allow more argumements

Author: smasongarrison

NEWS.md

@@ -1,3 +1,6 @@
+# BGmisc 1.3.2.1
+* Added ability to pass additional arguments to the ped2FOO functions
+
 # BGmisc 1.3.2
 * Added some more tests of identifyModel.R
 * Modified tests to be MKL friendly

R/buildPedigree.R

@@ -9,6 +9,7 @@
 #' @param momID character.  Name of the column in ped for the mother ID variable
 #' @param dadID character.  Name of the column in ped for the father ID variable
 #' @param famID character.  Name of the column to be created in ped for the family ID variable
+#' @param ... additional arguments to be passed to \code{\link{ped2com}}
 #' @details
 #' The general idea of this function is to use person ID, mother ID, and father ID to
 #' create an extended family ID such that everyone with the same family ID is in the
@@ -25,14 +26,17 @@
 #'
 #' @export
 #'
-ped2fam <- function(ped, personID = "ID", momID = "momID", dadID = "dadID", famID = "famID") {
+ped2fam <- function(ped, personID = "ID",
+                    momID = "momID", dadID = "dadID", famID = "famID",
+                    ...) {
   # Call to wrapper function
   .ped2id(ped = ped, personID = personID, momID = momID, dadID = dadID, famID = famID, type = "parents")
 }
 
 .ped2id <- function(ped,
                     personID = "ID", momID = "momID", dadID = "dadID",
-                    famID = "famID", type) {
+                    famID = "famID", type,
+                    ...) {
   # Turn pedigree into family
   pg <- ped2graph(ped = ped, personID = personID, momID = momID, dadID = dadID, adjacent = type)
 
@@ -79,7 +83,8 @@ ped2graph <- function(ped,
                       momID = "momID",
                       dadID = "dadID",
                       directed = TRUE,
-                      adjacent = c("parents", "mothers", "fathers")) {
+                      adjacent = c("parents", "mothers", "fathers"),
+                      ...) {
   # Check ped/data.fram
   if (!inherits(ped, "data.frame")) stop("ped should be a data.frame or inherit to a data.frame")
   # Handle adjacent argument
@@ -171,7 +176,8 @@ ped2graph <- function(ped,
 #' for creating paternal line IDs
 #' @export
 #'
-ped2maternal <- function(ped, personID = "ID", momID = "momID", dadID = "dadID", matID = "matID") {
+ped2maternal <- function(ped, personID = "ID",
+                         momID = "momID", dadID = "dadID", matID = "matID",...) {
   # Call to wrapper function
   .ped2id(ped = ped, personID = personID, momID = momID, dadID = dadID, famID = matID, type = "mothers")
 }
@@ -189,7 +195,9 @@ ped2maternal <- function(ped, personID = "ID", momID = "momID", dadID = "dadID",
 #' for creating maternal line IDs
 #' @export
 #'
-ped2paternal <- function(ped, personID = "ID", momID = "momID", dadID = "dadID", patID = "patID") {
+ped2paternal <- function(ped, personID = "ID",
+                         momID = "momID", dadID = "dadID",
+                         patID = "patID",...) {
   # Call to wrapper function
   .ped2id(ped = ped, personID = personID, momID = momID, dadID = dadID, famID = patID, type = "fathers")
 }

R/convertPedigree.R

@@ -204,8 +204,11 @@ ped2com <- function(ped, component,
 #' @inherit ped2com details
 #' @export
 #'
-ped2add <- function(ped, max.gen = 25, sparse = FALSE, verbose = FALSE, gc = FALSE, flatten.diag = FALSE, standardize.colnames = TRUE,
-                    tcross.alt.crossprod = FALSE, tcross.alt.star = FALSE) {
+ped2add <- function(ped, max.gen = 25, sparse = FALSE, verbose = FALSE,
+                    gc = FALSE,
+                    flatten.diag = FALSE, standardize.colnames = TRUE,
+                    tcross.alt.crossprod = FALSE, tcross.alt.star = FALSE,
+                    ...) {
   ped2com(
     ped = ped,
     max.gen = max.gen,
@@ -226,7 +229,13 @@ ped2add <- function(ped, max.gen = 25, sparse = FALSE, verbose = FALSE, gc = FAL
 #' @export
 #' @aliases ped2mt
 #'
-ped2mit <- ped2mt <- function(ped, max.gen = 25, sparse = FALSE, verbose = FALSE, gc = FALSE, flatten.diag = FALSE, standardize.colnames = TRUE, tcross.alt.crossprod = FALSE, tcross.alt.star = FALSE) {
+ped2mit <- ped2mt <- function(ped, max.gen = 25,
+                              sparse = FALSE,
+                              verbose = FALSE, gc = FALSE,
+                              flatten.diag = FALSE,
+                              standardize.colnames = TRUE,
+                              tcross.alt.crossprod = FALSE, tcross.alt.star = FALSE,
+                              ...) {
   ped2com(
     ped = ped,
     max.gen = max.gen,
@@ -246,7 +255,11 @@ ped2mit <- ped2mt <- function(ped, max.gen = 25, sparse = FALSE, verbose = FALSE
 #' @inherit ped2com details
 #' @export
 #'
-ped2cn <- function(ped, max.gen = 25, sparse = FALSE, verbose = FALSE, gc = FALSE, flatten.diag = FALSE, standardize.colnames = TRUE, tcross.alt.crossprod = FALSE, tcross.alt.star = FALSE) {
+ped2cn <- function(ped, max.gen = 25, sparse = FALSE, verbose = FALSE,
+                   gc = FALSE, flatten.diag = FALSE,
+                   standardize.colnames = TRUE,
+                   tcross.alt.crossprod = FALSE, tcross.alt.star = FALSE,
+                   ...) {
   ped2com(
     ped = ped,
     max.gen = max.gen,
@@ -266,6 +279,7 @@ ped2cn <- function(ped, max.gen = 25, sparse = FALSE, verbose = FALSE, gc = FALS
 #' @inherit ped2com details
 #' @export
 #'
-ped2ce <- function(ped) {
+ped2ce <- function(ped,
+                   ...) {
   matrix(1, nrow = nrow(ped), ncol = nrow(ped), dimnames = list(ped$ID, ped$ID))
 }