The MCMC Procedure

This subsection describes how to monitor transformation of an effect u when the students variable is an indexing subject variable. An indexing subject variable is an integer variable that takes value from one to the total number of unique subjects in a variable. In other words, the variable can be used as an index in a SAS array. The indexing subject variable does not need to be sorted for the example code in this section to work. An example of an indexing variable takes the values of (1 2 3 4 5 1 2 3 4 5), where the total number of observation is n=10 and the number of unique values is m=5.

The following statements create an indexing variable students in the data set a:

data a;
   input students @@;
   datalines;
1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10
;

The following statements run a random-effects model without any response variables. There are only random-effects parameters in the model; the program calculates the logit transformation of each effect, saves the results to the OUTPOST= data set, and produces Figure 73.22:

proc mcmc data=a monitor=(p) diag=none stats=none outpost=a1
   plots=none seed=1;
   array p[10];
   random u ~ n(0, sd=1) subject=students;
   p[students] = logistic(u);
   model general(0);
run;

proc print data=a1(obs=3);
run;

The ARRAY statement creates an array p of size 10, which is the number of unique values in students. The p array stores all the transformed values. The RANDOM statement declares u to be an effect with the subject variable students. The P[STUDENTS] assignment statement calculates the logit transformations of u and saves them in appropriate array elements—this is why the students variable must be an indexing variable. Because the students variable used in the p[] array is also the subject variable in the RANDOM statement, PROC MCMC can match each random-effects parameter with the corresponding element in array p. The MONITOR= option monitors all elements in p and saves the output to the a1 data set. The a1 data set contains variables p1–p10. Figure 73.22 shows the first three observations of the OUTPOST= data set.

The variable p1 is the logit transformation of the variable u_1, p2 is the logit transformation of the variable u_2, and so on.

The same idea works for a students variable that is unsorted. The following statements create an unsorted indexing variable students with repeated measures in each subject, fit the same model, and produce Figure 73.23:

data a;
   input students @@;
   datalines;
   1 1 1 3 5 3 4 5 3 1 5 5 4 4 2 2 2 2 4 3
;
proc mcmc data=a monitor=(p) diag=none stats=none outpost=a1
   plots=none seed=1;
   array p[5];
   random u ~ n(0, sd=1) subject=students;
   p[students] = logistic(u);
   model general(0);
run;

proc print data=a1(obs=3);
run;

There are five random-effects parameters in this example, and the array p also has five elements. The values p1–p5 are the transformations of u_1–u_5, respectively. The u variables are not sorted from u_1 to u_5 because PROC MCMC creates the names according to the order by which the subject variable appears in the input data set. Nevertheless, because students is an indexing variable, the first element p[1] stores the transformation that corresponds to students=1 (which is u_1), the second element p[2] stores the transformation that corresponds to students=2, and so on.

A non-indexing subject variable can take values of character literals (for example, names) or numerals (for example, ZIP code or a person’s weight). This section illustrates how to monitor functions of random-effects parameters in these situations.

Suppose you have unsorted character literals as the subject variable:

data a;
   input students$ @@;
   datalines;
   smith john john mary kay smith lizzy ben ben dylan
   ben toby abby mary kay kay lizzy ben dylan mary
;

A statement such as following does not work anymore because a character variable cannot be used as an array index:

p[students] = logistic(u);

In this situation, you usually need to do two things: (1) find out the number of unique values in the subject variable, and (2) create a numeric index variable that replaces the students array index. You can use the following statements to do the first task:

proc sql noprint;
   select count(distinct(students)) into :nuniq from a;
quit;
%put &nuniq;

The PROC SQL call counts the distinct values in the students variable and saves the count to the macro variable &nuniq. The macro variable is used later to specify the element size of the p array. In this example, the a data set contains 20 observations and 9 unique elements (the value of &nuinq).

The following statements create an Index variable in the a data set that is in the order by which the students names appear in the data set:

proc freq data=a order=data noprint;
   tables students / out=_f(keep=students);
run;

proc print data=_f;
run;

data a(drop=n);
   set a;
   do i = 1 to nobs until(students=n);
      set _f(keep=students rename=(students=n)) point=i nobs=nobs;
      Index = i;
   end;
run;

proc print data=a;
run;

The PROC FREQ call identifies the unique students names and saves them to the _f data set, which is displayed in Figure 73.24.

The DATA step steps through the a data set and creates an Index variable to match the order in which the students names appear in the data set. The new a data set^[36] is displayed in Figure 73.25.

Student smith is the first subject, and his Index value is one. The same student appears again in the sixth observation, which is given the same Index value. Now, this Index variable can be used to index the p array, in a similar fashion as demonstrated in previous programs:

data _f;
   set _f;
   subj = compress('p_'||students);
run;
proc sql noprint;
   select subj into :pnames separated by ' ' from _f;
quit;
%put &pnames;

proc mcmc data=a monitor=(p) diag=none stats=none outpost=a1
   plots=none seed=1;
   array p[&nuniq] &pnames;
   random u ~ n(0, sd=1) subject=students;
   p[index] = logistic(u);
   model general(0);
run;

proc print data=a1(obs=3);
run;

The first part of the DATA step and the PROC SQL call create array names for the p array that match the subject names in the students variable. It is not necessary to include these steps for the PROC MCMC program to work, but it makes the output more readable. The first DATA step steps through the _f data set and creates a subj variable that concatenates the prefix characters p_ with the names of the students. The PROC SQL calls put all the subj values to a macro called &pnames, which looks like the following:

p_smith p_john p_mary p_kay p_lizzy p_ben p_dylan p_toby p_abby

In the PROC MCMC program, the ARRAY statement defines an p array with size &nuniq (9), and use the macro variable &pnames to name the array elements. The P[INDEX] assignment statement uses the Index variable to find the correct array element to store the transformation. Figure 73.26 displays the first few observations of the OUTPOST=a1 data set.

There are nine random-effects parameters (u_smith, u_john, and so on). There are nine elements of the p array (p_smith, p_john, and so on); each is the logit transformation of corresponding u elements.

You can use the same statements for subject variables that are numeric non-indexing variables. The following statements create a students variable that take large numbers that cannot be used as indices to an array. The rest of the program monitors functions of the effect u. The output is not displayed here.

data a;
   call streaminit(1);
   do i = 1 to 20;
      students = rand("poisson", 20);
      output;
   end;
   drop i;
run;

proc sql noprint;
   select count(distinct(students)) into :nuniq from a;
quit;
%put &nuniq;

proc freq data=a order=data noprint;
   tables students / out=_f(keep=students);
run;

data a(drop=n);
   set a;
   do i = 1 to nobs until(students=n);
      set _f(keep=students rename=(students=n)) point=i nobs=nobs;
      Index = i;
   end;
run;

data _f;
   set _f;
   subj = compress('p_'||students);
proc sql noprint;
   select subj into :pnames separated by ' ' from _f;
   quit;
%put &pnames;

proc mcmc data=a monitor=(p) diag=none stats=none outpost=a1
   plots=none seed=1;
   array p[&nuniq] &pnames;
   random u ~ n(0, sd=1) subject=students;
   p[index] = logistic(u);
   model general(0);
run;

proc print data=a1(obs=3);
run;