From 700c92127f70939a912a84cd65c39f58744cff35 Mon Sep 17 00:00:00 2001 From: Laura Marshall Date: Mon, 4 Aug 2025 15:10:33 +0100 Subject: [PATCH 1/6] Fix documentation issues --- NEWS.md | 2 +- R/check.cols.R | 6 +++--- R/dsm_cor.R | 3 ++- R/dsm_varprop.R | 6 +++--- man/check.cols.Rd | 2 +- man/dsm.cor.Rd | 3 ++- man/dsm_cor.Rd | 3 ++- man/dsm_varprop.Rd | 6 +++--- 8 files changed, 17 insertions(+), 14 deletions(-) diff --git a/NEWS.md b/NEWS.md index 0194b16..3cd1b5e 100644 --- a/NEWS.md +++ b/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 diff --git a/R/check.cols.R b/R/check.cols.R index 8ed0fd1..a393a45 100644 --- a/R/check.cols.R +++ b/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 diff --git a/R/dsm_cor.R b/R/dsm_cor.R index bd8d41c..fe3354d 100644 --- a/R/dsm_cor.R +++ b/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. diff --git a/R/dsm_varprop.R b/R/dsm_varprop.R index b40cb7d..002dc18 100644 --- a/R/dsm_varprop.R +++ b/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 diff --git a/man/check.cols.Rd b/man/check.cols.Rd index a8017fd..187f88c 100644 --- a/man/check.cols.Rd +++ b/man/check.cols.Rd @@ -7,7 +7,7 @@ check.cols(ddf.obj, segment.data, observation.data, segment.area) } \arguments{ -\item{ddf.obj}{a \code{ddf} object from \code{\link{mrds}}} +\item{ddf.obj}{a \code{ddf} object from \code{\link[mrds]{mrds}}} \item{segment.data}{segment data as defined in \code{\link{dsm}}} diff --git a/man/dsm.cor.Rd b/man/dsm.cor.Rd index e4435b4..71334b1 100644 --- a/man/dsm.cor.Rd +++ b/man/dsm.cor.Rd @@ -29,7 +29,8 @@ result of calling \code{\link[base:order]{order}} must make sense.} \item{max.lag}{maximum lag to calculate at.} \item{resid.type}{the type of residuals used, see -\code{\link{residuals.gam}}. Defaults to \code{"scaled.pearson"} in the GAM +\code{\link[mgcv]{residuals.gam}}. Defaults to \code{"scaled.pearson"} +in the GAM case and \code{"normalized"} in the GAMM case (which are equivalent).} \item{fun}{the function to use, by default \code{\link[stats:cor]{cor}}, must take two diff --git a/man/dsm_cor.Rd b/man/dsm_cor.Rd index 2c2c6d5..d5f8a6c 100644 --- a/man/dsm_cor.Rd +++ b/man/dsm_cor.Rd @@ -29,7 +29,8 @@ result of calling \code{\link[base:order]{order}} must make sense.} \item{max.lag}{maximum lag to calculate at.} \item{resid.type}{the type of residuals used, see -\code{\link{residuals.gam}}. Defaults to \code{"scaled.pearson"} in the GAM +\code{\link[mgcv]{residuals.gam}}. Defaults to \code{"scaled.pearson"} +in the GAM case and \code{"normalized"} in the GAMM case (which are equivalent).} \item{fun}{the function to use, by default \code{\link[stats:cor]{cor}}, must take two diff --git a/man/dsm_varprop.Rd b/man/dsm_varprop.Rd index 5749545..7fc739e 100644 --- a/man/dsm_varprop.Rd +++ b/man/dsm_varprop.Rd @@ -22,7 +22,7 @@ predictions and just return model objects.} \item{var.type}{which variance-covariance matrix should be used (\code{"Vp"} for variance-covariance conditional on smoothing parameter(s), \code{"Vc"} for -unconditional). See \code{\link{gamObject}} for an details/explanation. If +unconditional). See \code{\link[mgcv]{gamObject}} for an details/explanation. If in doubt, stick with the default, \code{"Vp"}.} \item{var_type}{deprecated, use \code{var.type} instead.} @@ -64,7 +64,7 @@ used in the DSM. Note that we can use \code{var.type="Vc"} here (see \code{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 @@ -97,7 +97,7 @@ and Findlay, K.P. (2011). Chilean Blue Whales as a Case Study to Illustrate 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. } From 88175cc93c7fb967e53a27e7e33cd1575385e3a5 Mon Sep 17 00:00:00 2001 From: Laura Marshall Date: Mon, 4 Aug 2025 15:11:07 +0100 Subject: [PATCH 2/6] Fix maintainer field --- DESCRIPTION | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index fdf4fd4..d26d43f 100644 --- a/DESCRIPTION +++ b/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", @@ -51,4 +55,4 @@ Suggests: tweedie, testthat Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.1 +RoxygenNote: 7.3.2 From 81077e9659f096a273938532871afaaa93f4fdaf Mon Sep 17 00:00:00 2001 From: Laura Marshall Date: Mon, 4 Aug 2025 15:11:14 +0100 Subject: [PATCH 3/6] Bump package version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d26d43f..5bdacd7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -34,7 +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 From 77e7bad66dace901c5b1dddd8577162b60c11824 Mon Sep 17 00:00:00 2001 From: Laura Marshall Date: Mon, 4 Aug 2025 15:11:27 +0100 Subject: [PATCH 4/6] update Rbuildignore --- .Rbuildignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.Rbuildignore b/.Rbuildignore index a9fec17..97f5583 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -8,3 +8,5 @@ LICENSE ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^vignettes$ +Clarity.txt \ No newline at end of file From 31b871318136d77965cacacba3ee35ed25d06434 Mon Sep 17 00:00:00 2001 From: Laura Marshall Date: Mon, 4 Aug 2025 15:11:38 +0100 Subject: [PATCH 5/6] Setup rhub checking --- .github/workflows/rhub.yaml | 95 +++++++++++++++++++++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 .github/workflows/rhub.yaml diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml new file mode 100644 index 0000000..74ec7b0 --- /dev/null +++ b/.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 }} From b06e4a2d993621b469ee580c255b790c9cbb5329 Mon Sep 17 00:00:00 2001 From: Laura Marshall Date: Mon, 4 Aug 2025 15:14:33 +0100 Subject: [PATCH 6/6] pkgdown site build --- docs/404.html | 4 +- docs/LICENSE-text.html | 4 +- .../data_format/dsm-data-formatting.html | 8 +-- docs/articles/index.html | 4 +- .../articles/lines_gomex/mexico-analysis.html | 61 +++++++++--------- .../figure-html/dsm.xyvarplot-1.png | Bin 27621 -> 27615 bytes .../figure-html/visgam5-1.png | Bin 13928 -> 13918 bytes docs/authors.html | 16 +++-- docs/deps/bootstrap-5.3.1/bootstrap.min.css | 2 +- docs/index.html | 7 +- docs/news/index.html | 5 +- docs/pkgdown.yml | 6 +- docs/reference/block.info.per.su.html | 4 +- docs/reference/check.cols.html | 6 +- docs/reference/dsm-data.html | 4 +- docs/reference/dsm-package.html | 4 +- docs/reference/dsm.cor.html | 7 +- docs/reference/dsm.html | 4 +- docs/reference/dsm.var.gam.html | 4 +- docs/reference/dsm.var.movblk.html | 4 +- docs/reference/dsm.var.prop.html | 4 +- docs/reference/dsm_cor.html | 7 +- docs/reference/dsm_var_gam.html | 4 +- docs/reference/dsm_var_movblk.html | 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