Log: scab2.sas

 
 1          OPTIONS NONOTES NOSTIMER NOSOURCE NOSYNTAXCHECK;
 NOTE: ODS statements in the SAS Studio environment may disable some output features.
 73         
 74         /********************* scab2.sas (2018 verion) **********************/
 75         title 'Randomization Tests on the Scab Disease Data';
 76         
 77         data potato;
 78              infile '/folders/myfolders/441s18/Lecture/ScabDisease.data.txt';
 79              length condition $ 10.; /* Default length of character values is 8. */
 80              input condition $  infection;
 81              label infection = 'Ave percent surface covered';
 82         
 83         ods  select OverallANOVA;
 
 NOTE: The infile '/folders/myfolders/441s18/Lecture/ScabDisease.data.txt' is:
       Filename=/folders/myfolders/441s18/Lecture/ScabDisease.data.txt,
       Owner Name=root,Group Name=vboxsf,
       Access Permission=-rwxrwx---,
       Last Modified=11Feb2018:15:28:04,
       File Size (bytes)=578
 
 NOTE: 33 records were read from the infile '/folders/myfolders/441s18/Lecture/ScabDisease.data.txt'.
       The minimum record length was 0.
       The maximum record length was 16.
 NOTE: SAS went to a new line when INPUT statement reached past the end of a line.
 NOTE: The data set WORK.POTATO has 32 observations and 2 variables.
 NOTE: DATA statement used (Total process time):
       real time           0.00 seconds
       cpu time            0.01 seconds
       
 84         proc glm data=potato order=data;
 
 85              title2 'With proc glm for Comparison';
 86              class condition;
 87              model infection=condition;
 88         run;
 
 89         
 
 NOTE: PROCEDURE GLM used (Total process time):
       real time           0.05 seconds
       cpu time            0.05 seconds
       
 90         proc npar1way wilcoxon data=potato;
 
 91              title2 'Classical Kruskal-Wallis Test';
 92              class condition;
 93              var infection;
 94              exact / mc seed=77777 maxtime=300;
 95              /* It will never take 5 minutes, but just to be safe .... */
 96         run;
 
 NOTE: PROCEDURE NPAR1WAY used (Total process time):
       real time           0.42 seconds
       cpu time            0.20 seconds
       
 
 97         
 98         proc npar1way scores=data data=potato;
 99              title2 'Randomization Test';
 100             class condition;
 101             var infection;
 102             exact / mc seed=88888 maxtime=300;
 103        run;
 
 NOTE: PROCEDURE NPAR1WAY used (Total process time):
       real time           0.30 seconds
       cpu time            0.14 seconds
       
 
 104        
 105        /* Follow up with proc multtest. All 21 pairwise comparisons plus
 106              * Control vs. Average of Spring
 107              * Control vs. Average of Fall
 108              * Average of Spring vs. Average of Fall
 109         */
 110        
 111        proc multtest data=potato order=data
 112             permutation nsample=20000 seed=99999 ;
 113             title2 'Randomization multiple comparisons with proc multtest';
 114             class condition;
 115             /* Pairwise                                                 Bonferroni */
 116             contrast 'Control vs. Spring300'    1 -1  0  0  0  0  0;    /* 1.0000  */
 117             contrast 'Control vs. Spring600'    1  0 -1  0  0  0  0;    /* 1.0000  */
 118             contrast 'Control vs. Spring1200'   1  0  0 -1  0  0  0;    /* 1.0000  */
 119             contrast 'Control vs. Fall300'      1  0  0  0 -1  0  0;    /* 0.0888  */
 120             contrast 'Control vs. Fall600'      1  0  0  0  0 -1  0;    /* 1.0000  */
 121             contrast 'Control vs. Fall1200'     1  0  0  0  0  0 -1;    /* 0.0096  */
 122             contrast 'Spring300 vs. Spring600'  0  1 -1  0  0  0  0;
 123             contrast 'Spring300 vs. Spring1200' 0  1  0 -1  0  0  0;
 124             contrast 'Spring300 vs. Fall300'    0  1  0  0 -1  0  0;
 125             contrast 'Spring300 vs. Fall600'    0  1  0  0  0 -1  0;
 126             contrast 'Spring300 vs. Fall1200'   0  1  0  0  0  0 -1;
 127             contrast 'Spring600 vs. Spring1200' 0  0  1 -1  0  0  0;
 128             contrast 'Spring600 vs. Fall300'    0  0  1  0 -1  0  0;
 129             contrast 'Spring600 vs. Fall600'    0  0  1  0  0 -1  0;
 130             contrast 'Spring600 vs. Fall1200'   0  0  1  0  0  0 -1;
 131             contrast 'Spring1200 vs. Fall300'   0  0  0  1 -1  0  0;
 132             contrast 'Spring1200 vs. Fall600'   0  0  0  1  0 -1  0;
 133             contrast 'Spring1200 vs. Fall1200'  0  0  0  1  0  0 -1;
 134             contrast 'Fall300 vs. Fall600'      0  0  0  0  1 -1  0;
 135             contrast 'Fall300 vs. Fall1200'     0  0  0  0  1  0 -1;
 136             contrast 'Fall600 vs. Fall1200'     0  0  0  0  0  1 -1;
 137             /* Averages */
 138             contrast 'Control vs. Spring'       3 -1 -1 -1  0  0  0;
 139             contrast 'Control vs. Fall'         3  0  0  0 -1 -1 -1;
 140             contrast 'Spring vs. Fall'          0  1  1  1 -1 -1 -1;
 141             test mean(infection); /* Requests t-tests */
 142        run;
 
 NOTE: The multiple testing procedure for this run is not closed. In cases with badly heteroskedastic data, tests for individual 
       null hypotheses can have inflated familywise Type I error rates.
 NOTE: There were 32 observations read from the data set WORK.POTATO.
 NOTE: PROCEDURE MULTTEST used (Total process time):
       real time           0.31 seconds
       cpu time            0.30 seconds
       
 
 143        
 144        /* The only issue is Controll vs. Fall300. p = 0.0519, but it's an
 145           ESTIMATE of the p-value from a randomization test. Is it
 146           SIGNIFICANTLY above 0.05? */
 147        
 148        proc iml;
 NOTE: IML Ready
 149             title2 'Testing H0: p = 0.05 with a large-sample Z-test for proportions';
 150             p = 0.0519;
 150      !                  n = 20000;
 150      !                             Z = sqrt(n)*(p-0.05)/(0.05*0.95);
 151             print p Z;
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 160        OPTIONS NONOTES NOSTIMER NOSOURCE NOSYNTAXCHECK;
 173