Minor cleanups

R/ped_plot.R

@@ -461,10 +461,10 @@ plotPedList = function(plots, widths = NULL, groups = NULL, titles = NULL,
       newpeds = lapply(p, list)
     else { # if list of ped with plot arguments
       p1 = p[[1]]
-      if(inherits(p[[1]], "pedList"))
+      if(inherits(p1, "pedList"))
         class(p[[1]]) = "list"
-      else if (!is.ped(p[[1]]))
-        stop2("First element must be a `ped` object", p[[1]])
+      else if (!is.ped(p1))
+        stop2("First element must be a `ped` object", p1)
       newpeds = list(p)
     }
 

R/ped_utils.R

@@ -143,7 +143,6 @@ generations = function(x, what = c("max", "compMax", "indiv", "depth")) {
   N = length(x$ID)
   FIDX = x$FIDX
   MIDX = x$MIDX
-  FOU = which(FIDX == 0) # founders(x, internal = TRUE)
   NONFOU = which(FIDX > 0)
 
   dp = rep(1L, N) # depth = 1 for founders
@@ -375,20 +374,6 @@ generateLabs = function(x, n = 1, avoid = NULL, prefix = "") {
   .mysetdiff(cand, taken)[seq_len(n)]
 }
 
-# TODO: Delete - no longer used. Replaced by generateLabs
-# Utility function for generating numbered "NN" labels.
-# Returns "NN_i" where i increments largest j occurring as NN_j, NN.j or NN-j in input.
-nextNN = function(labs) { # labs a character vector
-  NNs = grepl("^NN", labs)
-  if(!any(NNs))
-    return("NN_1")
-  NNnum = suppressWarnings(as.numeric(sub("^NN[._-]?", "", labs[NNs])))
-  if(all(is.na(NNnum)))
-    return("NN_1")
-  nextNNnum = max(NNnum, na.rm = TRUE) + 1
-  return(sprintf("NN_%d", nextNNnum))
-}
-
 
 #' Pedigree component
 #'

R/readPed.R

@@ -140,5 +140,4 @@ readPed = function(pedfile, colSep = "", header = NA,
          locusAttributes = locusAttributes, missing = missing,
          sep = sep, sexCodes = sexCodes, addMissingFounders = addMissingFounders,
          validate = validate)
-
 }

README.Rmd

@@ -27,7 +27,12 @@ The goal of **pedtools** is to provide a lightweight, but comprehensive tool set
 
 **pedtools** is the hub of the **pedsuite**, a collection of R packages for pedigree analysis, including applications in forensic and medical genetics. The **pedsuite** has its own  [GitHub repository](https://github.com/magnusdv/pedsuite) and a dedicated [website](https://magnusdv.github.io/pedsuite/) offering more information.
 
-<span style="color:red;"> Try the **QuickPed** app for building and analysing pedigrees here: [https://magnusdv.shinyapps.io/quickped/](https://magnusdv.shinyapps.io/quickped/) </span>
+#### Citation
+If you use **pedtools** in a publication, please cite the book [Pedigree Analysis in R](https://shop.elsevier.com/books/pedigree-analysis-in-r/vigeland/978-0-12-824430-2)
+(Vigeland, 2021. Academic Press. ISBN:<span>9780128244302</span>).
+
+#### Online app
+Try the online app **QuickPed** for building and analysing pedigrees here: [https://magnusdv.shinyapps.io/quickped/](https://magnusdv.shinyapps.io/quickped/)
 
 
 ## Installation

README.md

@@ -22,16 +22,24 @@ loop breaking, and merging pedigrees. The plotting feature imports
 machinery from the
 [kinship2](https://CRAN.R-project.org/package=kinship2) package.
 
-**pedtools** is the hub of the **ped suite**, a collection of R packages
+**pedtools** is the hub of the **pedsuite**, a collection of R packages
 for pedigree analysis, including applications in forensic and medical
-genetics. The **ped suite** has its own [GitHub
+genetics. The **pedsuite** has its own [GitHub
 repository](https://github.com/magnusdv/pedsuite) and a dedicated
 [website](https://magnusdv.github.io/pedsuite/) offering more
 information.
 
-<span style="color:red;"> Try the **QuickPed** app for building and
-analysing pedigrees here: <https://magnusdv.shinyapps.io/quickped/>
-</span>
+#### Citation
+
+If you use **pedtools** in a publication, please cite the book [Pedigree
+Analysis in
+R](https://shop.elsevier.com/books/pedigree-analysis-in-r/vigeland/978-0-12-824430-2)
+(Vigeland, 2021. Academic Press. ISBN:9780128244302).
+
+#### Online app
+
+Try the online app **QuickPed** for building and analysing pedigrees
+here: <https://magnusdv.shinyapps.io/quickped/>
 
 ## Installation