Issue 84 crancheck

.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 }}

DESCRIPTION

@@ -13,13 +13,13 @@ Description: Enable users to evaluate long-term trends using a Generalized
     questions.  Methodology described in Murphy (2019) 
     <doi:10.1016/j.envsoft.2019.03.027>.
 Author: Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
-Version: 2.0.11
+Version: 2.0.11.9002
 Maintainer: Erik W Leppo <Erik.Leppo@tetratech.com>
 Depends:
     R (>= 3.5.0)
 License: GPL-3    
 LazyData: TRUE
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Imports:
     dataRetrieval,

NEWS

@@ -4,7 +4,22 @@ NEWS
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-02-12 12:03:12.250764
+    #> Last Update: 2024-07-25 13:50:16.146636
+
+# baytrends 2.0.11.9003
+
+- release 2024-07-26
+- docs: Add rhubv2 for testing befor posting to CRAN
+
+# baytrends 2.0.11.9002
+
+- refactor: Function impute to pass a dataframe with two columns named
+  left and right to fitdistrplus::fitdistcens
+
+# baytrends 2.0.11.9001
+
+- refactor: Function gamTestSeason to address logic error with
+  gamPenaltyCrit
 
 # baytrends 2.0.11
 

NEWS.rmd

@@ -20,6 +20,21 @@ knitr::opts_chunk$set(
 cat(paste0("Last Update: ",Sys.time()))
 ```
 
+# baytrends 2.0.11.9003
+
+- release 2024-07-26
+- docs: Add rhubv2 for testing befor posting to CRAN
+
+
+# baytrends 2.0.11.9002
+
+-   refactor: Function impute to pass a dataframe with two columns named left 
+and right to fitdistrplus::fitdistcens
+
+# baytrends 2.0.11.9001
+
+-   refactor: Function gamTestSeason to address logic error with gamPenaltyCrit
+
 # baytrends 2.0.11
 
 -   Release 2024-02-12

R/gamTestSeason.r

@@ -615,17 +615,17 @@ gamTestSeason <-function(df, dep, stat, layer=NA, analySpec, gamTable=TRUE, gamP
 
       # evaluate F-stat in ANOVA table     #04Feb2017
       FstatFlag <- ""
-      if(selectSetting==FALSE &&
-         (min(gamANOVAtbl$df, na.rm=TRUE) < gamPenaltyCrit[1] ||  #18Jul2018
+      if(selectSetting==FALSE &
+         (min(gamANOVAtbl$df, na.rm=TRUE) < gamPenaltyCrit[1] |  #18Jul2018
           max(gamANOVAtbl$F, na.rm=TRUE) > gamPenaltyCrit[2])) {  #18Jul2018
         gamANOVAtbl$Note <- '-'
-        if (length(gamANOVAtbl$df < gamPenaltyCrit[1] ||      #18Jul2018
+        if (length(gamANOVAtbl$df < gamPenaltyCrit[1] |      #18Jul2018
                    gamANOVAtbl$F > gamPenaltyCrit[2]) == 1 &  #18Jul2018
-            is.na(gamANOVAtbl$df < gamPenaltyCrit[1] ||       #18Jul2018
+            is.na(gamANOVAtbl$df < gamPenaltyCrit[1] |       #18Jul2018
                   gamANOVAtbl$F > gamPenaltyCrit[2])[1]) {    #18Jul2018
           FstatFlag <- ""                                     #18Jul2018
         } else {
-          gamANOVAtbl[gamANOVAtbl$df < gamPenaltyCrit[1] ||
+          gamANOVAtbl[gamANOVAtbl$df < gamPenaltyCrit[1] |
                         gamANOVAtbl$F > gamPenaltyCrit[2],"Note"] <- "F-stat maybe unreliable"
           FstatFlag <- "***"
         }
@@ -634,8 +634,8 @@ gamTestSeason <-function(df, dep, stat, layer=NA, analySpec, gamTable=TRUE, gamP
       # Output GAM ANOVA table          #04Feb2017
       if(gamTable) {
 
-        if(selectSetting==FALSE &&
-           (min(gamANOVAtbl$df, na.rm=TRUE) < gamPenaltyCrit[1] ||  #18Jul2018
+        if(selectSetting==FALSE &
+           (min(gamANOVAtbl$df, na.rm=TRUE) < gamPenaltyCrit[1] |  #18Jul2018
             max(gamANOVAtbl$F, na.rm=TRUE) > gamPenaltyCrit[2])) {  #18Jul2018
           .T("GAM Analysis of Variance.")
           print(knitr::kable(gamANOVAtbl[,],

R/imputeCensored.R

@@ -48,7 +48,7 @@ impute <-function(x, imputeOption="mid") {
 
 # Error traps ####
 
-  # Error trap ... make sure x variable is a qw class
+  # Error trap ... make sure x variable is a Surv class
   if (!(class(x) %in% c("Surv"))) {
     stop("input vector not of type Surv.")
   }
@@ -111,17 +111,17 @@ impute <-function(x, imputeOption="mid") {
   } else if (imputeOption == "uniform") {
     x3[not.miss] <- stats::runif(sum(not.miss), x[not.miss,1], x[not.miss,2])
   } else if (imputeOption == "norm") {
-    myData1 <- data.frame(x=x2[not.miss], left=x[not.miss,1]
-                          , right=x[not.miss,2])
-    fn1     <- fitdistrplus::fitdistcens(myData1, distr="norm")
+    myData1  <- data.frame(x=x2[not.miss], left=x[not.miss,1]
+                           , right=x[not.miss,2])
+    fn1     <- fitdistrplus::fitdistcens(myData1[,c("left", "right")], distr="norm")
     mu.norm <- fn1$estimate[1]
     sd.norm <- fn1$estimate[2]
     myData1$normExpec <- .ExpNmCens(myData1,dep="x",mu.norm,sd.norm)[,1]
     x3[not.miss] <- myData1$normExpec
   } else if (imputeOption == "lnorm") {
     myData1  <- data.frame(x=x2[not.miss], left=x[not.miss,1]
                            , right=x[not.miss,2])
-    fn1      <- fitdistrplus::fitdistcens(myData1, distr="lnorm")
+    fn1      <- fitdistrplus::fitdistcens(myData1[,c("left", "right")], distr="lnorm")
     mu.lnorm <- fn1$estimate[1]
     sd.lnorm <- fn1$estimate[2]
     myData1$lnormExpec <- .ExpLNmCens(myData1,dep="x",mu.lnorm,sd.lnorm)[,1]

inst/extdata/baytrends_LibraryCreation.Rmd

@@ -123,14 +123,15 @@ file.remove("NEWS.html")
 #setwd(paste0("./", myLibrary))
 devtools::document()
 ## Install New Package (locally)
-setwd("..") # return to root directory first
-devtools::install(myLibrary, quick=FALSE, reload=TRUE, build_vignettes = TRUE)
+#setwd("..") # return to root directory first
+devtools::install(".", quick=FALSE, reload=TRUE, build_vignettes = TRUE)
 
 # blank line above ensures no "updates" to packages.
 # ## Reload library
 # library(myLibrary, character.only = TRUE)
 # change wd back to package
-setwd(file.path(".", myLibrary))
+#setwd(file.path(".", myLibrary))
+help(package=(myLibrary))
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ```
 
@@ -158,6 +159,11 @@ Downstream dependancies
 devtools::revdep("baytrends")
 ```
 
+URL check
+```{r URL_Check}
+urlchecker::url_check()
+```
+
 
 ## Check
 
@@ -174,9 +180,11 @@ Check failures
 but puts it all in one place.  Have to run *after* using Check.
 ```{r CheckFailures, eval=FALSE}
 library(devtools)
-dir.check <- "C:\\Users\\Erik.Leppo\\OneDrive - Tetra Tech, Inc\\MyDocs_OneDrive\\GitHub\\baytrends.Rcheck"
+# dir.check <- "C:\\Users\\Erik.Leppo\\OneDrive - Tetra Tech, Inc\\MyDocs_OneDrive\\GitHub\\baytrends.Rcheck"
+dir.check <- file.path(dirname(getwd()), "baytrends.Rcheck")
 #
 check_failures(dir.check)
+# 20240726, no longer a function
 
 
 ```
@@ -199,7 +207,7 @@ check_for_cran() # win and linux
 check_on_linux()
 
 ```
-
+20240726, above no longer works since v2
 
 
 Run all Examples.