diff --git a/NAMESPACE b/NAMESPACE
index 07534a87..6b40eef6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -140,6 +140,14 @@ exportClasses(TraitADG)
 exportClasses(TraitAE)
 exportClasses(TraitAEG)
 exportClasses(TraitAG)
+exportMethods(makeCross)
+exportMethods(makeCross2)
+exportMethods(makeDH)
+exportMethods(randCross)
+exportMethods(randCross2)
+exportMethods(selectCross)
+exportMethods(self)
+exportMethods(setPheno)
 import(Rcpp)
 importFrom(R6,R6Class)
 importFrom(Rdpack,reprompt)
diff --git a/R/crossing.R b/R/crossing.R
index 32495504..bc6bd14d 100644
--- a/R/crossing.R
+++ b/R/crossing.R
@@ -8,7 +8,7 @@
 #' @param crossPlan a matrix with two column representing
 #' female and male parents. Either integers for the position in
 #' population or character strings for the IDs.
-#' @param nProgeny number of progeny per cross. May be a single value for all 
+#' @param nProgeny number of progeny per cross. May be a single value for all
 #' crosses or a vector with values for each cross.
 #' @param simParam an object of class \code{\link{SimParam}}. If
 #' \code{NULL}, the function uses the object named \code{SP} from the
@@ -40,22 +40,43 @@
 #' pop3 = makeCross(pop, crossPlan, nProgeny=c(1,2),simParam=SP)
 #' getPed(pop3)
 #' @export
-makeCross = function(pop, crossPlan, nProgeny=1,
-                     simParam=NULL, nThreads=NULL){
+setGeneric(
+  "makeCross",
+  function(pop, crossPlan, nProgeny=1, simParam=NULL, nThreads=NULL){
+    standardGeneric("makeCross")
+  }
+)
+
+#' @describeIn makeCross Method for \code{\link{Pop-class}}
+#' @export
+setMethod(
+  "makeCross",
+  signature(pop = "Pop"),
+  function(pop, crossPlan, nProgeny=1, simParam=NULL, nThreads=NULL){
+    .makeCross_internal(
+      pop=pop, crossPlan=crossPlan, nProgeny=nProgeny, simParam=simParam,
+      nThreads=nThreads)
+  }
+)
+
+# Internal implementation shared by makeCross methods
+#' @keywords internal
+.makeCross_internal = function(pop,crossPlan,nProgeny=1,
+                               simParam=NULL,nThreads=NULL){
   if(is.null(simParam)){
     simParam = get("SP",envir=.GlobalEnv)
   }
-  
+
   if(is.null(nThreads)){
     nThreads = simParam$nThreads
   }else{
     nThreads = as.integer(nThreads)
   }
-  
+
   if(pop@ploidy%%2L != 0L){
-    stop("You can not cross indiviuals with odd ploidy levels")
+    stop("You can not cross individuals with odd ploidy levels")
   }
-  
+
   if(is.character(crossPlan)){ #Match by ID
     crossPlan = cbind(match(crossPlan[,1], pop@id),
                       match(crossPlan[,2], pop@id))
@@ -63,12 +84,12 @@ makeCross = function(pop, crossPlan, nProgeny=1,
       stop("Failed to match supplied IDs")
     }
   }
-  
+
   if((max(crossPlan)>nInd(pop)) |
      (min(crossPlan)<1L)){
     stop("Invalid crossPlan")
   }
-  
+
   # Handle nProgeny
   if(length(nProgeny)==1){
     if(nProgeny>1){
@@ -77,11 +98,11 @@ makeCross = function(pop, crossPlan, nProgeny=1,
     }
   }else{
     stopifnot("Length of nProgeny must equal 1 or nrow(crossPlan)" = nrow(crossPlan)==length(nProgeny))
-    
+
     crossPlan = cbind(rep(crossPlan[,1], times=nProgeny),
                       rep(crossPlan[,2], times=nProgeny))
   }
-  
+
   tmp = cross(pop@geno,
               crossPlan[,1],
               pop@geno,
@@ -97,22 +118,22 @@ makeCross = function(pop, crossPlan, nProgeny=1,
               simParam$maleCentromere,
               simParam$quadProb,
               nThreads)
-  
+
   dim(tmp$geno) = NULL # Account for matrix bug in RcppArmadillo
-  
+
   rPop = new("RawPop",
              nInd=nrow(crossPlan),
              nChr=pop@nChr,
              ploidy=pop@ploidy,
              nLoci=pop@nLoci,
              geno=tmp$geno)
-  
+
   if(simParam$isTrackRec){
     hist = tmp$recHist
   }else{
     hist = NULL
   }
-  
+
   return(.newPop(rawPop=rPop,
                  mother=pop@id[crossPlan[,1]],
                  father=pop@id[crossPlan[,2]],
@@ -129,12 +150,12 @@ makeCross = function(pop, crossPlan, nProgeny=1,
 #'
 #' @description
 #' A wrapper for \code{\link{makeCross}} that randomly
-#' selects parental combinations for all possible combinantions.
+#' selects parental combinations for all possible combinations.
 #'
 #' @param pop an object of \code{\link{Pop-class}}
 #' @param nCrosses total number of crosses to make
-#' @param nProgeny number of progeny per cross. May be a single value for all 
-#' crosses or a vector with values equal to the number of crosses. If providing 
+#' @param nProgeny number of progeny per cross. May be a single value for all
+#' crosses or a vector with values equal to the number of crosses. If providing
 #' a vector, the values are randomly assigned to each cross.
 #' @param balance if using sexes, this option will balance the number
 #' of progeny per parent
@@ -163,37 +184,63 @@ makeCross = function(pop, crossPlan, nProgeny=1,
 #' pop2 = randCross(pop, 10, simParam=SP)
 #'
 #' @export
-randCross = function(pop, nCrosses, nProgeny=1,
-                     balance=TRUE, parents=NULL,
+setGeneric(
+  "randCross",
+  function(
+    pop, nCrosses, nProgeny=1, balance=TRUE, parents=NULL, ignoreSexes=FALSE,
+    simParam=NULL, nThreads=NULL){
+    standardGeneric("randCross")
+  }
+)
+
+#' @describeIn randCross Method for \code{\link{Pop-class}}
+#' @export
+setMethod(
+  "randCross",
+  signature(pop = "Pop"),
+  function(
+    pop, nCrosses, nProgeny=1, balance=TRUE, parents=NULL, ignoreSexes=FALSE,
+    simParam=NULL, nThreads=NULL){
+    .randCross_internal(
+      pop=pop, nCrosses=nCrosses, nProgeny=nProgeny, balance=balance,
+      parents=parents, ignoreSexes=ignoreSexes, simParam=simParam,
+      nThreads=nThreads)
+  }
+)
+
+# Internal implementation shared by randCross methods
+#' @keywords internal
+.randCross_internal = function(pop,nCrosses,nProgeny=1,
+                     balance=TRUE,parents=NULL,
                      ignoreSexes=FALSE,
                      simParam=NULL, nThreads=NULL){
   if(is.null(simParam)){
     simParam = get("SP",envir=.GlobalEnv)
   }
-  
+
   if(is.null(nThreads)){
     nThreads = simParam$nThreads
   }else{
     nThreads = as.integer(nThreads)
   }
-  
+
   if(is.null(parents)){
     parents = 1:pop@nInd
   }else{
     parents = as.integer(parents)
   }
-  
+
   n = length(parents)
   if(n<=1){
     stop("The population must contain more than 1 individual")
   }
-  
+
   # Handle nProgeny
   if(length(nProgeny)>1){
     stopifnot("Length of nProgeny must equal 1 or nCrosses" = nCrosses==length(nProgeny))
     nProgeny = nProgeny[sample(nCrosses, nCrosses)]
   }
-  
+
   if(simParam$sexes=="no" | ignoreSexes){
     crossPlan = sampHalfDialComb(n, nCrosses)
     crossPlan[,1] = parents[crossPlan[,1]]
@@ -229,7 +276,7 @@ randCross = function(pop, nCrosses, nProgeny=1,
       crossPlan[,2] = male[crossPlan[,2]]
     }
   }
-  
+
   return(makeCross(pop=pop, crossPlan=crossPlan, nProgeny=nProgeny,
                    simParam=simParam, nThreads=nThreads))
 }
@@ -294,9 +341,36 @@ randCross = function(pop, nCrosses, nProgeny=1,
 #' pop2 = selectCross(pop, nInd=4, nCrosses=8, simParam=SP)
 #'
 #' @export
-selectCross = function(pop, nInd=NULL, nFemale=NULL, nMale=NULL, nCrosses,
-                       nProgeny=1, trait=1, use="pheno", selectTop=TRUE,
-                       simParam=NULL, nThreads=NULL, ..., balance=TRUE){
+setGeneric(
+  "selectCross",
+  function(
+    pop, nInd=NULL, nFemale=NULL, nMale=NULL, nCrosses, nProgeny=1, trait=1,
+    use="pheno", selectTop=TRUE, simParam=NULL, nThreads=NULL, ..., balance=TRUE){
+    standardGeneric("selectCross")
+  }
+)
+
+
+#' @describeIn selectCross Method for \code{\link{Pop-class}}
+#' @export
+setMethod(
+  "selectCross",
+  signature(pop = "Pop"),
+  function(
+    pop, nInd=NULL, nFemale=NULL, nMale=NULL, nCrosses, nProgeny=1, trait=1,
+    use="pheno", selectTop=T, simParam=NULL, nThreads=NULL, ..., balance=TRUE){
+    .selectCross_internal(
+      pop=pop, nInd=nInd, nFemale=nFemale, nMale=nMale, nCrosses=nCrosses,
+      nProgeny=nProgeny, trait=trait, use=use, selectTop=selectTop,
+      simParam=simParam, nThreads=nThreads, ..., balance=balance)
+  }
+)
+
+# Internal implementation shared by selectCross methods
+#' @keywords internal
+.selectCross_internal = function(pop,nInd=NULL,nFemale=NULL,nMale=NULL,nCrosses,
+                       nProgeny=1,trait=1,use="pheno",selectTop=TRUE,
+                       simParam=NULL,nThreads=NULL,...,balance=TRUE){
   if(is.null(simParam)){
     simParam = get("SP",envir=.GlobalEnv)
   }
@@ -327,7 +401,7 @@ selectCross = function(pop, nInd=NULL, nFemale=NULL, nMale=NULL, nCrosses,
                       nThreads=nThreads, ...)
     parents = c(females,males)
   }
-  
+
   return(randCross(pop=pop, nCrosses=nCrosses, nProgeny=nProgeny,
                    balance=balance, parents=parents,
                    ignoreSexes=FALSE, simParam=simParam,
@@ -345,7 +419,7 @@ selectCross = function(pop, nInd=NULL, nFemale=NULL, nMale=NULL, nCrosses,
 #' @param crossPlan a matrix with two column representing
 #' female and male parents. Either integers for the position in
 #' population or character strings for the IDs.
-#' @param nProgeny number of progeny per cross. May be a single value for all 
+#' @param nProgeny number of progeny per cross. May be a single value for all
 #' crosses or a vector with values for each cross.
 #' @param simParam an object of class \code{\link{SimParam}}. If
 #' \code{NULL}, the function uses the object named \code{SP} from the
@@ -377,23 +451,44 @@ selectCross = function(pop, nInd=NULL, nFemale=NULL, nMale=NULL, nCrosses,
 #' pop3 = makeCross2(pop, pop, crossPlan, nProgeny=c(1,2),simParam=SP)
 #' getPed(pop3)
 #' @export
-makeCross2 = function(females, males, crossPlan, nProgeny=1, simParam=NULL,
+setGeneric(
+  "makeCross2",
+  function(females,males,crossPlan,nProgeny=1,simParam=NULL, nThreads=NULL){
+    standardGeneric("makeCross2")
+  }
+)
+
+#' @describeIn makeCross2 Method for \code{\link{Pop-class}}
+#' @export
+setMethod(
+  "makeCross2",
+  signature(females = "Pop", males = "Pop"),
+  function(females,males,crossPlan,nProgeny=1,simParam=NULL, nThreads=NULL){
+    .makeCross2_internal(
+      females=females, males=males, crossPlan=crossPlan, nProgeny=nProgeny,
+      simParam=simParam, nThreads=nThreads)
+  }
+)
+
+# Internal implementation shared by makeCross2 methods
+#' @keywords internal
+.makeCross2_internal = function(females,males,crossPlan,nProgeny=1,simParam=NULL,
                       nThreads=NULL){
   if(is.null(simParam)){
     simParam = get("SP",envir=.GlobalEnv)
   }
-  
+
   if(is.null(nThreads)){
     nThreads = simParam$nThreads
   }else{
     nThreads = as.integer(nThreads)
   }
-  
+
   if((females@ploidy%%2L != 0L) |
      (males@ploidy%%2L != 0L)){
-    stop("You can not cross indiviuals with odd ploidy levels")
+    stop("You can not cross individuals with odd ploidy levels")
   }
-  
+
   if(is.character(crossPlan)){ #Match by ID
     crossPlan = cbind(match(crossPlan[,1],females@id),
                       match(crossPlan[,2],males@id))
@@ -401,13 +496,13 @@ makeCross2 = function(females, males, crossPlan, nProgeny=1, simParam=NULL,
       stop("Failed to match supplied IDs")
     }
   }
-  
+
   if((max(crossPlan[,1])>nInd(females)) |
      (max(crossPlan[,2])>nInd(males)) |
      (min(crossPlan)<1L)){
     stop("Invalid crossPlan")
   }
-  
+
   # Handle nProgeny
   if(length(nProgeny)==1){
     if(nProgeny>1){
@@ -416,11 +511,11 @@ makeCross2 = function(females, males, crossPlan, nProgeny=1, simParam=NULL,
     }
   }else{
     stopifnot("Length of nProgeny must equal 1 or nrow(crossPlan)" = nrow(crossPlan)==length(nProgeny))
-    
+
     crossPlan = cbind(rep(crossPlan[,1], times=nProgeny),
                       rep(crossPlan[,2], times=nProgeny))
   }
-  
+
   tmp=cross(females@geno,
             crossPlan[,1],
             males@geno,
@@ -436,22 +531,22 @@ makeCross2 = function(females, males, crossPlan, nProgeny=1, simParam=NULL,
             simParam$maleCentromere,
             simParam$quadProb,
             nThreads)
-  
+
   dim(tmp$geno) = NULL # Account for matrix bug in RcppArmadillo
-  
+
   rPop = new("RawPop",
              nInd=nrow(crossPlan),
              nChr=females@nChr,
              ploidy=as.integer((females@ploidy+males@ploidy)/2),
              nLoci=females@nLoci,
              geno=tmp$geno)
-  
+
   if(simParam$isTrackRec){
     hist = tmp$recHist
   }else{
     hist = NULL
   }
-  
+
   return(.newPop(rawPop=rPop,
                  mother=females@id[crossPlan[,1]],
                  father=males@id[crossPlan[,2]],
@@ -468,14 +563,14 @@ makeCross2 = function(females, males, crossPlan, nProgeny=1, simParam=NULL,
 #'
 #' @description
 #' A wrapper for \code{\link{makeCross2}} that randomly
-#' selects parental combinations for all possible combinantions between
+#' selects parental combinations for all possible combinations between
 #' two populations.
 #'
 #' @param females an object of \code{\link{Pop-class}} for female parents.
 #' @param males an object of \code{\link{Pop-class}} for male parents.
 #' @param nCrosses total number of crosses to make
-#' @param nProgeny number of progeny per cross. May be a single value for all 
-#' crosses or a vector with values equal to the number of crosses. If providing 
+#' @param nProgeny number of progeny per cross. May be a single value for all
+#' crosses or a vector with values equal to the number of crosses. If providing
 #' a vector, the values are randomly assigned to each cross.
 #' @param balance this option will balance the number
 #' of progeny per parent
@@ -507,33 +602,60 @@ makeCross2 = function(females, males, crossPlan, nProgeny=1, simParam=NULL,
 #' pop2 = randCross2(pop, pop, 10, simParam=SP)
 #'
 #' @export
-randCross2 = function(females, males, nCrosses, nProgeny=1,
-                      balance=TRUE, femaleParents=NULL,
-                      maleParents=NULL, ignoreSexes=FALSE,
-                      simParam=NULL, nThreads=NULL){
+setGeneric(
+  "randCross2",
+  function(
+    females, males, nCrosses, nProgeny=1, balance=TRUE, femaleParents=NULL,
+    maleParents=NULL, ignoreSexes=FALSE, simParam=NULL, nThreads=NULL){
+    standardGeneric("randCross2")
+  }
+)
+
+#' @describeIn randCross2 Method for \code{\link{Pop-class}}
+#' @export
+setMethod(
+  "randCross2",
+  signature(females = "Pop", males = "Pop"),
+  function(
+    females, males, nCrosses, nProgeny=1, balance=TRUE, femaleParents=NULL,
+    maleParents=NULL, ignoreSexes=FALSE, simParam=NULL, nThreads=NULL){
+    .randCross2_internal(
+      females = females, males = males, nCrosses = nCrosses,
+      nProgeny = nProgeny, balance = balance, femaleParents = femaleParents,
+      maleParents = maleParents, ignoreSexes = ignoreSexes,
+      simParam = simParam, nThreads = nThreads)
+  }
+)
+
+# Internal implementation shared by randCross2 methods
+#' @keywords internal
+.randCross2_internal = function(
+    females, males, nCrosses, nProgeny=1, balance=TRUE, femaleParents=NULL,
+    maleParents=NULL, ignoreSexes=FALSE, simParam=NULL, nThreads=NULL){
+
   if(is.null(simParam)){
     simParam = get("SP",envir=.GlobalEnv)
   }
-  
+
   if(is.null(nThreads)){
     nThreads = simParam$nThreads
   }else{
     nThreads = as.integer(nThreads)
   }
-  
+
   #Set allowable parents
   if(is.null(femaleParents)){
     femaleParents = 1:females@nInd
   }else{
     femaleParents = as.integer(femaleParents)
   }
-  
+
   if(is.null(maleParents)){
     maleParents = 1:males@nInd
   }else{
     maleParents = as.integer(maleParents)
   }
-  
+
   if(simParam$sexes=="no" | ignoreSexes){
     female = femaleParents
     male = maleParents
@@ -549,16 +671,16 @@ randCross2 = function(females, males, nCrosses, nProgeny=1,
       stop("population doesn't contain any males")
     }
   }
-  
+
   # Handle nProgeny
   if(length(nProgeny)>1){
     stopifnot("Length of nProgeny must equal 1 or nCrosses" = nCrosses==length(nProgeny))
     nProgeny = nProgeny[sample(nCrosses, nCrosses)]
   }
-  
+
   nMale = length(male)
   nFemale = length(female)
-  
+
   if(balance){
     female = female[sample.int(nFemale, nFemale)]
     female = rep(female, length.out=nCrosses)
@@ -578,7 +700,7 @@ randCross2 = function(females, males, nCrosses, nProgeny=1,
     crossPlan[,1] = female[crossPlan[,1]]
     crossPlan[,2] = male[crossPlan[,2]]
   }
-  
+
   return(makeCross2(females=females, males=males,
                     crossPlan=crossPlan, nProgeny=nProgeny,
                     simParam=simParam, nThreads=nThreads))
@@ -591,7 +713,7 @@ randCross2 = function(females, males, nCrosses, nProgeny=1,
 #' population. Only works when sexes is "no".
 #'
 #' @param pop an object of \code{\link{Pop-class}}
-#' @param nProgeny number of selfed progeny per individual. May be a single value 
+#' @param nProgeny number of selfed progeny per individual. May be a single value
 #' for all or a vector providing values for each individual.
 #' @param parents an optional vector of indices for allowable parents
 #' @param keepParents should previous parents be used for mother and
@@ -619,19 +741,44 @@ randCross2 = function(females, males, nCrosses, nProgeny=1,
 #' pop2 = self(pop, simParam=SP)
 #'
 #' @export
-self = function(pop, nProgeny=1, parents=NULL, keepParents=TRUE,
-                simParam=NULL, nThreads=NULL){
-  
+setGeneric(
+  "self",
+  function(
+    pop, nProgeny=1, parents=NULL, keepParents=TRUE, simParam=NULL,
+    nThreads=NULL){
+    standardGeneric("self")
+  }
+)
+
+#' @describeIn self Method for \code{\link{Pop-class}}
+#' @export
+setMethod(
+  "self",
+  signature(pop = "Pop"),
+  function(
+    pop, nProgeny=1, parents=NULL, keepParents=TRUE, simParam=NULL,
+    nThreads=NULL){
+    .self_internal(
+      pop=pop, nProgeny=nProgeny, parents=parents, keepParents=keepParents,
+      simParam=simParam, nThreads = nThreads
+    )
+  }
+)
+
+# Internal implementation shared by self methods
+#' @keywords internal
+.self_internal = function(
+    pop,nProgeny=1,parents=NULL,keepParents=TRUE,simParam=NULL,nThreads=NULL){
   if(is.null(simParam)){
     simParam = get("SP",envir=.GlobalEnv)
   }
-  
+
   if(is.null(nThreads)){
     nThreads = simParam$nThreads
   }else{
     nThreads = as.integer(nThreads)
   }
-  
+
   if(is(pop,"MultiPop")){
     stopifnot(is.null(parents))
     pop@pops = lapply(pop@pops, self, nProgeny=nProgeny,
@@ -639,29 +786,29 @@ self = function(pop, nProgeny=1, parents=NULL, keepParents=TRUE,
                       simParam=simParam, nThreads=nThreads)
     return(pop)
   }
-  
+
   if(is.null(parents)){
     parents = 1:pop@nInd
   }else{
     parents = as.integer(parents)
   }
-  
+
   if(pop@ploidy%%2L != 0L){
     stop("You can not self aneuploids")
   }
-  
+
   # Handle nProgeny
   if(length(nProgeny)==1){
     crossPlan = rep(parents, each=nProgeny)
-    
+
   }else{
     stopifnot("Length of nProgeny must equal 1 or nInd(pop)" = nInd(pop)==length(nProgeny))
-    
+
     crossPlan = rep(parents, times=nProgeny)
   }
-  
+
   crossPlan = cbind(crossPlan,crossPlan)
-  
+
   tmp = cross(pop@geno,
               crossPlan[,1],
               pop@geno,
@@ -677,22 +824,22 @@ self = function(pop, nProgeny=1, parents=NULL, keepParents=TRUE,
               simParam$maleCentromere,
               simParam$quadProb,
               nThreads)
-  
+
   dim(tmp$geno) = NULL # Account for matrix bug in RcppArmadillo
-  
+
   rPop = new("RawPop",
              nInd=nrow(crossPlan),
              nChr=pop@nChr,
              ploidy=pop@ploidy,
              nLoci=pop@nLoci,
              geno=tmp$geno)
-  
+
   if(simParam$isTrackRec){
     hist = tmp$recHist
   }else{
     hist = NULL
   }
-  
+
   if(keepParents){
     return(.newPop(rawPop=rPop,
                    mother=pop@mother[crossPlan[,1]],
@@ -752,29 +899,52 @@ self = function(pop, nProgeny=1, parents=NULL, keepParents=TRUE,
 #' pop2 = makeDH(pop, simParam=SP)
 #'
 #' @export
-makeDH = function(pop, nDH=1, useFemale=TRUE, keepParents=TRUE,
-                  simParam=NULL, nThreads=NULL){
+setGeneric(
+  "makeDH",
+  function(
+    pop,nDH=1,useFemale=TRUE,keepParents=TRUE,simParam=NULL,nThreads=NULL){
+    standardGeneric("makeDH")
+  }
+)
+
+#' @describeIn makeDH Method for \code{\link{Pop-class}}
+#' @export
+setMethod(
+  "makeDH",
+  signature(pop = "Pop"),
+  function(
+    pop,nDH=1,useFemale=TRUE,keepParents=TRUE,simParam=NULL,nThreads=NULL){
+    .makeDH_internal(
+      pop=pop, nDH=nDH, useFemale=useFemale, keepParents=keepParents,
+      simParam=simParam, nThreads=nThreads)
+  }
+)
+
+# Internal implementation shared by .makeDH_internal methods
+#' @keywords internal
+.makeDH_internal = function(
+    pop,nDH=1,useFemale=TRUE,keepParents=TRUE,simParam=NULL,nThreads=NULL){
   if(is.null(simParam)){
     simParam = get("SP",envir=.GlobalEnv)
   }
-  
+
   if(is.null(nThreads)){
     nThreads = simParam$nThreads
   }else{
     nThreads = as.integer(nThreads)
   }
-  
+
   if(is(pop,"MultiPop")){
     pop@pops = lapply(pop@pops, makeDH, nDH=nDH, useFemale=useFemale,
                       keepParents=keepParents, simParam=simParam,
                       nThreads=nThreads)
     return(pop)
   }
-  
+
   if(pop@ploidy!=2){
     stop("Only works with diploids")
   }
-  
+
   if(useFemale){
     tmp = createDH2(pop@geno, nDH,
                     simParam$femaleMap,
@@ -790,22 +960,22 @@ makeDH = function(pop, nDH=1, useFemale=TRUE, keepParents=TRUE,
                     simParam$isTrackRec,
                     nThreads)
   }
-  
+
   dim(tmp$geno) = NULL # Account for matrix bug in RcppArmadillo
-  
+
   rPop = new("RawPop",
              nInd=as.integer(pop@nInd*nDH),
              nChr=pop@nChr,
              ploidy=pop@ploidy,
              nLoci=pop@nLoci,
              geno=tmp$geno)
-  
+
   if(simParam$isTrackRec){
     hist = tmp$recHist
   }else{
     hist = NULL
   }
-  
+
   if(keepParents){
     return(.newPop(rawPop=rPop,
                    mother=rep(pop@mother, each=nDH),
@@ -848,9 +1018,9 @@ sortPed = function(id, mother, father, maxCycle=100){
                       father=match(father, id),
                       motherID=as.character(mother),
                       fatherID=as.character(father))
-  
+
   unsorted = rep(TRUE, nInd)
-  
+
   for(gen in seq_len(maxCycle)){
     for(i in which(unsorted)){
       if(is.na(output$mother[i])&is.na(output$father[i])){
@@ -878,11 +1048,11 @@ sortPed = function(id, mother, father, maxCycle=100){
       }
     }
   }
-  
+
   if(any(unsorted)){
-    stop("Failed to sort pedigree, may contain loops or require a higher maxGen")
+    stop("Failed to sort pedigree, may contain loops or require a higher maxCycle")
   }
-  
+
   return(output)
 }
 
@@ -894,7 +1064,7 @@ sortPed = function(id, mother, father, maxCycle=100){
 #'
 #' @param founderPop a \code{\link{Pop-class}}
 #' @param id a vector of unique identifiers for individuals
-#' in the pedigree. The values of these IDs are seperate from
+#' in the pedigree. The values of these IDs are separate from
 #' the IDs in the founderPop if matchID=FALSE.
 #' @param mother a vector of identifiers for the mothers
 #' of individuals in the pedigree. Must match one of the
@@ -949,17 +1119,17 @@ pedigreeCross = function(founderPop, id, mother, father, matchID=FALSE,
   if(is.null(simParam)){
     simParam = get("SP",envir=.GlobalEnv)
   }
-  
+
   if(is.null(nThreads)){
     nThreads = simParam$nThreads
   }else{
     nThreads = as.integer(nThreads)
   }
-  
+
   if(simParam$sexes!="no"){
     stop("pedigreeCross currently only works with sex='no'")
   }
-  
+
   # Coerce input data
   id = as.character(id)
   mother = as.character(mother)
@@ -972,21 +1142,21 @@ pedigreeCross = function(founderPop, id, mother, father, matchID=FALSE,
   if(is.null(nSelf)){
     nSelf = rep(0, length(id))
   }
-  
+
   # Check input data
   stopifnot(!any(duplicated(id)),
             length(id)==length(mother),
             length(id)==length(father),
             length(id)==length(DH),
             length(id)==length(nSelf))
-  
+
   # Sort pedigree (identifies potential problems)
   ped = sortPed(id=id, mother=mother, father=father,
                 maxCycle=maxCycle)
-  
+
   # Create list for new population
   output = vector("list", length=length(id))
-  
+
   # Order and assign founders
   isFounder = is.na(ped$father) & is.na(ped$mother)
   motherIsFounder = is.na(ped$mother) & !is.na(ped$father)
@@ -1006,17 +1176,17 @@ pedigreeCross = function(founderPop, id, mother, father, matchID=FALSE,
     if(nFounder>founderPop@nInd){
       stop(paste("Pedigree requires",nFounder,"founders, but only",founderPop@nInd,"were supplied"))
     }
-    
+
     # Randomly assign individuals as founders
     founderPop = founderPop[sample.int(founderPop@nInd,nFounder)]
-    
+
     # isFounder
     n1 = 1
     n2 = sum(isFounder)
     founderPop@id[n1:n2] = id[isFounder]
     founderPop@mother[n1:n2] = mother[isFounder]
     founderPop@father[n1:n2] = father[isFounder]
-    
+
     # motherIsFounder
     n = sum(motherIsFounder)
     if(n>=1){
@@ -1026,7 +1196,7 @@ pedigreeCross = function(founderPop, id, mother, father, matchID=FALSE,
       founderPop@mother[n1:n2] = rep("0", n2-n1+1)
       founderPop@father[n1:n2] = rep("0", n2-n1+1)
     }
-    
+
     # fatherIsFounder
     n = sum(fatherIsFounder)
     if(n>=1){
@@ -1037,7 +1207,7 @@ pedigreeCross = function(founderPop, id, mother, father, matchID=FALSE,
       founderPop@father[n1:n2] = rep("0", n2-n1+1)
     }
   }
-  
+
   # Create individuals
   crossPlan = matrix(c(1,1),ncol=2)
   for(gen in seq_len(max(ped$gen))){
@@ -1069,14 +1239,14 @@ pedigreeCross = function(founderPop, id, mother, father, matchID=FALSE,
                                    nThreads=nThreads)
         }
       }
-      
+
       # Self?
       for(j in seq_len(nSelf[i])){
         output[[i]] = self(output[[i]],
                            simParam=simParam,
                            nThreads=nThreads)
       }
-      
+
       # Make the individual a DH?
       if(DH[i]){
         output[[i]] = makeDH(output[[i]],
@@ -1086,14 +1256,14 @@ pedigreeCross = function(founderPop, id, mother, father, matchID=FALSE,
       }
     }
   }
-  
+
   # Collapse list to a population
   output = mergePops(output)
-  
+
   # Copy over names
   output@id = id
   output@mother = mother
   output@father = father
-  
+
   return(output)
 }
diff --git a/R/phenotypes.R b/R/phenotypes.R
index 7af178ff..6d95f8aa 100644
--- a/R/phenotypes.R
+++ b/R/phenotypes.R
@@ -157,9 +157,50 @@ calcPheno = function(pop, varE, reps, p, traits, simParam=NULL){
 #' pop = setPheno(pop, varE=1)
 #'
 #' @export
-setPheno = function(pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL,
-                    reps=1, fixEff=1L, p=NULL, onlyPheno=FALSE,
-                    traits=NULL, simParam=NULL, ...){
+setGeneric(
+  "setPheno",
+  function(
+    pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL, reps=1, fixEff=1L, p=NULL,
+    onlyPheno=FALSE, traits=NULL, simParam=NULL){
+    standardGeneric("setPheno")
+  }
+)
+
+#' @describeIn setPheno Method for \code{\link{Pop-class}}
+#' @export
+setMethod(
+  "setPheno",
+  signature(pop = "Pop"),
+  function(
+    pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL, reps=1, fixEff=1L, p=NULL,
+    onlyPheno=FALSE, traits=NULL, simParam=NULL) {
+    .setPheno_internal(
+      pop=pop, h2=h2, H2=H2, varE=varE, corE=corE, reps=reps, fixEff=fixEff,
+      p=p, onlyPheno=onlyPheno, traits=traits, simParam=simParam
+    )
+  }
+)
+
+#' @describeIn setPheno Method for \code{\link{MultiPop-class}} objects
+#' @export
+setMethod(
+  "setPheno",
+  signature(pop = "MultiPop"),
+  function(
+    pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL, reps=1, fixEff=1L, p=NULL,
+    onlyPheno=FALSE, traits=NULL, simParam=NULL) {
+    .setPheno_internal(
+      pop=pop, h2=h2, H2=H2, varE=varE, corE=corE, reps=reps, fixEff=fixEff,
+      p=p, onlyPheno=onlyPheno, traits=traits,simParam=simParam
+    )
+  }
+)
+
+# Internal implementation shared by all setPheno methods.
+# @keywords internal
+.setPheno_internal = function(
+    pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL, reps=1, fixEff=1L, p=NULL,
+    onlyPheno=FALSE, traits=NULL, simParam=NULL) {
   if(is.null(simParam)){
     simParam = get("SP",envir=.GlobalEnv)
   }
@@ -339,9 +380,9 @@ setPheno = function(pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL,
 #' SP$setVarE(varE = trtVarELog)
 #' pop = newPop(founderPop)
 #' popLarge = randCross(pop, nCrosses = 1000)
-#' 
+#'
 #' meanVarFun = function(x) list(mean = mean(x), var = var(x))
-#' 
+#'
 #' #Latent phenotypes and parameters
 #' (phenoLog = pheno(pop))
 #' phenoLogLarge = pheno(popLarge)
@@ -364,7 +405,7 @@ setPheno = function(pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL,
 #' cbind(phenoLog = phenoLog[, 1],
 #'   phenoExpMeanLog0 = phenoExpMeanLog0,
 #'   phenoExpMeanExp1 = phenoExpMeanExp1)
-#' 
+#'
 #' tmp = cbind(phenoLog = phenoLogLarge[, 1],
 #'   phenoExpMeanLog0 = c(asLogNormal(phenoLogLarge[, 1])),
 #'   phenoExpMeanExp1 = c(asLogNormal(phenoLogLarge[, 1], meanLogShift = -trtVarPLog[1]/2)))
@@ -377,16 +418,16 @@ setPheno = function(pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL,
 #' abline(v= tmp2$phenoExpMeanExp1$mean, col = "red")
 #'
 #' #Convert multiple input traits
-#' asLogNormal(pheno(pop))
-#' try(asLogNormal(pheno(pop), meanLogShift = 0))
-#' asLogNormal(pheno(pop), meanLogShift = c(0, 1))
-#' asLogNormal(pheno(pop), meanLogShift = list(0, NULL))
-#' 
+#' asLogNormal(x = pheno(pop))
+#' try(asLogNormal(x = pheno(pop), meanlog = 0))
+#' asLogNormal(x = pheno(pop), meanlog = c(0, 1))
+#' asLogNormal(x = pheno(pop), meanlog = list(0, NULL))
+#'
 #' #Store the recoded trait manually
 #' pheno(pop)
 #' pop@pheno[, 1] = asLogNormal(pheno(pop)[, 1])
 #' pheno(pop)
-#' 
+#'
 #' #Apply and store the transformation automatically via SimParam$finalizePop()
 #' finalizePopDefault = SP$finalizePop
 #' SP$finalizePop = function(pop, simParam = SP, ...) {
@@ -395,7 +436,7 @@ setPheno = function(pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL,
 #' }
 #' pop = newPop(founderPop)
 #' pheno(pop)
-#' 
+#'
 #' #Apply and store the transformation automatically via SimParam$finalizePheno()
 #' SP$finalizePop = finalizePopDefault
 #' SP$finalizePheno = function(pheno, pop, simParam = SP, ...) {
@@ -533,12 +574,12 @@ asLogNormal <- function(x, meanLogShift = NULL) {
 #'               p = list(c(0.5, 0.5),
 #'                        p),
 #'               mean = trtMean, var = trtVarP)
-#' 
+#'
 #' #Store the recoded trait manually
 #' pheno(pop)
 #' pop@pheno[, 1] = asCategorical(pheno(pop)[, 1])
 #' pheno(pop)
-#' 
+#'
 #' #Apply and store the transformation automatically via SimParam$finalizePop()
 #' finalizePopDefault = SP$finalizePop
 #' SP$finalizePop = function(pop, simParam = SP, ...) {
@@ -547,7 +588,7 @@ asLogNormal <- function(x, meanLogShift = NULL) {
 #' }
 #' pop = newPop(founderPop)
 #' pheno(pop)
-#' 
+#'
 #' #Apply and store the transformation automatically via SimParam$finalizePheno()
 #' SP$finalizePop = finalizePopDefault
 #' SP$finalizePheno = function(pheno, pop, simParam = SP, ...) {
@@ -633,7 +674,7 @@ asCategorical = function(x, p = NULL, mean = 0, var = 1,
 #' @details If input trait is normal (Gaussian) then this function generates a
 #'   count trait by sampling from the Poisson generalised linear model.
 #'   As such, this function's output is stochastic.
-#' 
+#'
 #'   Specifically, it generates \code{y | x ~ Poisson(lambda)} with
 #'   \code{lambda = exp(meanLogShift + x)}. If the supplied latent values
 #'   \code{x} have mean \code{mu} and variance \code{sigma2}, then the
@@ -648,7 +689,7 @@ asCategorical = function(x, p = NULL, mean = 0, var = 1,
 #'   mean and to induce overdispersion, but it does not fully determine
 #'   the observed variance. If \code{x} already contains an added Gaussian
 #'   residual term, that latent variance contributes to the overdispersion as well.
-#' 
+#'
 #'   The name \code{meanLogShift} is used to emphasize that this argument
 #'   is an additional shift applied during transformation, not the primary
 #'   way to set the latent trait mean. In normal AlphaSimR workflow, the
@@ -730,7 +771,7 @@ asCategorical = function(x, p = NULL, mean = 0, var = 1,
 #' pheno(pop)
 #' pop@pheno[, 1] = asPoisson(pheno(pop)[, 1])
 #' pheno(pop)
-#' 
+#'
 #' #Apply and store the transformation automatically via SimParam$finalizePop()
 #' finalizePopDefault = SP$finalizePop
 #' SP$finalizePop = function(pop, simParam = SP, ...) {
@@ -739,7 +780,7 @@ asCategorical = function(x, p = NULL, mean = 0, var = 1,
 #' }
 #' pop = newPop(founderPop)
 #' pheno(pop)
-#' 
+#'
 #' #Apply and store the transformation automatically via SimParam$finalizePheno()
 #' SP$finalizePop = finalizePopDefault
 #' SP$finalizePheno = function(pheno, pop, simParam = SP, ...) {
diff --git a/man/asLogNormal.Rd b/man/asLogNormal.Rd
index f6eb0e09..05df6eba 100644
--- a/man/asLogNormal.Rd
+++ b/man/asLogNormal.Rd
@@ -103,10 +103,10 @@ hist(tmp[, "phenoExpMeanExp1"], main = paste0("Mean: ", v=tmp2$phenoExpMeanExp1$
 abline(v= tmp2$phenoExpMeanExp1$mean, col = "red")
 
 #Convert multiple input traits
-asLogNormal(pheno(pop))
-try(asLogNormal(pheno(pop), meanLogShift = 0))
-asLogNormal(pheno(pop), meanLogShift = c(0, 1))
-asLogNormal(pheno(pop), meanLogShift = list(0, NULL))
+asLogNormal(x = pheno(pop))
+try(asLogNormal(x = pheno(pop), meanlog = 0))
+asLogNormal(x = pheno(pop), meanlog = c(0, 1))
+asLogNormal(x = pheno(pop), meanlog = list(0, NULL))
 
 #Store the recoded trait manually
 pheno(pop)
diff --git a/man/makeCross.Rd b/man/makeCross.Rd
index c02cb1f3..a6dbcb32 100644
--- a/man/makeCross.Rd
+++ b/man/makeCross.Rd
@@ -2,9 +2,12 @@
 % Please edit documentation in R/crossing.R
 \name{makeCross}
 \alias{makeCross}
+\alias{makeCross,Pop-method}
 \title{Make designed crosses}
 \usage{
 makeCross(pop, crossPlan, nProgeny = 1, simParam = NULL, nThreads = NULL)
+
+\S4method{makeCross}{Pop}(pop, crossPlan, nProgeny = 1, simParam = NULL, nThreads = NULL)
 }
 \arguments{
 \item{pop}{an object of \code{\link{Pop-class}}}
@@ -13,7 +16,7 @@ makeCross(pop, crossPlan, nProgeny = 1, simParam = NULL, nThreads = NULL)
 female and male parents. Either integers for the position in
 population or character strings for the IDs.}
 
-\item{nProgeny}{number of progeny per cross. May be a single value for all 
+\item{nProgeny}{number of progeny per cross. May be a single value for all
 crosses or a vector with values for each cross.}
 
 \item{simParam}{an object of class \code{\link{SimParam}}. If
@@ -30,6 +33,11 @@ Returns an object of \code{\link{Pop-class}}
 Makes crosses within a population using a user supplied
 crossing plan.
 }
+\section{Functions}{
+\itemize{
+\item \code{makeCross(Pop)}: Method for \code{\link{Pop-class}}
+
+}}
 \examples{
 #Create founder haplotypes
 founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
diff --git a/man/makeCross2.Rd b/man/makeCross2.Rd
index 785adb8f..0f6fec13 100644
--- a/man/makeCross2.Rd
+++ b/man/makeCross2.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/crossing.R
 \name{makeCross2}
 \alias{makeCross2}
+\alias{makeCross2,Pop,Pop-method}
 \title{Make designed crosses}
 \usage{
 makeCross2(
@@ -12,6 +13,15 @@ makeCross2(
   simParam = NULL,
   nThreads = NULL
 )
+
+\S4method{makeCross2}{Pop,Pop}(
+  females,
+  males,
+  crossPlan,
+  nProgeny = 1,
+  simParam = NULL,
+  nThreads = NULL
+)
 }
 \arguments{
 \item{females}{an object of \code{\link{Pop-class}} for female parents.}
@@ -22,7 +32,7 @@ makeCross2(
 female and male parents. Either integers for the position in
 population or character strings for the IDs.}
 
-\item{nProgeny}{number of progeny per cross. May be a single value for all 
+\item{nProgeny}{number of progeny per cross. May be a single value for all
 crosses or a vector with values for each cross.}
 
 \item{simParam}{an object of class \code{\link{SimParam}}. If
@@ -39,6 +49,11 @@ Returns an object of \code{\link{Pop-class}}
 Makes crosses between two populations using a user supplied
 crossing plan.
 }
+\section{Functions}{
+\itemize{
+\item \code{makeCross2(females = Pop, males = Pop)}: Method for \code{\link{Pop-class}}
+
+}}
 \examples{
 #Create founder haplotypes
 founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
diff --git a/man/makeDH.Rd b/man/makeDH.Rd
index 4413f81c..3407f85a 100644
--- a/man/makeDH.Rd
+++ b/man/makeDH.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/crossing.R
 \name{makeDH}
 \alias{makeDH}
+\alias{makeDH,Pop-method}
 \title{Generates DH lines}
 \usage{
 makeDH(
@@ -12,6 +13,15 @@ makeDH(
   simParam = NULL,
   nThreads = NULL
 )
+
+\S4method{makeDH}{Pop}(
+  pop,
+  nDH = 1,
+  useFemale = TRUE,
+  keepParents = TRUE,
+  simParam = NULL,
+  nThreads = NULL
+)
 }
 \arguments{
 \item{pop}{an object of 'Pop' superclass}
@@ -38,6 +48,11 @@ Creates DH lines from each individual in a population.
 Only works with diploid individuals. For polyploids, use
 \code{\link{reduceGenome}} and \code{\link{doubleGenome}}.
 }
+\section{Functions}{
+\itemize{
+\item \code{makeDH(Pop)}: Method for \code{\link{Pop-class}}
+
+}}
 \examples{
 #Create founder haplotypes
 founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)
diff --git a/man/pedigreeCross.Rd b/man/pedigreeCross.Rd
index 48ecaee5..6244f0b9 100644
--- a/man/pedigreeCross.Rd
+++ b/man/pedigreeCross.Rd
@@ -22,7 +22,7 @@ pedigreeCross(
 \item{founderPop}{a \code{\link{Pop-class}}}
 
 \item{id}{a vector of unique identifiers for individuals
-in the pedigree. The values of these IDs are seperate from
+in the pedigree. The values of these IDs are separate from
 the IDs in the founderPop if matchID=FALSE.}
 
 \item{mother}{a vector of identifiers for the mothers
diff --git a/man/randCross.Rd b/man/randCross.Rd
index e5e4e290..c5546847 100644
--- a/man/randCross.Rd
+++ b/man/randCross.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/crossing.R
 \name{randCross}
 \alias{randCross}
+\alias{randCross,Pop-method}
 \title{Make random crosses}
 \usage{
 randCross(
@@ -14,14 +15,25 @@ randCross(
   simParam = NULL,
   nThreads = NULL
 )
+
+\S4method{randCross}{Pop}(
+  pop,
+  nCrosses,
+  nProgeny = 1,
+  balance = TRUE,
+  parents = NULL,
+  ignoreSexes = FALSE,
+  simParam = NULL,
+  nThreads = NULL
+)
 }
 \arguments{
 \item{pop}{an object of \code{\link{Pop-class}}}
 
 \item{nCrosses}{total number of crosses to make}
 
-\item{nProgeny}{number of progeny per cross. May be a single value for all 
-crosses or a vector with values equal to the number of crosses. If providing 
+\item{nProgeny}{number of progeny per cross. May be a single value for all
+crosses or a vector with values equal to the number of crosses. If providing
 a vector, the values are randomly assigned to each cross.}
 
 \item{balance}{if using sexes, this option will balance the number
@@ -43,8 +55,13 @@ Returns an object of \code{\link{Pop-class}}
 }
 \description{
 A wrapper for \code{\link{makeCross}} that randomly
-selects parental combinations for all possible combinantions.
+selects parental combinations for all possible combinations.
 }
+\section{Functions}{
+\itemize{
+\item \code{randCross(Pop)}: Method for \code{\link{Pop-class}}
+
+}}
 \examples{
 #Create founder haplotypes
 founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
diff --git a/man/randCross2.Rd b/man/randCross2.Rd
index 8b2c00a5..8df069b0 100644
--- a/man/randCross2.Rd
+++ b/man/randCross2.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/crossing.R
 \name{randCross2}
 \alias{randCross2}
+\alias{randCross2,Pop,Pop-method}
 \title{Make random crosses}
 \usage{
 randCross2(
@@ -16,6 +17,19 @@ randCross2(
   simParam = NULL,
   nThreads = NULL
 )
+
+\S4method{randCross2}{Pop,Pop}(
+  females,
+  males,
+  nCrosses,
+  nProgeny = 1,
+  balance = TRUE,
+  femaleParents = NULL,
+  maleParents = NULL,
+  ignoreSexes = FALSE,
+  simParam = NULL,
+  nThreads = NULL
+)
 }
 \arguments{
 \item{females}{an object of \code{\link{Pop-class}} for female parents.}
@@ -24,8 +38,8 @@ randCross2(
 
 \item{nCrosses}{total number of crosses to make}
 
-\item{nProgeny}{number of progeny per cross. May be a single value for all 
-crosses or a vector with values equal to the number of crosses. If providing 
+\item{nProgeny}{number of progeny per cross. May be a single value for all
+crosses or a vector with values equal to the number of crosses. If providing
 a vector, the values are randomly assigned to each cross.}
 
 \item{balance}{this option will balance the number
@@ -51,9 +65,14 @@ Returns an object of \code{\link{Pop-class}}
 }
 \description{
 A wrapper for \code{\link{makeCross2}} that randomly
-selects parental combinations for all possible combinantions between
+selects parental combinations for all possible combinations between
 two populations.
 }
+\section{Functions}{
+\itemize{
+\item \code{randCross2(females = Pop, males = Pop)}: Method for \code{\link{Pop-class}}
+
+}}
 \examples{
 #Create founder haplotypes
 founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
diff --git a/man/selectCross.Rd b/man/selectCross.Rd
index b237928c..c467127f 100644
--- a/man/selectCross.Rd
+++ b/man/selectCross.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/crossing.R
 \name{selectCross}
 \alias{selectCross}
+\alias{selectCross,Pop-method}
 \title{Select and randomly cross}
 \usage{
 selectCross(
@@ -19,6 +20,22 @@ selectCross(
   ...,
   balance = TRUE
 )
+
+\S4method{selectCross}{Pop}(
+  pop,
+  nInd = NULL,
+  nFemale = NULL,
+  nMale = NULL,
+  nCrosses,
+  nProgeny = 1,
+  trait = 1,
+  use = "pheno",
+  selectTop = T,
+  simParam = NULL,
+  nThreads = NULL,
+  ...,
+  balance = TRUE
+)
 }
 \arguments{
 \item{pop}{an object of \code{\link{Pop-class}}}
@@ -75,6 +92,11 @@ of intermediate populations created. This reduces RAM usage
 and simplifies code writing. Note that this wrapper does not
 provide the full functionality of either function.
 }
+\section{Functions}{
+\itemize{
+\item \code{selectCross(Pop)}: Method for \code{\link{Pop-class}}
+
+}}
 \examples{
 #Create founder haplotypes
 founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
diff --git a/man/self.Rd b/man/self.Rd
index 1dc8f70b..eac7e4b0 100644
--- a/man/self.Rd
+++ b/man/self.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/crossing.R
 \name{self}
 \alias{self}
+\alias{self,Pop-method}
 \title{Self individuals}
 \usage{
 self(
@@ -12,11 +13,20 @@ self(
   simParam = NULL,
   nThreads = NULL
 )
+
+\S4method{self}{Pop}(
+  pop,
+  nProgeny = 1,
+  parents = NULL,
+  keepParents = TRUE,
+  simParam = NULL,
+  nThreads = NULL
+)
 }
 \arguments{
 \item{pop}{an object of \code{\link{Pop-class}}}
 
-\item{nProgeny}{number of selfed progeny per individual. May be a single value 
+\item{nProgeny}{number of selfed progeny per individual. May be a single value
 for all or a vector providing values for each individual.}
 
 \item{parents}{an optional vector of indices for allowable parents}
@@ -38,6 +48,11 @@ Returns an object of \code{\link{Pop-class}}
 Creates selfed progeny from each individual in a
 population. Only works when sexes is "no".
 }
+\section{Functions}{
+\itemize{
+\item \code{self(Pop)}: Method for \code{\link{Pop-class}}
+
+}}
 \examples{
 #Create founder haplotypes
 founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)
diff --git a/man/setPheno.Rd b/man/setPheno.Rd
index 9c107235..3395e20b 100644
--- a/man/setPheno.Rd
+++ b/man/setPheno.Rd
@@ -2,6 +2,8 @@
 % Please edit documentation in R/phenotypes.R
 \name{setPheno}
 \alias{setPheno}
+\alias{setPheno,Pop-method}
+\alias{setPheno,MultiPop-method}
 \title{Set phenotypes}
 \usage{
 setPheno(
@@ -18,6 +20,34 @@ setPheno(
   simParam = NULL,
   ...
 )
+
+\S4method{setPheno}{Pop}(
+  pop,
+  h2 = NULL,
+  H2 = NULL,
+  varE = NULL,
+  corE = NULL,
+  reps = 1,
+  fixEff = 1L,
+  p = NULL,
+  onlyPheno = FALSE,
+  traits = NULL,
+  simParam = NULL
+)
+
+\S4method{setPheno}{MultiPop}(
+  pop,
+  h2 = NULL,
+  H2 = NULL,
+  varE = NULL,
+  corE = NULL,
+  reps = 1,
+  fixEff = 1L,
+  p = NULL,
+  onlyPheno = FALSE,
+  traits = NULL,
+  simParam = NULL
+)
 }
 \arguments{
 \item{pop}{an object of \code{\link{Pop-class}} or
@@ -99,6 +129,13 @@ breeding programs. In this case, varE is set to the plot error and
 reps is set to the number of plots per entry. The resulting phenotype
 represents the entry-means.
 }
+\section{Functions}{
+\itemize{
+\item \code{setPheno(Pop)}: Method for \code{\link{Pop-class}}
+
+\item \code{setPheno(MultiPop)}: Method for \code{\link{MultiPop-class}} objects
+
+}}
 \examples{
 #Create founder haplotypes
 founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)