Merge pull request #57 from R-Computing-Lab/makelinks

Makelinks

Author: smasongarrison

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BGmisc
 Title: An R Package for Extended Behavior Genetics Analysis
-Version: 1.3.4.1
+Version: 1.3.5
 Authors@R: c(
     person("S. Mason", "Garrison", , "garrissm@wfu.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4804-6003")),
@@ -33,8 +33,10 @@ Imports:
     kinship2,
     Matrix,
     stats,
-    stringr
+    stringr,
+    methods
 Suggests: 
+    corrplot,
     dplyr,
     EasyMx,
     knitr,

NAMESPACE

@@ -5,16 +5,19 @@ export(allGens)
 export(calculateRelatedness)
 export(checkIDs)
 export(checkSex)
+export(com2links)
 export(comp2vech)
 export(createGenDataFrame)
 export(dropLink)
 export(evenInsert)
+export(extractSummaryText)
 export(famSizeCal)
 export(fitComponentModel)
 export(identifyComponentModel)
 export(inferRelatedness)
 export(makeInbreeding)
 export(makeTwins)
+export(parseTree)
 export(ped2add)
 export(ped2ce)
 export(ped2cn)
@@ -26,6 +29,7 @@ export(ped2mit)
 export(ped2paternal)
 export(plotPedigree)
 export(readGedcom)
+export(readWikifamilytree)
 export(recodeSex)
 export(related_coef)
 export(relatedness)

NEWS.md

@@ -1,10 +1,18 @@
+# BGmisc 1.3.5
+* Add com2links function that converts components to kinship links
+* Add tests for com2links
+* Add function to extract family tree from wiki family tree template
+* Add tests for readWikifamilytree
+* Create vignette for adjacency matrix methods
+* Silences invisible list for plot
+
 # BGmisc 1.3.4.1
 * Hot fix to resolve issue with list of adjacency matrix not loading saved version
 * Reoptimized generation calculation
 
 # BGmisc 1.3.4
 * Added alternative (and faster) methods to create the adjacency matrix
-* Add tests for comparison of adjacency matrix methods
+* Add tests for comparison of adjacency matrix build methods
 * Added Royal Family pedigree
 
 # BGmisc 1.3.3

R/checkSex.R

@@ -166,23 +166,23 @@ recodeSex <- function(
   }
 
   # Recode as "F" or "M" based on code_male, preserving NAs
-  if (!is.null(code_male) & !is.null(code_female)) {
+  if (!is.null(code_male) && !is.null(code_female)) {
     # Initialize sex_recode as NA, preserving the length of the 'sex' column
     ped$sex_recode <- recode_na
     ped$sex_recode[ped$sex == code_female] <- recode_female
     ped$sex_recode[ped$sex == code_male] <- recode_male
     # Overwriting temp recode variable
     ped$sex <- ped$sex_recode
     ped$sex_recode <- NULL
-  } else if (!is.null(code_male) & is.null(code_female)) {
+  } else if (!is.null(code_male) && is.null(code_female)) {
     # Initialize sex_recode as NA, preserving the length of the 'sex' column
     ped$sex_recode <- recode_na
     ped$sex_recode[ped$sex != code_male & !is.na(ped$sex)] <- recode_female
     ped$sex_recode[ped$sex == code_male] <- recode_male
     # Overwriting temp recode variable
     ped$sex <- ped$sex_recode
     ped$sex_recode <- NULL
-  } else if (is.null(code_male) & !is.null(code_female)) {
+  } else if (is.null(code_male) && !is.null(code_female)) {
     # Initialize sex_recode as NA, preserving the length of the 'sex' column
     ped$sex_recode <- recode_na
     ped$sex_recode[ped$sex != code_female & !is.na(ped$sex)] <- recode_male

R/convertPedigree.R

@@ -144,7 +144,7 @@ ped2com <- function(ped, component,
     if (verbose) cat("Resuming: Constructed matrix...\n")
     jss <- readRDS(checkpoint_files$jss)
     iss <- readRDS(checkpoint_files$iss)
-    list_of_adjacencies <- list(iss=iss, jss=jss)
+    list_of_adjacencies <- list(iss = iss, jss = jss)
   } else {
 
   list_of_adjacencies <- compute_parent_adjacency(
@@ -177,7 +177,7 @@ ped2com <- function(ped, component,
     }
     # Garbage collection if gc is TRUE
     if (gc) {
-      rm(parList, lens,list_of_adjacencies)
+      rm(parList, lens, list_of_adjacencies)
       gc()
     }
   }
@@ -264,7 +264,7 @@ ped2com <- function(ped, component,
 
   # r is I + A + A^2 + ... = (I-A)^-1 from RAM
   # could trim, here
-  while (mtSum != 0 & count < maxCount) {
+  while (mtSum != 0 && count < maxCount) {
     r <- r + newIsPar
     gen <- gen + (Matrix::rowSums(newIsPar) > 0)
     newIsPar <- newIsPar %*% isPar