-------------------------------------------------------------------------------------------------
       log:  C:\MyDocs\MPH\Text\SecondEdition\WebDoFiles\4.11.Sepsis.log
  log type:  text
 opened on:  30 Dec 2007, 20:16:09

. *  4.11.Sepsis.log
. *
. *  Simple logistic regression of mortal status at 30 days (fate) against
. *  baseline APACHE II score (apache) in a random sample of septic patients
. *
. use C:\WDDtext\4.11.Sepsis.dta, clear

. summarize fate apache

    Variable |       Obs        Mean    Std. Dev.       Min        Max
-------------+--------------------------------------------------------
        fate |        38    .4473684    .5038966          0          1
      apache |        38    19.55263    11.30343          0         41

. glm fate apache, family(binomial) link(logit)

Iteration 0:   log likelihood = -15.398485  
Iteration 1:   log likelihood =   -14.9578  
Iteration 2:   log likelihood = -14.956086  
Iteration 3:   log likelihood = -14.956085  

Generalized linear models                          No. of obs      =        38
Optimization     : ML                              Residual df     =        36
                                                   Scale parameter =         1
Deviance         =  29.91217061                    (1/df) Deviance =  .8308936
Pearson          =  66.34190718                    (1/df) Pearson  =  1.842831

Variance function: V(u) = u*(1-u)                  [Bernoulli]
Link function    : g(u) = ln(u/(1-u))              [Logit]

                                                   AIC             =  .8924255
Log likelihood   = -14.95608531                    BIC             = -101.0409

------------------------------------------------------------------------------
             |                 OIM
        fate |      Coef.   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
      apache |   .2012365   .0609004     3.30   0.001      .081874     .320599
       _cons |  -4.347806   1.371623    -3.17   0.002    -7.036138   -1.659474
------------------------------------------------------------------------------

. predict logodds, xb

. generate prob = exp(logodds)/(1 + exp(logodds))

. list apache fate logodds prob in 1/3

     +---------------------------------------+
     | apache    fate     logodds       prob |
     |---------------------------------------|
  1. |     16   Alive   -1.128022   .2445263 |
  2. |     25    Dead    .6831065   .6644317 |
  3. |     19   Alive   -.5243126   .3718444 |
     +---------------------------------------+

. sort apache

. label variable prob "Probability of Death"

. scatter fate apache || line prob apache, yaxis(2) color(red)    ///
>     , ylabel(0 1, valuelabel angle(0))                          ///
>       ylabel(, axis(2) angle(0) labcolor(red) tlcolor(red))     ///
>       ytitle(,axis(2) color(red))                               ///
>       yscale(titlegap(-8)) xlabel(0(10)40) legend(off)

. log close
       log:  C:\MyDocs\MPH\Text\SecondEdition\WebDoFiles\4.11.Sepsis.log
  log type:  text
 closed on:  30 Dec 2007, 20:16:11
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