options ls=80;
libname barley 'barley_data';
proc freq data=barley.comb;where MWG036B ^= '.' and RISIC10A ^= '.';
table MWG036B*RISIC10A;
run;
proc nlin data=barley.comb; where MWG036B ^= '.' and RISIC10A ^= '.';
 R=.0267; /* Recombination fraction from the linkage map */
 parms a=1 r1=0 to .0267 by .01 mu=76;
 bounds 0 <=r1 <= R;
 r2=(R-r1)/(1-2*r1);
 if MWG036B='A' and RISIC10A='A' then x=r1*r2/(1-R);
 if MWG036B='B' and RISIC10A='B' then x=1-r1*r2/(1-R);
 if MWG036B='A' and RISIC10A='B' then x=r1*(1-r2)/R;
 if MWG036B='B' and RISIC10A='A' then x=r2*(1-r1)/R;
 model env9=mu-2*a*x;
run;
proc glm data=barley.comb;where MWG036B ^= '.' and RISIC10A ^= '.';
class MWG036B RISIC10A;
model env9=MWG036B RISIC10A;
lsmeans MWG036B RISIC10A;
run;