Log:scab1.sas

 
 1          OPTIONS NONOTES NOSTIMER NOSOURCE NOSYNTAXCHECK;
 55         
 56         /********************* scab1.sas ***************************/
 57         title 'Scab Disease Data';
 58         
 59         data potato;
 60              infile '/folders/myfolders/ScabDisease.data.txt';
 61              length condition $ 10.; /* Default length of character values is 8. */
 62              input condition $  infection;
 63              label infection = 'Ave percent surface covered';
 
 NOTE: The infile '/folders/myfolders/ScabDisease.data.txt' is:
       Filename=/folders/myfolders/ScabDisease.data.txt,
       Owner Name=root,Group Name=vboxsf,
       Access Permission=-rwxrwx---,
       Last Modified=08Jan2016:21:27:35,
       File Size (bytes)=576
 
 NOTE: 32 records were read from the infile '/folders/myfolders/ScabDisease.data.txt'.
       The minimum record length was 16.
       The maximum record length was 16.
 NOTE: The data set WORK.POTATO has 32 observations and 2 variables.
 NOTE: DATA statement used (Total process time):
       real time           0.01 seconds
       cpu time            0.01 seconds
       
 64         proc freq;
 
 65              tables condition;
 66         
 
 NOTE: There were 32 observations read from the data set WORK.POTATO.
 NOTE: PROCEDURE FREQ used (Total process time):
       real time           0.04 seconds
       cpu time            0.04 seconds
       
 67         proc means;
 
 68              class condition;
 69              var infection;
 70         
 
 NOTE: There were 32 observations read from the data set WORK.POTATO.
 NOTE: PROCEDURE MEANS used (Total process time):
       real time           0.03 seconds
       cpu time            0.04 seconds
       
 71         proc glm;
 
 72              class condition;
 73              model infection = condition / clparm;
 74              /* clparm gives CIs for contrasts down in the estimate statements. */
 75              /* Pairwise multiple comparisons */
 76              lsmeans condition / pdiff tdiff adjust = tukey;
 77              lsmeans condition / pdiff tdiff adjust = bon;
 78              lsmeans condition / pdiff tdiff adjust = scheffe;
 79              /* Test some custom contrasts. Beware of alphabetical order:
 80                 Control Fall1200 Fall300 Fall600 Spring1200 Spring300 Spring600*/
 81              contrast 'Overall test for comparison' condition 1 -1  0  0  0  0  0,
 82                                                     condition 1  0 -1  0  0  0  0,
 83                                                     condition 1  0  0 -1  0  0  0,
 84                                                     condition 1  0  0  0 -1  0  0,
 85                                                     condition 1  0  0  0  0 -1  0,
 86                                                     condition 1  0  0  0  0  0 -1;
 87         
 88              contrast 'Av. of Fall vs. Control'   condition 3 -1 -1 -1  0  0  0;
 89              contrast 'Av. of Spring vs. Control' condition 3  0  0  0 -1 -1 -1;
 90              contrast 'Fall vs. Spring'           condition 0  1  1  1 -1 -1 -1;
 91         
 92              contrast 'Spring Amount'             condition 0  0  0  0  1 -1  0,
 93                                                   condition 0  0  0  0  0  1 -1;
 94         
 95              contrast 'Fall Amount'               condition 0  1 -1  0  0  0  0,
 96                                                   condition 0  0  1 -1  0  0  0;
 97         
 98              contrast 'Spr vs. Fall for 300 lbs.' condition 0  0  1  0  0 -1  0;
 99              contrast 'Spr vs. Fall for 600 lbs.' condition 0  0  0  1  0  0 -1;
 100             contrast 'Spr vs. Fall, 1200 lbs'    condition 0  1  0  0 -1  0  0;
 101        
 102             /* Estimate and CI for Control vs. Fall 1200 (F = t^2) */
 103             estimate 'Control vs. Fall 1200'     condition 1 -1  0  0  0  0  0;
 104             estimate 'Control vs. Mean of Fall'
 105                      condition 3 -1 -1 -1  0  0  0 / divisor = 3;
 106        
 107        /* Scheffe critical value for a test of s contrasts is critval * (p-1)/s.
 108           For p=7 means and a single contrast, it's critval *  (7-1)/1 */
 
 NOTE: PROCEDURE GLM used (Total process time):
       real time           2.14 seconds
       cpu time            0.83 seconds
       
 109        proc iml;
 
 NOTE: IML Ready
 110             title2 'Critical value for all possible 1-df Scheffe F-tests';
 111             numdf = 6;
 111      !                   /* p-1 = Numerator degrees of freedom for initial test */
 112             dendf = 25;
 112      !                   /* n-p = Denominator degrees of freedom for initial test */
 113             alpha = 0.05;
 114             critval = finv(1-alpha,numdf,dendf);
 114      !                                            print critval;
 115             ScheffeCritval = critval*numdf;
 115      !                                      print ScheffeCritval;
 116        
 NOTE: Exiting IML.
 NOTE: PROCEDURE IML used (Total process time):
       real time           0.02 seconds
       cpu time            0.02 seconds
       
 117        proc iml;
 
 NOTE: IML Ready
 118             title2 'Table of Scheffe critical values for COLLECTIONS of contrasts';
 119             numdf = 6;
 119      !                   /* Numerator degrees of freedom for initial test */
 120             dendf = 25;
 120      !                   /* Denominator degrees of freedom for initial test */
 121             alpha = 0.05;
 122             critval = finv(1-alpha,numdf,dendf);
 123             zero = {0 0};
 123      !                    S_table = repeat(zero,numdf,1);
 123      !                                                     /* Make empty matrix */
 124             /* Label the columns */
 125             namz = {"Number of Contrasts in followup F-test"
 126                     "    Scheffe Critical Value"};
 127             mattrib S_table colname=namz;
 128             do i = 1 to numdf;
 129                s_table(|i,1|) = i;
 130                s_table(|i,2|) = numdf/i *  critval;
 131             end;
 132             reset noname;
 132      !                    /* Makes output look nicer in this case */
 133             print "Initial test has"  numdf " and " dendf "degrees of freedom."
 134                   "Using significance level alpha = " alpha;
 135             print s_table;
 136        
 137             /* Example of subsetting vs. contrasts */
 138        
 NOTE: Exiting IML.
 NOTE: PROCEDURE IML used (Total process time):
       real time           0.03 seconds
       cpu time            0.03 seconds
       
 139        proc glm;
 
 140             title2 'Test differences among treatments excluding control';
 141             title3 'Using contrasts of all means (traditional)';
 142             class condition;
 143             model infection = condition;
 144             contrast 'Differences excluding control' condition 0  1 -1  0  0  0  0,
 145                                                      condition 0  0  1 -1  0  0  0,
 146                                                      condition 0  0  0  1 -1  0  0,
 147                                                      condition 0  0  0  0  1 -1  0,
 148                                                      condition 0  0  0  0  0  1 -1;
 
 NOTE: PROCEDURE GLM used (Total process time):
       real time           0.37 seconds
       cpu time            0.16 seconds
       
 149        proc glm;
 
 150             title2 'Test differences among treatments excluding control';
 151             title3 'Subset the data by excluding control';
 152             where condition ne 'Control'; /* Case sensitive */
 153             class condition;
 154             model infection = condition;
 155        
 156        
 157        OPTIONS NONOTES NOSTIMER NOSOURCE NOSYNTAXCHECK;
 169