revdepcheck

R/datasets.R

@@ -1821,10 +1821,7 @@ NULL
 #' Hand, D. J., F. Daly, A. D. Lunn, K. J. McConway and E. Ostrowski (1994).
 #' \emph{A Handbook of Small Datasets}, Chapman and Hall/CRC, London.
 #' 
-#' Egyptian Skull Development, StatLib Data and Story Library, 
-#' \url{https://dasl.datadescription.com/Stories/EgyptianSkullDevelopment.html}
 #' @source
-#' 
 #' D. J. Hand, F. Daly, A. D. Lunn, K. J. McConway and E. Ostrowski (1994).
 #' \emph{A Handbook of Small Datasets}, Chapman and Hall/CRC, London.
 #' @keywords datasets

cran-comments.md

@@ -1,7 +1,6 @@
 ## Test environments
-* local Windows 7 install, R version 4.2.1 (2022-06-23 ucrt)
-* local Windows 10 install, R 4.0.2
-* win-builder R Under development (unstable) (2022-09-25 r82916 ucrt)
+* local Windows 10 install, R 4.3.1 (2023-06-16 ucrt)
+* win-builder R Under development (unstable) (2023-09-03 r85052 ucrt)
 * win-builder R version 4.2.1 (2022-06-23 ucrt)
 
 ## R CMD check results
@@ -15,15 +14,18 @@ There were no ERRORs or WARNINGS or NOTES.
 
 ## revdepcheck results
 
-We checked 9 reverse dependencies (4 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 9 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
  * We failed to check 0 packages
 
 
 ## Comments
 
-This is a minor release, to fix an error in the CITATION file
+This is a major release, without much new or changed functionality, but with all documentation now
+in roxygen format.
+
+
 
 
 

revdep/README.md

@@ -0,0 +1,24 @@
+# Platform
+
+|field    |value                                     |
+|:--------|:-----------------------------------------|
+|version  |R version 4.3.1 (2023-06-16 ucrt)         |
+|os       |Windows 10 x64 (build 19042)              |
+|system   |x86_64, mingw32                           |
+|ui       |RStudio                                   |
+|language |(EN)                                      |
+|collate  |English_Canada.utf8                       |
+|ctype    |English_Canada.utf8                       |
+|tz       |America/Toronto                           |
+|date     |2023-09-04                                |
+|rstudio  |2022.07.2+576 Spotted Wakerobin (desktop) |
+|pandoc   |3.1.2 @ C:\PROGRA~1\Pandoc\pandoc.exe     |
+
+# Dependencies
+
+|package |old   |new   |Δ  |
+|:-------|:-----|:-----|:--|
+|heplots |1.4-2 |1.6.0 |*  |
+
+# Revdeps
+

revdep/checks/Guerry/new/Guerry.Rcheck/00check.log

@@ -0,0 +1,57 @@
+* using log directory 'C:/R/projects/heplots/revdep/checks/Guerry/new/Guerry.Rcheck'
+* using R version 4.3.1 (2023-06-16 ucrt)
+* using platform: x86_64-w64-mingw32 (64-bit)
+* R was compiled by
+    gcc.exe (GCC) 12.2.0
+    GNU Fortran (GCC) 12.2.0
+* running under: Windows 10 x64 (build 19042)
+* using session charset: UTF-8
+* using options '--no-manual --no-build-vignettes'
+* checking for file 'Guerry/DESCRIPTION' ... OK
+* checking extension type ... Package
+* this is package 'Guerry' version '1.8.1'
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking whether package 'Guerry' can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking 'build' directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of 'data' directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from 'inst/doc' ... OK
+* checking files in 'vignettes' ... OK
+* checking examples ... OK
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in 'inst/doc' ... OK
+* checking running R code from vignettes ... NONE
+  'MultiSpat.Rmd' using 'UTF-8'... OK
+  'guerry-multivariate.Rmd' using 'UTF-8'... OK
+* checking re-building of vignette outputs ... SKIPPED
+* DONE
+Status: OK

revdep/checks/Guerry/new/Guerry.Rcheck/00install.out

@@ -0,0 +1,16 @@
+* installing *source* package 'Guerry' ...
+** package 'Guerry' successfully unpacked and MD5 sums checked
+** using staged installation
+** data
+*** moving datasets to lazyload DB
+** demo
+** inst
+** help
+*** installing help indices
+*** copying figures
+** building package indices
+** installing vignettes
+** testing if installed package can be loaded from temporary location
+** testing if installed package can be loaded from final location
+** testing if installed package keeps a record of temporary installation path
+* DONE (Guerry)

revdep/checks/Guerry/new/Guerry.Rcheck/Guerry-Ex.R

@@ -0,0 +1,228 @@
+pkgname <- "Guerry"
+source(file.path(R.home("share"), "R", "examples-header.R"))
+options(warn = 1)
+options(pager = "console")
+library('Guerry')
+
+base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
+base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
+cleanEx()
+nameEx("Angeville")
+### * Angeville
+
+flush(stderr()); flush(stdout())
+
+### Name: Angeville
+### Title: Data from d'Angeville (1836) on the population of France
+### Aliases: Angeville
+### Keywords: datasets
+
+### ** Examples
+
+library(Guerry)
+library(sp)
+library(RColorBrewer)
+
+data(Guerry)
+data(gfrance)
+data(Angeville)
+
+gf <- gfrance     # the SpatialPolygonsDataFrame
+
+# Add some Angeville variables, transform them to ranks
+gf$Mortality       <- rank(Angeville$Mortality)
+gf$Marriages       <- rank(Angeville$Marriages)
+gf$Legit_births    <- rank(Angeville$Legit_births)
+gf$Illeg_births    <- rank(Angeville$Illeg_births)
+gf$Farmers         <- rank(Angeville$Farmers)
+gf$Schoolchildren  <- rank(Angeville$Schoolchildren)
+
+# plot them on map of France
+my.palette <- rev(brewer.pal(n = 9, name = "PuBu"))
+spplot(gf, 
+       c("Mortality", "Marriages", "Legit_births",  "Illeg_births", "Farmers", "Schoolchildren"),
+       names.attr = c("Mortality", "Marriages", "Legit_births",  
+                      "Illeg_births", "Farmers", "Schoolchildren"),
+       layout=c(3,2), 
+       as.table=TRUE, 
+       col.regions = my.palette, 
+       cuts = 8, # col = "transparent",
+       main="Angeville variables")
+
+
+
+
+
+cleanEx()
+nameEx("Guerry")
+### * Guerry
+
+flush(stderr()); flush(stdout())
+
+### Name: Guerry
+### Title: Data from A.-M. Guerry, "Essay on the Moral Statistics of
+###   France"
+### Aliases: Guerry
+### Keywords: datasets
+
+### ** Examples
+
+library(car)
+data(Guerry)
+
+# Is there a relation between crime and literacy?
+
+# Plot personal crime rate vs. literacy, using data ellipses. 
+#    Identify the departments that stand out
+set.seed(12315)
+with(Guerry,{
+	dataEllipse(Literacy, Crime_pers,
+		levels = 0.68,
+  	ylim = c(0,40000), xlim = c(0, 80),
+  	ylab="Pop. per crime against persons",
+  	xlab="Percent who can read & write",
+  	pch = 16,
+  	grid = FALSE,
+  	id = list(method="mahal", n = 8, labels=Department, location="avoid", cex=1.2),
+  	center.pch = 3, center.cex=5,
+  	cex.lab=1.5)
+  # add a 95% ellipse
+	dataEllipse(Literacy, Crime_pers,
+		levels = 0.95, add=TRUE,
+  	ylim = c(0,40000), xlim = c(0, 80),
+  	lwd=2, lty="longdash",
+  	col="gray",
+  	center.pch = FALSE
+  	)
+
+  # add the LS line and a loess smooth.
+  abline( lm(Crime_pers ~ Literacy), lwd=2)	
+  lines(loess.smooth(Literacy, Crime_pers), col="red", lwd=3)
+  }
+  	)
+
+# A corrgram to show the relations among the main moral variables
+# Re-arrange variables by PCA ordering.
+
+library(corrgram)
+corrgram(Guerry[,4:9], upper=panel.ellipse, order=TRUE)
+
+
+
+
+cleanEx()
+nameEx("gfrance")
+### * gfrance
+
+flush(stderr()); flush(stdout())
+
+### Name: gfrance
+### Title: Map of France in 1830 with the Guerry data
+### Aliases: gfrance
+### Keywords: datasets spatial
+
+### ** Examples
+
+library(sp)
+data(gfrance)
+names(gfrance)  ## list @data variables
+plot(gfrance)   ## just show the map outline
+
+# Show basic choropleth plots of some of the variables
+spplot(gfrance, "Crime_pers")
+
+# use something like Guerry's pallete, where dark = Worse
+my.palette <- rev(RColorBrewer::brewer.pal(n = 9, name = "PuBu"))
+spplot(gfrance, "Crime_pers", col.regions = my.palette, cuts = 8)
+
+
+spplot(gfrance, "Crime_prop")
+
+# Note that spplot assumes all variables are on the same scale for comparative plots
+# transform variables to ranks (as Guerry did)
+
+## Not run: 
+##D local({
+##D   gfrance$Crime_pers <- rank(gfrance$Crime_pers)
+##D   gfrance$Crime_prop <- rank(gfrance$Crime_prop)
+##D   gfrance$Literacy <- rank(gfrance$Literacy)
+##D   gfrance$Donations <- rank(gfrance$Donations)
+##D   gfrance$Infants <- rank(gfrance$Infants)
+##D   gfrance$Suicides <- rank(gfrance$Suicides)
+##D    	
+##D   spplot(gfrance, c("Crime_pers", "Crime_prop", "Literacy", "Donations", "Infants", "Suicides"), 
+##D     layout=c(3,2), as.table=TRUE, main="Guerry's main moral variables")
+##D }) 
+## End(Not run)
+
+
+
+cleanEx()
+nameEx("gfrance85")
+### * gfrance85
+
+flush(stderr()); flush(stdout())
+
+### Name: gfrance85
+### Title: Map of France in 1830 with the Guerry data, excluding Corsica
+### Aliases: gfrance85
+### Keywords: datasets spatial
+
+### ** Examples
+
+data(gfrance85)
+require(sp)
+plot(gfrance85)   # plot the empty outline map
+
+# extract some useful components
+df <- data.frame(gfrance85)[,7:12]       # main moral variables
+xy <- coordinates(gfrance85)             # department centroids
+dep.names <- data.frame(gfrance85)[,6]
+region.names <- data.frame(gfrance85)[,5]
+col.region <- colors()[c(149,254,468,552,26)]
+
+if (require(spdep)) {
+  lw <- nb2listw(poly2nb(gfrance85))       # neighbors list
+}
+
+# plot the map showing regions by color with department labels
+op <-par(mar=rep(0.1,4))
+plot(gfrance85,col=col.region[region.names])
+text(xy, labels=dep.names, cex=0.4)
+par(op)
+
+
+
+
+
+graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+cleanEx()
+nameEx("propensity")
+### * propensity
+
+flush(stderr()); flush(stdout())
+
+### Name: propensity
+### Title: Distribution of crimes against persons at different ages
+### Aliases: propensity
+### Keywords: datasets
+
+### ** Examples
+
+data(propensity)
+## maybe str(propensity) ; plot(propensity) ...
+
+
+
+### * <FOOTER>
+###
+cleanEx()
+options(digits = 7L)
+base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
+grDevices::dev.off()
+###
+### Local variables: ***
+### mode: outline-minor ***
+### outline-regexp: "\\(> \\)?### [*]+" ***
+### End: ***
+quit('no')