* Fisher analysis;

* Set working directory (Put your directory in place of xxxxxx);
  %let dir = c:\xxxxxx;
  %let dir = c:\documents and settings\jbaldwin\Desktop\Fisher manuscript new2\Revisions;

* Load all of the SAS macros;
  %include "&dir.\fisher macros.sas";

* Import data;
  PROC IMPORT OUT=histories DATAFILE= "&dir.\data by zones.xlsx" 
    DBMS=EXCEL2007 REPLACE; sheet="Data"; 
    GETNAMES=YES; MIXED=NO; SCANTEXT=YES; USEDATE=YES; SCANTIME=YES;
  run;

* Duplicate data so that "All Zones" is a new zone (so SAS "by" statement can be used);
  data histories;
    set histories;
	output;
	Zone = "All";
	output;
  run;

* Sort by zone;
  proc sort data=histories out=histories;
    by zone;
  run;

* Set the number of seasons;
  %let nSeasons = 8;

* Perform analyses of each model;
*        Prob of presence: psiType = dot, Year, logit;
*             Persistence: phiType = dot, 0, Year;
*   Detection probability: pType = dot, Year, TwoGroup, YearTwoGroup;

  %Analysis(histories,8,psiType=dot,phiType=dot,pType=dot)
  %Analysis(histories,8,psiType=dot,phiType=dot,pType=Year)
  %Analysis(histories,8,psiType=dot,phiType=Year,pType=dot)
  %Analysis(histories,8,psiType=dot,phiType=Year,pType=Year)
  %Analysis(histories,8,psiType=Year,phiType=dot,pType=dot,gconv=1E-08)
  %Analysis(histories,8,psiType=Year,phiType=dot,pType=Year)
  %Analysis(histories,8,psiType=Year,phiType=Year,pType=dot)
  %Analysis(histories,8,psiType=Year,phiType=Year,pType=Year)
  %Analysis(histories,8,psiType=dot,phiType=0,pType=dot)
  %Analysis(histories,8,psiType=dot,phiType=0,pType=Year)
  %Analysis(histories,8,psiType=Year,phiType=0,pType=dot)
  %Analysis(histories,8,psiType=Year,phiType=0,pType=Year)
  %Analysis(histories,8,psiType=dot,phiType=0,pType=TwoGroup)
  %Analysis(histories,8,psiType=dot,phiType=dot,pType=TwoGroup)
  %Analysis(histories,8,psiType=dot,phiType=Year,pType=TwoGroup)
  %Analysis(histories,8,psiType=Year,phiType=0,pType=TwoGroup)
  %Analysis(histories,8,psiType=Year,phiType=dot,pType=TwoGroup)
  %Analysis(histories,8,psiType=Year,phiType=Year,pType=TwoGroup)
  %Analysis(histories,8,psiType=dot,phiType=0,pType=YearTwoGroup)
  %Analysis(histories,8,psiType=dot,phiType=dot,pType=YearTwoGroup)
  %Analysis(histories,8,psiType=dot,phiType=Year,pType=YearTwoGroup)
  %Analysis(histories,8,psiType=Year,phiType=0,pType=YearTwoGroup)
  %Analysis(histories,8,psiType=Year,phiType=dot,pType=YearTwoGroup)
  %Analysis(histories,8,psiType=Year,phiType=Year,pType=YearTwoGroup)
  %Analysis(histories,8,psiType=logit,phiType=dot,pType=dot)
  %Analysis(histories,8,psiType=logit,phiType=dot,pType=Year)
  %Analysis(histories,8,psiType=logit,phiType=dot,pType=TwoGroup)
  %Analysis(histories,8,psiType=logit,phiType=dot,pType=YearTwoGroup)
  %Analysis(histories,8,psiType=logit,phiType=0,pType=dot)
  %Analysis(histories,8,psiType=logit,phiType=0,pType=Year)
  %Analysis(histories,8,psiType=logit,phiType=0,pType=TwoGroup)
  %Analysis(histories,8,psiType=logit,phiType=0,pType=YearTwoGroup)
  %Analysis(histories,8,psiType=logit,phiType=Year,pType=dot)
  %Analysis(histories,8,psiType=logit,phiType=Year,pType=Year)
  %Analysis(histories,8,psiType=logit,phiType=Year,pType=TwoGroup)
  %Analysis(histories,8,psiType=logit,phiType=Year,pType=YearTwoGroup)

* Combine estimates of detection probabilities;
  data ae;
    set aedotdotdot
	    aedotdotYear
	    aedotYeardot
	    aedotYearYear
	    aeYeardotdot
	    aeYeardotYear
	    aeYearYeardot
	    aeYearYearYear
		aedot0dot
		aedot0Year
		aeYear0dot
		aeYear0Year
        aedot0TwoGroup
        aedotdotTwoGroup
        aedotYearTwoGroup
        aeYear0TwoGroup
        aeYeardotTwoGroup
        aeYearYearTwoGroup
		aedot0YearTwoGroup
		aedotdotYearTwoGroup
		aedotYearYearTwoGroup
		aeYear0YearTwoGroup
		aeYeardotYearTwoGroup
		aeYearYearYearTwoGroup
		aelogitdotdot
		aelogitdotYear
		aelogitdotTwoGroup
		aelogitdotYearTwoGroup
		aelogit0dot
		aelogit0Year
		aelogit0TwoGroup
		aelogit0YearTwoGroup
		aelogitYeardot
		aelogitYearYear
		aelogitYearTwoGroup
		aelogitYearYearTwoGroup;
  run;

* Combine AIC values;
  data AIC;
    set fsdotdotdot
	    fsdotdotYear
	    fsdotYeardot
	    fsdotYearYear
	    fsYeardotdot
	    fsYeardotYear
	    fsYearYeardot
	    fsYearYearYear
		fsdot0dot
		fsdot0Year
		fsYear0dot
		fsYear0Year
        fsdot0TwoGroup
        fsdotdotTwoGroup
        fsdotYearTwoGroup
        fsYear0TwoGroup
        fsYeardotTwoGroup
        fsYearYearTwoGroup
		fsdot0YearTwoGroup
		fsdotdotYearTwoGroup
		fsdotYearYearTwoGroup
		fsYear0YearTwoGroup
		fsYeardotYearTwoGroup
		fsYearYearYearTwoGroup
		fslogitdotdot
		fslogitdotYear
		fslogitdotTwoGroup
		fslogitdotYearTwoGroup
		fslogit0dot
		fslogit0Year
		fslogit0TwoGroup
		fslogit0YearTwoGroup
		fslogitYeardot
		fslogitYearYear
		fslogitYearTwoGroup
		fslogitYearYearTwoGroup
;

  proc sort data=AIC out=AIC;
    by zone AIC;
  data AIC total;
    set AIC;
	by zone;
	retain minAIC total;
	if first.zone then do; minAIC = AIC; total = 0; end;
	deltaAIC = AIC - minAIC;
	AICWt = exp(-deltaAIC/2);
	total = total + AICWt;
	output AIC;
	if last.zone then output total;
  run;
  data total;
    set total;
	keep zone total;
  data AIC;
    set AIC;
	keep zone model AIC deltaAIC AICWt;
  data AIC;
    merge AIC total;
	drop total;
    by zone;
	AICWt = AICWt/total;
  run;

* Parameter estimates;
  data pe;
    set pedotdotdot
	    pedotdotYear
	    pedotYeardot
	    pedotYearYear
	    peYeardotdot
	    peYeardotYear
	    peYearYeardot
	    peYearYearYear
		pedot0dot
		pedot0Year
		peYear0dot
		peYear0Year
        pedot0TwoGroup
        pedotdotTwoGroup
        pedotYearTwoGroup
        peYear0TwoGroup
        peYeardotTwoGroup
        peYearYearTwoGroup
		pedot0YearTwoGroup
		pedotdotYearTwoGroup
		pedotYearYearTwoGroup
		peYear0YearTwoGroup
		peYeardotYearTwoGroup
		peYearYearYearTwoGroup
		pelogitdotdot
		pelogitdotYear
		pelogitdotTwoGroup
		pelogitdotYearTwoGroup
		pelogit0dot
		pelogit0Year
		pelogit0TwoGroup
		pelogit0YearTwoGroup
		pelogitYeardot
		pelogitYearYear
		pelogitYearTwoGroup
		pelogitYearYearTwoGroup
;

* Save output summaries;
  PROC EXPORT DATA= WORK.AIC 
    OUTFILE= "&dir.\fisher summary 2012-08-10.xlsx" DBMS=EXCEL2007 REPLACE;
    SHEET="AIC";
  PROC EXPORT DATA= WORK.PE 
    OUTFILE= "&dir.\fisher summary 2012-08-10.xlsx" DBMS=EXCEL2007 REPLACE;
    SHEET="ParameterEstimates";
  PROC EXPORT DATA= WORK.AE 
    OUTFILE= "&dir.\fisher summary 2012-08-10.xlsx" DBMS=EXCEL2007 REPLACE;
    SHEET="AdditionalEstimates";
  PROC EXPORT DATA= WORK.Histories
    OUTFILE= "&dir.\fisher summary 2012-08-10.xlsx" DBMS=EXCEL2007 REPLACE;
    SHEET="Histories";
  run;