Recommendations, Analyses, and Data for Health Services Research, Diagnosis, and Prognosis Clinic
Click
here for older notes
Current Notes
2019-4-1
Rachel Koch, Surgery
*I need help with coding of string variables from Redcap and then would like to confirm that I am using the correct test to compare groups given my data and perhaps also to discuss ways to find the most interesting results from all of the data. Mentor confirmed, may be late.
2019-3-18
Jenna Dombroski, Biomedical Engineering
- Request: Maria and I are students in Dr. Damon’s PHAR 8328 Experimental Design course. My project is to test the efficacy of a vaccine I have developed to prevent 4T1 breast cancer in a Balb/c mouse model. Maria’s project is to synthesize a dual functionalized liposome which will target and kill circulating tumor cells in the bloodstream before they can form a distant metastasis. Our questions are related to pilot studies, sample size and avoiding bias.
- Maria: colon cancer metastasis. Studying a protein which comes out of cancer cells when they move through blood to other parts of the body. Staining and cancer cell images; protein appears as spots (puncta) on the cell surface in imaging. Getting 10-15 images of the puncta in the cell line. Needing to analyze the puncta on image (define, number - variation of puncta across cells - and size, typical shape, distribution/location). Using ImageJ partical analysis function. Will eventually build an AI. Staining/imaging process is long. Cell sizes are approximately the same.
- Advice: Could look at density of distribution of puncta across cells. When measuring multiple units which mimic/influence each other (where there is less variability), more cells do not necessarily contribute new information. Could look at nearest-neighbor distances to evaluate distribution/location. In presenting, state assumptions (e.g. that cells are the same size). If two measurements are highly correlated (variable clusters) don't need to compare across both measurements, only one. Will help to establish the dimensions that you need to deal with, in order to organize output of interest. Recommend to follow-up with animal research biostats clinic. Recommend displaying all raw data with current data, due to number of cell lines. Scatterplot: number of puncta by another characteristic, colored by cell line. Could look into research of characterizing data on a sphere (contact Tom Stewart for contacts), parallel coordinate plots.
- Jenna: Testing efficacy of vaccine in mouse model. Has performed pilot study: 3 test/3 control. Initial results: reduced tumor size. Goal: reduced growth, increased survival. Primary endpoint is time until death, following all mice for 6 weeks maximum (time until established tumor size). Measuring tumor size with imaging, every 2 days. Batch effect of housing mice together is unknown; assumed no effect.
- Advice: Longitudinal profile recording size of the tumor over time would give most information/more power, using an endpoint of tumor size. Make a decision about how long to follow the mice (e.g. at end of 6 weeks, end follow-up of all mice). For full study, the researcher taking tumor measurements will need to be blinded.
2019-3-04
Brett Byram, Biomedical Engineering (VUSE)
- We are interested in doing A/B testing of some images as a way to assess improvement, but we would like to have a brief chat about the experimental design and how to analyze the data before we go farther. Outcome: Grant/abstract *Two images, which one better, or are they similar? Question: Which is image is preferred by physician? *Design: Want to assess consistency, as well. 10 images, repeated. *Could assign 0.5 point to answer "C" (similar). *Could not do binary, could do a "slider" and capture how much a physician prefers the image. *If have small number of readers, they need to read more images. Then can checked intra rater reliability, and assume that these readers will be the same as the population of all readers. *Could also do three images, three sliders. Or instruct readers to assess the first, and then compare the others to the first one.
2019-2-11
Lara Harvey, Gyn
- A comparison of surgeon times and scores on 3 simulation trainer tasks before and after a training session in Haiti. Question regarding best statistical test to compare times and scores.
- No funding support expected.
- 7 surgeons testing 3 skill sets in laparoscopic surgery technique; want to evaluate time and OSATS score pre- and post-intervention. Recommended to use descriptive tables and figures to describe data. Inferential stats not recommended due to small sample size. Wilcoxon rank-sum may be used.
Alexander Hawkins
- Overview: Robotic surgery, with articulated instruments and the ability to perform delicate dissection in the pelvis, has been thought to offer an advantage to traditional laparoscopy. The specific aim is to determine if there is a difference in the rate of negative margin status between patients undergoing laparoscopic versus robotic resection
- Data: National Cancer Database
- Design: Retrospective cohort of laparoscopic and robotic approach for patients undergoing resection for rectal cancer.
- Endpoint: negative margin status
- Funding: Will apply for VICTR biostatistics voucher
- Recommendations:
- Adjust for potential confounding due to surgeon choice using propensity score methods.
- Seek biostatistics voucher
- The hours of support required for this project are projected to fit within the standard voucher.
2019-2-04
Reza Ehsanian, PM & R
- Design: Cross sectional population based study.
- Data set: Comprehensive pain reports categorically defined as head, spine, trunk, and limb pain; smoking history; demographics; medical history from a total of 2,307 subjects from the 2003-2004 National Health and Nutrition Examination Survey obtained from the Centers for Disease Control.
- Objective: Examine the interrelationship between smoking and pain.
- Have questions about the analysis conducted. Want double check our methods and potentially receive input on how to improve analysis.
- No funding support expected, mentor to attend by phone.
- Result of discussion: best course of action to obtain the data and start over, in order to appropriately defend the analysis. Since smoking is a key variable of interest, use pack-years, time since quitting, multi-level smoking status (e.g. never, former, current).
Yuri Kim, General surgery
- Would like to conduct a retrospective review of comparing clinical outcomes in trauma icu patients who received palliative care intervention.
- VICTR voucher, mentor confirmed.
- Trauma subjects with palliative consult or no consult
- Need sample size
- Outcomes: utilization: LOS, cost '
- Propensity vs. regression: see Frank Harrell's write up at hbiostat.org/doc/bbr.pdf
- Frank: back up, consider what factors are important in real time.
2019-1-28
Jake Hughey, Biomedical Informatics
- I am using the SD to identify medications that are associated with false positive drug screen results (where the sample initially tests positive by immunoassay, but then negative by the gold standard mass spec). I would like to know if my approach, which is based on constructing 2-way contingency tables, is reasonable.
- Background of study: Immunoassays designed to recognize specific drug or class of drug. Then confirmed based on a more specific assay (standard practice). Immunoassays can recognize other molecules/compounds than what they're designed for. Systematically going through SD to use lab test results along with medication information to determine which drugs associated with false positive screen.
- Question of interest: What is the probability of having a false positive screen (of a particular sample having a positive screen result and a negative confirmation result)?
- Output measurement: 0 (screen negative) or 1 (screen pos, conf neg). Retrospective review of what medications the patient had an order for in the previous 30 days (arbitrary amount of time, drug likely to be in urine by that time). Only prereq: patient had their very first visit at least 30 days prior to screen (urine sample), in order to know what medications they're on. Analysis excludes patients who had both positive screen and positive confirmation. There is a small percentage of patients who have negative screen and positive confirmation, but they don't fit well into the study framework. Two of the medication compounds are similar/overlapping, however the medications tested are fairly distinct. Each observation is an individual screen, so the same patient may have multiple observations. Confidence of capturing medication data in patients. (OTCs are not documented, PCP may not be at Vanderbilt, brand names/generic are grouped together into same variable. Testing 700 ingredients across screens. Looking at correlations in medication usage, calculating pairwise Pearson correlations between top ~20 ingredients.
- Recommendations: Look at confidence intervals instead of p-values, as CIs will give information about magnitude. Candidates that need to be in the combination are the ones which are not independent of each other/those which co-occur a lot (based on raw counts): use a logistic model including all of these combinations and the second-order interaction of those which co-occur a lot. Need at least 200 events ("1" outcomes in the dataset) to stabilize the logistic model (at least 5 people - not measurements but actual people - must have had a false positive on that medication for that medication to be included.) Could extend the available data by stacking the data/combining data from all screens; correct later for faking the sample size.
2019-1-7
Aaron Brill, Radiology and Epidemiology
- Project: 35,000 patients treated between 1946 and 1968 for hyperthyroidism with different combinations of I-131, anti thyroid drugs and surgery. Mortality data updated thru 2015 on 90%. Therapy not randomized. Much Co morbidity and biased treatment allocation. Known small radiation risk. To avoid potential radiation risk anti thyroid drugs used preferentially. Need to look at how different outcomes correlate with therapy, including effects on longevity, a potentially positive effect. Data regarding I-131 risk has been analyzed in collaboration with NCI but has not included drug and surgical therapy and as the initial study PI I want to look at the data as a Phase 4 type study to look at unexpected correlations and need to find a statistical approach and a statistician interested and skilled in using the available tools needed for such an analysis. Data at NCI and their collaboration will be needed.
- Hoping to have a more clear analysis plan by M Jan 14
- Advised to call it an 'epidemiological cohort study' rather than Phase IV study.
- With many comorbidities, database will need thousands of outcome events to use individual comorbidities. May need to use comorbidity index to approximate impact of comorbidities present. Will need to choose the appropriate comorbidity index for your project.
- If dataset has baseline information collected prior to treatment allocation, then a propensity score could be included as a covariate in a regression model. What were the physicians thinking when they made the treatment allocation? Factors may include calendar time, etc.
- Swedish paper excludes many patients in their cohort, which may cast doubt on methods. Comorbidities could be included directly as covariates.
Jae Jeong (JJ) Yang, Epidemiology
- Project: I am working on a cohort study to examine the associations of baseline characteristics (i.e., lifestyle and dietary factors) with weight change during follow-up using a multivariate mixed effects model. I would like to have your comments on how to select adjustment variables for our mixed models.
- 18000 patients in dataset with baseline time point. Outcome is continuous variable of weight. Exclude patients with severe disease at baseline. When a patient develops a severe disease, they are excluded, and when a patients reaches age 70, they are excluded from study. Data from Southern Comm Cohort Study. Follow-up data is collected at yearly intervals.
- What are primary covariates of interest? Lifestyle, psychosocial factors, medical hx. With all covariates included in model, some are significant and some are not.
- If goal is inference, recommended not to use a variable selection procedure and to include all variables. Automatic variable selection causes CIs to become too small and type I error rate is not protected. If goal is prediction, can use a variable selection method.
- Due to size of cohort, the number of covariates included in the model are not a concern.
- Analysis done by sex and race.
- Outcome variable should be what you measure in the follow-up and baseline variables could be nonlinear. (For age and weight, could put variable + variable^2; or could put an interaction term in as a secondary analysis.)
- One model: baseline covariates. Second model: baseline and follow-up covariates. (Test R^2 for change/effect of follow-up time points.) Third model: include interaction terms.
- If lack of follow-up is due to baseline characteristics is related to issues other than baseline characteristics, need to state in limitations.
2018-12-17
Shawniqua Williams Roberson, Neurology
- Seeking VICTR biostatistics voucher
- We conducted a 35-question survey among epilepsy patients in the outpatient clinic to explore racial and socioeconomic differences in attitudes toward epilepsy care. Hypothesis: African Americans express less trust in their providers and greater perception of dangers of surgery than other populations. Question: would like assistance in developing statistical analysis plan and statistician support for completing the analysis.
- Prelim analysis done on 36 subjects. Would like to complete analysis and produce paper.
- Survey pulled from literature (prev published in Canada). n=144 (123 able to be analyzed; 20 unable to complete, 1 aborted during interview) Survey delivered as an interview. Qs about epilepsy are categorical/binary. Qs about providers are Likert scale. Demographic Qs are categorical/ordinal. Data are in REDCap, exported into Excel.
- Goals: validate survey, produce demographics, inferential analysis looking at relationships between race, attitudes towards providers and towards surgery.
- Next steps: In StarBrite, go to Funding > Apply Here. At one point (under Resources part of application) it'll ask for the type of support you want, specify a biostatistics voucher. The VICTR voucher is flat-priced and will automatically populate the budget. In Documents, will need to put together a 5-page written application. (Tom will send a template for this 5-page document by email.) Correspond with Tom to agree on stats section, before submitting application.
Brenda Pun,
- Seeking VICTR biostatistics voucher
- As part of my DNP dissertation I worked on a survey to ICU interprofessionals about teamwork and healthywork environment. My dissertation focused on those data from one site as a pilot study. Since then I have worked with a national professional society to collect the same data from 6000+ ICU professionals nationally. I am planning to submit a VICTR resource request for the funding to support the statistical analyses of the national dataset.
- Goal: implement critical care bundle. premise: teamwork matters. resurveyed staff 14 months after initial survey. AITCS and HWE scales given to all staff in critical care in 68 hospitals. collaborative is all anonymous; incorporated the dan-rosh (sp?) method to pair pre/post responses. (30% of post-collab responses possibly to be paired with pre)
- Now: secondary analysis in this project. 1. descriptive at baseline. 2. what factors influence teamwork scores? 3. is there a difference before/after collaborative? 4. are there any predictors of this change pre/post?
- Funding: funding secured through professional organization. Would need a contract (through the cost center): funding would go to you, the researcher, then would come to biostats as the analysis is done. Able to apply for VICTR voucher, if you like.
- Deadline: aiming to have manuscript out by end of spring 2019.
- Thomas Stewart to be in touch via email to follow-up.
2018-12-03
Sophia Delpe, Urology
- Seeking VICTR biostatistics voucher, mentor confirmed.
- Our study is a cross sectional survey sent to women >18. We would like to look at the prevalence of fecal incontinence and the relationship between that and psychosocial disorders/social interaction.
- Questionnaire on REDcap assessing toileting behavior. Approx 4789 patients.
- More of a descriptive study, so should describe the distribution of responses in results (e.g. histograms). To assess bivariate relationships, recommended to present cross-tabulations for categorical and likert-scale questions. Could use regression models: tendency to stay home modeled by symptoms, etc. Next steps for future work would be to control for covariates (age).
2018-11-12
Caroline Thomas, Pediatric Pulmonology
- Seeking VICTR biostatistics voucher.
- Retrospective chart review of pediatric patients with obstructive sleep apnea, who underwent tonsillectomy and adenoidectomy, and were then placed on positive airway pressure (PAP). We would like to determine whether there are predictors of adherence to PAP, specifically looked at: sex, race, insurance, weight, BMI, developmental status, presence of genetic disorder/autism/and/or psychiatric disorder, age of diagnosis of OSA, initial findings on sleep report, time to initiation of PAP post-surgery, other surgeries, presence of PAP titration study, presence of comorbid sleep disorders, follow up visits to sleep clinic, use of auto or fixed PAP settings, use of psychotropic medications, and data of nightly usage from PAP downloads.
- Adherence outcome measured as hours in first 6 months of use; adherence is at least 4 hours per night. n=117, download data for 67. Other variables of interest: development/neurodevelopment (prior diagnosis) and binary verbal variable.
- Statistical software recommendations: previous use of Stata so will continue to use. Missing data will likely be approached with multiple imputation.
- Suggestions: Descriptive statistics by adherence. Covariates: baseline CPAP score, age, development, verbal, (possibly) weight, interaction between age and developmental status. For analysis, stick to 6-8 parameters in the analysis, due to sample size of 67.
- Next steps: 1) Send Tom Stewart an email to get started with VICTR biostats voucher and work to get something together for abstract (due December).
Alexander Sherry, Radiation Oncology
- Seeking VICTR voucher
- Prospective trial of concurrent chemoradiation in adjuvant treatment of breast cancer. Our question regards a power calculation for our primary aim. Would be happy to provide more details (protocol) prior to meeting.
- Feasibility study. Primary aim of grade 3/4 clinician-derived toxicity during treatment (binary endpoint) sample size calculation of 17, but VICTR studio questions.
- Recommendations: Perform precision analysis to give estimate of yield of study regardless of how big a difference is there. With feasibility study, main objectives are to show that you can get patients enrolled (within reasonable time, resources, etc.) and that you can measure what you're trying to measure. To derive and validate another quantitative measure in the feasibility study could allow for more efficient full study. A "feasibility/measurement study".
- Concerns: To not distinguish grade 3/4 toxicity, requires more samples. Could possibly consider ordinal regression, depending on proportions of 3/4. Ask what estimating and bump SS up by factor of 10, or be aware and transparent about what the current SS can show. Noise requires more samples. Typical SS is 384 for MOE of 0.1. Non-inferiority SS are even larger.
2018-11-05
Alan Tate, ENT Clinical Instructor Faculty
- Trying to export REDCap data with certain criteria and then categorize. Previously attended a REDCap clinic.
- Study involves voice patients, about five years of data. Four groups, voice therapy alone, PT alone, and combo VT and PT. Observational study; patients selected group, essentially. Two questions: how were they different at baseline, and how were they different after therapy. Could look at differences in groups at baseline using bivariate approach. Then, perhaps multivariate approach to second question.
- Possible biostat voucher. Email Tom Stewart for VICTR application.
Christopher Gray, Neuro/Stroke
- Requests assistance with data interpretation for a review of current Kcentra protocol for intracranial hemorrhage.
- Previous clinic visit on Thurs, Sep 13, 2018: Requested advice on how to present data meaningfully. Advised to 1) look at outcome (death at 30 days) in a logistic regression with the size of the bleed as the independent variable, and 2) look at severity of rankin at 30 days using proportional regression.
*Feedback. Don't use correlation for binary variables. Try to show change in Rankin with profile plot--current plot does not show change well. Trying to define question? Not clear--right now all subjects got Kcentra, weight based dosing. Hospital may switch to standard dosing, if weight based is not effective. Stick to outcome of probability of success of treatment--
2018-10-29
David W. Bearl, Pediatric Cardiology
- My proposed project is evaluation of liver studies (labs, MRI, elastography) pre- heart transplant for Fontan patients (all have liver disease pre, which is known) and then evaluating those patients post- heart transplant (that is not known).
- n = 31 since started doing transplants for kids in 1987. Repeat evaluation at 6mo and 1yr post-tx.
- Two steps: (1) feasibility: show you can actually collect the data for the larger study. Estimate pt-to-pt variability; rates/patterns of missing data; (2) larger study with other hospitals: proper sample size needed for this (powered based on feasibility study).
- Best option for small population: ask 'based on where the patient started, where did they end up?' Can make use of gap between follow-up evaluations as a variable, if the gap varies by patient.
- With half the patients, better to show descriptive statistics (graphs and tables).
Shawniqua Williams Roberson, Neurology
- Purpose: Preparing preliminary data for an upcoming career development award submission. Several quantitative EEG metrics have been recorded on patients with ICU delirium of varying etiologies. Would like to use these preliminary data to build a model that uses the qEEG metrics to predict the etiology of delirium. Need guidance on: 1) how much data is needed to build this model 2) what statistical tools to use (multivariate logistic regression?)
- Applying for Faculty Research Scholarship in next cycle (February). Hoping for guidance on how to analyse preliminary data with respect to an aim in the grant.
- Aims of research: Evaluating quantitative frontal EEG to monitor for delirium continuously, producing numeric output. (1) Is it better than traditional EEG? (2) Can we distinguish different etiologies for delirium; Is there a dominant one, at which we can direct clinical decision-making? (3) Does qfEEG predict adverse outcomes? (Note: qfEEG is a subset of traditional EEG which doesn't require an EEG reader.)
- Data: 25 patients, 89 assessments. (Measurements taken at least twice per day, over the course of up to two weeks. Summarised down to a single number within the window for each assessment.)
- Suggested analyses: (1) random-intercept model (accounts for the fact that observations within a patient will be more highly correlated with each other): RASS ~ covariates + random intercept per pt. In scatterplots, put RASS score on y-axis since its the outcome. Depending on sample size, you could possibly allow for a non-linear association between variables. Could possibly focus on hypoactive patients only. Ordinal regression model with random-intercept, since RASS is ordinal and scale is small. (Not every statistical program will have ordinal regression with random-intercept, so may have to revert back to linear regression with random-intercept.) With 4 different predictors from the EEG and 89 assessment, should have enough to look at non-linear associations. (2) To differentiate etiologies, need patients with all types of etiologies and take the qfEEG. Regression is one method for creating that prediction tool. Once the tool is developed, collect more data and see how the tools perform making those predictions on the new data. Preliminary steps for etiologies: see how etiologies show up in graphical displays. (3) Depends on what you do during steps 1 & 2. Potentially its own separate predictive model with different features seen in the data. A lot of data will be needed for all models.
2018-10-22
Joseph Wong, Biomedical Informatics
- Purpose: Building upon a prior project–we have measured satisfaction, health literacy, and computer attitude regarding the patient portal prior the eStar EHR migration. We now want to measure these same factors with the new, eStar-based patient portal. From the original 6000 survey respondents, 3000 have volunteered to be contacted again.
- Previous clinic visits on Th 8/16 & Th 9/06: Investigating determinants of patient satisfaction with an online patient portal (My Health at Vanderbilt). Had previously built univariate linear regression models for satisfaction score and had selected factors for a multiple linear regression model. Recommended to add histograms. Recommended to include only up to a quadratic term and a linear term in the model. Recommended to use square root transformation on the Health Result Function, rather than the logarithm, and to include both the square root and linear terms in the model.
- Previously tested satisfaction usage before eStar update (using old pt portal) using ordered logistic regression. Next step is to test satisfaction with eStar. Needs to know what to measure and get thoughts for data collection.The same individuals agreed to be followed up with the eStar satisfaction. Satisfaction scale is 12-60.
- To fix odds ratios in ordered logistic regression, need to transform (square root or cube root - cannot use log due to zeroes) count (click) variables and then use interquartile ranges, rather than raw values, as change in one click is negligible. Do transformation before implementing regression model. Easiest: do transformation, divide by iqr, use those values in the regression; interpretation made by change in IQR. (Demonstration of restricted cubic spline in Stata: can calculate odds ratios but beta values cannot be interpreted.) Can model all count variables this way. Test statement will allow to test the overall impact.
- Compare satisfaction pre-EPIC to post_EPIC with Wilcoxon signed-rank or paired t-test. Not interested in testing computer literacy as it may not have changed in the previous six-months. 3000 individuals agreed to be recontacted. Best to keep the survey short; only plan to ask the 12 satisfaction questions. Keep in mind that people may respond differently to satisfaction questions if previously at end of longer survey and now shorter survey. Other test options: use same model already built, Bland-Altman plot, identify what may correlate with a decline in satisfaction. To calculate session times to include in the model. Could look at post- scores as a function of pre- scores, nonlinearly. Could compare domains of satisfaction score to see if the weighting is equal.
2018-10-01
Brooklynn Bailey, MMC Dept of Family & Community Medicine
- Clinic Follow-up from 8/20:
- We are exploring the relationship among PTSD symptoms in our sample of young women exposed to interpersonal violence. 17 symptoms are assessed via clinical interview and are scored from 0-8. Prior to our first clinic visit, I had ran network analyses in R, with concerns pertaining to sample size. We have since ran hierarchical cluster analyses as recommended to us to compare to the network results. We are returning to get feedback on these results and recommendations for next steps.
- Current state: cross-sectional data; n = 68; 17 PTSD symptoms assessed through interview (each scored 0-8): not likely to be any 1s (each scored for presence and severity); histograms have been created by cluster, as recommended from last time (zero-inflated data: should report on number of 0 responses but overlay the probability distribution only over results 1+); results of cluster analysis (ward's method) with bootstrapping (open to suggestions on this front); a second cluster analysis based on presence of symptoms alone. * Analysis performed in R - function cluster methods are ward D and euclidean. Bootstrap method used is unknown (code used not available during clinic).
- Concerns: some variables may not be grouped because of low variation/smaller sample (C8/B2/C12) are these clustered together because of low variability? These are all rare symptoms; are they grouped together only because of this or are they actually correlated? What is stability of bootstrapping?
- Previously there was a question about sample size, so wanted to view variability of responses in available data. Matrix of pairwise probabilities for how often symptoms correlate in % of bootstraps. Probabilities should be either close to 1 or close to 0, so you'll see what clusters often go together; if getting values in middle of range, there is more variability in the way variables are clustered.
- Need to think about the cutoff for what determines a cluster. There are algorithms for determining this cutoff, but they are very computational/use cross-validation. This may be something to handle via email after looking at code. Also need to think about adjusting the number of clusters.
- Q: How could we tie these back to original network analyses and validate? A: There is a very tight connection between the clustering and the network analyses because both based off correlation matrices. Once you've ID'd that you have stable clusters, you can do network analyses within each cluster to generate partial correlations.
- Q: Is the last symptom to separate out more central than other symptoms? (Interested in identifying centrality.) A: With longitudinal data centrality of the symptoms makes more sense, so not useful in cross-sectional data. (If unable to reject null, unable to detect clusters in stable way. Clusters perform better with more data, therefore sample size may be issue.)
- Next steps: Brooklynn to send code to Dr. Stewart for review. Stability question to be answered after viewing code.
2018-09-24
Christine Rukasin, Medicine/Allergy, Pulmonary and Critical Care
- I am doing a survey based study evaluating anxiety and drug allergy testing. This is a series of surveys with repetition of questions at different point in time. I would like assistance in strategies to best analyze the results, visualization/diagrams of results and suggested sample size. * Expected Outcome: Protocol with no expected funding support, Abstract, Other. Possible VICTR voucher? Still time before analysis is needed. *Graphical display of data. Could sum questions for a total score. 100 is a reasonable number of subjects. Could also plot mean score by number of tests/measures per subject to assess learning effects. Compute correlation with subject characteristics and total score. Tom will send email with VICTR application.
Satya (Nanu) Das, Medicine/Oncology
- We are performing a retrospective analysis assessing whether gastrointestinal cancer patients (at Vanderbilt) who experience immune-related adverse events while on immunotherapy experience improved outcomes (PFS,OS,duration of response) compared to patients who do not experience these events. I would like to briefly touch on my data collection and the statistical methodology for my future analysis.
- Expected Outcome: Abstract, Other
- All subjects on immune therapy are eligible. How to disentangle treatment for event and treatment? We don't know how long they need to be on therapy. Could do "landmark" analysis, analyze one outcome (AE), then the next outcome. This is all subjects--with smaller sample, focus on high resolution variables.
WALK IN: Parisa Samimi, Uro gynecology
- Possible VICTR, prospective study looking at correlation between patient satisfaction and am labs (no lab vs. routine labs). Do not know sample size needed. Do not know baseline satisfaction, or any baseline data. Question needs refinement--need to specify question and definitions. Could also search current literature for baseline satisfaction level--to get baseline data.
2018-09-17
Mallory Hacker, Neurology
- Study Objective: To improve the identification and referral of patients who may have spasticity to a physician who is an expert in the diagnosis and treatment of spasticity through the development of a bedside physical exam referral tool for primary care physicians and nurse practitioners. * Hypothesis: A simple limited bedside physical examination guide enhances the ability of primary care providers to correctly and reliably identify residents in a long-term care facility who may have spasticity and appropriately refer them to a specialist for spasticity evaluation. * Question: Are the sensitivity and negative predictive values the most appropriate to report for this study? * Expected Outcome: Other * Present as a 2x2 table (most will want to see), report PPv and NPV. Calculate SP SN, but not as primary number. Could do a figure to show proportion correctly diagnosed. Should we use Kappa? No--not the point. Also check instructions for authors.
Sean Collon, VUSM Global Health
- Teleophthalmology screening in Nepal–comparing in person decision making of ophthalmic technicians with limited screening resources to decision making of ophthalmologits reviewing photographs of the same patients. For each patient, technician and MD record a diagnosis for each eye and a plan for each patient based on their respective information (in person exam with limited equipment vs. viewing photos remotely), diagnoses and plans grouped into broad categories, then agreement compared to determine utility of device in the screening camp setting. * Expected Outcome: VICTR Biostatistics voucher *Could separate by anterior and posterior, would make sense in this context. Could also do each diagnosis separately, then order in order of agreement. Agreement on treatment plan not useful when diagnosis did not agree, limit to when diagnosis did not agree. For agreement, could do a 2x2 table (MD/Tech). Calculate agreement. Two eyes from each patient--correlated measures. Could treat as independent. Can compute confidence intervals for all measures.
*Could put voucher in under local mentor name--although students may be eligible.
2018-08-20
Brooklynn Bailey, Meharry Vanderbilt Alliance
- I recently was introduced to the network approach to psychopathology at a conference this year. I would like to explore the network structure of DSM-IV PTSD symptoms in my sample of young adult women who have recently experienced interpersonal violence. I have taught myself how to conduct network and related analyses in R; however, I have some questions related to my small sample size and the adequacy of my findings given this limitation. In general, I could use guidance on methods for analyzing this symptom data to better understand the presentation of posttraumatic psychopathology in this population. *Possible VICTR voucher-contact Tom if interested. * Research question: how are PTSD symptoms related to each other in this sample of young women? *Sample size ~70 *Using Lasso right now * Consider using histograms to examine structure of symptom data. Could do simple variable clustering with bootstrapping with replacement, less complex than current approach.
Rohini Chakravarthy, Meharry Vanderbilt Alliance
- We have surveyed a cohort of 3000 patients using an IOM survey on social determinants of health. We are interested in seeing which are most predictive of outcomes (as measured by A1C at time of study and potentially its progression). I think multilevel modeling may be useful but am not sure how to proceed and whether this makes sense for a VICTR voucher application. Data collection is complete.
*First step is further refining question; are we looking at med adherence, incidence, or AIC?
*Multiple regression may be right approach, even in the presence of colinearity. Could do voucher or continue to come to clinic for more assistance.
2018-08-13
Jessica Heft, Urology/Urogynecology
- We will be conducting a survey of young women and assessing their physical activity and how that relates to pelvic floor dysfunction. We will be using several standardized questionnaires and need assistance with methodology/patient recruitment expectations/statistical planning. Project is in the design phase.
- VICTR Voucher to cover biostat support-can set up database alone. May ask for VICTR support for gift cards.
- Propose email based survey examining relationship between athleticism and stress incontinence.
- Concern is over the representatives of the respondents.
- Recommend using slider bar for questions when possible.
2018-08-06
Zeb White, Hearing & Speech Sciences
- A new, experimental 40-question parent-report measure was developed by our lab in order to better understand parent-child interaction in stuttering. This instrument was administered to 68 parents of children who do and do not stutter. We are attempting to understand the differences between the two groups (parents of children who stutter vs parents of children who do not stutter) and identify if the instrument correlates with other parent-report measures regarding stuttering severity and consequences. * We would like guidance in selecting appropriate statistical tests to answer relevant research questions. * Data collection is complete. * Range of stuttering severity, not "true" group. Kids could range from ~4% of words to ~15%. Really is a range (0% to ---). About 30 in each "group". BUT, could include previously excluded kids which would increase sample size considerably. * Wish to reduce items on survey, perhaps group questions? * Questions developed from advice given to parents and from literature on parent intervention. This survey administered at time 0, prior to intervention/therapy. * Could look at correlation; parent response by RYCS; does the degree of stuttering correlate with the RYCS? Could use Goodman gamble. * Small sample size to do 40 analyses--use caution with multiple tests like Wilcoxen. * May consider dropping "never" and "always", extreme responses. * 40 x 40 correlation matrix could show what questions are highly correlated, and drop highly correlated. * Redundancy analysis could work * Cronbachs alpha on questions that should measure the same thing * Could force questions into groups based in clinical (e.g. timing)
2018-07-30
Margaret Adgent, General Pediatrics
- *Overview
- I am updating an analysis from an observational cohort study regarding maternal prenatal vitamin use and childhood asthma. Pregnant women were enrolled and interviewed; they were recontacted 4+ years later to answer questions about their children’s health. There is substantial loss to follow up (70%), and I am interested in applying inverse probability weights to address possible selection bias due to loss to follow up.
~1900 met inclusion for the secondary analysis, ~500 responded and had exposure. Goal is to compare folic acid use before pregnancy to those who started after.
Should summarize the differences between groups (those with follow up and without)--see how different they are. There is and fairly even split between groups.
Use 1/prob
Wt. table to check values, check for large values
Contact Jill Shell re: collaboration in peds. Possible Chris Slaughter.
2018-07-23
Laurie Samuels, Biostatistics
- The project uses Medicare claims data to look at regional rates of variation in a particular surgical procedure, and I would love to get feedback from more senior biostatisticians. Looking at regional variation in colon resection. Have three years of data. Several issues, one is difficulty in identifying denominator. Dartmouth health atlas could be useful for methods.
2018-06-05
Brenda Pun, Pulmonary
- As part of my DNP dissertation I worked on a survey to ICU interprofessionals about teamwork and healthywork environment. My dissertation focused on those data from one site as a pilot study. Since then I have worked with a national professional society to collect the same data from 6000+ ICU professionals nationally. I am planning to submit a VICTR resource request for the funding to support the statistical analyses of the national dataset.
- Stage of project (select one): Data collection completed
- Data collection method (select one): Survey
- Data management system (select one): Redcap
- Expected outcome (check all that apply): VICTR Biostatistics voucher
- Investigator experience (select one): Independent investigator
2018-05-21
Natalie Covington, Hearing & Speech Sciences
- We are planning a study in which we would like to sub-classify patients with traumatic brain injury based on their memory “profiles” (patterns of impaired and intact memory performance across a battery of tasks); we would like to discuss possible methods for classifying patients into subtypes (e.g. latent profile analysis; k-means clustering; etc).
- Stage of project (select one): Design
- Data collection method (select one): Other
- Data management system (select one): Spreadsheet
- Expected outcome (check all that apply): Protocol with no expected funding support
- Investigator experience (select one): Graduate/Medical Student
2018-05-14
Wendi Mason, Medicine / Pulmonary
- To compare a new practice model (prospective) employing telehealth strategies of telemonitoring and telesupport to previous year’s model of standard practice (retrospective chart review) to determine effect on hospitalization rate, illnesses and other complications, compliance, and rate of decline in patients with Idiopathic Pulmonary Fibrosis.
- Stage of project (select one): Design
- Data collection method (select one): Case report form/data form
- Data management system (select one): REDCap
- Expected outcome (check all that apply): VICTR Biostatistics voucher
- Investigator experience (select one): Independent investigator
2018-05-14
Jessica Heft, ObGyn/Urogyn
Background:
- Retrospective cohort comparing two surgical approaches (open vs. laparoscopic). Will be looking at perioperative complications and outcomes.
- Stage of project (select one): Design
- Data collection method (select one): Data are exported in electronic format
- Data management system (select one): REDCap
- Expected outcome (check all that apply): VICTR Biostatistics voucher
- Investigator experience (select one): Resident or fellow
Discussion & Action Items:
- Perfect confounding between surgeon and surgical technique.
- Jessica will coordinate with Thomas Stewart to develop a statistical analysis plan for submission of an application for VICTR voucher.
2018-05-07
Yolanda McDonald, Human and Organizational Development
- The editor-in-chief of the American Journal of Public Health asked for us to test for interaction indicating that there is heterogeneity across the 4 size-specific ORs . I found some information on Research Gate. However, I would still like to discuss the test or test(s) option. The manuscript is Minor Revision status.
- Stage of project (select one): Data collection complete
- Data collection method (select one): Other
- Data management system (select one): Other
- Expected outcome (check all that apply): Other
- Investigator experience (select one): Independent investigator
2018-04-23
James Andry, Neurology - Sleep
- Please provide a short description of your project and the questions you’d like to address: The primary goal of this study is to evaluate whether the features measured by an aggregated set of consumer-grade activity monitors can predict a given patient’s successful treatment with CPAP. Our study design also supports the secondary goal of validating the sleep parameters measured by these devices in aggregate. Would like to discuss statistical methods for measuring correlation between sleep parameters from consumer-grade devices (test device) and polysomnography (gold-standard).
- Stage of project (select one): Design complete but no enrollment/data collection
- Data collection method (select one): Data are exported in electronic format
- Data management system (select one): Spreadsheet (e.g. Excel)
- Expected outcome (check all that apply): Protocol with no expected funding support, VICTR Biostatistics voucher
- Investigator experience (select one): Independent investigator
2018-04-23
Alexander Langerman, Otolaryngology
- Please provide a short description of your project and the questions you’d like to address: Using qualitative research, we’ve identified subgroups of patients who have differing opinions on how they trust their physicians. I’d like to develop a quantitative diagnostic of these perceptions.
- Stage of project (select one): Design
- Data collection method (select one): Survey
- Data management system (select one): REDCap
- Expected outcome (check all that apply): Other
- Investigator experience (select one): Independent investigator
2018-04-09
Ellen Kelly
- Please provide a short description of your project and the questions you’d like to address: We have developed an instrument to assess parents’ perceptions of their communicative interactions with their children. We need assistance with evaluating the instrument and analyzing the data we have collected to date.
- Stage of project (select one): Data collection underway
- Data collection method (select one): Case report form/data form
- Data management system (select one): REDCap
- Expected outcome (check all that apply): Protocol with no expected funding support, Other
- Investigator experience (select one): Independent investigator
Briana Furch, Infectious Disease
- Please provide a short description of your project and the questions you'd like to address: I'm not sure which type of analysis I should do in order to compare 4 different disease states and their associated biomarkers (variables) at different time points. I also want to look at these disease states to asses normal variance.
- Eligible for departmental collaboration plan, if in place?: no
- Stage of project (select one): Design
- Data collection method (select one): Other
- Data management system (select one): REDCap
- Expected outcome (check all that apply): Protocol with no expected funding support, Grant
- Investigator experience (select one): Independent investigator
- Name of Mentor: John Koethe
2018-04-02
Paul Slocum with William Stuart Reynolds (mentor), OB/GYN
- Please provide a short description of your project and the questions you'd like to address:
Assessing pain in women with synthetic pelvic mesh and outcomes after treatment.
Would like to come to biostats clinic to obtain VICTR research voucher. We have a prospectively collected case series of patients with pelvic pain who underwent mesh removal.
- Eligible for departmental collaboration plan, if in place?: no
- Stage of project (select one): Data collection completed
- Data collection method (select one): Data are exported in electronic format
- Data management system (select one): REDCap
- Expected outcome (check all that apply): VICTR Biostatistics voucher
- Investigator experience (select one): Resident or fellow
2018-03-26
2018-03-19
Ray Blind, faculty, Department of Medicine, with two undergraduate students
There is a lot of data correlating IV drug use with hepatitis, and hepatitis with liver cancer, but no studies have correlated IV drug use with liver cancer, to our knowledge. We used the synthetic derivative to attempt to correlate IV drug use with liver cancer and need help deciding which stats tests to apply to the data.
Recommendations:
- Best approach would be to follow a cohort of IV drug users to see whether they develop liver cancer; next-best would be a case-control study comparing the odds of being an IV drug user among people with liver cancer compared to people in a reasonable comparison (control) group. The hard part is deciding what that control group should be.
- Here is an introductory explanation of case-control studies: http://www.bmj.com/about-bmj/resources-readers/publications/epidemiology-uninitiated/8-case-control-and-cross-sectional
- To visualize 2x2 data (for example, IV drug use by cancer) graphically, you can make a jittered scatterplot. This gives the same information as a table, but it can be helpful to see the information presented in more than one way.
2018-03-12
2018-03-05
Dupree Hatch, Pediatrics
- Please provide a short description of your project and the questions you’d like to address:
I have two projects that I would like to discuss the design of a statistical analysis (if there is time):
We have a large national database that contains data on ~20% of all very low birth weight infants. We would like to a) describe the use of mechanical ventilation in these infants (# of days, etc.), b) quantify the inter-center variation in the # of ventilator days/infants and c) define the contributions of specific practice variables (ventilator modalities, sedation regimens) to the observed variation in ventilator days/patient.
I would like to discuss the statistical analysis to quantify the variation and to test the practice factors to attempt to determine what, if any of them are driving variation.
The second study I would like to discuss if time allows concerns alarms from mechanical ventilators. We have built an internal database of ~30000 hours of ventilator alarms. I would like to describe some of the factors that are associated with high alarm burden (patient size, ventilator mode, time of day, etc.) in a future effort to intervene on those factors that are modifiable. I would like to discuss how to handle the clustering at the patient level since we have hundreds, sometimes thousands, of alarms within a single patient and how to adjust for that when I look at the different patient and practice factors.
- Stage of project (select one): Design
- Data collection method (select one): Data are exported in electronic format
- Data management system (select one): Spreadsheet (e.g. Excel)
- Expected outcome (check all that apply): Protocol with no expected funding support, Grant, Other
- Investigator experience (select one): Independent investigator
- Notes from clinic:
- Chris Slaughter has a collaboration plan with Pediatrics but is currently busy; Dr. Hatch came to clinic for preliminary discussion
- For the first project:
- 200--300 centers; 10--200 very-low-birthweight births per center per year; 6--7 years of data. Temporal trends are likely but seasonal trends are not.
- Interested in quantifying the resource utilization (number of ventilator days)
- Even the descriptive statistics are challenging for this project, because some of the babies die, and ventilator use is a measure of both how sick the baby is and of usual practice at that particular center. It's possible that the best approach will consist of a mixture model that incorporates both time to death and ventilator days while alive.
- Some babies are transferred from their original NICU. Rather than excluding these babies from the study cohort, we recommend including them in the cohort, but censoring them at the time of transfer, to minimize bias.
- For the second project:
- The dataset contains 40k ventilation hours for 400--500 babies. About 15% of the patients get switched from one mode to another
- It will definitely be important to include patient characteristics in the model for this project; it may be less important to do patient-level clustering, depending on the data structure and the overall goal of the analysis.
2018-02-12
Nitya Venkat, Undergraduate Student, Vanderbilt Brain Institute.
In our study, we programmed a MATLAB script and Arduino micro-controller to deliver visual and tactile stimuli to subjects. We then collect responses (numerical: 0 -100) from subjects as well as questionnaire responses on a Likert scale (1-6). We are hoping to address how to deal with the issue of normality in the data as it relates to parametric tests. We are also hoping to ask about which post-hoc tests to do, what means to correlate and generally how to make the most of our data. We also have questions about how to correlate our Likert responses to our measurement data that is numerical but not on an interval.
W. Stuart Reynolds, postdoctoral fellow, Urology.
My project is concerned with base-line clinical characteristics of women with and without overactive bladder, including general demographic and clinical data, along with condition-specific data and results of quantitative sensory testing, with which to phenotype participants. I am interested in phenotyping, specifically using data-driven statistical methods, such as clustering, and would like advice regarding these and other novel techniques, including machine learning, that may be applicable to my data. I am planning to submit for a VICTr voucher for biostatistical support.
2018-02-05
Lou Posey, medical student
The acute phase response is the body’s biological response to combat bleeding, infection, hypoxia, and tissue dysfunction following an injury. This system is tightly regulated such that a post-injury response that is either too small or too robust can result in deleterious patient outcomes. This trend has long been observed in clinical practice, yet the validation of clinical markers of the acute phase response (also known as acute phase reactants) in correlation with poor outcomes is underreported. Using the synthetic derivative database, we aim to correlate vascular complications (namely venous thromboses) with elevation in acute phase markers such as CRP. Moreover, we will record associated platelet levels surrounding the vascular complications to depict a consumptive coagulopathy.
Currently, there are no quantitative markers to predict the risk of a DVT; as such, we hope to show the divergence of elevated CRP and platelet trough as a novel predictor of thrombosis. This could change VTE prophylaxis guidelines in both the pediatric and adult populations.
Lauren Marlar, PUBH student
Sample size calculation and and test selection for class assignment.
Problem: Calculate the sample size required for a randomized controlled trial comparing two treatment groups and a control group. The primary end point is a 5% weight loss by the last session. Assume that only 5% of the participants in the control group will lose at least 5%. Assume that 20% of the people who start the program will drop out.
Note: We were instructed to go to the Clinic if we needed assistance. (Note from Laurie Samuels: Dan Byrne confirmed that he suggested that students in this class attend clinic for help with power calculations.)
2017-11-13
Claire, Lo. Medical student.
I have data and preliminary analyses from a repeated measures longitudinal study assessing the impact of variable exercise intensity and volume on inflammatory markers (hs-CRP, IL-6, epinephrine). I am trying to create generalized linear models for the data and I'm not sure where to start (or if GLMs are the most appropriate model for this data set).
2017-10-30
Sarah Diehl, Hearing and speech sciences (doctoral student)
The speech perceptual characteristics of people with dysarthria due to chorea can vary tremendously (Darley, Aronson, & Brown, 1969a). The current study aims to identify distinct clusters of speech perceptual characteristics within a group of 51 speakers with dysarthria resulting from Huntington’s disease (HD). All speakers will be within a mild speech severity range.
Raters (4 graduate students complete, 6 to be recruited) completed a speech perceptual characteristics checklist for each person with HD. The speech perceptual characteristics checklist contains 38 items separated into 7 separate dimensions as follows: pitch characteristics (1-4), loudness (1-9), vocal quality (10-18), respiration (19-21), prosody (22-31), articulation (32-36), and general impression dimension (37-38). The general impression dimension also includes an estimated percent intelligibility (without formal calculation) and graduate students’ proposed dysarthria type. Each checklist item is rated individually on the ordinal scale from 1 (normal) to 7 (very severe).
The following research questions will be addressed in this study:
- What are the speech perceptual characteristics consistent with diagnosis of HD and how do they compare to previous literature on hyperkinetic dysarthria?
- Are there distinct clusters of speech perceptual characteristics within speakers with mild dysarthria due to HD?
- If distinct clusters of speech characteristics exist within speakers with HD, do the individuals who belong to the same cluster also share other disease- or treatment-related features (i.e. type of medications, number of CAG repeats, and the length of disease duration)?
Our questions for the meeting are primarily focused on the cluster analysis, however, we may bring additional questions at that time. We plan to present preliminary results at a conference in mid November. We will bring full data for the first 4 raters.
Recommendations:
- Do not do statistical tests comparing groups on the 38 items that went into the cluster analysis. It would be reasonable to do tests on things like medication use, etc., that did not go into the cluster analysis.
- To show group differences visually, consider plotting the first two principal components using colors for the different clusters, and/or making a parallel coordinates plot
- With so few patients relative to the number of items, the clusters are likely to be unstable, although if the plots show large separation between groups, this may be less of a concern
- Consider trying a few different clustering methods to see whether they all suggest the same four clusters
- Consider sparse principal components analysis, and either cluster on some or all of the principal components, or use the PCA results to help you decide which variables to cluster on
- For a manuscript, present intra- and inter-rater reliability
Supisara Tintara, Nephrology (medical student)
We are studying the tissue sodium levels in peritoneal dialysis patients compared to controls without kidney disease. My question is determining whether the sodium levels in dialysis patient is different from the sodium levels in the controls. Also, are sodium levels different among age, race, or gender in controls and dialysis patients.
Recommendations:
- Because some of the data has been published already, focus on two comparisons, using Wilcoxon rank-sum tests: PD vs. HD and PD vs. control
- For comparisons involving race and gender, use descriptive plots rather than statistical tests (because the group sizes are very small)
2017-10-23
Petrice Cogswell, Radiology (resident)
Analysis of survey response data from survey polling radiology programs directors of attitudes towards MD-PhD vs non-PhD residents. I verified that the distribution of respondents (program size and
PhD residents) is representative of the polled group and would like to continue with assistance on the statistical analysis.
2017-10-16
Petrice Cogswell, Radiology (resident)
Survey on radiology program directors toward MD PhD residents and resident research. The responses were likert scale, how do you view PhD residents vs non PhD score -2, -1, 0, 1, 2 representing much worse, worse, similar, better, much better in multiple areas. Question: is there a statistical test to evaluate this type of data?
Recommendations:
- First step: see how comparable the responders are to the non-responders (or the whole set of programs) in terms of # residents, # MD/PhD residents, NIH funding amount
- From there we can talk about statistical testing. We will probably want to use a finite-population correction since the whole population = 63 programs
- Regardless of comparability, descriptive statistics (10 out of 23... etc.) will still be interesting to report
Yolanda McDonald, Human & Organizational Development/Peabody College (Faculty)
Project Title: An environmental justice review of drinking water quality in the United States, 2011-2015
Abstract:
Despite the need for potable water for human life and EPA regulation of U.S. public water systems, there has not been a comprehensive study to quantify disparities in residential drinking water. This research systematically reviews results of the National Primary Drinking Water Regulations (2011-2015) by community water systems at the county-level. This study utilizes an environmental justice framework to (1) elucidate if legally enforceable drinking water quality standards differ based on community race/ethnicity, socioeconomic status, and rural-urban classification and (2) determine if communities with predominantly underrepresented groups are disproportionately burdened with repeat violations of drinking water violations.
Data Sources and Variables:
Dependent Variable:
Drinking water violations for arsenic, atrazine, chlorine, coliform (Pre -TCR), coliform (TCR), combined uranium, di(2-ethylhexyl) adipate, di(2-ethylhexyl) phthalate, nitrates, nitrate-nitrite, lead and copper rule, radium, TTHM, TCE, haloacetic Acids, and Trichlorethane were downloaded from the Safe Drinking Water Information System (SDWIS) federal reporting services for the years 2011-2015 (N = 58,018). Of the violations, there were N = 30,981 repeat violations. Violations and repeat violations were operationalized as dichotomous variables (0 = no violation, 1 = violation).
Explanatory Variables:
Race/ethnicity and socioeconomic status variables were obtained from the U.S. Census, American Community Survey, 5-year estimate (2011-2015) and were operationalized as continuous variables measured as proportions. The rural-urban classification is based on the USDA’s Rural Utilities Service (USDA RU) definition of rural. Rural-urban classification was operationalized as dichotomous variables (0 = urban, 1 = rural).
Data structure:
The database structure format is one violation per row, Public Water System ID (PWSID) is the unique identifier. A PWSID may appear more than once in the database. For example, a PWSID could have multiple violations during the study year. The column data points are violations, race/ethnicity, SES, and rural-urban classification.
Proposed Data Analysis Strategy:
The unit of analysis is county-level. Descriptive statistics were run to characterize the data. Correlation matrix measured the magnitude and direction of association between water violations and explanatory variables. To determine the relationship between water violations and the explanatory variables univariable and multivariable logistic regression analyses were used. The Variance Inflation (VIF) diagnostic was used to detect multicollinearity in the multivariable and interactions analyses. To detect confounding, all explanatory variables unadjusted odds ratio were compared to adjusted odds ratio to determine if there was a change of ≥ or ≤ 10% in the odds ratio (Szklo and Nieto 2014). And, multivariable logistic regression was used to adjust for confounding (Pourhoseingholi, Baghestani and Vahedi 2012). The Pearson goodness-of-fit statistic was used to compare the observed values to the expected. Covariates that had a likelihood ratio P value of <0.050 (two-tailed) and an odds ratio that did not cross 1.00 with a 95% confidence interval were considered to be statistically significant in the univariable and multivariable analyses.
Questions:
Do we need to adjust for water systems, i.e. counties vary in the number of community water systems that service the area? If so, which of these options are recommended?
a. Do we need to adjust the variance estimators of the estimated coefficients to account for the variance within the county, i.e. robust standard errors using clusters?
b. Weight counties by population served by the community water systems?
c. Stratify by community water system size (i.e. number of people served): Small Level 1 ≤ 3,300; Small Level II 3,301 ≤10,000; Medium 10,001 ≤ 50,000; and Large ≥ 50,001.
Do you recommend that we use Pearson goodness-of-fit statistic to compare the observed values to the expected?
Do you recommend post-hoc analysis for logistic regression? If yes, are there different post-hoc test for interaction terms?
Recommendations:
- We are concerned because we don't know the number of times each system was tested. If it's not possible to get this information, one possibility might be to simulate data to try to get a sense of the possible scope of the impact of frequency-of-testing
- The overall project seems like a good fit for a VICTR voucher or short-term biostatistics support (its scope is too large for clinic). To inquire about short-term biostats support, email Yu Shyr, Chair. Another possibility might be working with a student (email Jeffrey Blume, director of graduate studies).
- Will need to keep in mind: some systems get swallowed up into other systems.
- Longitudinal data analysis won't be feasible without the complete testing data (we would need the non-violations in addition to the violations).
- Next level (after other issues resolved): geospatial correlation (tricky, though, because of the upstream/downstream issue)
2017-10-02
Kelly Schuering, Internal Medicine/Vanderbilt Familiar Faces (medical student), with Ed Vasilevskis (mentor; Department of Medicine, Division of General Internal Medicine and Public Health)
This study is looking at the prevalence of housing instability, risk factors for instability, and utilization of community resources among patients working with the Vanderbilt Familiar Faces program. Our research questions are as follows:
Primary: Among patients with high health care utilization working with the Vanderbilt Familiar Faces staff, what is the prevalence of housing instability, potential future housing instability, and secure housing and what factors predict this?
Secondary: What community resources are people using to help address housing instability and how would individuals describe their relationship with those resources? What predicts whether patients are connected to resources to assist with finding housing?
Data will be collected through a self-administered redcap survey on an ipad while patients are in the hospital.
Our analysis plan is as below:
Housing stability (ordinal):
- Pearson’s chi-squared or Fisher’s exact test, depending on n in each category
- Ordinal regression (vs. multinomial?)
We plan to include the following variables in the regression based on literature review and experiences with similar populations: consistent income (binary), employment (binary), current substance abuse (binary), legal history (binary), and current/recent intimate partner violence (binary)
Resource usage (binary):
- Pearson’s chi-squared or Fisher’s exact test, depending on n in each category
- Logistical regression
Based primarily on our experiences as there is not literature in this area, we plan to include having an outside case manager/social worker (binary), having a regular monthly income (binary), history of drug use (binary), and current housing stability status (categorical) in this logistical regression.
Since our multivariable analysis will not be able to account for every potential confounder, we will also conduct a sensitivity analysis to determine how big of an effect an additional cofounder would have to be to change the observed relationship.
Finally, we will also do a subanalysis of the pre-identified VFF patients compared with those who were assigned to the VFF team due to risk and bed space. This binary variable could also be included in the multivariable analyses.
I was hoping to get feedback on the above analysis plan and input on how many variables can realistically be included in the regressions if the estimated sample size is 200. I am also hoping to get an estimate for how much time we would need to purchase from biostats in order to get the above analysis completed.
Recommendations:
For the binary outcome, the best-case scenario would involve 100 patients per outcome group, in which case it would be reasonable to adjust for 5 covariates in the regression model. Pre-specifying the covariates without looking at the data would preserve the Type I error rate, but with an exploratory analysis like this, that might not be your highest priority. If you are planning to present the analysis as exploratory and don't need to prespecify the model, a good starting place would be to look at plots and descriptive statistics for all variables by outcome group, and then to look at a scatterplot/correlation matrix and also to make a variable-clustering plot to get a sense of whether some variables can be used to "represent" others.
An ordinal logistic regression would be appropriate for the ordinal outcome, but depending on the sizes in the groups, you may need to collapse two of the outcome groups.
Possibilities for longer-term help: VICTR voucher and/or contacting Dr. Yu Shyr, Chair, to see whether short-term help is available.
2017-09-25
Christian Okitondo, Psychiatry (Staff)
Topic: Increased tendency for proximal proprioceptive errors in limb bisection for individuals with autism spectrum disorder is not mitigated by too use.
Previous studies involving tool use tasks have shown that typically developing (TD) individuals commit distal errors in limb bisection after using tools, presumably due to perceptual extension of the peri-hand space.
Given that individuals with ASD are less susceptible to visual override of veridical proprioceptive information in other proprioceptive paradigms, we hypothesized that individuals with ASD would not demonstrate these distal errors after tool use.
Questions I would to address:
How to incorporate repeated measure on my ANOVA?
For each subject, I have a pre training means and post training means.
How to explain the repeated measure ANOVA to the world with no statistical background?
Ricky Shinall, Surgery (Assistant Professor)
I have a dataset consisting of about 350 responses to a quality of life instrument that has not been previously validated. I would like to get an estimate on the biostatistical effort needed to analyze the data for consistency and validity in order to obtain a VICTR voucher.
2017-09-18
Devika Nair, Nephrology (Postdoc)
Attending this clinic is part of a requirement for my Biostatistics I class that I am attending for my
MSCI, but I do have a question related to one of my projects.
I'm interested in exploring the coping behaviors of African American patients with advanced, non-dialysis dependent CKD. Based on what is available in the literature (which is limited), minority patients in general use religious coping to deal with the stresses of chronic illness. African American patients in particular seem to use denial/avoidant coping mechanisms. I believe that these coping mechanisms could in part explain why many of these patients disengage and disappear when the need for dialysis is mentioned. I believe that these behaviors are more related to cultural differences, rather than socioeconomic status or educational level.
If I am trying to illustrate a causal mechanism for why AA patients with adv CKD disappear when dialysis is mentioned (independent of their SES/educational status), would the best study design be to compare AA patients of both low and high SES, or would it be to compare AA patients with low SES with patients of other races with low SES?
Recommendations:
- You are welcome to come back to clinic, but as a member of the Nephrology division you are also welcome to work directly with Thomas Stewart
- Recruit patients across a range of SES's; will probably want to limit to patients who are either AA or white, due to likely low numbers in other groups
Baldeep Pabla, GI (Fellow)
Also attending clinic as part of a requirement for Biostatistics I class for
MSCI; particular project involves looking at a predefined set of SNPs in patients with and without GI cancer or metaplasia. Current literature suggests that environmental factors may play a greater role than genetics in the development of these conditions.
Recommendations:
- You are welcome to come back to clinic, but as a member of the Gastroenterology division you may be able to work directly with Chris Slaughter
- Identifying appropriate controls for this study will be tricky
2017-09-11
Shaina Willen, Clinical Fellow (Pediatric Hematology/Oncology)
I am preparing a VICTR proposal to study the impact of biomarkers of lung injury on complications in children and adults with sickle cell disease. I would like some assistance with my statistical analysis plan and how to determine power and sample size calculations.
- for enrolled patients, look at previous 3 years then follow forward 2 years
- 250 children & 300 adults seen at clinic
- plasma & DNA samples
- outcome is pain and acute chest syndrome
- 3 genotypes and plasma biomarkers
- believe 2,2 genotype will have increased pain and chest syndrome (1,1 (26%) 1,2 (55%) 2,2 (19%))
- look at incident rate at 1 yr and 2 yr; poisson model; need to know what difference would be expected between the groups
- sample size - graph of incidence rate that can be detected vs sample size needed
- Simplest approach: find confidence interval formula for a Poisson rate; assume lowest true rate and solve for n such that multiplicative margin of error is 1.5 with 0.95 confidence
- Simplest confidence interval is lambda +- 1.96 * sqrt(lambda / n); once you have an upper limit on lambda can solve for n to give acceptable margin of error for lambda
- Would be better to get the multiplicative margin of error for the ratio of two Poisson rates (to simplify we may assume the sample size in each group is the lowest of the three genotype group sizes)
- See http://statsdirect.com/help/rates/compare_crude_incidence_rates.htm
Alice Hoyt, faculty (Medicine/Allergy)
The aims of this R21 are to determine the preparedness and knowledge of K-12 schools on the topics of asthma and food allergy, then to pilot an asthma telemedicine program.
2017-08-28
Ricky Shinall (Surgery)
Palliative care consultation has been shown to reduce utilization in end of life care, but this hasn’t been rigorously studied in trauma patients.
I have access to Vanderbilt’s trauma registry which can be cross referenced against the palliative care registry to identify patients with palliative care consultation. I’d like to discuss the procedures for creating a propensity matched comparison of patients with and without palliative care consultation to compare resource utilization between the two groups. I’d also like to get a sense of the complexity of this analysis and the amount of effort from a biostatistician it would take to complete it.
Propensity score model resource:
https://statcomp2.app.vumc.org/VisualPruner/
Katie Tippey (Anesthesiology)
We did a card sorting projects where each participant sorted 4 decks of index cards.
We recorded the time it took them to sort and notes based on asking them to think aloud while they sorted the cards.
We created annotated files of photos of their final sorting arrangement and have created a raw data set based on these photos.
We think we may want to use factor analysis on this raw data set but are unsure both if this is the appropriate analysis and, if so, how to perform this analysis.
Resources:
http://fharrell.com/doc/bbr.pdf section 16.1
2017-08-14
Nicolas Forget (Emergency Department)
- Perception of collaboration between doctors and nurses in Guyana
- Pre- and post-team-building exercise, then 4-6w later
- 27 participants with 2 dropouts by the end; 15 nurses, 10 doctors at the end
- Issue of using means vs. proportions for Likert scales; want to look at disagreements of perception before and after training
- Nurses used more spread of answers than doctors
- 2 demographic variables, 15 Likert questions; need to combine into a single global scale for graphical individual profiles and for stat analysis
- Can do a formal analysis of variability of responses within subject, e.g. compute the SD over 15 questions within subject and see if nurses have more variation than doctors
- Main analysis on mean
- Form within-person difference from baseline (paired data)
- Do 2-sample (unpaired) t-test comparing these differences - nurses vs doctors
- Be sure to graph all measurements (on summary score)
- Pre-post design often provides an upper limit to an intervention effect
2017-07-24
Maureen Saint Georges Chaumet (fellow)
Project description: I am starting a project that compares the cosmetic outcomes of 3 different laceration closure methods in kids: sutures, tape and glue. I will also be looking at several secondary outcomes.
Overall, study design seems reasonable. Recommended that parents rate the cosmetic outcome of the laceration in addition to 3 reference pictures. If parent's responses can be captured via an online Redcap survey, consider the possibility of a sliding scale response.
Recommend 90 hours of biostat work. (Does not involve writing more than one manuscript)
Samuel Younger (Nurse Practitioner)
Interested in determining sample size and best statistical approach. HLM-SEM vs Path analysis?
Research Abstract
Many organizations are looking to their staff to creatively engage in improving the safety of patients. Further, within the Magnet health care environment, transformational leadership is the theory that has been promoted as core to the achievement of patient outcomes, thus is the core focus of this study. The purpose of this research is to examine the role that leaders play in bringing together elements of a safety culture and a climate of innovation that support and enable staff to engage creatively in improving the quality and safety of patient care. There is little empirical evidence in the nursing literature related to patient safety in an innovative climate, and none could be found that study the leadership behaviors of nursing managers that are conducive to an innovation climate and impact on patient safety outcomes in a Magnet designated, Academic Medical Center. Therefore, this study seeks to fill that gap in knowledge and expand the leadership and innovation literature to include patient safety within a Magnet work environment.
This research uses a multi-level, cross-sectional, descriptive correlational design aimed at examining the relationship between nurse manager transformational leadership and front line nurse rated patient safety score, and to further investigate how, if any, does communication and feedback about error and the innovation climate influence the relationship. The independent variables in this study are transformational and transactional leadership. The dependent variable is front line nurse rated patient safety score. The innovation climate is proposed to be a mediating variable. Feedback and communication is proposed to be a moderator variable between transformational leadership and patient safety score. The variables will be measured through an online survey based the three validated and reliable survey instruments (54 questions): the MLQ-5x short (MLQ-5x), the Team Climate Inventory-short (TCI), and Feedback and Communication About Error and Patient Safety Grade (subscales of the AHRQ Hospital Survey on Patient Safety Culture) which are all appropriate for collecting data about the perceptions of front line nurses.
If findings confirm these relationships, then in order to impact outcomes, nursing managers may need to be adept at navigating and promoting the complex nature of innovation through communication and establishing an innovation climate. In this context, leadership facilitates communication and an understanding of the innovation climate, which supports creative solutions to patient outcomes and improved quality, in this case, patient safety. On a practical level, this study will contribute to a greater understanding of how to prepare future nursing leaders for the challenges of a changing healthcare landscape through an understanding of what behaviors are necessary to generate innovative and safe care delivery models.
H1a: There is a significant, positive relationship between nurse managers’ transformational leadership as measured by the Multifactor Leadership Questionnaire (MLQ-5X) and nurses’ perception of patient safety as measured by patient safety grade (AHRQ HSOPSC).
H1b: There is a significant, positive relationship between nurse managers’ transactional leadership as measured by the Multifactor Leadership Questionnaire (MLQ-5X) and nurses’ perception of patient safety as measured by patient safety grade (AHRQ HSOPSC).
H1c: There is a significant relationship between nurse managers transactional leadership as measured by the Multifactor Leadership Questionnaire (MLQ-5X) and nurses’ perception of patient safety as measured by patient safety grade (AHRQ HSOPSC), but to a lesser degree than transformational leadership. Included per our discussion on transformational leadership predicting quality above and beyond that of transactional leadership.
H2a: There is a significant relationship between nurse managers’ transformational leadership as measured by the Multifactor Leadership Questionnaire (MLQ-5X) and innovation climate as measured by the Team Climate Inventory (TCI-short).
H2b: There is a significant negative relationship between nurse manager’s transactional leadership as measured by the Multifactor Leadership Questionnaire (MLQ-5X) and innovation climate as measured by the Team Climate Inventory (TCI-short).
H3: The relationship between nurse manager transformational leadership as measured by the Multifactor Leadership Questionnaire (MLQ-5X) and nurses’ perception of patient safety as measured by patient safety grade (AHRQ HSOPSC), will be mediated by innovation climate as measured by the Team Climate Inventory (TCI-short).
H4: The relationship between transformational leadership and patient safety grade will be moderated by feedback and communication about error. In terms of this relationship, transformational leadership will have a stronger, positive relationship with patient safety scores when feedback and communication about error is high.
2017-07-10
Ryan Skeens (fellow)
This is a patient activation measure survey conducted on parents/caregivers of NICU patients. Survey will be conducted at NICU enrollment, NICU discharge, and 30 day after discharge. The hypothesis is that patient activation measure will decrease at NICU discharge but increase over time (30 day after discharge). In addition, characters such as social economic status that links to high patient activation measure will be identified.
The measure has been validated and used by mentor team. This is a fellowship project, and Ryan will apply an internal grant for the 6-9 months project. Further,
CTSA support will be explored.
Recommendations:
- Sample size is fixed based on fellowship time. Power and sample size should be calculated accordingly.
- Keep the measure in the continuous form (0-100) instead of dichonimization.
- Consider to have CTSA statistician's early involvement at the design stage. Given this involves design, grant writing, data collection, data analysis, and manuscript preparation, a 90 hour work maybe needed.
- As prediction is involved (identify characters that are related to high measures), model validation should be considered.
2017-06-19
2017-06-12
Danxia Yu, Epidemiology (faculty)
We will examine the associations of diet quality scores (assessed at baseline) with body weight change (from baseline to following visits) in a prospective cohort study. Generalized estimating equation model has been used in other studies, which we are not familiar with. We need statistical inputs on this model and the power estimation. We also would like to find a statistician whom we may work with on this project. Thank you.
Recommendations:
- If dropout is not random, either GLS with a serial correlation structure or a linear mixed-effects model would be more appropriate than GEE.
- Do not collapse the diet variables into quintiles; leave them as continuous variables
- For the power calculation, it may be possible to ask for conditional approval to have access to a subset of the data to get estimates of the quantities needed for a power calculation.
- You can do a simplified power calculation with just one wave of data, and argue that the power will be higher when there are more data points per person.
- Possibly useful R packages: longpower (thank you for bringing this to our attention!), pwr (in particular, the pwr.f2.test function).
- Simulation could also be a useful approach, but it would also require some background information about the standard deviations of the variables
Joshua Cohn, Urologic Surgery (clinical fellow)
I have two questionnaire-based databases on overactive bladder that I have merged. I would like to use this data to develop a model that predicts bother based on symptoms and comorbidities and prioritizes necessary treatments. I am not sure if cluster analysis is the best way to do this.
Recommendations:
2017-06-05
Paul Yoder, Special Education (faculty)
I'd like evaluation of area under the curve (AUC) as a way to quantify the magnitude of the between treatment-group-difference and its confidence interval for RCT with repeated measures of the dependent variable. A reference for an example is
Gallop, R. J., Dimidjian, S., Atkins, D. C., & Muggeo, V. (2011). Quantifying treatment effects when flexibly modeling individual change in a nonlinear mixed effects model. J Data Sci, 9, 221-241.
Recommendations:
- Email Hakmook Kang to talk about the possibility of working through the KC biostatistics core to get an estimate of how many children and timepoints you would need to do the flexible-breakpoint approach discussed in the article
- We also discussed an approach using restricted cubic splines. It's possible that this approach would let you use fewer subjects; it may be useful even though you are expecting a linear relationship
Bryan Hill, OB/GYN (fellow)
This is a follow up from recommendations from 5/15/2017 regarding a logistic regression model of post operative complications as the output variable and clinical and demographic variables as the independent variables. The recommendations, in summary were:
1) Treating the outcome as an ordinal, rather than binary, variable if there are enough people in the additional groups
2) Look at the cross-tabulation between physician and sling type to see whether it is feasible to include both
3) Leave the continuous variables as is (do not categorize them). May want to consider log-transforming age.
4) Try variable clustering to see which variables may be collinear/redundant
5) Consider combining less important (less interesting) variables into a score
Goal for the session: to discuss results of the model.
Recommendations:
2017-05-29
No clinic---Memorial Day
2017-05-22
2017-05-15
Bryan Hill, Fellow, Gynecology
Reporting complications after surgery are important for quality improvement. Two methods of finding complications are: 1) administrative data from diagnosis codes and 2) key-word search from a manual chart review. We suspect the administrative reporting method under-reports complications. The primary aim of the study is to determine sensitivity and specificity of the administrative method compared to the manual reporting method. The secondary aim is to determine which risk factors are associated with having a complication.
We think that creating a logistic regression model would help address our secondary aim. Our plan is the following: setting the output as "complication present (1)" and using the variables: asa class, age, body-mass index, setting (outpatient or inpatient), sling type, attending, if a concomitant procedure was done, anesthesia time, operation time, smoking history, diabetes, and prior surgery.
Question #1: We need guidance on how many variables we can include in our model. Some have high numbers, and some are quite low.
#2 Some variables may influence each other. For example, sling type is heavily dependent on attending (they like to chose a particular brand or type). How do we adjust our model for that?
#3 It is known that older patients are more likely to experience complications. How do we determine if age is independently associated with "complication presence" versus just being a confounder influencing other variables?
Files we plan to append: data dictionary, STATA file, table of variables with total numbers of responses.
Recommendations:
- In deciding which categories to collapse, look at the sample overall (not by complication status)
- To increase power, consider treating the outcome as an ordinal, rather than binary, variable if there are enough people in the additional groups
- Look at the cross-tabulation between physician and sling type to see whether it is feasible to include both
- Leave the continuous variables as is (do not categorize them). May want to consider log-transforming age.
- Try variable clustering to see which variables may be collinear/redundant
- Consider combining less important (less interesting) variables into a score
- For binary logistic regression, we generally want to have 10--20 people in the smaller outcome group for every degree of freedom (continuous variable or single category) in the model
- If you apply for VICTR funding, we recommend the larger time amount if you are interested in a publication or presentation. In your application, you can cite these notes as evidence that you have been to a biostatistics clinic.
Mike Temple, Biomedical Informatics, faculty
I am comparing the results of 2 surveys and need help calculating p-values and odds ratios to determine significance between the 2 surveys.
I am using R
Recommendations:
- Get more information about the survey design (especially number of people surveyed) so that you can compare the response rates in 2012 and 2016. If they are not close to each other, it will be harder to justify comparing the results of the two surveys
- If possible, get info about demographic makeup of the people surveyed in 2012 and 2016 from the organization's records. If, for example, the mean age of respondents is very different from the known mean age of the people surveyed, you will know that in at least that one aspect, the respondents are not representative of the people surveyed.
- Chi-squared tests should be fine if the categories are exhaustive (but this is secondary to the nonresponse issue)
- If possible, get more info about the outcomes and model specifications used for the regressions in Table 3.
2017-05-08
Chirayu Patel, resident physician, radiation oncology
The project is VEEP-C - Visually Enhanced Education for Prostate Cancer, a randomized, controlled trial to assess the impact of a visual presentation on prostate cancer treatment decision-regret, anxiety, satisfaction, and patient-reported symptoms, in the radiation oncology department. The expected accrual for patients was 112 patients based on 120 prostate cancer patient consultations seen within a 6-month timeframe. Unfortunately, due to a drop in consultations, only ~30 patients have been accrued, and only 1 patient has completed external beam radiation therapy over a 6 month timeframe (other have undergone brachytherapy, surgery, active surveillance, or are still deciding).
1. The sample size is based on an instrument which only 1 patient has completed. As originally written, the study is not feasible. Determination of new outcome and sample size?
2. Role for interim analysis on secondary outcomes?
3. Thoughts on closing the trial due to poor accrual?
2017-05-01
Cara Singer, PhD Student, Speech and Hearing
- This project investigates speech-language imbalances in children. We are interested in the best way to measure imbalances using five standardized tests. Simple range scatter and standard deviation have been discussed. We are also interested in the best way to analyze whether increased synchrony between the five tests is associated with a decrease in stuttering frequency based on two years of development.
Hatun Zengin-Bolatkale, Faculty, Hearing and Speech
The purpose of the present study was to longitudinally assess sympathetic arousal (i.e., physiological correlate of emotional reactivity) of preschool-age children with persisting stuttering (CWPS), those who recover from stuttering (CWRS), and their normally fluent peers (CWNS) during a stressful picture-naming task. The apriori research questions/ hypotheses are as following:
The first question addressed whether change in SCL in response to stress at initial testing - close to the onset of stuttering - is associated with stuttering chronicity (i.e., persistence vs. recovery). We hypothesized that children whose stuttering persists, compared to those who recover and those who do not stutter, would exhibit increased skin conductance reactivity to a stressful picture naming task at their initial testing (i.e., prior to stuttering resolution for children who recover).
The second question addressed whether change in SCL in response to stress - approximately 18 months after their first testing – is associated with stuttering chronicity (persistent vs. recovered patterns). We hypothesized that children whose stuttering persists, compared to those who recovered and those who do not stutter, would exhibit increased skin conductance reactivity to a stressful picture naming task at 18 months-post-initial testing (i.e., after stuttering resolution for children who recover).
The third question addressed whether changes in SCL in response to stress are associated with changes in stuttering frequency. We hypothesized that for children who persist, compared to children who recover and children who do not stutter, increased skin conductance reactivity would be associated with increases in stuttering frequency.
We would like help from the clinic with the analyses of the hypotheses above, especially for #3.
2017-04-24
2017-04-17
Works-In-Progress
2017-03-27
Sarah Diehl, Hearing and Speech Sciences , PhD student
* Questions for the clinic:
1. After removing the ratings that have a mean score of 2 or below, there will be ratings that will highly correlate. Should we first do something like a multi-dimensional scaling approach to identify dimensions and then a cluster analysis to see how these dimensions cluster? Or do we throw all ratings (potentially 38 if none receive a mean score of 2 or below – realistically perhaps something like 20 to 25) into a cluster analysis.
2. If we expect at least 2 or 3 clusters, what is a reasonable sample size given the number of items we have on the rating scale?
3. What do we need to put into a proposal that is going to use cluster analysis? What kind of information is critical?
4. Is there another approach that would work better than cluster analysis?
Gurjeet Birdee, Health Services Research, Faculty.
- The objective of this study was to measure the energy expenditure (oxygen consumption O2/kg/min) of adults practicing common yoga movements. For each individual, participants were asked to do movements in a standing position, lying position, and seated position (body orientation). In addition, each movement was done with different variations serially. In addition, participants were asked to walk at low and moderate intensities to compare energy expenditure of a comparative aerobic exercise to yoga.
The main questions we would like addressed:
What is the best approach to measure if there was significant variation between individuals for mean energy expenditure by body orientation?
What is the best approach to measure if there was significant variation between individuals for each movement?
When considering if variation exists above, should we take into account resting energy expenditure for each individual?
2017-03-20
Cara Singer, Hearing and Speech Sciences, PhD student
- This project investigates differences in skin conductance levels in children who stutter and are persisting, children who stuttered and recovered, and children who do not stutter. All children were followed 3-4 times across a two year period. At each visit, skin conductance levels were measured during a neutral video and speaking task, a positive emotion-inducing video and speaking task, and a negative emotion-inducing video and speaking task. We would like to discuss the best statistical models for our hypotheses.
- Note that at each timepoint, there are 7 skin conductance measures (a "baseline" and 6 other measures)
- Recommendations:
- Keep all possible timepoints from all possible subjects. Do not exclude subjects based on their trajectories or baseline characteristics
- Use continuous versions of the stuttering outcomes if possible; at a minimum, collapse the outcomes into 5 ordinal categories
- Use a longitudinal mixed-effects model. Each subject will contribute 1, 2, or 3 rows depending on how many of the timepoints they have. You can model severity as a function of time-1 severity, age, sex, the seven time-1 conductance measures (or a reduction thereof; try a redundancy analysis first), time in days, and squared time in days, with random effects for subject (and possibly time and squared time). We recommend a continuous-time correlation structure, but this might be tricky with the mixed-effects model; generalized least squares might work better.
- If we can get a clear, simple plan and the analysis is not a multi-step analysis and the dataset is clean (and tall and thin, with the relevant time-1 variables and non-identifying subject ID on each row), we may be able to conduct the analysis during a clinic.
- Starting next month, we will be able to take on longer short-term projects for a charge.
- The Kennedy Center statistics core may also be able to do this. If you come back to a clinic, please remind us to invite Hakmook.
2017-02-27
Kristy Broman, Surgery Resident
Method to compare standardized incidence ratios using SEER data
2017-02-20
Katie McGinnis (MPH candidate)
(followup from last two weeks)
Recommendations:
- For each overall question category, try a scatterplot of a) the means and b) the standard deviations for each item, with staff values on the x-axis and parent values on the y-axis (or vice-versa). Label each point with the question number or a short phrase to identify it
- Do variable clustering within the staff items and the parent items, to see which items tend to be answered similarly by the same person (hcavar in stata)
- Rather than doing several univariate analyses comparing the relationship between the demographic items and each survey item, do a single regression analysis for each survey item, with all the demographic items included in the model at once. Collapse the categorical items into 2 or at most 3 categories, and just assign numeric values (e.g. 1--5) to the levels in the binned continuous items like distance and treat those as continuous variables (so they will have just one term in the model). Actually, though, drop distance altogether and just use travel time. The overall F-statistic from the regression will tell you whether anything in the model matters. The best approach would be a proportional odds model, but ordinary regression will be next best.
- It's ok to take the means of means (across items in a particular category) and talk about those, but there aren't enough data points to warrant a statistical test.
2017-02-13
Katie McGinnis (MPH candidate)
(followup from last week)
Recommendations:
- Instead of doing t-tests, do wilcoxon rank-sum test (only 5 response options)
- Rather than overlaying the parent and staff histograms, show the parent mean as a dot on the staff histograms
- Do the "dot-histograms" by hospital because the hospitals are so different, even if tests comparing hospitals are not significant
- Don't put too much weight on the p-values; this is exploratory research with relatively small sample sizes
- For the two similar staff questions, run a correlation on the responses to help justify using only one of the questions. Use a Spearman rank correlation.
- We don't think it would make sense to take the mean of the responses for the parent "how often" questions
- For any set of questions, it could be interesting to order the means to see which questions had the highest or lowest means, but it wouldn't make sense to do a statistical test comparing the means of the different items.
2017-02-06
Antje Mefferd, Hearing and Speech Sciences
I’m an assistant professor in the Hearing and Speech Science department and I’m currently preparing a manuscript. I would like to have someone take a look at the analysis that I completed to make sure they are correct. I’m a bit unsure about some things (assign fixed and random effects, reporting of degrees of freedom). I have my data in excel spreadsheets and can share it ahead of time.
The topic is how the tongue and the jaw change in their range of motion during various speech tasks (speaking typical, loud, slow, clear). These speech tasks are used in speech therapy to help people with brain diseases (Parkinson’s disease) to be better understood. In this data set I look at this in just one group of speakers (healthy speakers).
Participants complete 5 repetitions for each task (5 reps x 4 tasks = 20 data points from each participant). There are 11 females and 10 males in this study (sex has a significant main effect due to anatomical differences between males and females, but it is typically not statistically controlled for in our field in repeated measures). There are three measures – tongue movement, jaw movement , and the acoustics. For all three I need to analyze task effects in separate analyses.
I also need to look at how changes in tongue movements predict changes in acoustics and how well changes in jaw movements predict change sin acoustics using data of typical to loud speech, typical to clear speech, typical to slow speech -- this time regressions within females and within males.
In the meeting I would like to make sure that I ran these analyses correctly and also would like to verify that I used to correct degrees of freedom in my write-up.
Recommendations: 1. For primary analysis, either ANOVA using each subject's mean or mixed-effects model with fixed effect for task and random effects for subject would be fine. 2. For secondary analysis, it would be best to use the same
approach (either one mean data point per person per task, or a mixed-effects model). If doing mixed effects model for secondary analysis, be careful with the interpretation of R-squared.
Katie McGinnis (MPH candidate)
I have questions about my MPH Thesis project, specifically related to the best options for comparing some of my variables and running a few other statistical tests
Practicum in Kenya; originally a needs assessment, not designed for research. 16-page staff surveys (n= 94) & parent surveys (n= 69) from 2 children's hospitals, plus demographic data. Hoping to compare parent responses to staff responses in some way. Challenges: 1. parents are responding about 1 child but staff are responding about all children, and 2. for some items, the response scales for parents and staff are slightly or very different. She is comfortable treating the response options as numeric (taking the mean would be meaningful to her). The thesis does not have to contain a formal statistical analysis.
Recommendation for next steps: For survey items where the response scales are the same, continue the exploratory data analysis by plotting histograms for the staff responses, and then marking the mean of the parent responses on the x-axis.
2017-01-30
Frances Anderson, MPH Global Health
I am an MPH Global Health track student and I need some assistance with ANOVA analysis on my thesis project. My project is an evaluation of Minnesota's TB screening of refugees and immigrants across four counties in the state. The data I am looking at for ANOVA includes mean days to initiation (TB testing) and mean days to disposition. There are some outliers in the data that I need to consider dropping. I seek advisement in this, completing the test, and if ANOVA is not appropriate for this dataset finding a new test.
2017-01-09
Joshua Cockroft, MD student
We are looking to design and validate a new psychometric scale that measures a patient/client's trust in new providers. Though psychometric scales currently exist that measure trust in healthcare systems, trust in existing personal providers, and measures of global trust, there is currently no scale described in the literature that specifically measures trust in new providers. The hope is that such a scale would be of use in many underserved populations, particularly those populations with histories of either substance use disorder or severe mental illness, who are not regularly active participants within the healthcare system. We would hope to be able to use such a survey to measure the effect of this specific type of trust on outcomes such as healthcare service utilization. Like other healthcare trust-related scales, this scale would likely be a Likert-scale with questions that would span multiple domains of trust (i.e. competence, dependability). As there is no current gold standard for this type of measurement, advice on important considerations for internal validation would be greatly appreciated. We may consider the validation of this scale in multiple sub-populations if able. Conceptualization of this scale will be derived from the literature and our own qualitative research.
2016-12-19
Angela Maxwell-Horn, MD, Assistant Professor of Developmental Pediatrics, Monroe Carell Jr. Children’s Hospital at Vanderbilt
I am a pediatrician wanting to do a study about the effectiveness of a medication to treat ADHD symptoms in children with autism. I would like to come to a biostats clinic to help me figure out what type of analysis that I should do and how many subjects I need to effectively power my study. I have attached a copy of my study proposal.
- Recommend a randomized cross-over study design with double blinding if possible
- Select a side-effect measurement tool
- Clearly state inclusion/exclusion criteria
Heather Limper, Center for Clinical Quality and Implementation Research
"I would like to get some help with execution of times series analysis using STATA (ideally)."
2016-11-21
Katie McGinnis, MPH Candidate, Global Health
Perform surveys in three children hospitals on parents and staff. 69 respondents from parents and 97 from staff.
Parents survey: demographics about parents and children, how the experiences in hospital impact parents and children, patient satisfaction
Staff survey: demographics, education, child's hospitalization needs
Research questions: what do you think caused the child's illness? The language barrier in receiving proper care? The correlation between child's experience in hospital and staff's education and experience.
Survey matrices are similar in parents' survey and in staff's survey (a dozen of likert-scale questions). Want to check the correspondence between parents' responses and staff's. First check if parents agree with each other. Code the answer to each question as 1,2,3,4,5. Summarize the score of each question across all the patients. Small SD is an indication of better agreement between parents. Second check the consensus of staff. Third, to evaluate the staff's characteristics, compare staff's responses to parents' consensus; to evaluate the parents' characteristics, compare parents' responses to staff's consensus. Take the difference between staff's response and parents' consensus as outcome, fit a regression model on providers' characteristics.
Could generate a summary score over multiple questions in one category (Rockwood's index).
2016-10-17
Samantha Gustafson, Hearing and Speech Sciences
VICTR application for dissertation research. EEG measures for speech sound processing in quiet and in noise. Looking for age effects. How does the effect of noise change with age? Proposed analysis based on linear regression. Expects one EEG measure to be more sensitive than the other. Second question is to look for mediator with EEG response and how well they do behaviorally depending on age. Particularly tricky how to size a study for an exploratory mediation analysis. Have replaced repeated measures ANOVA with a linear model. Each EEG task takes 10 minutes. Two listening conditions, same task. Quiet vs noise order is randomized. Half of participants hear "da" and the other half receive "ga" (randomized). Model: EEG = intercept + age effect + noise/quiet + age x noise/quiet interaction. Can use generalized least squares (correlation structure irrelevant except don't assume the correlation is zero, since only 2 times per subject) or repeated measures ANOVA if very careful to use the correction for correlation (if can handle interaction between group (noise/quiet) and age). But GLS is ideal. Need to check normality assumption of residuals.
Power of a test of interaction is much lower than a test of main effect (difference in slopes vs. slope not being flat). Data not available for making initial guess of sample size required to achieve a given precision or power. Only thought is related to a minimum possible sample size - the size needed to estimate a difference in mean EEG for an adult with very good precision. The SD of the noise-quiet difference is used here. Once the acceptable margin of error (half-width of 0.95 confidence interval for the mean difference) is determined can plug in formulas related to precision - see e.g.
http://fharrell.com/doc/bbr.pdf . Beware: sample size needed for interaction is easily 4 times as large.
Alec Pawlukiewicz, Neuroscience and Psychiatry
Effect of exercise on neuro cognitive testing. Database of 20,000 participants - 9,000 after exclusions. Control for covariates sex, age, education level, # prior concussions. Interested in matched analysis. Not having enough controls. Suggested using full qualifying sample without matching, to maximize power and avoid any arbitrariness in how matches are determined. Non-matched analysis requires careful specification of the statistical model.
Several neuro scores are given by the test. If scales are continuous enough can use the standard multiple regression linear model if analyze one score at a time. May need to model age as a smooth nonlinear effect and perhaps likewise for education. Age and education may be co-linear. Variable of major interest is exercise (binary). Need to consider whether exercise may interact with age, sex, etc. What about type of exercise? For variables such as # prior concussions a quadratic effect often suffices.
Dillon Pruett, Hearing and Speech Sciences
Respiratory sinus arrhythmia. Comparing in children who do not stutter, stutter and persist, stutter and stop. They watch a video followed by a task, and this is repeated with different videos/tasks. Baseline re-measured at the end.
Question about whether to form groups or to have a continuous-time longitudinal model with stuttering measures as the response variables (without categorization). Answer questions by estimating difference in means over time. Need to interpret the result in a clinically meaningful way. Need to adjust for baseline stuttering measure as a covariate. This might possibly be interacted with the intervention effect. Need to carefully formulate the linear model and account for within-subject correlation using something like GLS or mixed effects models (the latter is mainly used if there are more than 2 or 3 measurements over time within subject).
2016-10-10
Omair Khan, Center for Research on Men's Health
- "I would like to request some time to talk to another statistician about exploratory factor analysis I am doing in R with the psych package. This procedure is fairly new to me and I have some questions that I would like help with."
2016-09-19
Mary Lauren Neel, Neonatal
- Association between ITSP and illness severity score
- Association between parenting style (PSDQ) and infant adoptation.
Mark Tyson, Urology
- Bladder neck size on incontinence, controlling for BMI, age, preop score, disease status, and stitch.
- Restricted cubic spline examples: MSCI Biostat II STATA
2016-09-12
Dillon Pruett, PhD student in the dept of hearing and speech sciences working with Dr. Robin Jones
- I'm working on a project involving longitudinal data with children who stutter and persist, children who stutter and recover, and children who do not stutter.
2016-08-29
Scott Karpowicz
- Matched design, 1:1, 1:many, BOOM
- match on socio-economic, clinical factors, etc.
- Change point analysis
- see if readmission rates change at time of policy implementation
- REQUEST FOR VICTR SUPPORT: Clinic statisticians recommend a 90 hour voucher.
2016-07-25
Sam Gannon
VICTR
- Developing a randomized controlled clinical trial in mental literacy. Working notion, to increase mental literacy, communications which in turn increase mental health outcomes.
- Submit concept paper to NIMental Health. Questions to address and want to get statistical expertise.
- Questions: 4 educational arms and a control group for a total of groups. Setting community mental health clinics
Metric for outcome measure clinician reports notes - self management, behavioral adherence to protocol and rate of compliance
These response measures are known to be correlated.
Intervention: different educational programs. Control will have standard of care.
- Consider cluster randomization. Figure out how many clinics that you will have access to. Five arms note one clinic receive one arm.
- How to assess "fidelity"? Recording data consistently. Approach with assessment for some of inter-rater reliability.
How do you capture your outcome? If survey or standard form then it will be much easier to make results consistent. For example if reporting is done through
RedCap, you will have the opportunity to formalize or standardize process.
- Mediation analysis (Baron & Kenny, structural equation modeling). First you need to show that your intervention has an association with response variable. Mediator will be communication for example
. What factors mediate the intervention?
- * (Y~X) Education is associated with improved mental health.
- * (X~M) Education works through health literacy and/or communication(Mediators) to improve mental health.
- Will I benefit from cross-over design? We believe that once knowledge is gained it will be difficult to have a "wash out". Cross over design will be more appropriate to a set up such the development of new drug with clear wash out.
- Question from biostatisticians: do you need 4 arms? Can you combine some of these educational programs.
- Transient effect: Is it common in the literacy literature and look into other clinical studies such as in diabetes which require behavioral changes. There are issues of relapse and maintaining adherence.
- Timeline: Extend two years follow up time to address the "transient effect" although most studies have short follow up. Can you follow up subjects on StarPanel to show that you can address long term effects. Need to sit down with statitiscians to address realistically the multiple issues. How many clinics do you think that you could have access to? Recruitment time? How many subjects are needed?
- Consider short term effects and long term outcomes. Can you design you study pragmatically without too much effort to collect data? Using the real set up Dr. entries for follow up assessment.
- Recommendation: Follow up with VICTR voucher and statistician for help with proposal.
2016-07-18
Heather Lillimoe
General Surgery Resident
I am currently in the process of designing a research study pertaining to resident feedback within the department of surgery. My hope is to utilize REDCap for my primary mode of obtaining data. I was hoping to meet with a biostatistician as I apply for VICTR funding for the study. It involves an educational timeout before an operation. This is a 3rd year rotation in plastic surgery. There is an iphone app to do a competency rating.
- Survey - baseline assessment - residents and attendings - 85 questions
- Additional survey after rotation
Cara Singer
I am a
PhD student in the Department of Hearing and Speech Sciences. I would like to attend the biostat clinic today (if possible) to discuss appropriate analyses for a study I am conducting under the mentorship of Robin Jones (Developmental Stuttering Lab). The study is investigating whether a risk factor assessment (a mix of categorical and continuous variables) can predict stuttering persistence. 70-80% spontaneously recover. Would like to identify those likely to persist, in advance, for focusing therapy. Multiple risk factors have been identified. Empirical evidence for supporting predictive ability of the risk factors is sought.
- Children previously seen - diagnostic visit; 4y ago; stuttering up to 18m; English is primary language
- New follow-up for status at one point in time
- Baseline variables that originate from continuous measurements (e.g., age at onset) need to be analyzed as continuous variables
- Include baseline stuttering severity as a predictor
- With a maximum of 150 children the maximum number of candidate predictors might be around 10 if the outcome variable is almost continuous (it's worse if outcome is almost binary)
- Stuttering is multi-dimensional, e.g., some children may reduce amount of speaking because of the problem, so they seem to stutter less
- May consider a compound summary of all the outcome measures, e.g., average rank across children; clinical ranking of scenarios can also be used
- Dependent variable needs to have at least 5 frequently levels and be ordered or continuous
- If there is one standout, popular scale, that one could be used by itself
- Empirical variable selection requires an enormous sample size to reliably find the "right variables" so it's best not to use selection procedures; can find various approximations to the model for clinical non-computerized application
- Data reduction methods (variable clustering, principle components, redundancy analysis) can be useful for effectively reducing the number of predictors to use in the multivariable model
2016-06-20
Chris Brown, Internal Medicine Resident
- To go over analysis produced by VICTR biostatisticians
2016-05-09
Kazeem Oshkoya, Division of Clinical Pharmacology, Dr. Dan Roden's Lab
Data analysis on blood sample storage and drug concentration - look at whether a gel absorbs too much of a drug in the blood to make drug assessment accurate enough. Measured at baseline and 4h. Need to know how to describe the base value. Triplicate measurements available. More interested in relative comparison.
- Best to present all the raw data
- Might use 3 quartiles (25th and 75th percentiles and median) as descriptive stats and use Wilcoxon signed rank test for testing for a difference between baseline and 4h
- There's also two types of samples - same study repeated with different samples, sample drug concentration
- Only have 2 patients; plan to have 5 later
- Better to not average over the 3 replicates - may hide variability
- Bland-Altman plot (mean-difference plot) is a good way to show agreement and whether variation is stable over base levels. If band of variability expands going from left to right, this is an indication that perhaps the analysis should be done on the log concentration scale.
- Other useful ways to summarize data: mean absolute difference between estimated and true concentrations - separately by no gel and gel
- Can also show mean absolute differences between replicates ignoring the true concentrations
- There are problems with lower limit of detection, representing missing values that are not randomly missing; ordinary analysis may be problematic
Jessica Dennis, Lea Davis, Genetic Medicine
Modeling lab values to look for genetic variation; data from the synthetic derivative
- Interested in variation over time within patient
- Variants are summarized into polygenetic risk scores
- Difficulty in interpreting results if patients are being treated for the lab abnormality being studies
- How to define time zero?
- May want to ignore records corresponding to post-Rx periods
- Started with HDL
- Side study: confirm that med initiation that is supposed to modify HDL really does
- Simplest longitudinal analyses:
- Compute within-patient Gini's mean difference to correlation with gen. risk score; asks whether gen. risk is correlated with variability
- Similar but summarize with the median to correlate gen. risk with overall height of the longitudinal records
- Summarize entire longitudinal record with slope and intercept; AUC and relate summary measures to gen. risk score
- Would be useful to summarize the data using representative patients after clustering on mean HDL, shape, number of observations, maximum time gap between any two measurements
- Another type of analysis: summarize each patient using the 9 deciles of HDL; use these deciles to predict polygen. risk score
- Does not take time ordering into account
- Might add a slope or shape summary to the deciles
2016-05-02
Amanda Peltier, Department of Neurology
Discuss Aims and power analysis for R01
2016-04-11
Jake Landes, PT, DPT Vanderbilt Sports Medicine, Rehabilitation Services
- I am a physical therapist in the Sports Medicine outpatient department and we are planning two studies that we would like to discuss. Primarily, though, we would like to discuss a prospective observational study we will be performing this coming school year with overhead athletes – we will be looking at the relationship of core strength to the likelihood of shoulder injury in overhead athletes. We plan to test the athletes’ core strength at start of their season and then collect data on injuries and time lost from playing their sport during the season. Specifically, we have questions about what our number of subjects should be in order to determine a difference and what we will need to do statistically in order to analyze the data.
- Outcomes: number of days (or proportion) lost during the season due to shoulder injuries
- Need information on the proportion of athletes who would get shoulder injury during a season. Sample size needed would be large if the proportion is very low.
- Could use logistic regression to examine association between core strength and incidence of injury
- Consider other factors that could affect shoulder injury such as the type of sport, number of years practicing, etc. These factors can be adjusted for in the regression model.
- To calculate the sample size, need to specify the outcome, type of analysis used, the meaningful difference (effect size: odds ratio of injury upon one unit change in core strength) you want to detect, and some preliminary data on the outcome measurements (rate or variation). A rule of thumb: 20 cases of injury are needed for each factor you'd like to analyze.
- Consider choosing a type of sports with the greatest association between core strength and shoulder injury.
- how to quantify core strength, a single summary score?
- A second study I am wondering about is an Anterior Cruciate Ligament Reconstruction study where we are going to compare a group of patients in a home based program versus standard care (control). We are wanting to do a feasibility study this year in our clinic, and I think it will be a prospective case-control study, or maybe prospective cohort—we also want to know about N size and analysis after ward.
- Enroll 7 patients in one month. Feasibility study.
2016-03-14
Katherine McDonell, Neurology
- Parkinson's disease - norepinephrine; VICTR application
- Original intention peripheral blood pressure support
- Interested in a combined medication regiment
- Goal to get nor. into CNS
- Propose to study n=16 patients
- Need dose titration 100mg bid -> 600mg 3/day
- Which dose do patients tend to end up with?
- Is a safety & tolerability study, partly dose-finding
- Patient response that is monitored is blood pressure - minimizing orthostatic symptoms without side effects; target supine BP plus headaches, dizzyness, mania; symptoms are of primary emphasis
- Is there an accepted symptom summary scale? If not may need to just count the number of symptoms present
- But dose adjustments are clinical adjustments based on a symptom "gestalt"
- Target for analysis is final dose
- Need SD of dose; best available data will probably come from what doses are used long-term in clinical practice; we'll assume this is a stand-in for the final tolerable dose
- Once a useful SD estimate is found, it can be used to compute the likely margin of error in estimating the population mean required dose when n=16, with say 0.95 confidence. The margin of error is the half-width of the confidence interval.
- Would be good to know what evidence exists for the usefulness of plasma drug concentrations in estimating the final required dose
2016-02-22
Reagan Leverett, MD, MS, Assistant Professor, Department of Radiology, Women's Imaging
- PQI project. Two types of images (new vs. old method) were performed for each patient.
- Examine the agreement between the two methods based on the paired data (kappa stat). Readings are ordinal values.
- Let a few radiologists read the two sets of images in random order to study the agreement.
- May need a couple of hundreds of patients, and a few (2 to 6) radiologists. (also want to have good agreement between radiologists, that is, readings of a certain method do not heavily depend on the experiences of radiologists).
2016-02-01
Akshitkumar Mistry
Reserved spot for consulting with Chris F. about meta-analysis
2016-01-25
Stephen Patrick, Assistant Professor of Pediatrics and Health Policy, Division of Neonatology
- Mary-Margaret Fill, TDH EIS
- Neonatal abstinence syndrome and long term outcomes
- Merge TennCare data with educational data
- Suggest regression model with traditional covariate adjustment unless need to do special matching (family, neighborhood)
- Biggest assumptions: children move away from TN for reasons unrelated to potential educational achievement
- Confounding: women giving birth to infant with NAS may tend to be different from those not having an NAS child; need to adjust for all factors related to this that might be associated with educational outcome
- Also what is the effect of school on test scores?
- Birth records have mother's educational level, zip code, tobacco use
- Matching records may be challenged by mother changing last name
- Might also look at infant and mother utilization of services, diagnosis of ADHD, etc.; cross-correlate with educational achievement
2016-01-04
Here is the feedback I received on my application: Power analysis never should involve having a power of detecting a previously observed (and probably measured with bias) effect. Power should always be defined as the probability of detecting a minimal clinically meaningful effect. Also, this type of study is more suited for justifying sample size on the basis of precision of an effect of interest (usually a difference or a correlation). Precision is stated as a margin of error e.g. half-width of a confidence interval. Please revise Section E of the proposal and feel free to attend a clinic to discuss.
What was initially written: Power Analyses: Previous researchers have found moderate relationships between trauma severity and pain symptoms (r = .29; Poundja, Fikretoglu, & Brunet, 2006). Power analyses using unadjusted effect size from this study based on their sample size of 130 suggest a necessary sample size of at least 97 for the present study to reveal similar effects. Power
analyses of the results of studies of the relationships between trauma severity, pain severity, experiential avoidance, and anxiety sensitivity (Gootzeit, 2014; Ruiz-Párraga & López-Martínez, 2015) suggest that a sample size of 144-158 is necessary to find these associations. The hypotheses outlined above will be tested through bivariate correlation and
linear regression analyses. Specifically, relationships among variables of interest (Hypotheses 1A, 1B, 2A, 2B) will be assessed through Pearson product-moment correlation analyses to determine the strength of the association among these constructs in our sample. Tests of moderation (Hypotheses 2C, 3) will be tested using multiple linear regression with
cross-products of the variables of interest to assess the interaction between predictors. All analyses will be carried out on either SPSS 22 (IBM, 2013) or the R statistical package (R Development Core Team, 2010)
- See Chapter 8, P. 8-12 of http://fharrell.com/doc/bbr.pdf - suggest using the r=0 curve. This approach is using the margin of error based on 0.95 confidence limits. E.g.: "With a sample size of N subjects we can estimate the correlation coefficient between two variables to within a margin of +/- xx with 0.95 confidence (see graph)."
- Important to prioritize the comparisons and to report them in this pre-specified order so that no multiplicity corrections will be needed
- A regression model that allows for interaction between time since trauma and amount of trauma would allow for estimation of the time-decay or enhancement of memories-effect. The time interaction effect may be nonlinear.
2015 Dec 14
Sachin Patel, Psychiatry
- Animal model for exposure to stress, long at differential response to stress
- Interested in susceptibility to stress
- Measure of anxiety is a key measure (high = more anxious)
- Each animal has a baseline measure
- Would be good to do a Tukey mean-difference plot (Bland-Altman plot) to be sure that the delta is an adequate summary of the two measures
- Also watch for floor and ceiling effects
- Using the delta as a continuous stress response measure will optimize power and minimize arbitrariness
- Discussed regression to the mean
- Problem with choice of anxiety measure out of many
- A composite measure may help, e.g., average z-score or average rank; can do Spearman rho rank correlation on the result, against another variable; can describe variability in ranks across anxiety measures
- Otherwise analyses of disparate measures can be hard to reconcile
2015 Dec 7th
Pierce Trumbo
- Shade tree clinic, where patients do not have insurance or do not have enough insurance can get medical service.
- Primary outcomes: number of ER visits, length of hospital length of stay. Will compare before and after pts visited the clinic.
- N=680 patients and estimate to have ~300 meet inclusion (time span between first visit and last visit greater or equal to 1 year).
- Need estimate for VICTR application. Suggest for $5000.
2015 Nov 30th
Andrew T. Hale, Medical Scientist Training Program
- Need a quote for biostatistical support for a VICTR grant submission
- Want to assess the association between brain tumor grade (total 128, 93 1s and 35 2s) and gender, age at diagnosis, Edema (0-3), draining vein, necrosis, location (8 different location).
- Will apply for VICTR voucher in amount of $2000.
Christopher John Prendergast, Tracy McGregor
- We will specifically be seeking some guidance regarding graphical representation of data related to statin doses in children and adolescents.
Christopher Lee Brown
- Discussed analysis for reviewer's comments
2015 Nov 23rd
Mark A. Clay, Divisions of Cardiology and Critical Care
- The purpose of the study was to evaluate whether patients with single ventricle physiology undergoing the second stage of surgical palliation, who’s length to weight ratio was >90% were at higher risk for increased ICU length of stay, ventilator times, and increased non-invasive ventilation when compared to those whose length for weight was <90%. Analyzing the data with the Mann-Whitney U Test there was a statistically significant difference between ICU length of stay and ventilator hours for those with weight for length >90% compared to those <90%. However, I attempted to analyze the data again with Spearman’s to see if there was a correlation between increasing z-score percentile and there was no statistically significant correlation.
- Clinic question: Has the data been analyzed appropriately to answer the question? Should I be concerned that Spearman’s correlation did not show a statistically significant correlation between the variables even though there was a statistically significant difference between the groups? Should I use and how might I best demonstrate association or risk related to weight for length z-score >90% with linear regression?
Rebekah Griesenauer (Conley), Biomedical Engineering
- I am designing a study for a small group of human subjects to test the feasibility of a new tool that I designed for breast cancer assessment using medical images. I would like some guidance on effective study designs for a small number of patients and for determining the accuracy of a new tool when there is no current clinical equivalent to compare to.
- Need a measureble outcome to calculate the required sample size
2015 Nov 16th
Aaron C. Shaver, M.D., Ph.D. Assistant Professor of Pathology, Microbiology, and Immunology
- The csv consists of sample ID, the covariates I want to test (age as an integer and categorical variable; poor.risk through transcription, which are all categorical variables; and num.muts, which is an integer) and the OS and PFS data (for censoring rows, 0=censored and 1=dead). I would like to include the interaction between age and poor.risk, because I have biological reason to believe that that interaction is relevant. My questions concern: measuring goodness of fit of the model; how to interpret the interaction term; how to estimate power, given the large number of covariates and small sample size
2015 Nov 9th
Fernanda Maruri
- "If possible I would like some help interpreting results of 2 Wilcoxon Rank Sum tests in which one is significant and the other is not."
- Compare
Jessica Kaitlin Campbell
- The goal of the project is to examine the impact that the palliative care unit has had on the medical intensive care unit in terms of patient length of stay and mortality. I have collected data regarding some parameters per and post opening of the palliative care unit. I am interested in the best approach in analyzing the data.
- Have data a year before and a year after the unit opened. Want to compare LOS and mortality in MICU. Both groups had palliative consult, only some patients after went to the palliative care unit.
- Wil apply for VICTR biostat support. Suggest for $5000 study.
2015 Nov 2nd
Gabriella D. Cozzi
- GDM project analysis. Associaion between hoursehold income and education with the five primary endpoints.
Michael Chomat
- To discuss experimental study design and data analysis for a project within REDCaps
- Two REDCap data base can be merged based on common identifier.
Jamie Robine
- R questions about fitting logistic regression model and plotting the figure.
2015 Oct 19th
Rebecca Cox, Psychology
- I am working with the data from the National Comorbidity Survey Replication, a nationally representative sample used to estimate prevalence rates of psychological disorders. I have questions about what types of analyses to use with a complex sampling design that includes strata, clusters, and weights.
*Suggest review survey document to specify correct strata, clusters and weightings variables
*Set up complex survey design effects in SPSS complex module.
- Subpopulation command in stead of subset anaysis.
2015 Oct 5th
Stevenson, David, Health Policy
- Stratified cluster randomized trial.
- Intervention group: predicted mortality risk score obtained for all the patients, based on which "top patients" will be provided with hospice and will be expected to get better life quality. Control group: standard care. Individual agencies (50 in total) will be randomized to intervention/control group.
- Cutoff of risk score may vary within and across the sites. Information obtained from prediction model: median life expectancy, probabilities of death during certain time periods.
- If the primary outcome is continuous, would need SD to calculate sample size. If it's the time to event, we will need expected median time in each group.
- Consider the flexible/sequential design, having pilot sites included in the final analysis.
- Biostat resources: VICTR Voucher (35 hours). Dr. Matt Shotwell
Conor McWade, ED, PhD student
- Apply for Voucher (90 hours)
- Have collected car collision/victims data, demographics of the passengers, road characteristics.
- Define collision as fatal vs serious.
- Aim to develop a prediction model to predict the severity of collision based on location, time, etc.
2015 Sep 28
Katrina, Electrical Engineering
- Our study is on incidence of eye disease seen at Vanderbilt. We have data on 33,000 patients looking at incidence of disease and I would like to discuss how to best analyze this data.
- Whether incidence at Vanderbilt can represent incidence in Nashville
Scott
- I was hoping to come to biostats clinic today to get some help with sample size calculations for my project.
- Cross over design. Within subject correlation is 0.7. Need power calculation.
Wes Clord
- Power analysis of survival analysis
2015 Sep 21
Jose A Arriola, PGY 3 - Psychiatry
- "I plan to implement a different type of interview in the first episode psychosis outpatient clinic at Vanderbilt Psychiatric Hospital and investigate how it contributes to improve adherence and management. The type of interview is called Shared decision making approach which is a little bit different to what we are used to. I am planning to train the MDs and providers on this technique and then compare measurable outcomes before and after the training. The outcomes would be no-show clinic rates, hospitalizations, etc. (things that are recorded automatically on the patient's chart). "
- Statistical tests: Wilcoxon signed rank test for continuous outcomes, and McNemar's test for binary outcome
- Primary outcome: number of times that pt did not show up within 3 months raning 0-4. Proportional odds logistic model to analyze. num of no show after intervention ~ number of no show before intervention + age + gender
- Sample size calculation: use PS for paried binary outcome
Tamara Moyo, Hem/Onc
- Want to correlate the resistanze to therapy based on imaging with cell signal
- Wilcoxon signed rank test (paired t-test); Wilcoxon rank sum test (two group t-test)
- Mixed-effects model to adjust for other covariates.
2015 Sep 14
Mhd Wael Alrifai, Neonatology
- Name of project: Paretneral Protein Calculator (PPC)
- Type: Randomized controlled clinical trial, un-blinded
- Help needed: Discussing the primary and secondary outcomes, designing the database
- Study status: IRB approved, enrollment starting next week
- Research question: the effect of intervention on the accuracy of protein prescription. The primary endpoint is the ratio of target days to total days (target days are the days when prescriptions are given with correct amount).
Sudipa Sarkar
- My research topic is on the effect of statins on non-alcoholic fatty liver disease
- retrospective cohort study.
Michael C. Dewan, Department of Neurological Surgery
- I am interested in discussing sample size calculations. We are conducting a clinical trial evaluating the effectiveness of a prophylactic antiepileptic drug (levetiracetam) in brain tumor patients. For 14 days following surgery, patients will be randomized to either drug or no drug. The primary outcome is the development of a clinical seizure and the follow-up time to primary endpoint is 14 days.
Shruti
- I would like to address a few questions regarding sample size calculation for a translational study on the role of alternate complement activation in sickle cell lung disease
2015 Aug 24
Christopher Brown
- Retrospective cross-sectional study on heart failure patients.
- Outcome is the low potassium, related to urine output per hour.
Maya Yiadom, Emergence Medicine
- Criteria for giving EKG to diagose STEMI.
- Trigger criteria: typical symptom, atypical S
Megan Pask, Tricia Russ, BME
- Compare CT values between four groups.
- Use non parametric test: Kruskal Wallis test (ANOVA), Wilcoxon Rank sum test (two sample -t-test)
2015 Aug 17
Karl Zelik, Assistant Professor of Mechanical Engineering, Assistant Professor of Physical Medicine & Rehabilitation
- sample size calculations for a grant proposal
2015 Aug 3
Lan Wu, PMI
- Had questions about VICTR proposal review. Suggest use Wilcoxon Rank Sum test or Wilcoxon Signed Rank test to compare between and within subjects
- Try to identify subset of b-cell in this set of subjects - will be able to provide descriptive statistics
- Consent 60 subjects will estimate to have 30 subjects. Will quantify b-cell and compare b-cell among two different locations. First get a percentage of b-cell of the mixture then calculate the absolute number of b-cell per gram tissue.
- Will find SD from preliminary data and calculate required sample size based on that.
2015 June 29
Aaron Noll, VMS IV
- retrospective chart review of 1750 patients. correlation between screening exam results with 15 diseases. 923 patients had actual visits within two years (gold standard of disease).
- Analysis data set: two-by-two tables based on 923 patients. Compare demographics between 923 patients with (1750-923) patients.
- I am currently finishing a research project that is regarding various diagnoses that are able to be picked up on a screening exam (for diabetic retinopathy). To this point, I have calculated the following values for the 16 diagnoses of relevance: true positives/negatives, false positives/negatives, positive/negative predictive values, and sensitivities/specificities. However, I am unsure what the best test is to determine statistical significance or importance of these numbers--eg, do I use a 95% CI, odds ratio, etc. One issue with these results is that although I have a very large sample size for the initial screened population (over 900), many of the diagnoses have less than 5-10 true positive results.
- Zero or close to zero number in certain cells. Wilson confidence interval. binom.confint() of binom package.
2015 June 22
Nelleke van Wouwe, Department of Neurology
- We are working on a grant and we have some questions about a power calculation for a Repeated Measures ANOVA (based on effect size from a previous study).
2015 June 15
Daniel J. Miller, Department of Psychology, Psychological Sciences
- Discussion about microstimulation data to develop a test of the hypothesis that stimulating two areas in the brain from which evoked movements differ produces a blend of those movements (endpoint neuronal encoding)
- Need help understanding how to organize the data in order to build a model to explain physiological results (e.g., how the dual stimulation sites interact)
- Suggest apply for a $5000 VICTR voucher.
Kendall Anne Ulbrich, Pediatrics
- I am requesting assistance in figuring out statistical significance. We see a trend in the data with the diagnosis of chronic lung disease leading to increased risk of death after trach placement vs other diagnosis.
- Babies in NICU, outcome is alive/died, want to compare chronic lung disease to other diagnosis.
- There were ~15 diagnosis, among whom 12 had chronic lung disease.
- Total 115 babies (25 died in NICU). Primary outcome is the death in NICU. 8 (or 11) babies who had lung disease and died.
- Plot Kaplan-Meier curve first for description, use log-rank test.
- Can use Cox proportional hazard model to analyze the association between lung disease and survival in NICU.
- Could also apply for a $2000 VICTR voucher.
2015 June 1
Robert Lentz, cardiology
- My project is looking at radiation-induced atrial fibrillation, specifically in patients with breast and lung cancers. I have raw data extracted from the Synthetic Derivative and am hoping for some guidance regarding my data analysis plan and how I might be able to best display my data.
- There are ~3000 breast cancer pts (125 had AF), ~2000 lung cancer pts.
- To test the association between radiation and AF, include all pts (y=AF, x=radiation y/n, cancer side); then take subset of pts who had radiation, fit a model of radiation dose/side with AF.
- Length of follow up is different for all patients. Can use survival analysis. If certain proportion of pts died before developing AF, should treat those pts as competing risks events.
- If apply for VICTR voucher, suggest $5000.
Robert K. Tunney, Jr., Cardiology Resident
- Email: My research is investigating statin dose intensification according to the ACC/AHA 2013 Cholesterol Guidelines in post-ACS patients. I am interested in performing logistic regression analysis on ~300 patients and potentially Spearman rank r correlation coefficient.
- Two groups: historic control and intervention group. Binary outcome. Primary aim is to assess the outcome difference between groups.
- Chi-sq test and multivariable logistic regression can be used to test the primary hypothesis.
- Suggest propensity score adjustment.
- Will apply VICTR voucher in amount of $2000.
2015 May 11
Zac Cox, PharmD, BCPS
- Email: I would like to request a biostats clinic reservation on Monday 5/11 from 12-1 for a comparative effectiveness research project. The main question is selection of the best primary outcome to maximize power for a population size that will be fixed (secondary to funding and patient enrollment). Our second question is the best statistical analysis method for 3 independent continuous variables (ANOVA vs the 2 experimental groups independently compared to the standard of care comparison arm). Please let me know if you would like me to send anything in advance.
- Use continuous outcome to maximize power
- Wilcoxon rank sum test to compare two new treatment groups to the standard care group
- Multivariable linear model adjusting for baseline weight and treatment regimen
Michelle K. Roach, Obstetrics and Gynecology
- Email: We will be completing a retrospective chart review looking at pregnancy and delivery outcomes in women with gestataional diabetes. We plan to use RedCap database for data entry.
2015 Apr 27
Aaron Noll, Medical Student
- I am a third year medical student working on a research project that is evaluating the teleretinal imaging program at the Nashville VA Hospital. I attended one of your clinics about a month and a half ago and greatly appreciate the help I received at that time. I have now completed my data collection and am moving on to the data analysis portion of the research, and would like to discuss my revised project with you to see what the best way is for me to proceed.
- As an overview, I am looking into the teleretinal screening program to evaluate its efficiency and its accuracy at diagnosing abnormalities other than diabetic retinopathy (the true purpose). I have recorded the data on the following topics:
- Demographics (Age, sex, ethnicity)
- Months from consult entry to screening
- Days from screening until note loaded to chart
- Screening diagnoses, diagnoses found at subsequent visits, and diagnoses found at previous visits
- No-show rate for the screenings
- Consult timing
- Months since prior screenings and clinic visits
- Had imaging readings and clinic diagnosis on ~1700 subjects. There were 18 diagnosis categories, looking at their agreement.
- Will apply for VICTR voucher. Suggest $2000 for up to 35 hours
2015 Apr 20
Lexy Morvant, Pediatric
- NICU data analysis
- time trend of gestational age when receiving ECMO (Y2004-2014) for C-section babies. To evaluate the effect of policy change (increase gestational age for C-section baby in 2007) on ECMO.
- Only have the information on birth year available. Fit a linear regression model
- Also have the information on the total number of all ECMO babies. With an assumption that the proportion of C-section babies remains the same, could fit a poisson linear regression model.
2015 Apr 13
Jared
- I have a retrospective dataset of patients who underwent a new cochlear implant programming procedure. The data contain pre- and post-intervention objective performance data, demographic data, and information about the cochlear implant type and location. I am trying to develop model(s) that can answer the following questions: 1) How can we predict whether a patient will be a responder to re-programming? 2) Which variables are most predictive of change in performance from baseline?
- 177 patients.
- Endpoint: measurement performance (0-100)
- Predictors: 15 ~ 20
- Fit a multivariable linear regression model. Predictor importance can be measured based on the model.
2015 Mar 9
Taylor Leath
- We attended a biostats clinic on February 23rd to develop a statistical plan. Now that we have a dataset completed, we are having difficultly with our regression models and would appreciate your input.
2015 Feb 23
Katie Rizzone, M.D., Clinical Instructor, Orthopaedics and Rehabilitation
- I would like to request a methods clinic (to review my methods) for a retrospective chart review study on female college athletes and stress fractures I am writing an IRB for.
Taylor Leath
I would like to reserve a time on Monday, February 23rd to develop an appropriate statistical plan for our study and dataset. I've attached the study protocol which details our specific aims and hypotheses. Our primary questions:
1) Is linear regression the appropriate model to use? Predictors would be sex, age, years of education, participant's current health, trauma exposure and religiosity (all continuous except for sex), and the outcome variable would be each of the individual health states (GOSE 2-8). If so, this would mean six different regression models for the six health states?
2) Alternatively, would it be more appropriate to develop one regression model that includes the health state (GOSE 2-8) as an additional predictor?
3) Do we have sufficient sample size to answer our study questions? Current n=2156 after exclusions.
4) We would also like to show whether the utility values for each of the six health states are significantly different from one another-- would that simply be a within-subjects ANOVA with pairwise comparisons?
5) Should we consider transforming the worse-than-death values?
2015 Jan 12
Dr. Heidi J. Silver, Ph.D., R.D Research Associate Professor of Medicine
- Study of diet intervention, body composition, insulin resistance, lipo.
- Could apply for a VICTR voucher of $4000.
2014 Dec 15
Amos M. Sakwe, Department of Biochemistry and Cancer Biology, Meharry Medical College
2014 Nov 24
Paula DeWitt, Center for Biomedical Ethics and Society; Madhu Murphy, pediatric cardiac intensive care unit
Email: We are wanting to test the effectiveness of a “journey board” (see attachment) designed to better prepare parents for their child’s stay and eventual discharge from Vanderbilt’s pediatric cardiac intensive care unit. This will entail giving self-administered surveys with preparedness and satisfaction items to parents of children hospitalized in the pediatric ICU immediately before and immediately after the parent has been exposed to a 15-minute educational intervention using the journey board. The intervention will take place in the child’s hospital room (or another room in the unit) and will consist of a clinician walking the parent through the journey board, and answering any questions the parent may have. Immediately before this, a researcher (not the clinician) will approach the parent, explain the study, and ask if the parent would like to participate. If yes, the parent will be given two short (5-10 minute) self-administered surveys to complete. He/she will be asked to complete one prior to the intervention and one immediately after the intervention. The data will be used to assess the effectiveness of the journey board in preparing parents, and we would like your advice concerning numbers of parents we will need to interview to obtain statistical significance and statistical techniques to be used.
- Frank's note: Design is confounded with time/fatigue/learning. Also there is little precedent for doing a pre-post study with such little time between pre and post. I think you will need to do a randomized study to attribute any effect to the intervention. Randomize 1/2 of families to get the intervention, 1/2 to get the prevailing treatment, and give survey at the "after" time point for both groups.
Amma N. Bosompem, MPH graduate student
I'm a graduate student in the Masters of Public Health program who will be looking at treatment completion rates in a specific population for my thesis. I need some guidance on study design and what analyses are appropriate given my sample size.
- TB clinic in Nashville, 203 cases (information on case only) in year 2013.
- Treatment: completed vs not completed (refused, lost to follow up, etc.)
- Research question: 1. treatment completion rate. 2. the association between patient's characteristics and treatment completion.
- Prepare data set as http://biostat.mc.vanderbilt.edu/wiki/Main/DataTransmissionProcedures
- Is there an association between country of origin and acceptance of treatment (accepted vs. no accepted)
- Apply logistic regression analysis (dichotomous or binary response variable) and include the variables of interest. *General rule of thumb the smaller sample size/10 will help you assess your regression power or how many variables you can include in regression model *N=48 that refused and will be the limiting sample size in regression analysis
- Country of origin main factor and will have to think of best way of grouping *The covariates of interest: Age as continuous non-linear; gender, marital (married vs. non-married) and country of origin
2014 Nov 17
Mary Van Meter, medical student
My project is looking at the cost of packaging surgical instrument trays (possiblly using regression) and calculating the percentage of instruments used in trays across various Gyn specialties.
- Total number of instruments used per tray (25-100), usually less than 50% is used.
- Will compare unnecessary cost between specialty
- Will apply for VICTR voucher. A standard $2000 is appropriate.
- Patients underwent liver transplant who had plastic stent to treat leak, about 20-30% needed mental stent later
- Want to predict early whether patient needs mental or not so pt does not need to surfer pain
- The current data only gives conditional needs to mental if had plastic already
- Suggest do descriptive statistics and plan bigger study to develop prediction model
- Use R for internal validation and calibration using bootstrapping method (rms package)
2014 Nov 3
Monica Ledoux
I am an adjunct at Vanderbilt's Dermatology department, working with Zhengzheng Tang from biostats on microbiome and skin and would like to know the biostat budget for VICTR application(s)
- Want to know the relationship between Cortisone treatment and bacterial change.
- Each subject will be his own control: cortisone on one arm and no cortisone on the other. Each arm will be tested at two sites, one normal skin and one tape stripping skin. Observe bacterial change. Therefore, each subject will have 4 tested samples and each sample measured twice (total 8 per person)
- Look at treatment effect on normal skin. Suggest amount of $2000.
2014 Sept 29
Bryan I. Hartley, MD Department of Radiology
Review an abstract.
- There are limitations of pre post design. Many factors will affect the outcome besides the intervention like time.
- Box plot with raw data to explore the distribution
- Can use Wilcoxon signed rank test to compare continuous outcomes before and after
- Consider ANCOVA (Analysis of Covariance) to analyze post while adjust for pre specified covariates like previous experience
Adam P. Bregman, MD, MBA, Annette Ilg, Vanderbilt Internal Medicine Resident
I am starting a project with Dr. Anthony Langone in the renal transplant division and I have come across some questions with my redcap database that I would like to ask
- Retro spective study of post renal transplant patients. Follow those patients for two years to observe a rare event.
- Describe users characteristics. Some pts took medication for entire 6 months, some stopped prior 6 months for certain reasons, some retook it later. Can consider using certain amount of time to define user.
- Binary/categorical variables can be described as frequency and percentage
2014 Sept 22
Kasim Ortiz, Sociology, Doctoral Student
I’d like to obtain assistance with a project I completed this summer while attending the Fenway Summer Institute on LGBT Population Health. I used a dataset that permitted me to analyze the effects of states having restrictions on same-sex marriage on smoking, extending previous work by examining these impacts among racial minorities that are sexual minorities. My findings were counterintuitive to previously published work, insofar that I did not find where states restricting same-sex marriage policies had a negative impact on smoking among racial sexual minorities. The dataset is the Social Justice Sexuality Project.
Most previously published papers examining the effects of same-sex marriage policies on the health of LGBT populations have utilized GEE in their statistical analyses. However, I was having problems getting GEE models to converge with the cross sectional data I am using and thus I utilized GLM for the binomial family with adjustments for state clustering (vce) using STATA. I’m apprehensive about wrapping up the manuscript out of fear that I might get a ton of push back because of the methodology I’ve chosen. Also I was having problems with conducting post-hoc analyses on some of the interactions that I included in the analysis (sample sizes kept changing across models preventing me from appropriately conducting likelihood ratio tests). Thus, I wanted to obtain statistical advice on the differences between the two and consultation on how I should proceed. It is my understanding that R is utilized predominantly and since I am learning R in my statistical sequence this year, I thought this would be a great opportunity to compare STATA with R on a question that I’m invested in and a dataset that I’m familiar with.
- Logistic regression model with robust standard error is appropriate.
Robin Jones, Assistant professor
We have two questions regarding our project on respiratory sinus arrhythmia (RSA) and stuttered disfluencies.
We are interested in how that RSA (respiratory sinus arrhythmia, parasympathetic activity on the heart) is associated with speech disfluencies. RSA during various tasks is influenced by it’s baseline value, thus, in our model we need to account for baseline RSA in some way. When running a model predicting stuttered disfluencies with RSA during an emotional speaking task, should we use a) RSA during the task and RSA at baseline as covariates, or b) create a residualized difference score of RSA during task relative to baseline as a covariate? With option “a” we would be using two covariates in the model (RSA during task & RSA at baseline), whereas with option “b” we would be using only one (RSA difference score).
- Could include baseline RSA if colinearity is not an issue.
I would like to verify that our analytic plan is the most appropriate. We are using a Generalized Linear Regression with Negative Binomial Distribution. We are using this distribution because stuttered disfluencies are not normally distributed.
- Generalized Linear Regression with Negative Binomial Distribution is good.
The model for our 3rd research question: Is the relationship between RSA and stuttered disfluencies different for children who stutter versus children who do not stutter during various emotion conditions. We used a 3-way interaction (as well as the various 2-way permutations) to assess this: RSA*Group*Condition. However, when running this model, I am not getting an intercept term. Is the model flawed in some way?
Lastly, we have some outliers, and I am curious on what is the preferable way to handle this: 1) next case imputation, 2) log transformation, 3) square root transformation?
- Take into account the correlation within each subject.
- Might have carry-over effects between different periods. Could test on equivalent carry-over effects.
2014 Sept 15
Stacy S. Klein-Gardner, Ph.D. Biomedical Engineering
My data that I would like to analyze is survey data from a Likert scale that I believe to generate interval data. I am attaching the raw data to this message. We can focus only on the first spreadsheet as the analysis will be the same for all. The data that is shown includes pre and post data from each of three summers of educational intervention. On the spreadsheet, I have entered the data first under the summer in which the intervention and testing took place. I then moved the data around to indicate which summer it was for the student. For example a student may have come first the first time in 2012, 2013, or 2014. She may have come only one summer or she may have repeated the program. My question is: Does repeated participation in the intervention improve the impact that the program has on the measures indicated by this survey? Is one summer sufficient to increase this measure?
Background
- Outreach for engineering education
- looking at data from engineering camp for girls (looking for changes in self- efficacy)
- self- efficacy- feeling that you can accomplish something in your life (this scale has been validated) * some girls have participated for one year, some have participated for about three years
Research Question:
* interested to see if there is an effect of attending camp for more than one year
- also interested in differences in pre-post scores for the one year attended by student
Suggestions:
- descriptive statistics: consider summary statistics across different categories (i.e. pre and post scores by different school types, year of study, grades)
- Consider repeated measures type analysis (longitudinal data analysis) for assessment of slope over time (year) of self-efficacy variable
- Per question of interest - may need to reformat data to “long style or vertical format” (i.e. have row 1 id=1: 2012 post self-efficacy score, row 2 id=1: 2013 post, row 3 id=1 2014 post self-efficacy score, etc. for each of the girls)
- adjust for age , school type (consider the role of additional potential confounders)
- Consider applying for VICTR funding– for assistance in repeated measures type of analysis.
- Need to account for the correlated nature of data and verification of assumptions (such as in Mixed effects modeling or generalized least squares)
- Account for the missing data
- Limitation: lack of control group (there is no way to conclude that the program is the only thing that is improving self efficacy)
- pre vs. post score for any given year
- consider doing boxplots for each of the pre and post scores for each year (these can serve as your summary statistics)
- Univariate analysis: Wilcoxon Signed rank test to see if there is a difference between the distributions of pre and post scores (data in horizontal format works)
- cautioned combining the pre-scores over the three years, and post scores over the three years (year may be a confounder and impact trend of the data)
- pre vs. post study (may see a difference, however no guarantee that improvement is from the program- not an randomized controlled trial)
- Motivated and selected group of girls and may have higher self-efficacy baseline score (pre) - consider comparing self-efficacy scores with those reported in other studies among girls.
2014 Sep 8
Jason Winnick, MPB
I perform biomedical research where the sample sizes are generally approximately 6 to 10 per group. The primary outcome variables are usually something like counterregulatory hormones levels, glucose in fusion rates, or muscle glucose uptake. I will be submitting an R01 in October and I would like to receive your advice regarding the estimation of sample size. In addition there may be the potential to receive statistical assistance over the life of the grant if it's funded.
- Two primary endpoints; one with greatest variability (glucose infusion rate needed to maintain desired blood glucose level) has most variability and hence will be conservative to plan for
- 10 with type I DM 10 without
- Other covariates: age, insulin required to maintain blood glucose, HbA1c
- Baseline liver glycogen assessment
- Start with 3 hour fructose infusion to stimulate liver glucose update vs. saline infusion (randomized), then insulin infusion then 2 hour period where become hypoglycemic (using clamp)
- Need a good estimate of the standard deviation across patients for infusion rate - use the dog data taking all relevant time periods and stratify by liver glycogen to compute 12 SDs; then we can compute an averaging by averaging the variances and taking the square root
- Need clinically relevant difference (in mean infusion rates) not to miss: estimate 1 mg/Kg/min
- Language for grant application something like: The power calculation was based on a 2-sample t-test without covariate adjustment for HbA1c, age, etc. The actual statistical test will be ANCOVA adjusting for these factors, which will increase the actual power a bit (increase would be more had the sample size been larger; the sample size chosen has a penalty for estimating the effects of the baseline covariates).
- Last aim: most general way to assess to to fit a smooth function of time to the longitudinal (serial) measurements, separately for each of two groups, and test for differences in shape of the two curves. A convenient choice is to fit a quadratic function of time to each curve. This increases power over individual time point tests. Suggested statistical method: generalized least squares or mixed effects linear model.
- Suggested contacting Li Wang to tell her that a VICTR voucher is in the works
2014 Aug 18
Cecilia Di Pentima, Zachary Willis, Pediatric
- Want to assess the impact of the implementation of an ASP on antibiotics use.
- Monthly antimicrobials (AMs) use in days from 2009-2012 April. Data from many hospitals including Vanderbilt. Want to compare Vanderbilt to ALLCHA.
- ASP intervention started 2012 March at Vanderbilt. Can see less use of AMs after intervention.
- The comparison of pre and post might be biased by other factors like time not just by intervention. Institution effect is hard to assess since all institutions started intervention at different times.
- Also needs to adjust for other factors like date for seasonal effect.
- Linear model of VCG ~ intervention + rcs(time)
- Better to have individual data for all the hospitals which had both pre and after data to assess intervention effect using mixed-effects model, or just compare between hospitals using data after intervention to see whether Vanderbilt does better than others
- Consider get Vanderbilt rank among all CHA
2014 July 21
Kelvin Moses, Urologic Surgery
- wants to do a pilot study to get preliminary results for a grant submission.
- requesting data from Southern Community Cohort Study (SCCS). Needs power analysis and statistical plan for the data request.
- applying for VICTR biostats support for funding for this prelim project. Needs estimate.
- about 3200 men enrolled. max follow-up 10 years. about half finished the whole study period.
- Prediction of screening frequency by baseline characteristics. Association between prostate cancer stage and frequency of screening.
- all patient self-reported data, at 5 year and 10 year. (have you had screening within the last year?)
- GEE model of screening frequency (recent screening yes/no at 5 year, 10 year) on age, race, interaction between age and race, ...
- Ordinal logistic regression model of prostate cancer stage/grade on screening frequency (need be carefully defined) prior to diagnosis. Need consider different follow-up of the patients.
- Contact Li Wang(li.wang@vanderbilt.edu) for budget estimate.
Austin Beason, summer medical student, MOON Group
- How can I determine the required sample size (i.e. number of subjects or raters) for interval estimation of the Kappa statistic for an intraobserver and interobserver study with multiple raters? Our number of subjects is currently 20 (N=20) and our current number of raters is 27 (n=27). Further, we are hoping the given sample size will give at least 80% power at the 0.05 level of significance (two-sided).
- >library(kappaSize)
14July14
April Barnado, Leslie Crofford, Division of Rheumatology
- Email: I am submitting an early career grant for a starter type project due August 1 and needed help with performing and writing up power/sample size calculations.
- Specific Aim #1: identify group of lupus patients of about 1135. Lupus nephritis patients of about 400. Nephritis is severity indicator.
- Specific Aim #2: Determine the association between ED use and meeting standards of quality of care in management of SLE and in the treatment of SLE nephritis, as defined by the Quality Indicator Set for SLE. For aims #2, I would likely be performing Chi squared tests comparing 3 groups (non, occasional, and frequent ER users) for most of those sub-aims.
- Specific Aim #3: Determine the association between ED use and corticosteroid use in SLE and SLE nephritis. For aim #3, I would likely be using multiple linear regression.
- For binary outcomes, use logistic regression with adjustment of other confounders.
- Ratio will be treated as continuous variable and will be analyzed using general linear model.
- Hypothesis: more ED use will have higher steroid dose. Will analyze current steroid dose and #ED visits in the past 12 months. Steroid dose will be a ordered categorical variable with 4 levels. Can use Chi-square test. Proportional odds model can be used to adjust for other confounders.
- Grant due Aug 1st, need to be done July 21st.
Taylor Leath, Trauma in Surgical Sciences
- Survey on quality of life (N=1000). There are 7 GOSE questions about health states (0-100). Can describe the distribution for each GOSE. Predictors include gender, age, and years of education.
- Want to compare between GOSE scores. Multiple comparison issues (21 comparisons).
- Can use mixed-effects model taking into account of within subject correlation.
Ola Oluwole, Medicine
- N=36 patients who had CLL transplant with two types (8 vs. 27). Want to compare survival between two groups.
- Time from transplant to death or relapse. Sample size is limited. Mainly descriptive. Want to write manuscript.
- Can apply for voucher of $4000.
23June14
Neelam Patel, Medical Student
- I am fourth year medical student doing a project for dermatology. We are doing a meta-analysis of pediatric vitiligo patients to assess which populations need thyroid studies performed. I have a spreadsheet of the data. I need help analyzing it.
- Research question: the percentage of thyroid abnormalities in pediatric vitiligo patients.
- Only have aggregated data. Could have an overall estimate of percentage. Also could explore the variability between studies.
- Apply for a $2000 Voucher.
Tyler Kendrick, Anesthesiology, Medical Student
- One-year prospective study. Will record the numbers of surgeries in Ethiopia (an African country) and the number of perioperative mortalities.
- Sample size calculation to reach a desirable precision of mortality rate estimate.
28April14
Wei Xie, Computer Science, Brad Malin, DBMI
- we want to find out if the IRLS estimation algorithm is reversible -- e.g., given only the Fisher information matrix and scoring function (and \beta coefficients), can we go back to the original Y or X matrices
- Context is confidentiality with data coming from multiple sites, with each site's data maintained independently, and controlled
- How to do model diagnostics without residuals?
- Does the distributed computing model lead to good statistical modeling practice? E.g.: covariate transformations, Y transformation, normality of residuals [could compute residual vector separately by center and share an ECDF of the residuals)
- How often are practitioners of distributed statistical analysis assuming linearity of covariate effects? Being careful about transforming Y or modeling Y robustly?
- Can't reverse the process to solve for an individual's datum if model is full rank, n > p, no parameter is devoted to only one subject, residual vector is secret
- If a single parameter is devoted to 5 subjects at one site, may possibly be able to solve for a summary statistic for the 5 (e.g., race has 4 levels and one of the levels only applies to 5 subjects at a site)
- May be able to discern that one site has an overall better level of Y than another site
- Not able to get a robust sandwich covariance matrix estimator if residual vector is not provided; sandwich estimation requires U matrix not just U vector
- Even if residuals are available, it may not be possible to work backwards to an individual from a given site because estimates come from a global beta vector over all sites
- We seldom use OLS with health care data; the need for weighted X'X (X'VX) instead of X'X as used in OLS makes the identification problem more difficult in general, because V is a function of the current beta estimate (for all sites combined)
- Worthwhile working out the special case where Y is binary and there is a single X that is binary or polytomous, and there is no special knowledge (e.g., k subjects are of type x and all have the same Y)
- Worth taking another look at data squashing
Neil Templeton, Engineering, CHBE
- Metabolic flux analysis
- Rate of metabolite turnover
- Which metabolic phenotypes are produced in high titre-achieving production processes
- Protein therapeutics; cost of production
- 14 conditions (cell lines); correlations between fluxes (80 reactions- flux, mass spec); looking for up-regulation
- 80 Spearman rank correlations x 14; each correlation 10 observations (clones)
- Two controls; secondary controls
- Independent experimental units: clones, manipulations of cell lines
- See if a unified model would be a better approach than pairwise analysis
- Must be able to precisely estimate a quantity such as a correlation coefficient in order to be reliable in picking "winners" across reactions
- Low precision (low number of independent experimental units) implies low probability of selecting the optimum reaction/condition
- Dimensionality is high enough that an "omics" method may be needed
- Recommend contining discussion at a Tuesday or Friday clinic
14April14
Elizabeth Morse, RN, MSN, FNP-BC, MPH Vanderbilt University School of Nursing
- My project involves survey data of 220 Spanish and Arabic-speaking patients in the Center for Women's Health. I've completed all of the descriptive statistics but need help with the correlations. For example, I know from having surveyed patients myself that those patients who reported speaking "Arabic only" at home were more likely to self-report speaking English "not very well", but I don't know how to express this statistically.
- To test association between two variables A and B,
- If A is a continuous variable and B is categorical variable, use Kruskal Wallis test (or Wilcoxon rank-sum test)
- If A and B are both categorical variables, use chi-square test
- If A is ordinal variable and B is binary, use chi-square trend test
- If A and B are both continuous variables, use spearman's correlation coefficient.
31Mar14
Brett Byram, BME
* Clinical image degradation with ultrasound
- What are major factors of degradation? Pulling apart mechanisms.
- Clinical target: liver tumors/biopsy; visualize needle
- What is the best study design?
- Ask trained readers to assess utility of image
- Discusssed hypothesis testing vs estimation study
- One estimand could be the mean absolute number of levels different
- Can relate an ordinal measure to quantitative measures of image quality
- Can estimate # patients needed if have a reliable estimate of the standard deviation of an absolute difference of interest
- May consider progressively ruining an image to see when it becomes uninterpretable
- One goal is to develop a model to predict expert's quality rating from multiple quantitative physics-based measures
- May consider an ordinal response model / multinomial model
10Feb14
Steve Kahn, General Surgery Fellow
- can't arrive before 1pm on Wednesdays, so attending Monday clinic
- "I am going to perform an email survey of surgical residents (approx 5500 in the US) and wanted to know what you think an appropriate response rate would be and the best method to do statistical analysis (rough draft of survey attached). Or should the questions be revised to facilitate a better statistical analyisis?"
- make the variable as continuous as possible using sliding bar
Philip Budge, Fellow, Division of Infectious Diseases
- grant proposal relating to the development of new diagnostic technologies for neglected tropical diseases
- Survey on two cohorts, VA-based cohort and university-based cohort.
- Outcome: global physical and mental health score. Pain is part of global score, and also a barrier to level of reintegration success. Could calculate a global score without pain. Could examine how pain correlates with reintegration and outcome.
- A specific question (meaning of life) in two standardized questionnaire. Could include both in the model predicting outcome.
27Jan14
Stephanie Fecteau, Psychiatry Post-Doc
- Cortisol measures 3 per day
- % of increase because times not noted accurately
- Need Bland-Altman plot to check proper transformation: post - pre vs. (post + pre)/2 or log(post) - log(pre) vs. geometric mean of pre and post
- want the transformation that makes the graph flat and random
- 1/2 of families received a service dog after 3 weeks
- Suggest longitudinal analysis using 3 daily x 15 weeks, allowing for correlation; only one day per week
- Correlation structure based on approximate time of measurements in days + fraction of day
- Model smooth time trend, allowing for separate trend in those randomized to service dog; check for shape change between two groups
- Easiest-to-interpret method generalized least squares with AR1 continuous-time correlation structure
David Dantzler and Donald Lynch, Cardiovascular Medicine
- ECMO: what predicts survival to hospital discharge; initiated by cardiac surgeons
- Collecting patients from last 2 years (N=60 so far)
- Discussed margin of error of 0.1 in estimating a single probability with n=96
- Alternate endpoints: LOS, censor on death, i.e. Y=time to successful discharge
- Or: ordinal outcome Y=1, 2, 3, ... longest LOS, dead = longest LOS + 1; effective sample size almost equal to # subjects
- Also have Glasgow coma scale at discharge; could factor into ordinal outcome
- May be possible to use a complex high-information scale to derive a severity of illness-based score that is then used to predict mortality
- Has reduced many variables to one
- What to do with patients who died before ECMO was available?
13Jan14
Mitchell Odom, VUMC 3rd year medical student, Department of Neurosurgery.
I am currently helping with a project that requires a survey be employed, and we are creating an original one to send out. I would like to get some expert opinions on the questions that we ask, and to make sure we are honing in on what we're really looking for.
- CTE - Chronic Traumatic Encephalitis caused by multiple concussions. Survey is designed to ask questions about awareness of CTE among parents of young athletes (junior high and high school). The plan is to distribute the survey using Vanderbilt connections with local high schools.
- Recommendations:
- Maximize response rate (by giving parents incentives of some sort)
- Ensure that the survey is brief
- Make sure the responses are anonymous
- Use numbers instead of categories
- Simplify the language
- Branch questions
- Incorporate visual analog scale (instead of categories)
- Order questions in a logical way
Older Notes