Issue 174

.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

@@ -16,13 +16,13 @@ Description: A simple way of fitting detection functions to distance sampling
     Horvitz-Thompson-like estimator) if survey area information is provided. See
     Miller et al. (2019) <doi:10.18637/jss.v089.i01> for more information on
     methods and <https://distancesampling.org/resources/vignettes.html> for example analyses.
-Version: 2.0.0.9013
+Version: 2.0.1
 URL: https://github.com/DistanceDevelopment/Distance/
 BugReports: https://github.com/DistanceDevelopment/Distance/issues
 Language: en-GB
 Depends:
     R (>= 4.1.0),
-    mrds (>= 3.0.0)
+    mrds (>= 3.0.1)
 Imports:
     dplyr,
     methods,

NEWS.md

@@ -7,6 +7,7 @@
 * Truncation distances greater than the largest cutpoint value for binned data are no longer permitted as these cause fitting issues. (Issue #175)
 * print.dht_result now displays estimates for groups as well as individuals by default when group size is present. (Issue #178)
 * Issues a warning when truncation is provided as a character but without the explicit % sign. (Issue #166) 
+* Fix sample ordering issue in dht2 for the S1, S2 and O1 encounter rate variance estimators. (Issue #174)
 
 Enhancements
 

R/ER_var_f.R

@@ -24,8 +24,8 @@ ER_var_f <- function(erdat, innes, binomial_var=FALSE){
   }else{
 
     # sort the data if we use O2/O3 estimators
-    if(any(erdat$er_est %in% c("O2", "O3"))){
-      warning("Using O2 or O3 encounter rate variance estimator, assuming that sorting on Sample.Label is meaningful", immediate. = TRUE, call. = FALSE)
+    if(any(erdat$er_est %in% c("O1", "O2", "O3", "S1", "S2"))){
+      warning("Using one of O1, O2, O3, S1 or S2 encounter rate variance estimators, assuming that sorting on Sample.Label is meaningful.", immediate. = TRUE, call. = FALSE)
       if(!is.numeric(erdat$Sample.Label)){
         warning("Additionally, Sample.Label is not numeric, this may cause additional issues", immediate. = TRUE, call. = FALSE)
       }