Merge pull request #1 from mayer79/release_candidate

release candidate ready

.Rbuildignore

@@ -1,5 +1,11 @@
-^\.Rproj\.user$
+^LICENSE\.md$
 ^cran-comments\.md$
 ^doc$
 ^Meta$
-^confintr\.Rproj$
+^packaging.R$
+[.]Rproj$
+^backlog$
+^cran-comments.md$
+^logo.png$
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -4,3 +4,6 @@
 .Ruserdata
 doc
 Meta
+inst/doc
+/doc/
+/Meta/

DESCRIPTION

@@ -1,38 +1,37 @@
 Type: Package
 Package: confintr
 Title: Confidence Intervals
-Version: 0.1.1
-Date: 2020-06-29
+Version: 0.1.2
+Date: 2022-01-28
 Authors@R: 
     person(given = "Michael",
            family = "Mayer",
            role = c("aut", "cre"),
            email = "mayermichael79@gmail.com")
 Maintainer: Michael Mayer <mayermichael79@gmail.com>
-Description: Calculates classic and/or bootstrap confidence
-    intervals for many parameters such as the population mean, variance,
-    interquartile range (IQR), median absolute deviation (MAD), skewness,
-    kurtosis, Cramer's V, odds ratio, R-squared, quantiles (incl. median),
+Description: Calculates classic and/or bootstrap confidence intervals for
+    many parameters such as the population mean, variance, interquartile
+    range (IQR), median absolute deviation (MAD), skewness, kurtosis,
+    Cramer's V, odds ratio, R-squared, quantiles (incl. median),
     proportions, different types of correlation measures, difference in
     means, quantiles and medians. Many of the classic confidence intervals
     are described in Smithson, M. (2003, ISBN: 978-0761924999). Bootstrap
     confidence intervals are calculated with the R package 'boot'. Both
     one- and two-sided intervals are supported.
-License: GPL(>= 2)
-URL: https://github.com/mayer79/confintr
-BugReports: https://github.com/mayer79/confintr/issues
+License: GPL (>= 2)
 Depends: 
     R (>= 3.1.0)
-VignetteBuilder: 
-    knitr
 Encoding: UTF-8
-LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.0
-Imports: 
-    stats,
-    boot
+RoxygenNote: 7.1.1
+URL: https://github.com/mayer79/confintr
+BugReports: https://github.com/mayer79/confintr/issues
 Suggests: 
-    knitr,
     rmarkdown,
-    testthat
+    knitr,
+    testthat (>= 3.0.0)
+VignetteBuilder: knitr
+Config/testthat/edition: 3
+Imports: 
+    boot,
+    stats

NEWS.md

@@ -1,3 +1,11 @@
+# confintr 0.1.2
+
+This is a maintenance release only, 
+
+- getting rid of the CRAN note on LazyData,
+- updating to testthat v3, and
+- using a more elegant way to generate/update the package.
+
 # confintr 0.1.1
 
 - Added confidence intervals for the odds ratio via stats::fisher.test.

README.md

@@ -41,7 +41,7 @@ install.packages("confintr")
 Latest version from github:
 ``` r
 library(devtools)
-install_github("mayer79/confintr", subdir = "release/confintr")
+install_github("mayer79/confintr")
 ```
 
 ## Teaser

backlog/concordance.R

@@ -0,0 +1,32 @@
+library(survival)
+n <- 100
+y <- sample(0:1, n, T)
+x <- runif(n)
+S <- Surv(rexp(n), sample(0:1, n, TRUE, prob = c(0.1, 0.9)))
+
+conc_measure <- function(x, y, what = "AUC") {
+
+  conc <- survival::concordance(y ~ x)
+
+  if (what == "AUC") {
+    stopifnot(all(y == 1 | y == 0))
+    out <- conc$concordance
+  } else if (what == "SomersD") {
+    out <- conc$concordance * 2 - 1
+  } else if (what == "HarrellsC") {
+    stopifnot(is.Surv(y))
+    out <- conc$concordance
+  }
+  out
+}
+
+conc_measure(x, S, "HarrellsC")
+Hmisc::rcorr.cens(x, S)
+
+MetricsWeighted::AUC(y, x)
+
+# AUC: y binary and default timewt
+# Harrell's c-statistic: y survival
+# (Somers' d + 1) / 2: y continuous
+# var: somer / 4
+

cran-comments.md

@@ -1,7 +1,27 @@
-## Resubmission
+This is mainly a maintenance release:
 
-- Resubmission reason: forgot rmarkdown package in suggests.
+- removing testthat::context()
+- getting rid of CRAN note on LazyData
+- improving the way how the package itself is being generated.
 
-- Fixed wrong "VignetteIndexEntry".
+## Checks
 
-- Added confidence intervals for the odds ratio via stats::fisher.test.
+### Local check seems fine
+
+`devtools::check()` result:
+
+   WARNING
+  'qpdf' is needed for checks on size reduction of PDFs
+
+0 errors √ | 1 warning x | 0 notes √
+
+### Online checks seem fine as well:
+
+- check_win_devel()
+- check_rhub()
+
+checking for detritus in the temp directory ... NOTE
+  Found the following files/directories:
+    'lastMiKTeXException'
+
+0 errors √ | 0 warnings √ | 1 note x

packaging.R

@@ -1,98 +1,88 @@
-#=====================================================================================
-# BUILD THE PACKAGE
-#=====================================================================================
+#=============================================================================
+# Put together the package
+#=============================================================================
 
-if (FALSE) {
-  library(boot)
-  lapply(list.files("R", full.names = TRUE), source)
-}
+# WORKFLOW: UPDATE EXISTING PACKAGE
+# 1) Modify package content and documentation.
+# 2) Increase package number in "use_description" below.
+# 3) Go through this script and carefully answer "no" if a "use_*" function
+#    asks to overwrite the existing files. Or just skip that function call.
 
 library(usethis)
-library(devtools)
 
-# Create a new package
-dir.create(file.path("release"))
-pkg <- file.path("release", "confintr")
-
-create_package(
-  pkg,
+# Sketch of description file
+use_description(
   fields = list(
     Title = "Confidence Intervals",
     Type = "Package",
-    Version = "0.1.1",
+    Version = "0.1.2",
     Date = Sys.Date(),
     Description = "Calculates classic and/or bootstrap confidence intervals for many parameters such as the population mean, variance, interquartile range (IQR), median absolute deviation (MAD), skewness, kurtosis, Cramer's V, odds ratio, R-squared, quantiles (incl. median), proportions, different types of correlation measures, difference in means, quantiles and medians. Many of the classic confidence intervals are described in Smithson, M. (2003, ISBN: 978-0761924999). Bootstrap confidence intervals are calculated with the R package 'boot'. Both one- and two-sided intervals are supported.",
     `Authors@R` = "person('Michael', 'Mayer', email = 'mayermichael79@gmail.com', role = c('aut', 'cre'))",
-    URL = "https://github.com/mayer79/confintr",
-    BugReports = "https://github.com/mayer79/confintr/issues",
     Depends = "R (>= 3.1.0)",
-    VignetteBuilder = "knitr",
-    License = "GPL(>= 2)",
     LazyData = NULL,
-    Maintainer = "Michael Mayer <mayermichael79@gmail.com>"),
-  open = FALSE)
+    Maintainer = "Michael Mayer <mayermichael79@gmail.com>"
+  ),
+  roxygen = TRUE
+)
+
+use_gpl_license(2)
+use_github_links() # use this if this project is on github
 
-file.copy(file.path(pkg, "DESCRIPTION"), to = getwd(), overwrite = TRUE)
-# Use package has no option to look for pkg, so we first copy description from pkg, modify it and move back
+# Your files that do not belong to the package itself (others are added by "use_* function")
+use_build_ignore(c("^packaging.R$", "[.]Rproj$", "^backlog$",
+                   "^cran-comments.md$", "^logo.png$"), escape = FALSE)
+
+# Required external packages
 use_package("stats", "Imports")
 use_package("boot", "Imports")
-use_package("knitr", "Suggests")
-use_package("rmarkdown", "Suggests")
-use_package("testthat", "Suggests")
-
-# Set up other files -------------------------------------------------
-# use_readme_md()
-# use_news_md()
-# use_cran_comments()
-# use_testthat()
-
-# Copy readme etc.
-file.copy(c("NEWS.md", "README.md", "cran-comments.md", "DESCRIPTION", ".Rbuildignore"),
-          pkg, overwrite = TRUE)
-
-# Copy R scripts and document them
-if (!dir.exists(file.path(pkg, "R"))) {
-  dir.create(file.path(pkg, "R"))
-}
-file.copy(list.files("R", full.names = TRUE), file.path(pkg, "R"), overwrite = TRUE)
-devtools::document(pkg)
 
-# Tests
-if (!dir.exists(file.path(pkg, "tests"))) {
-  dir.create(file.path(pkg, "tests"))
-}
-file.copy("tests", pkg, recursive = TRUE)
-# test(pkg)
+# If your code uses the pipe operator %>%
+# use_pipe()
+
+# If your package contains data. Google how to document
+# use_data()
+
+# Add short docu in Markdown (without running R code)
+use_readme_md()
+
+# Longer docu in RMarkdown (with running R code). Often quite similar to readme.
+use_vignette("confintr")
+
+# If you want to add unit tests
+use_testthat()
+# use_test("test-cor.R")
+
+# On top of NEWS.md, describe changes made to the package
+use_news_md()
 
 # Add logo
 use_logo("logo.png")
-dir.create(file.path(pkg, "man", "figures"))
-file.copy(file.path("man", "figures", "logo.png"),
-          file.path(pkg, "man", "figures", "logo.png"))
-
-if (TRUE) {
-  # Copy vignette
-  # use_vignette(name = "confintr", title = "confintr")
-  dir.create(file.path(pkg, "vignettes"))
-  dir.create(file.path(pkg, "doc"))
-  dir.create(file.path(pkg, "Meta"))
-  file.copy(list.files("vignettes", full.names = TRUE),
-            file.path(pkg, "vignettes"), overwrite = TRUE)
-
-  devtools::build_vignettes(pkg)
-}
 
-# Check
-check(pkg, manual = TRUE)
+# If package goes to CRAN: infos (check results etc.) for CRAN
+use_cran_comments()
 
-# Create
-build(pkg)
 
-# Install
-install(pkg)
+#=============================================================================
+# Finish package building (can use fresh session)
+#=============================================================================
 
-check_win_devel(pkg)
+library(devtools)
+
+document()
+test()
+build_vignettes()
+check(manual = TRUE, cran = TRUE)
+build()
+# build(binary = TRUE)
+install()
 
-check_rhub(pkg)
+# Run only if package is public(!) and should go to CRAN
+if (FALSE) {
+  check_win_devel()
+  check_rhub()
 
-devtools::release(pkg)
+  # Wait until above checks are passed without relevant notes/warnings
+  # then submit to CRAN
+  release()
+}