Fix notes, update package to use roxygen and add github actions.

.Rbuildignore

@@ -1,3 +1,9 @@
+genlogo.R
+^_pkgdown\.yml$
+^figure$
+^pkgdown$
+^Meta$
+^doc$
 #All packages
 ^.*\.Rproj$
 ^\.Rproj\.user$
@@ -15,3 +21,12 @@
 #Specific
 ^raw-image*$
 ^articles*$
+^\.github$
+#Vignette cache
+^cran-comments[.].*$
+^vignettes/.*[.](pdf|PDF)$
+^vignettes/.*[.](r|R)$
+^vignettes/[.]install_extras$
+^vignettes/.*_cache$
+^vignettes/.*_files$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,32 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+      - name: Check
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
+        shell: Rscript {0}

.gitignore

@@ -1,9 +1,18 @@
-.Rproj.user
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
-*.pper
-*.pper
-.DS_Store
-.Rproj.user/AF86C25B/pcs/source-pane.pper
-.Rproj.user/AF86C25B/pcs/windowlayoutstate.pper
-*.pper
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/

BioStatR.Rproj

@@ -14,4 +14,6 @@ LaTeX: pdfLaTeX
 
 BuildType: Package
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageBuildArgs: --force
 PackageCheckArgs: --as-cran
+PackageRoxygenize: rd,collate,namespace,vignette

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: BioStatR
 Type: Package
 Title: Initiation à La Statistique Avec R
-Version: 3.1.1
-Date: 2019-01-26
+Version: 3.1.2
+Date: 2021-03-13
 Depends: R (>= 2.10)
 Imports: ggplot2 
 Authors@R: c(
@@ -16,6 +16,6 @@ LazyData: yes
 License: GPL-3
 Encoding: UTF-8
 Classification/MSC:
-URL: http://www-irma.u-strasbg.fr/~fbertran/, https://github.com/fbertran/BioStatR
-BugReports: https://github.com/fbertran/BioStatR/issues
-RoxygenNote: 6.1.1
+URL: http://www-irma.u-strasbg.fr/~fbertran/, https://github.com/fbertran/BioStatR/
+BugReports: https://github.com/fbertran/BioStatR/issues/
+RoxygenNote: 7.1.1

NAMESPACE

@@ -1,14 +1,23 @@
-import(ggplot2)
-importFrom("grDevices", "colorRampPalette", "gray")
-importFrom("graphics", "hist", "par", "persp", "rect")
-importFrom("stats", "as.formula", "lm", "qchisq", "qf", "qnorm",
-           "quantile", "sd")
+# Generated by roxygen2: do not edit by hand
 
-# functions
-export(cvar) 
-export(eta2) 
-export(panel.hist) 
-export(poi.ci) 
-export(binom.ci) 
-export(plotcdf2) 
-export(gg_qqplot)
+export(binom.ci)
+export(cvar)
+export(eta2)
+export(gg_qqplot)
+export(panel.hist)
+export(plotcdf2)
+export(poi.ci)
+import(ggplot2)
+importFrom(grDevices,colorRampPalette)
+importFrom(grDevices,gray)
+importFrom(graphics,hist)
+importFrom(graphics,par)
+importFrom(graphics,persp)
+importFrom(graphics,rect)
+importFrom(stats,as.formula)
+importFrom(stats,lm)
+importFrom(stats,qchisq)
+importFrom(stats,qf)
+importFrom(stats,qnorm)
+importFrom(stats,quantile)
+importFrom(stats,sd)

NEWS.md

@@ -1,3 +1,7 @@
+# BioStatR 3.1.2
+
+* Update to Roxygen and fix CRAN notes.
+
 # BioStatR 3.1.1
 
 * Update of the reference to the book in the description file.

R/BioStatR-package.R

@@ -0,0 +1,32 @@
+#' BioStatR
+#' 
+#' Motivation: Package compagnon du livre Initiation à la statistique avec R.
+#' Il contient les codes des chapitres du livre ainsi que les solutions des
+#' exercices mais aussi d'autres compléments à découvrir.
+#' 
+#' 
+#' @name BioStatR
+#' @docType package
+#' @references F. Bertrand, M. Maumy-Bertrand, Initiation à la Statistique avec
+#' R, 3ème edition, ISBN:9782100782826, Dunod, Paris, 2018.
+#' @references \emph{Initiation à la Statistique avec R}, Frédéric Bertrand, 
+#' Myriam Maumy-Bertrand, 2018, ,
+#' \url{https://www.dunod.com/sciences-techniques/initiation-statistique-avec-r-cours-exemples-exercices-et-problemes-corriges-0},
+#' \url{https://github.com/fbertran/BioStatR/} et
+#' \url{https://fbertran.github.io/BioStatR/}
+#' 
+#' @importFrom grDevices colorRampPalette gray
+#' @importFrom graphics hist par persp rect
+#' @importFrom stats as.formula lm qchisq qf qnorm quantile sd
+#' @import ggplot2
+#' 
+#' @examples
+#' set.seed(314)
+#' 
+NULL
+
+
+
+
+
+

R/binom.ci.R

@@ -1,55 +1,82 @@
-binom.ci <- function (x, n, conf.level = 0.95, method = c("Wilson", "exact", "Wald", 
-    "all")) 
-{
-    method <- match.arg(method)
-    bc <- function(x, n, conf.level, method) {
-        nu1 <- 2 * (n - x + 1)
-        nu2 <- 2 * x
-        ll <- if (x > 0) 
-            x/(x + qf(1/2 + conf.level/2, nu1, nu2) * (n - x + 1))
-        else 0
-        nu1p <- nu2 + 2
-        nu2p <- nu1 - 2
-        pp <- if (x < n) 
-            qf(1/2 + conf.level/2, nu1p, nu2p)
-        else 1
-        ul <- ((x + 1) * pp)/(n - x + (x + 1) * pp)
-        zcrit <- -qnorm((1-conf.level)/2)
-        z2 <- zcrit * zcrit
-        p <- x/n
-        cl <- (p + z2/2/n + c(-1, 1) * zcrit * sqrt((p * (1 - 
-            p) + z2/4/n)/n))/(1 + z2/n)
-        if (x == 1) 
-            cl[1] <- -log(conf.level)/n
-        if (x == (n - 1)) 
-            cl[2] <- 1 + log(conf.level)/n
-        asymp.lcl <- x/n - qnorm(1/2+conf.level/2) * sqrt(((x/n) * 
-            (1 - x/n))/n)
-        asymp.ucl <- x/n + qnorm(1/2+conf.level/2) * sqrt(((x/n) * 
-            (1 - x/n))/n)
-        res <- rbind(c(ll, ul), cl, c(asymp.lcl, asymp.ucl))
-        res <- cbind(rep(x/n, 3), res)
-        switch(method, Wilson = res[2, ], exact = res[1, ], Wald = res[3, 
-            ], all = res, res)
-    }
-    if ((length(x) != length(n)) & length(x) == 1) 
-        x <- rep(x, length(n))
-    if ((length(x) != length(n)) & length(n) == 1) 
-        n <- rep(n, length(x))
-    if ((length(x) > 1 | length(n) > 1) & method == "all") {
-        method <- "Wilson"
-        warning("method=all will not work with vectors...setting method to Wilson")
-    }
-    if (method == "all" & length(x) == 1 & length(n) == 1) {
-        mat <- bc(x, n, conf.level, method)
-        dimnames(mat) <- list(c("Exact", "Wilson", "Wald"), 
-            c("PointEst", "Lower", "Upper"))
-        return(mat)
-    }
-    mat <- matrix(ncol = 3, nrow = length(x))
-    for (i in 1:length(x)) mat[i, ] <- bc(x[i], n[i], conf.level = conf.level, 
-        method = method)
-    dimnames(mat) <- list(rep("", dim(mat)[1]), c("PointEst", 
-        "Lower", "Upper"))
-    mat
-}
+#' Intervalles de confiance pour une proportion
+#' 
+#' Cette fonction permet de calculer plusieurs types d'intervalles de confiance
+#' pour une proportion.
+#' 
+#' 
+#' @param x Nombre de succès
+#' @param n Nombre d'essais
+#' @param conf.level Niveau de confiance recherché pour l'intervalle
+#' @param method Type d'intervalle de confiance à calculer : intervalle de
+#' "Wilson", intervalle "exact" de Clopper-Pearson, intervalle asymptotique de
+#' "Wald" ou tous les trois "all"
+#' @return \item{matrix}{Limites des intervalles de confiance demandés.}
+#' @author Frédéric Bertrand\cr \email{frederic.bertrand@@math.unistra.fr}\cr
+#' \url{http://www-irma.u-strasbg.fr/~fbertran/}\cr 
+#' Maumy-Bertrand\cr \email{myriam.maumy@@math.unistra.fr}\cr
+#' \url{http://www-irma.u-strasbg.fr/~mmaumy/}
+#' @seealso \code{\link{binom.test}}, \code{\link{binom.ci}},
+#' \code{\link{poi.ci}}
+#' @references F. Bertrand, M. Maumy-Bertrand, Initiation à la Statistique avec
+#' R, Dunod, 3ème edition, 2018.
+#' @keywords univar
+#' @examples
+#' 
+#' binom.ci(5,10,method="all")
+#' 
+#' @export binom.ci
+binom.ci <- function (x, n, conf.level = 0.95, method = c("Wilson", "exact", "Wald", 
+    "all")) 
+{
+    method <- match.arg(method)
+    bc <- function(x, n, conf.level, method) {
+        nu1 <- 2 * (n - x + 1)
+        nu2 <- 2 * x
+        ll <- if (x > 0) 
+            x/(x + qf(1/2 + conf.level/2, nu1, nu2) * (n - x + 1))
+        else 0
+        nu1p <- nu2 + 2
+        nu2p <- nu1 - 2
+        pp <- if (x < n)
+            qf(1/2 + conf.level/2, nu1p, nu2p)
+        else 1
+        ul <- ((x + 1) * pp)/(n - x + (x + 1) * pp)
+        zcrit <- -qnorm((1-conf.level)/2)
+        z2 <- zcrit * zcrit
+        p <- x/n
+        cl <- (p + z2/2/n + c(-1, 1) * zcrit * sqrt((p * (1 - 
+            p) + z2/4/n)/n))/(1 + z2/n)
+        if (x == 1) 
+            cl[1] <- -log(conf.level)/n
+        if (x == (n - 1)) 
+            cl[2] <- 1 + log(conf.level)/n
+        asymp.lcl <- x/n - qnorm(1/2+conf.level/2) * sqrt(((x/n) * 
+            (1 - x/n))/n)
+        asymp.ucl <- x/n + qnorm(1/2+conf.level/2) * sqrt(((x/n) * 
+            (1 - x/n))/n)
+        res <- rbind(c(ll, ul), cl, c(asymp.lcl, asymp.ucl))
+        res <- cbind(rep(x/n, 3), res)
+        switch(method, Wilson = res[2, ], exact = res[1, ], Wald = res[3, 
+            ], all = res, res)
+    }
+    if ((length(x) != length(n)) & length(x) == 1) 
+        x <- rep(x, length(n))
+    if ((length(x) != length(n)) & length(n) == 1) 
+        n <- rep(n, length(x))
+    if ((length(x) > 1 | length(n) > 1) & method == "all") {
+        method <- "Wilson"
+        warning("method=all will not work with vectors...setting method to Wilson")
+    }
+    if (method == "all" & length(x) == 1 & length(n) == 1) {
+        mat <- bc(x, n, conf.level, method)
+        dimnames(mat) <- list(c("Exact", "Wilson", "Wald"), 
+            c("PointEst", "Lower", "Upper"))
+        return(mat)
+    }
+    mat <- matrix(ncol = 3, nrow = length(x))
+    for (i in 1:length(x)) mat[i, ] <- bc(x[i], n[i], conf.level = conf.level, 
+        method = method)
+    dimnames(mat) <- list(rep("", dim(mat)[1]), c("PointEst", 
+        "Lower", "Upper"))
+    mat
+}

R/cvar.R

@@ -1,4 +1,27 @@
-cvar <- function(x){100*sd(x)/mean(x)}
-
-
-
+#' Coefficient de variation
+#' 
+#' Calcule coefficent de variation d'une série statistique
+#' 
+#' Le coefficient de variation est égal à l'écart-type corrigé divisé par la
+#' moyenne. Il est exprimé en pourcents.
+#' 
+#' @param x Un vecteur numérique
+#' @return \item{num}{Valeur du coefficient de variation exprimé en pourcents}
+#' @author Frédéric Bertrand\cr \email{frederic.bertrand@@math.unistra.fr}\cr
+#' \url{http://www-irma.u-strasbg.fr/~fbertran/}\cr 
+#' Maumy-Bertrand\cr \email{myriam.maumy@@math.unistra.fr}\cr
+#' \url{http://www-irma.u-strasbg.fr/~mmaumy/}
+#' @seealso \code{\link{mean}}, \code{\link{sd}}
+#' @references F. Bertrand, M. Maumy-Bertrand, Initiation à la Statistique avec
+#' R, Dunod, 3ème edition, 2018.
+#' @keywords univar
+#' @examples
+#' 
+#' data(Europe)
+#' cvar(Europe[,2])
+#' 
+#' @export cvar
+cvar <- function(x){100*sd(x)/mean(x)}
+
+
+