fix major issue with re-ordering of dii and f vectors

  - caused major issues and errors in makeA relatedness matrices
  - reason was code tried to transpose perm vector of a permutation matrix instead of using invPerm
  - permutation matrices class "pMatrix" have perm slot as EITHER row index or column index vector
  - converting perm slot from row to column index vectors (or vice versa) requires usinv invPerm and NOT transposing matrix then taking perm slot
  - note this is not an issue where makeAinv.fuzzy() reorders f and dii vectors because the fsOrd1 matrix is not a pMatrix but ngCMatrix

R/makeAinv.R

@@ -294,12 +294,12 @@ makeAinv.default <- function(pedigree, f = NULL,
   Ainv <- crossprod(fsOrd, Ainv) %*% fsOrd
   if(ptype == "D"){
       Ainv@Dimnames <- list(as.character(pedalt[, 1]), NULL)
-      f <- Cout[[3]][t(fsOrd)@perm][-seq(nggroups)]
-      dii <- Cout[[4]][t(fsOrd)@perm][-seq(nggroups)]
+      f <- Cout[[3]][invPerm(fsOrd@perm)][-seq(nggroups)]
+      dii <- Cout[[4]][invPerm(fsOrd@perm)][-seq(nggroups)]
   } else {
       Ainv@Dimnames <- list(as.character(pedigree[, 1]), NULL)
-      f <- c(rep(0, nggroups), Cout[[3]][t(fsOrd)@perm][(nggroups+1):(nggroups + eN)])
-      dii <- c(rep(0, nggroups), Cout[[4]][t(fsOrd)@perm][(nggroups+1):(nggroups + eN)])
+      f <- c(rep(0, nggroups), Cout[[3]][invPerm(fsOrd@perm)][(nggroups+1):(nggroups + eN)])
+      dii <- c(rep(0, nggroups), Cout[[4]][invPerm(fsOrd@perm)][(nggroups+1):(nggroups + eN)])
     }
   if(!is.null(ggroups) && !gOnTop){ 
      permute <- as(as.integer(c(seq(eN+1, N, 1), seq(eN))), "pMatrix")

R/makeTinvDF.R

@@ -229,8 +229,8 @@ makeDiiF.default <- function(pedigree, f = NULL, ...){
             as.integer(0),			#number genetic groups
 	    as.integer(fmiss - 1))		#first f to calculate (not supplied)
   fsOrd <- as(as.integer(renPed), "pMatrix")
-  f <- Cout[[3]][t(fsOrd)@perm]
-  dii <- Cout[[4]][t(fsOrd)@perm]
+  f <- Cout[[3]][invPerm(fsOrd@perm)]
+  dii <- Cout[[4]][invPerm(fsOrd@perm)]
 
 
  return(list(D = Diagonal(x = dii, n = N),
@@ -265,8 +265,8 @@ makeDiiF.numPed <- function(pedigree, f = NULL, ...){
             as.integer(0),			#number genetic groups
 	    as.integer(fmiss))			#first f to calculate (not supplied)
   fsOrd <- as(as.integer(renPed), "pMatrix")
-  f <- Cout[[3]][t(fsOrd)@perm]
-  dii <- Cout[[4]][t(fsOrd)@perm]
+  f <- Cout[[3]][invPerm(fsOrd@perm)]
+  dii <- Cout[[4]][invPerm(fsOrd@perm)]
 
 
  return(list(D = Diagonal(x = dii, n = N),