Log:uvtubes.sas

 
 1          OPTIONS NONOTES NOSTIMER NOSOURCE NOSYNTAXCHECK;
 55         
 56         /********************* uvtubes.sas ***********************/
 57         title 'Fungus Tube data in univariate format';
 58         
 59         data mould1;
 60              infile '/folders/myfolders/tubes.data.txt' firstobs=2  missover;
 61               /* missover makes data omitted at the end of a line missing. */
 62              input line mcg rep day  AML AMS AMld   PML PMS PMld   AMslp PMslp SWeight;
 63              label mcg     = 'Fungus Type'
 64                    rep     = 'Replication (1-4)'
 65                    AML     = 'AM Length'    AMS = 'AM Number of Sclerotia'  AMld = 'AM Leading Edge'
 66                    PML     = 'PM Length'    PMS = 'PM Number of Sclerotia'  PMld = 'PM Leading Edge'
 67                    AMslp   = 'AM Least-squares Slope'
 68                    PMslp   = 'PM Least-squares Slope'
 69                    SWeight = 'Slerotial Weight';
 70              Tube = 1000*rep + mcg; /* 4-digit tube identifier */
 71              Length = (AML+PML)/2;
 72              Sclerotia = (AMS+PMS)/2;
 73              /* Zero sclerotia were recorded as missing. */
 74              if Sclerotia=. then Sclerotia=0;
 75              Slope = (AMslp+PMslp)/2;
 76              if Tube ne 1213; /* Getting rid of the outlier, based on science. */
 77         
 78         /* Fungus grew past the end of some tubes after day 10 so it was really a 10-day
 79            experiment, but day 14 has slopes and weight of sclerotia. These variables will
 80            still be available in mould1, with one non-missing value for each tube. */
 81         
 
 NOTE: The infile '/folders/myfolders/tubes.data.txt' is:
       Filename=/folders/myfolders/tubes.data.txt,
       Owner Name=root,Group Name=vboxsf,
       Access Permission=-rwxrwx---,
       Last Modified=25Mar2016:08:32:33,
       File Size (bytes)=20782
 
 NOTE: 336 records were read from the infile '/folders/myfolders/tubes.data.txt'.
       The minimum record length was 59.
       The maximum record length was 69.
 NOTE: Missing values were generated as a result of performing an operation on missing values.
       Each place is given by: (Number of times) at (Line):(Column).
       46 at 71:19    61 at 72:22    312 at 75:20   
 NOTE: The data set WORK.MOULD1 has 322 observations and 17 variables.
 NOTE: DATA statement used (Total process time):
       real time           0.01 seconds
       cpu time            0.01 seconds
       
 82         data mould2;
 
 83              set mould1;
 84              if day < 11;
 85         
 
 NOTE: There were 322 observations read from the data set WORK.MOULD1.
 NOTE: The data set WORK.MOULD2 has 230 observations and 17 variables.
 NOTE: DATA statement used (Total process time):
       real time           0.00 seconds
       cpu time            0.00 seconds
       
 86         proc print;
 
 87              var Tube mcg rep day Length Sclerotia;
 88         
 
 NOTE: There were 230 observations read from the data set WORK.MOULD2.
 NOTE: PROCEDURE PRINT used (Total process time):
       real time           0.37 seconds
       cpu time            0.37 seconds
       
 89         proc freq;
 
 90              title2 'Sample sizes';
 91              tables day*mcg / norow nocol nopercent missing;
 92         
 
 NOTE: There were 230 observations read from the data set WORK.MOULD2.
 NOTE: PROCEDURE FREQ used (Total process time):
       real time           0.07 seconds
       cpu time            0.07 seconds
       
 93         proc tabulate;
 
 94              title2 'Mean Length';
 95              class day mcg;
 96              var Length;
 97              table (day all),(mcg all) * (mean*Length);
 98         
 
 NOTE: There were 230 observations read from the data set WORK.MOULD2.
 NOTE: PROCEDURE TABULATE used (Total process time):
       real time           0.04 seconds
       cpu time            0.05 seconds
       
 99         proc glm;
 
 100             title2 'Proc glm just for the mean plot';
 101             class day mcg;
 102             model Length = day|mcg;
 103        
 
 NOTE: PROCEDURE GLM used (Total process time):
       real time           0.63 seconds
       cpu time            0.22 seconds
       
 104        proc mixed cl;
 
 105             title2 'Unstructured Covariance Matrix';
 106             class day mcg;
 107             model Length = day|mcg;
 108             repeated / type=un subject=tube;
 109             lsmeans mcg / pdiff adjust=bon;
 110        /* Test linear growth starting with day 2. H0 is
 111                                  mu1  mu2  mu3  mu4  mu5  mu6  mu7  mu8  mu9  mu10
 112           mu2-mu3 = mu3-mu4  <=>  0    1   -2    1    0    0    0    0    0    0
 113           mu3-mu4 = mu4-mu5  <=>  0    0    1   -2    1    0    0    0    0    0
 114           mu4-mu5 = mu5-mu6  <=>  0    0    0    1   -2    1    0    0    0    0
 115           mu5-mu6 = mu6-mu7  <=>  0    0    0    0    1   -2    1    0    0    0
 116           mu6-mu7 = mu7-mu8  <=>  0    0    0    0    0    1   -2    1    0    0
 117           mu7-mu8 = mu8-mu9  <=>  0    0    0    0    0    0    1   -2    1    0
 118           mu8-mu9 = mu9-mu10 <=>  0    0    0    0    0    0    0    1   -2    1
 119        */
 120             contrast 'LinearAfter2'
 121                               day 0    1   -2    1    0    0    0    0    0    0,
 122                               day 0    0    1   -2    1    0    0    0    0    0,
 123                               day 0    0    0    1   -2    1    0    0    0    0,
 124                               day 0    0    0    0    1   -2    1    0    0    0,
 125                               day 0    0    0    0    0    1   -2    1    0    0,
 126                               day 0    0    0    0    0    0    1   -2    1    0,
 127                               day 0    0    0    0    0    0    0    1   -2    1;
 128        
 129        /* Finally, test whether an ar(1) is good enough */
 130        
 
 NOTE: Convergence criteria met.
 NOTE: PROCEDURE MIXED used (Total process time):
       real time           0.27 seconds
       cpu time            0.26 seconds
       
 131        proc mixed method=ml;
 
 132             title2 'Full model for Sigma is unstructured';
 133             class day mcg;
 134             model Length = day|mcg;
 135             repeated / type=un subject=tube;
 136        
 
 NOTE: Convergence criteria met.
 NOTE: PROCEDURE MIXED used (Total process time):
       real time           0.13 seconds
       cpu time            0.13 seconds
       
 137        proc mixed method=ml;
 
 138             title2 'Reduced model for Sigma is AR(1)';
 139             class day mcg;
 140             model Length = day|mcg;
 141             repeated / type=ar(1) subject=tube;
 142        
 
 NOTE: Convergence criteria met.
 NOTE: PROCEDURE MIXED used (Total process time):
       real time           0.09 seconds
       cpu time            0.08 seconds
       
 143        proc iml;
 
 NOTE: IML Ready
 144             title2 'Difference between chi-squared values is chi-squared';
 145             Chisquare = 382.99-219.86;
 145      !                                 df=54-1;
 145      !                                          pvalue = 1-probchi(Chisquare,df);
 146             print Chisquare df pvalue;
 147        
 148        
 149        
 150        OPTIONS NONOTES NOSTIMER NOSOURCE NOSYNTAXCHECK;
 162