diff --git a/NAMESPACE b/NAMESPACE
index 2594253a..796f782a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -133,6 +133,14 @@ 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 d84be75f..8fb88419 100644
--- a/R/crossing.R
+++ b/R/crossing.R
@@ -31,8 +31,29 @@
 #' pop2 = makeCross(pop, crossPlan, simParam=SP)
 #'
 #' @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)
   }
@@ -42,7 +63,7 @@ makeCross = function(pop,crossPlan,nProgeny=1,
     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),
@@ -102,7 +123,7 @@ 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
@@ -132,7 +153,33 @@ makeCross = function(pop,crossPlan,nProgeny=1,
 #' pop2 = randCross(pop, 10, simParam=SP)
 #'
 #' @export
-randCross = function(pop,nCrosses,nProgeny=1,
+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){
@@ -250,7 +297,34 @@ 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,
+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)){
@@ -324,7 +398,28 @@ selectCross = function(pop,nInd=NULL,nFemale=NULL,nMale=NULL,nCrosses,
 #' pop2 = makeCross2(pop, pop, crossPlan, simParam=SP)
 #'
 #' @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)
@@ -336,7 +431,7 @@ makeCross2 = function(females,males,crossPlan,nProgeny=1,simParam=NULL,
   }
   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),
@@ -397,7 +492,7 @@ 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.
@@ -432,10 +527,37 @@ 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)
   }
@@ -528,8 +650,34 @@ 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)
   }
@@ -639,8 +787,31 @@ 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)
   }
@@ -756,7 +927,7 @@ 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)
 }
@@ -769,7 +940,7 @@ 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
diff --git a/R/phenotypes.R b/R/phenotypes.R
index 0f4120f9..f329d87e 100644
--- a/R/phenotypes.R
+++ b/R/phenotypes.R
@@ -152,9 +152,50 @@ 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)
   }
@@ -315,9 +356,9 @@ setPheno = function(pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL,
 #' SP$setVarE(varE = trtVarELog)
 #' pop = newPop(founderPop)
 #' popLarge = randCross(pop, nCrosses = 1000)
-#' 
+#'
 #' meanVarFun = function(x) list(mean = mean(x), var = var(x))
-#' 
+#'
 #' #Latent phenotypes and parameters
 #' (phenoLog = pheno(pop))
 #' phenoLogLarge = pheno(popLarge)
@@ -339,7 +380,7 @@ setPheno = function(pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL,
 #' cbind(phenoLog = phenoLog[, 1],
 #'   phenoExpMeanLog0 = phenoExpMeanLog0,
 #'   phenoExpMeanExp1 = phenoExpMeanExp1)
-#' 
+#'
 #' tmp = cbind(phenoLog = phenoLogLarge[, 1],
 #'   phenoExpMeanLog0 = c(asLogNormal(phenoLogLarge[, 1])),
 #'   phenoExpMeanExp1 = c(asLogNormal(phenoLogLarge[, 1], meanlog = -trtVarPLog[1]/2)))
@@ -357,12 +398,12 @@ setPheno = function(pop, h2=NULL, H2=NULL, varE=NULL, corE=NULL,
 #' try(asLogNormal(x = pheno(pop), meanlog = 0))
 #' asLogNormal(x = pheno(pop), meanlog = c(0, 1))
 #' asLogNormal(x = pheno(pop), meanlog = list(0, NULL))
-#' 
+#'
 #' #Store the recoded trait manually
 #' pheno(pop)
 #' pop@pheno[, 1] = asLogNormal(x = pheno(pop)[, 1])
 #' pheno(pop)
-#' 
+#'
 #' #Apply and store the transformation automatically via SimParam$finalizePop()
 #' SP$finalizePop = function(pop, simParam = SP) {
 #'   pop@pheno[, 1] = asLogNormal(x = pheno(pop)[, 1])
@@ -481,12 +522,12 @@ asLogNormal <- function(x, meanlog = NULL) {
 #'               p = list(c(0.5, 0.5),
 #'                        p),
 #'               mean = trtMean, var = trtVarP)
-#' 
+#'
 #' #Store the recoded trait manually
 #' pheno(pop)
 #' pop@pheno[, 1] = asCategorical(x = pheno(pop)[, 1])
 #' pheno(pop)
-#' 
+#'
 #' #Apply and store the transformation automatically via SimParam$finalizePop()
 #' SP$finalizePop = function(pop, simParam = SP) {
 #'   pop@pheno[, 1] = asCategorical(x = pheno(pop)[, 1])
diff --git a/man/makeCross.Rd b/man/makeCross.Rd
index 4dee9d31..8d1996eb 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}}}
@@ -27,6 +30,11 @@ 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 721492ed..2829af4b 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.}
@@ -36,6 +46,11 @@ 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 46a649a8..90a95fab 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}
@@ -36,6 +46,11 @@ 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 487944cd..3ef09c93 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 d300e0a7..0af43d84 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(
@@ -14,6 +15,17 @@ 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}}}
@@ -39,8 +51,13 @@ 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 608321be..ae0974e5 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.}
@@ -47,9 +61,14 @@ 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 8baf6e90..a9aa2680 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}}}
@@ -73,6 +90,11 @@ 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 64df6ec9..05ad8332 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(
@@ -12,6 +13,15 @@ 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}}}
@@ -35,6 +45,11 @@ 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 aa3866e0..ba65e489 100644
--- a/man/setPheno.Rd
+++ b/man/setPheno.Rd
@@ -2,9 +2,40 @@
 % Please edit documentation in R/phenotypes.R
 \name{setPheno}
 \alias{setPheno}
+\alias{setPheno,Pop-method}
+\alias{setPheno,MultiPop-method}
 \title{Set phenotypes}
 \usage{
 setPheno(
+  pop,
+  h2 = NULL,
+  H2 = NULL,
+  varE = NULL,
+  corE = NULL,
+  reps = 1,
+  fixEff = 1L,
+  p = NULL,
+  onlyPheno = FALSE,
+  traits = NULL,
+  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,
@@ -93,6 +124,13 @@ 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)