Merge branch 'release-1.2.0' into release

.github/workflows/build.yml

@@ -36,7 +36,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
     steps:
         - name: Checking out the repository
-          uses: actions/checkout@v3
+          uses: actions/checkout@v4
 
         - name: Setting up pandoc
           uses: r-lib/actions/setup-pandoc@v2

.github/workflows/linter.yml

@@ -24,7 +24,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
         - name: Checking out the repository
-          uses: actions/checkout@v3
+          uses: actions/checkout@v4
 
         - name: Setting up R
           uses: r-lib/actions/setup-r@v2
@@ -40,20 +40,22 @@ jobs:
           run: |
             library(lintr)
             excluded_files <- list(
-              "vignettes/Sampling_and_ML_estimation.Rmd:29"
+              "vignettes/Sampling_and_ML_estimation.Rmd" = 29,
+              "R/probdist-class.R" = c(25, 29, 38, 40, 43),
+              "R/prepEta.R" = 2
             )
             style_rules <- list(
               T_and_F_symbol_linter(), assignment_linter(), brace_linter(),
               commas_linter(), commented_code_linter(), todo_comment_linter(),
-              cyclocomp_linter(), equals_na_linter(),
+              equals_na_linter(),
               function_left_parentheses_linter(), infix_spaces_linter(),
-              line_length_linter(), no_tab_linter(), absolute_path_linter(),
+              line_length_linter(), whitespace_linter(), absolute_path_linter(),
               pipe_continuation_linter(),
-              semicolon_linter(), seq_linter(), single_quotes_linter(),
+              semicolon_linter(), seq_linter(), quotes_linter(),
               spaces_inside_linter(), spaces_left_parentheses_linter(),
               trailing_blank_lines_linter(), trailing_whitespace_linter(),
               undesirable_function_linter(), undesirable_operator_linter(),
-              unneeded_concatenation_linter()
+              unnecessary_concatenation_linter()
             )
-            lint_package(linters = style_rules, exclusions = excluded_files)
+            expect_lint_free(linters = style_rules, exclusions = excluded_files)
           shell: Rscript {0}

.github/workflows/pkgdown.yaml

@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.1.1
-Date: 2024-02-26 15:11:55 UTC
-SHA: d3942e5b524eb80d5cabfc6cdd5fecb48f5f3a50
+Version: 1.2.0
+Date: 2024-09-26 06:14:26 UTC
+SHA: aac7a6b6cc93a891f567efa812c71ea719d34713

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TruncExpFam
 Title: Truncated Exponential Family
-Version: 1.1.1
-Date: 2024-02-26
+Version: 1.2.0
+Date: 2024-09-26
 Authors@R:
 	c(
 		person(
@@ -27,7 +27,7 @@ Description: Handles truncated members from the exponential family of
 License: GPL-3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Imports: methods, invgamma, rmutil
 Suggests:
     knitr,

LICENSE

@@ -19,7 +19,7 @@ GNU General Public License for most of our software; it applies also to
 any other work released this way by its authors.  You can apply it to
 your programs, too.
 
-  When we speak of free software, we are referring to freedom, not
+  When we speak of free software, we are refering to freedom, not
 price.  Our General Public Licenses are designed to make sure that you
 have the freedom to distribute copies of free software (and charge for
 them if you wish), that you receive source code or can get it if you
@@ -111,7 +111,7 @@ menu, a prominent item in the list meets this criterion.
 
   1. Source Code.
 
-  The "source code" for a work means the preferred form of the work
+  The "source code" for a work means the prefered form of the work
 for making modifications to it.  "Object code" means any non-source
 form of a work.
 

NAMESPACE

@@ -94,8 +94,33 @@ export(mlEstimationTruncDist)
 export(natural2parameters)
 export(parameters2natural)
 export(probdist)
+export(ptrunc)
+export(ptruncbeta)
+export(ptruncbinom)
+export(ptruncchisq)
+export(ptrunccontbern)
+export(ptruncexp)
+export(ptruncgamma)
+export(ptruncinvgamma)
+export(ptruncinvgauss)
+export(ptrunclnorm)
+export(ptruncnbinom)
+export(ptruncnorm)
+export(ptruncpois)
+export(qtrunc)
+export(qtruncbeta)
+export(qtruncbinom)
+export(qtruncchisq)
+export(qtrunccontbern)
+export(qtruncexp)
+export(qtruncgamma)
+export(qtruncinvgamma)
+export(qtruncinvgauss)
+export(qtrunclnorm)
+export(qtruncnbinom)
+export(qtruncnorm)
+export(qtruncpois)
 export(rtrunc)
-export(rtrunc.beta)
 export(rtrunc_direct)
 export(rtruncbeta)
 export(rtruncbinom)

NEWS.md

@@ -1,3 +1,13 @@
+# TruncExpFam 1.2.0
+
+* Implemented `ptrunc()` and `qtrunc()` for all distributions (issue #54)
+* Refactoring (issue #104, #112)
+* Fixed bugs related to using the Negative Binomial with `mu` instead of `prob` (issue #107)
+* Fixed domain validation on Negative Binomial and Inverse Gamma
+* Added domain validation to `rtrunc(..., faster = TRUE)` (issue #109)
+* Added `faster` argument to `rtrunc()` aliases (issue #110)
+* Improved calculation of cumulative densities (issue #113)
+
 # TruncExpFam 1.1.1
 
 * Fixed `UseMethod()` no longer forwarding local variables from the generic on R-devel (issue #103)

R/TruncExpFam-package.R

@@ -32,7 +32,7 @@
 #' }
 #' @note Found a bug? Want to suggest a feature? Contribute to the scientific
 #' and open source communities by opening an issue on our home page.
-#' Check the "BugReports" field on \code{packageDescription("TruncExpFam")} for
+#' Check the "BugReports" field on `packageDescription("TruncExpFam")` for
 #' the URL.
 #' @importFrom methods new is
 #' @importFrom stats dbinom dgamma dlnorm dnorm dpois pbinom pgamma plnorm pnorm

R/attachDistroAttributes.R

@@ -5,5 +5,5 @@ attachDistroAttributes <- function(sample, family, parms) {
     attr(sample, "truncation_limits") <- parms[c("a", "b")]
     attr(sample, "continuous") <- family_attributes$cont
   }
-  return(sample)
+  sample
 }

R/averageT.R

@@ -10,5 +10,4 @@ averageT <- function(y) {
   } else {
     out <- colMeans(Ty)
   }
-  return(out)
 }

R/beta.R

@@ -7,14 +7,19 @@
 #' @param shape2 positive shape parameter beta
 #' @rdname rtrunc
 #' @export
-rtrunc.beta <- function(n, shape1, shape2, a = 0, b = 1) {
+rtruncbeta <- function(n, shape1, shape2, a = 0, b = 1, faster = FALSE) {
   class(n) <- "trunc_beta"
-  sampleFromTruncated(mget(ls()))
+  if (faster) {
+    family <- gsub("trunc_", "", class(n))
+    parms <- mget(ls())[grep("^faster$|^n$|^family$", ls(), invert = TRUE)]
+    return(rtrunc_direct(n, family, parms, a, b))
+  } else {
+    parms <- mget(ls())[grep("^faster$", ls(), invert = TRUE)]
+    return(sampleFromTruncated(parms))
+  }
 }
 
-#' @rdname rtrunc
-#' @export
-rtruncbeta <- rtrunc.beta
+rtrunc.beta <- rtruncbeta
 
 #' @export
 dtrunc.trunc_beta <- function(y, shape1, shape2, eta, a = 0, b = 1, ...) {
@@ -40,12 +45,13 @@ empiricalParameters.trunc_beta <- function(y, ...) {
   beta <- alpha * (1 / amean - 1)
   parms <- c(shape1 = alpha, shape2 = beta)
   class(parms) <- "parms_beta"
-  return(parms)
+  parms
 }
 
+#' @method sufficientT trunc_beta
 sufficientT.trunc_beta <- function(y) {
   # Calculates the sufficient statistic T(y)
-  return(suff.T = cbind(log(y), log(1 - y)))
+  suff.T <- cbind(log(y), log(1 - y))
 }
 
 #' @export
@@ -55,17 +61,17 @@ natural2parameters.parms_beta <- function(eta, ...) {
   if (length(eta) != 2) stop("Eta must be a vector of two elements")
   parms <- c(shape1 = eta[[1]], shape2 = eta[[2]])
   class(parms) <- class(eta)
-  return(parms)
+  parms
 }
 
 #' @export
 parameters2natural.parms_beta <- function(parms, ...) {
   # parms: The parameters shape and rate in a beta distribution
   # returns the natural parameters
   eta <- prepEta(c(parms[1], parms[2]), class(parms))
-  return(eta)
 }
 
+#' @method getYseq trunc_beta
 getYseq.trunc_beta <- function(y, y.min = 0, y.max = 1, n = 100) {
   # needs chekking
   mean <- mean(y, na.rm = TRUE)
@@ -75,9 +81,10 @@ getYseq.trunc_beta <- function(y, y.min = 0, y.max = 1, n = 100) {
   out <- seq(lo, hi, length = n)
   out <- out[out > 0 & out < 1] # prevents NaN as sufficient statistics
   class(out) <- class(y)
-  return(out)
+  out
 }
 
+#' @method getGradETinv parms_beta
 getGradETinv.parms_beta <- function(eta, ...) {
   # eta: Natural parameter
   # return the inverse of E.T differentiated with respect to eta' : p x p matrix
@@ -90,5 +97,5 @@ getGradETinv.parms_beta <- function(eta, ...) {
   term.12 <- -(1 + 2 * (x + y)) / (2 * (x + y) ^ 2)
   term.2 <- (x * (x + 2 * x * y + 2 * y * (1 + y))) / (2 * y ^ 2 * (x + y) ^ 2)
   A_inv <- matrix(c(term.1, term.12, term.12, term.2), ncol = 2)
-  return(A = solve(A_inv))
+  solve(A_inv)
 }