Fix cran issues

.Rbuildignore

@@ -8,3 +8,5 @@ LICENSE
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^vignettes$
+Clarity.txt

.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

@@ -4,7 +4,11 @@ License: GPL (>= 2)
 Title: Density Surface Modelling of Distance Sampling Data
 LazyLoad: yes
 Authors@R: 
-  c(person(given=c("David", "L."),
+  c(person(given=c("Laura"),
+           family="Marshall",
+           email = "lhm@st-andrews.ac.uk" , 
+           role = "cre"),
+    person(given=c("David", "L."),
            family="Miller",
            role=c("aut")),
     person(given="Eric",
@@ -30,7 +34,7 @@ Description: Density surface modelling of line transect data. A Generalized
     of animal abundance from distance sampling (also presence/absence and strip
     transect) data. Several utility functions are provided for model checking,
     plotting and variance estimation.
-Version: 2.3.3.9001
+Version: 2.3.4
 Language: en-GB
 Encoding: UTF-8
 URL: https://github.com/DistanceDevelopment/dsm
@@ -51,4 +55,4 @@ Suggests:
     tweedie,
     testthat
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.2

NEWS.md

@@ -1,7 +1,7 @@
 # dsm 2.3.4
 
 - fix bug where if predictions were NA (e.g., predictions outside the soap boundary), all variances were NA due to propagation (#4)
-
+- fix CRAN NOTES regarding documentation links and special characters.
 
 # dsm 2.3.3
 

R/check.cols.R

@@ -2,9 +2,9 @@
 #'
 #' Internal function to check that supplied `data.frames` have the correct
 #' columns and checks that sample labels are all unique.
-#' @param ddf.obj a `ddf` object from [`mrds`][mrds]
-#' @param segment.data segment data as defined in [`dsm`][dsm]
-#' @param observation.data observation data as defined in [`dsm`][dsm]
+#' @param ddf.obj a `ddf` object from \code{\link[mrds]{mrds}}
+#' @param segment.data segment data as defined in \code{\link{dsm}}
+#' @param observation.data observation data as defined in \code{\link{dsm}}
 #' @param segment.area area of segments
 #' @return nothing, but throws an error if something went wrong
 #' @author David Lawrence Miller

R/dsm_cor.R

@@ -10,7 +10,8 @@
 #' @param Segment.Label label for the segments (default: `Segment.Label`).The
 #' result of calling [`order`][base::order] must make sense.
 #' @param resid.type the type of residuals used, see
-#' [`residuals.gam`][residuals.gam]. Defaults to `"scaled.pearson"` in the GAM
+#' \code{\link[mgcv]{residuals.gam}}. Defaults to `"scaled.pearson"`
+#' in the GAM
 #' case and `"normalized"` in the GAMM case (which are equivalent).
 #' @param fun the function to use, by default [`cor`][stats::cor], must take two
 #' column vectors as arguments.

R/dsm_varprop.R

@@ -24,7 +24,7 @@
 #'
 #' Note that we can use `var.type="Vc"` here (see `gamObject`), which is the
 #' variance-covariance matrix for the spatial model, corrected for smoothing
-#' parameter uncertainty. See Wood, Pya & S{\"a}fken (2016) for more
+#' parameter uncertainty. See Wood, Pya & Säfken (2016) for more
 #' information.
 #'
 #' Models with fixed scale parameters (e.g., negative binomial) do not require
@@ -65,7 +65,7 @@
 #' Methods to Estimate Abundance and Evaluate Conservation Status of Rare
 #' Species. Conservation Biology 25(3), 526-535.
 #'
-#' Wood, S.N., Pya, N. and S{\"a}fken, B. (2016) Smoothing parameter and model
+#' Wood, S.N., Pya, N. and Säfken, B. (2016) Smoothing parameter and model
 #' selection for general smooth models. Journal of the American Statistical
 #' Association, 1-45.
 #'
@@ -75,7 +75,7 @@
 #' @param trace for debugging, see how the scale parameter estimation is going.
 #' @param var.type which variance-covariance matrix should be used (`"Vp"` for
 #' variance-covariance conditional on smoothing parameter(s), `"Vc"` for
-#' unconditional). See [`gamObject`][gamObject] for an details/explanation. If
+#' unconditional). See \code{\link[mgcv]{gamObject}} for an details/explanation. If
 #' in doubt, stick with the default, `"Vp"`.
 #' @param var_type deprecated, use `var.type` instead.
 #' @export