diff --git a/R/convertPedigree.R b/R/convertPedigree.R
index 4123c4c..84c1662 100644
--- a/R/convertPedigree.R
+++ b/R/convertPedigree.R
@@ -12,7 +12,7 @@
#' @param tcross.alt.crossprod logical. If TRUE, use alternative method of using Crossprod function for computing the transpose
#' @param tcross.alt.star logical. If TRUE, use alternative method of using \%\*\% for computing the transpose
#' @param ... additional arguments to be passed to \code{\link{ped2com}}
-#' @details The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions".
+#' @details The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions". For more advanced scenarios and detailed explanations, consult this vignette.
#' @export
#'
ped2com <- function(ped, component,
@@ -156,8 +156,6 @@ ped2com <- function(ped, component,
# compute rel <- tcrossprod(rsq)
if (gc) {
rm(isPar, newIsPar)
- }
- if (gc) {
gc()
}
if (verbose) {
@@ -166,8 +164,6 @@ ped2com <- function(ped, component,
r2 <- r %*% Matrix::Diagonal(x = sqrt(isChild), n = nr)
if (gc) {
rm(r, isChild)
- }
- if (gc) {
gc()
}
if (verbose) {
@@ -201,9 +197,7 @@ ped2com <- function(ped, component,
#' Take a pedigree and turn it into an additive genetics relatedness matrix
#' @inheritParams ped2com
-#' @details The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions".
-#' For more advanced scenarios and detailed explanations, consult this vignette.
-
+#' @inherit ped2com details
#' @export
#'
ped2add <- function(ped, max.gen = Inf, sparse = FALSE, verbose = FALSE, gc = FALSE, flatten.diag = FALSE, standardize.colnames = TRUE,
@@ -224,7 +218,7 @@ ped2add <- function(ped, max.gen = Inf, sparse = FALSE, verbose = FALSE, gc = FA
#' Take a pedigree and turn it into a mitochondrial relatedness matrix
#' @inheritParams ped2com
-#' @details The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions".
+#' @inherit ped2com details
#' @export
#' @aliases ped2mt
#'
@@ -245,7 +239,7 @@ ped2mit <- ped2mt <- function(ped, max.gen = Inf, sparse = FALSE, verbose = FALS
#' Take a pedigree and turn it into a common nuclear environmental relatedness matrix
#' @inheritParams ped2com
-#' @details The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions".
+#' @inherit ped2com details
#' @export
#'
ped2cn <- function(ped, max.gen = Inf, sparse = FALSE, verbose = FALSE, gc = FALSE, flatten.diag = FALSE, standardize.colnames = TRUE, tcross.alt.crossprod = FALSE, tcross.alt.star = FALSE) {
@@ -265,7 +259,7 @@ ped2cn <- function(ped, max.gen = Inf, sparse = FALSE, verbose = FALSE, gc = FAL
#' Take a pedigree and turn it into an extended environmental relatedness matrix
#' @inheritParams ped2com
-#' @details The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions".
+#' @inherit ped2com details
#' @export
#'
ped2ce <- function(ped) {
diff --git a/man/Null.Rd b/man/Null.Rd
index b51c24f..24fc71d 100644
--- a/man/Null.Rd
+++ b/man/Null.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helper.R
+% Please edit documentation in R/helpGeneric.R
\name{Null}
\alias{Null}
\title{Compute the null space of a matrix}
diff --git a/man/SimPed.Rd b/man/SimPed.Rd
index 1d70f0f..79dd1f9 100644
--- a/man/SimPed.Rd
+++ b/man/SimPed.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helper.R
+% Please edit documentation in R/helpGeneric.R
\name{SimPed}
\alias{SimPed}
\title{SimPed (Deprecated)}
diff --git a/man/allGens.Rd b/man/allGens.Rd
index 2f7efe0..6bc6d9e 100644
--- a/man/allGens.Rd
+++ b/man/allGens.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/famSizeCal.R
+% Please edit documentation in R/calculateFamilySize.R
\name{allGens}
\alias{allGens}
\title{allGens
diff --git a/man/calculateH.Rd b/man/calculateH.Rd
index 9fe2415..0894f0c 100644
--- a/man/calculateH.Rd
+++ b/man/calculateH.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/formula.R
+% Please edit documentation in R/computeRelatedness.R
\name{calculateH}
\alias{calculateH}
\title{Falconer's Formula
diff --git a/man/calculateRelatedness.Rd b/man/calculateRelatedness.Rd
index 81f7a3b..259ff8b 100644
--- a/man/calculateRelatedness.Rd
+++ b/man/calculateRelatedness.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/formula.R
+% Please edit documentation in R/computeRelatedness.R
\name{calculateRelatedness}
\alias{calculateRelatedness}
\title{Calculate Relatedness Coefficient}
diff --git a/man/efunc.Rd b/man/efunc.Rd
index 31ef25f..f51dcc9 100644
--- a/man/efunc.Rd
+++ b/man/efunc.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helper.R
+% Please edit documentation in R/helpGeneric.R
\name{efunc}
\alias{efunc}
\title{Error Function}
diff --git a/man/evenInsert.Rd b/man/evenInsert.Rd
index 010b627..2dae39c 100644
--- a/man/evenInsert.Rd
+++ b/man/evenInsert.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/evenInsert.R
+% Please edit documentation in R/insertEven.R
\name{evenInsert}
\alias{evenInsert}
\title{evenInsert
diff --git a/man/famSizeCal.Rd b/man/famSizeCal.Rd
index 60e20a9..e51f95e 100644
--- a/man/famSizeCal.Rd
+++ b/man/famSizeCal.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/famSizeCal.R
+% Please edit documentation in R/calculateFamilySize.R
\name{famSizeCal}
\alias{famSizeCal}
\title{famSizeCal
diff --git a/man/hazard.Rd b/man/hazard.Rd
index c701a19..fa0430c 100755
--- a/man/hazard.Rd
+++ b/man/hazard.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/dataDoc.R
+% Please edit documentation in R/documentData.R
\docType{data}
\name{hazard}
\alias{hazard}
diff --git a/man/inbreeding.Rd b/man/inbreeding.Rd
index a8fad43..d85149e 100755
--- a/man/inbreeding.Rd
+++ b/man/inbreeding.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/dataDoc.R
+% Please edit documentation in R/documentData.R
\docType{data}
\name{inbreeding}
\alias{inbreeding}
diff --git a/man/inferRelatedness.Rd b/man/inferRelatedness.Rd
index cf30820..961de7e 100644
--- a/man/inferRelatedness.Rd
+++ b/man/inferRelatedness.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/formula.R
+% Please edit documentation in R/computeRelatedness.R
\name{inferRelatedness}
\alias{inferRelatedness}
\title{Infer Relatedness Coefficient}
diff --git a/man/nullToNA.Rd b/man/nullToNA.Rd
index 7efae0c..4bccb4b 100644
--- a/man/nullToNA.Rd
+++ b/man/nullToNA.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helper.R
+% Please edit documentation in R/helpGeneric.R
\name{nullToNA}
\alias{nullToNA}
\title{nullToNA}
diff --git a/man/ped2add.Rd b/man/ped2add.Rd
index ad87012..581a5b9 100644
--- a/man/ped2add.Rd
+++ b/man/ped2add.Rd
@@ -41,6 +41,5 @@ generations as there are in the data.}
Take a pedigree and turn it into an additive genetics relatedness matrix
}
\details{
-The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions".
-For more advanced scenarios and detailed explanations, consult this vignette.
+The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions". For more advanced scenarios and detailed explanations, consult this vignette.
}
diff --git a/man/ped2ce.Rd b/man/ped2ce.Rd
index a736557..f4c1efa 100644
--- a/man/ped2ce.Rd
+++ b/man/ped2ce.Rd
@@ -13,5 +13,5 @@ ped2ce(ped)
Take a pedigree and turn it into an extended environmental relatedness matrix
}
\details{
-The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions".
+The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions". For more advanced scenarios and detailed explanations, consult this vignette.
}
diff --git a/man/ped2cn.Rd b/man/ped2cn.Rd
index 0d7e3eb..e4b8e84 100644
--- a/man/ped2cn.Rd
+++ b/man/ped2cn.Rd
@@ -41,5 +41,5 @@ generations as there are in the data.}
Take a pedigree and turn it into a common nuclear environmental relatedness matrix
}
\details{
-The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions".
+The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions". For more advanced scenarios and detailed explanations, consult this vignette.
}
diff --git a/man/ped2com.Rd b/man/ped2com.Rd
index 67daf5f..1f35587 100644
--- a/man/ped2com.Rd
+++ b/man/ped2com.Rd
@@ -47,5 +47,5 @@ generations as there are in the data.}
Take a pedigree and turn it into a relatedness matrix
}
\details{
-The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions".
+The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions". For more advanced scenarios and detailed explanations, consult this vignette.
}
diff --git a/man/ped2fam.Rd b/man/ped2fam.Rd
index c3db0a7..0620d15 100644
--- a/man/ped2fam.Rd
+++ b/man/ped2fam.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/family.R
+% Please edit documentation in R/buildPedigree.R
\name{ped2fam}
\alias{ped2fam}
\title{Add an extended family ID variable to a pedigree}
diff --git a/man/ped2graph.Rd b/man/ped2graph.Rd
index 0564b1f..cf90526 100755
--- a/man/ped2graph.Rd
+++ b/man/ped2graph.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/family.R
+% Please edit documentation in R/buildPedigree.R
\name{ped2graph}
\alias{ped2graph}
\title{Turn a pedigree into a graph}
diff --git a/man/ped2maternal.Rd b/man/ped2maternal.Rd
index 8cc0a8b..3822684 100755
--- a/man/ped2maternal.Rd
+++ b/man/ped2maternal.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/family.R
+% Please edit documentation in R/buildPedigree.R
\name{ped2maternal}
\alias{ped2maternal}
\title{Add a maternal line ID variable to a pedigree}
diff --git a/man/ped2mit.Rd b/man/ped2mit.Rd
index 530ca4e..520c986 100644
--- a/man/ped2mit.Rd
+++ b/man/ped2mit.Rd
@@ -42,5 +42,5 @@ generations as there are in the data.}
Take a pedigree and turn it into a mitochondrial relatedness matrix
}
\details{
-The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions".
+The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions". For more advanced scenarios and detailed explanations, consult this vignette.
}
diff --git a/man/ped2paternal.Rd b/man/ped2paternal.Rd
index b88fabb..719097d 100755
--- a/man/ped2paternal.Rd
+++ b/man/ped2paternal.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/family.R
+% Please edit documentation in R/buildPedigree.R
\name{ped2paternal}
\alias{ped2paternal}
\title{Add a paternal line ID variable to a pedigree}
diff --git a/man/potter.Rd b/man/potter.Rd
index 100a164..1fff502 100755
--- a/man/potter.Rd
+++ b/man/potter.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/dataDoc.R
+% Please edit documentation in R/documentData.R
\docType{data}
\name{potter}
\alias{potter}
diff --git a/man/related_coef.Rd b/man/related_coef.Rd
index b48fc0d..1111298 100644
--- a/man/related_coef.Rd
+++ b/man/related_coef.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helper.R
+% Please edit documentation in R/helpGeneric.R
\name{related_coef}
\alias{related_coef}
\title{related_coef (Deprecated)}
diff --git a/man/relatedness.Rd b/man/relatedness.Rd
index 0ae4832..f84740d 100644
--- a/man/relatedness.Rd
+++ b/man/relatedness.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helper.R
+% Please edit documentation in R/helpGeneric.R
\name{relatedness}
\alias{relatedness}
\title{relatedness (Deprecated)}
diff --git a/man/resample.Rd b/man/resample.Rd
index ae2aa85..67246be 100644
--- a/man/resample.Rd
+++ b/man/resample.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helper.R
+% Please edit documentation in R/helpGeneric.R
\name{resample}
\alias{resample}
\title{Resample Elements of a Vector}
diff --git a/man/rmvn.Rd b/man/rmvn.Rd
index fe3be9b..a293947 100644
--- a/man/rmvn.Rd
+++ b/man/rmvn.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helper.R
+% Please edit documentation in R/helpGeneric.R
\name{rmvn}
\alias{rmvn}
\title{rmvn}
diff --git a/man/sizeAllGens.Rd b/man/sizeAllGens.Rd
index 47e1afd..e477c19 100644
--- a/man/sizeAllGens.Rd
+++ b/man/sizeAllGens.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/famSizeCal.R
+% Please edit documentation in R/calculateFamilySize.R
\name{sizeAllGens}
\alias{sizeAllGens}
\title{sizeAllGens
diff --git a/man/try_na.Rd b/man/try_na.Rd
index e5abb2e..0f8fdde 100644
--- a/man/try_na.Rd
+++ b/man/try_na.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helper.R
+% Please edit documentation in R/helpGeneric.R
\name{try_na}
\alias{try_na}
\title{modified tryCatch function}
diff --git a/vignettes/pedigree.html b/vignettes/pedigree.html
index edc6f3d..0b13234 100644
--- a/vignettes/pedigree.html
+++ b/vignettes/pedigree.html
@@ -416,7 +416,7 @@ Single Pedigree Visualization
plotPedigree() function.
# Plot the simulated pedigree
plotPedigree(df_ped)
+
#> Did not plot the following people: 10032
#> $plist
#> $plist$n
@@ -598,7 +598,7 @@ Visualizing Multiple Pedigrees Side-by-Side
# Plot the 4-generation pedigree
plotPedigree(df_ped_4, width = 1)
-
+
#> $plist
#> $plist$n
#> [1] 2 5 10 12