Prepare CRAN release v0.7.2

Author: magnusdv

NEWS.md

@@ -2,6 +2,8 @@
 
 * Internal reorganisation, moving the Shiny code to `inst/shiny/app.R`.
 
+* `launchApp()` is now the main launching function, with `runKLINK()` as an alias.
+
 * Fixes a minor regression error in the previous version.
 
 

R/KLINK-package.R

@@ -3,10 +3,10 @@
 
 ## usethis namespace: start
 #' @rawNamespace import(shiny, except = c(singleton, is.singleton))
-#' @import shinydashboard
 #' @import gt
 #' @import openxlsx
 #' @import pedtools
+#' @import shinydashboard
 ## usethis namespace: end
 NULL
 

R/data.R

@@ -1,6 +1,6 @@
 #' Built-in linkage map
 #'
-#' A genetic map including 9 pairs of linked STR markers
+#' A genetic map including 9 pairs of linked STR markers.
 #'
 #' @format A data frame with 18 rows and 5 columns.
 #'
@@ -9,14 +9,13 @@
 
 #' Dataset for a paternity case
 #'
-#' A list of two pedigrees forming the hypotheses in a paternity case: H1 (AF is
-#' the father of CH) and H2 (unrelated). AF and CH are genotyped with 11 marker.
+#' A list of two pedigrees forming the hypotheses in a paternity case: H1 (`AF` is
+#' the father of `CH`) and H2 (unrelated). `AF` and `CH` are genotyped with 11
+#' markers, with allele frequencies from `forrel::NorwegianFrequencies`.
 #'
 #' @format A list of two pedigrees, named H1 and H2.
 #'
 #' @examples
-#' library(forrel)
-#'
-#' plotPedList(paternity, marker = "SE33")
-#' kinshipLR(paternity)
+#' pedtools::plotPedList(paternity, marker = "SE33")
+#' forrel::kinshipLR(paternity)
 "paternity"

R/karyo.R

@@ -22,6 +22,11 @@ karyogram = function(markerdata, cols = KARYOPALETTE, bgcol = "gray92") {
          pch = 21, pt.cex = 2.2, pt.bg = cols[1:9], bty = "n")
 }
 
+
+
+# Hardcoded parameters ----------------------------------------------------
+
+
 CHROM.MB = c(247.2, 242.9, 199.5, 191.3, 180.9, 170.9, 158.8, 146.3, 140.3,
              135.4, 134.4, 132.3, 114.1, 106.4, 100.3,  88.8,  78.8, 76.1,
              63.8,  62.4,  46.9,  49.7)

R/launchApp.R

@@ -1,6 +1,6 @@
 #' Launch KLINK
 #'
-#' This launches the shiny app KLINK.
+#' This launches the KLINK app. `runKLINK()` is a synonym for `launchApp()`.
 #'
 #' @return No return value, called for side effects.
 #'

R/writeResult.R

@@ -14,6 +14,7 @@
 #' @return NULL
 #'
 #' @examples
+#' \donttest{
 #' # Built-in dataset `paternity`
 #' peds = paternity
 #' map = LINKAGEMAP
@@ -31,7 +32,7 @@
 #'             outfile = tmp)
 #'
 #' # openxlsx::openXL(tmp)
-#'
+#' }
 #' @export
 writeResult = function(resultTable, pedigrees, linkageMap, markerData,
                        outfile, notes = NULL, fam = NULL) {

README.Rmd

@@ -35,7 +35,7 @@ install.packages("KLINK")
 
 Then you may start KLINK as follows:
 ```{r, eval = F}
-KLINK::runKLINK()
+KLINK::launchApp()
 ```
 
 ```{r, echo = F}

README.md

@@ -28,7 +28,7 @@ install.packages("KLINK")
 Then you may start KLINK as follows:
 
 ``` r
-KLINK::runKLINK()
+KLINK::launchApp()
 ```
 
 <img src="man/figures/screenshot-klink.png" width="100%" />