Log:scab2.sas

 
 1          OPTIONS NONOTES NOSTIMER NOSOURCE NOSYNTAXCHECK;
 NOTE: ODS statements in the SAS Studio environment may disable some output features.
 71         
 72         /********************* scab2.sas (2020 version) **********************/
 73         title 'Randomization Tests on the Scab Disease Data';
 74         
 75         data potato;
 76              infile '/home/brunner0/441s20/ScabDisease.data.txt';
 77              length condition $ 10.; /* Default length of character values is 8. */
 78              input condition $  infection;
 79              label infection = 'Ave percent surface covered';
 80         
 81         ods  select OverallANOVA;
 
 NOTE: The infile '/home/brunner0/441s20/ScabDisease.data.txt' is:
       Filename=/home/brunner0/441s20/ScabDisease.data.txt,
       Owner Name=brunner0,Group Name=oda,
       Access Permission=-rw-r--r--,
       Last Modified=04Jan2020:16:00:45,
       File Size (bytes)=578
 
 NOTE: 33 records were read from the infile '/home/brunner0/441s20/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
       user cpu time       0.00 seconds
       system cpu time     0.00 seconds
       memory              754.46k
       OS Memory           29096.00k
       Timestamp           03/29/2020 02:59:01 PM
       Step Count                        62  Switch Count  3
       Page Faults                       0
       Page Reclaims                     165
       Page Swaps                        0
       Voluntary Context Switches        29
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           264
       
 
 82         proc glm data=potato order=data;
 83              title2 'With proc glm for Comparison';
 84              class condition;
 85              model infection=condition;
 86         run;
 
 87         
 
 NOTE: PROCEDURE GLM used (Total process time):
       real time           0.03 seconds
       user cpu time       0.04 seconds
       system cpu time     0.00 seconds
       memory              3836.46k
       OS Memory           31416.00k
       Timestamp           03/29/2020 02:59:01 PM
       Step Count                        63  Switch Count  3
       Page Faults                       0
       Page Reclaims                     585
       Page Swaps                        0
       Voluntary Context Switches        22
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           744
       
 
 88         proc means data = potato order=data;
 89              class condition; var infection;
 90         run;
 
 NOTE: There were 32 observations read from the data set WORK.POTATO.
 NOTE: PROCEDURE MEANS used (Total process time):
       real time           0.03 seconds
       user cpu time       0.02 seconds
       system cpu time     0.01 seconds
       memory              8372.78k
       OS Memory           38844.00k
       Timestamp           03/29/2020 02:59:01 PM
       Step Count                        64  Switch Count  1
       Page Faults                       0
       Page Reclaims                     2182
       Page Swaps                        0
       Voluntary Context Switches        24
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           0
       
 
 91         
 92         proc npar1way wilcoxon data=potato;
 93              title2 'Classical Kruskal-Wallis Test';
 94              class condition;
 95              var infection;
 96              exact / mc seed=77777 maxtime=300;
 97              /* It will never take 5 minutes, but just to be safe .... */
 98         run;
 
 NOTE: PROCEDURE NPAR1WAY used (Total process time):
       real time           2.53 seconds
       user cpu time       0.17 seconds
       system cpu time     0.02 seconds
       memory              14797.34k
       OS Memory           44716.00k
       Timestamp           03/29/2020 02:59:04 PM
       Step Count                        65  Switch Count  1
       Page Faults                       0
       Page Reclaims                     4371
       Page Swaps                        0
       Voluntary Context Switches        792
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           896
       
 
 99         
 100        proc npar1way scores=data data=potato;
 101             title2 'Randomization Test';
 102             class condition;
 103             var infection;
 104             exact / mc seed=88888 maxtime=300;
 105        run;
 
 NOTE: PROCEDURE NPAR1WAY used (Total process time):
       real time           0.31 seconds
       user cpu time       0.12 seconds
       system cpu time     0.01 seconds
       memory              3146.09k
       OS Memory           46132.00k
       Timestamp           03/29/2020 02:59:04 PM
       Step Count                        66  Switch Count  1
       Page Faults                       0
       Page Reclaims                     541
       Page Swaps                        0
       Voluntary Context Switches        627
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           696
       
 
 106        
 107        /* Follow up with proc multtest. All 21 pairwise comparisons plus
 108              * Control vs. Average of Spring
 109              * Control vs. Average of Fall
 110              * Average of Spring vs. Average of Fall
 111         */
 112        
 113        proc multtest data=potato order=data
 114             permutation nsample=20000 seed=99999 ;
 115             title2 'Randomization multiple comparisons with proc multtest';
 116             class condition;
 117             /* Pairwise                                                 Bonferroni */
 118             contrast 'Control vs. Spring300'    1 -1  0  0  0  0  0;    /* 1.0000  */
 119             contrast 'Control vs. Spring600'    1  0 -1  0  0  0  0;    /* 1.0000  */
 120             contrast 'Control vs. Spring1200'   1  0  0 -1  0  0  0;    /* 1.0000  */
 121             contrast 'Control vs. Fall300'      1  0  0  0 -1  0  0;    /* 0.0888  */
 122             contrast 'Control vs. Fall600'      1  0  0  0  0 -1  0;    /* 1.0000  */
 123             contrast 'Control vs. Fall1200'     1  0  0  0  0  0 -1;    /* 0.0096  */
 124             contrast 'Spring300 vs. Spring600'  0  1 -1  0  0  0  0;
 125             contrast 'Spring300 vs. Spring1200' 0  1  0 -1  0  0  0;
 126             contrast 'Spring300 vs. Fall300'    0  1  0  0 -1  0  0;
 127             contrast 'Spring300 vs. Fall600'    0  1  0  0  0 -1  0;
 128             contrast 'Spring300 vs. Fall1200'   0  1  0  0  0  0 -1;
 129             contrast 'Spring600 vs. Spring1200' 0  0  1 -1  0  0  0;
 130             contrast 'Spring600 vs. Fall300'    0  0  1  0 -1  0  0;
 131             contrast 'Spring600 vs. Fall600'    0  0  1  0  0 -1  0;
 132             contrast 'Spring600 vs. Fall1200'   0  0  1  0  0  0 -1;
 133             contrast 'Spring1200 vs. Fall300'   0  0  0  1 -1  0  0;
 134             contrast 'Spring1200 vs. Fall600'   0  0  0  1  0 -1  0;
 135             contrast 'Spring1200 vs. Fall1200'  0  0  0  1  0  0 -1;
 136             contrast 'Fall300 vs. Fall600'      0  0  0  0  1 -1  0;
 137             contrast 'Fall300 vs. Fall1200'     0  0  0  0  1  0 -1;
 138             contrast 'Fall600 vs. Fall1200'     0  0  0  0  0  1 -1;
 139             /* Averages */
 140             contrast 'Control vs. Spring'       3 -1 -1 -1  0  0  0;
 141             contrast 'Control vs. Fall'         3  0  0  0 -1 -1 -1;
 142             contrast 'Spring vs. Fall'          0  1  1  1 -1 -1 -1;
 143             test mean(infection); /* Requests t-tests */
 144        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
       user cpu time       0.32 seconds
       system cpu time     0.00 seconds
       memory              1178.37k
       OS Memory           45224.00k
       Timestamp           03/29/2020 02:59:05 PM
       Step Count                        67  Switch Count  1
       Page Faults                       0
       Page Reclaims                     77
       Page Swaps                        0
       Voluntary Context Switches        13
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           48
       
 
 145        
 146        /* The only issue is Controll vs. Fall300. p = 0.0519, but it's an
 147           ESTIMATE of the p-value from a randomization test. Is it
 148           SIGNIFICANTLY above 0.05? */
 149        
 150        proc iml;
 NOTE: IML Ready
 151             title2 'Testing H0: p = 0.05 with a large-sample Z-test for proportions';
 152             p = 0.0519;
 152      !                  n = 20000;
 152      !                             Z = sqrt(n)*(p-0.05)/sqrt(0.05*0.95);
 153             print p Z;
 154        quit;
 NOTE: Exiting IML.
 NOTE: PROCEDURE IML used (Total process time):
       real time           0.01 seconds
       user cpu time       0.01 seconds
       system cpu time     0.00 seconds
       memory              509.50k
       OS Memory           44964.00k
       Timestamp           03/29/2020 02:59:05 PM
       Step Count                        68  Switch Count  1
       Page Faults                       0
       Page Reclaims                     133
       Page Swaps                        0
       Voluntary Context Switches        11
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           8
       
 
 155        
 156        /* Try a bigger MC sample size: 200 thousand. */
 157        
 158        proc multtest data=potato order=data
 159             permutation nsample=200000 seed=99999 ;
 160             title2 'Bigger MC sample size: See Control vs. Fall300';
 161             class condition;
 162             /* Pairwise                                                 Bonferroni */
 163             contrast 'Control vs. Spring300'    1 -1  0  0  0  0  0;    /* 1.0000  */
 164             contrast 'Control vs. Spring600'    1  0 -1  0  0  0  0;    /* 1.0000  */
 165             contrast 'Control vs. Spring1200'   1  0  0 -1  0  0  0;    /* 1.0000  */
 166             contrast 'Control vs. Fall300'      1  0  0  0 -1  0  0;    /* 0.0888  */
 167             contrast 'Control vs. Fall600'      1  0  0  0  0 -1  0;    /* 1.0000  */
 168             contrast 'Control vs. Fall1200'     1  0  0  0  0  0 -1;    /* 0.0096  */
 169             contrast 'Spring300 vs. Spring600'  0  1 -1  0  0  0  0;
 170             contrast 'Spring300 vs. Spring1200' 0  1  0 -1  0  0  0;
 171             contrast 'Spring300 vs. Fall300'    0  1  0  0 -1  0  0;
 172             contrast 'Spring300 vs. Fall600'    0  1  0  0  0 -1  0;
 173             contrast 'Spring300 vs. Fall1200'   0  1  0  0  0  0 -1;
 174             contrast 'Spring600 vs. Spring1200' 0  0  1 -1  0  0  0;
 175             contrast 'Spring600 vs. Fall300'    0  0  1  0 -1  0  0;
 176             contrast 'Spring600 vs. Fall600'    0  0  1  0  0 -1  0;
 177             contrast 'Spring600 vs. Fall1200'   0  0  1  0  0  0 -1;
 178             contrast 'Spring1200 vs. Fall300'   0  0  0  1 -1  0  0;
 179             contrast 'Spring1200 vs. Fall600'   0  0  0  1  0 -1  0;
 180             contrast 'Spring1200 vs. Fall1200'  0  0  0  1  0  0 -1;
 181             contrast 'Fall300 vs. Fall600'      0  0  0  0  1 -1  0;
 182             contrast 'Fall300 vs. Fall1200'     0  0  0  0  1  0 -1;
 183             contrast 'Fall600 vs. Fall1200'     0  0  0  0  0  1 -1;
 184             /* Averages */
 185             contrast 'Control vs. Spring'       3 -1 -1 -1  0  0  0;
 186             contrast 'Control vs. Fall'         3  0  0  0 -1 -1 -1;
 187             contrast 'Spring vs. Fall'          0  1  1  1 -1 -1 -1;
 188             test mean(infection); /* Requests t-tests */
 189        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           2.22 seconds
       user cpu time       2.23 seconds
       system cpu time     0.00 seconds
       memory              847.21k
       OS Memory           45224.00k
       Timestamp           03/29/2020 02:59:07 PM
       Step Count                        69  Switch Count  1
       Page Faults                       0
       Page Reclaims                     51
       Page Swaps                        0
       Voluntary Context Switches        13
       Involuntary Context Switches      3
       Block Input Operations            0
       Block Output Operations           48
       
 
 190        
 191        proc iml;
 NOTE: IML Ready
 192             title2 'Another large-sample Z-test of H0: p = 0.05';
 193             p = 0.0515;
 193      !                  n = 200000;
 193      !                              Z = sqrt(n)*(p-0.05)/sqrt(0.05*0.95);
 194             print p Z;
 195        quit;
 NOTE: Exiting IML.
 NOTE: PROCEDURE IML used (Total process time):
       real time           0.01 seconds
       user cpu time       0.01 seconds
       system cpu time     0.00 seconds
       memory              501.15k
       OS Memory           44964.00k
       Timestamp           03/29/2020 02:59:07 PM
       Step Count                        70  Switch Count  1
       Page Faults                       0
       Page Reclaims                     133
       Page Swaps                        0
       Voluntary Context Switches        11
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           8
       
 
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 200        
 201        OPTIONS NONOTES NOSTIMER NOSOURCE NOSYNTAXCHECK;
 212