Merge pull request #126 from TGuillerme/master

v1.8 release

.github/workflows/R-CMD-check.yaml

@@ -1,18 +1,10 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - MCMCglmm
-      - main
-      - master
-      - release
+    branches: [main, master, release]
   pull_request:
-    branches:
-      - MCMCglmm
-      - main
-      - master
-      - release
+    branches: [main, master, release]
 
 name: R-CMD-check
 
@@ -26,73 +18,34 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release', vignettes: ', "--ignore-vignettes"), build_args = ("--no-bulid-vignettes"'}
-          - {os: macOS-latest, r: 'release', vignettes: ', "--ignore-vignettes"), build_args = ("--no-bulid-vignettes"'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      RGL_USE_NULL: true
-      _R_CHECK_CRAN_INCOMING_: true # Seemingly not set by --as-cran
-      _R_CHECK_FORCE_SUGGESTS_: false # CRAN settings
-      R_COMPILE_AND_INSTALL_PACKAGES: 'never'
-      _R_CHECK_THINGS_IN_CHECK_DIR_: false
-      R_REMOTES_STANDALONE: true
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      _R_CHECK_CRAN_INCOMING_USE_ASPELL_: false # Set to true when can figure how to install aspell on Windows
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+      R_KEEP_PKG_SOURCE: yes
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = c("soft", "Config/Needs/check")),
-                  ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor),
-                     ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get install ghostscript texlive-latex-base texlive-latex-extra texlive-fonts-recommended texlive-fonts-extra
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = c("soft", "Config/Needs/check"))
-       #   pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran" ${{ matrix.config.vignettes }}),
-                               error_on = "error", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          error-on: '"error"'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,31 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}

.travis.yml

@@ -25,4 +25,4 @@ r_packages:
 
 
 after_success:
-  - Rscript -e 'library(covr); codecov(token = "5f041826-63f1-47fa-b4a8-9a32633f47fa")'
+  - Rscript -e 'library(covr); codecov(token = "14042dcc-32e4-418a-b5ca-fa368414b775")'

DESCRIPTION

@@ -1,10 +1,14 @@
 Package: dispRity
 Title: Measuring Disparity
-Author: Thomas Guillerme [aut, cre, cph],
-		Mark N Puttick [aut, cph]
+Authors@R: c(person("Thomas", "Guillerme", role = c("aut", "cre", "cph"),
+										   email = "[email protected]",
+										   comment = c(ORCID = "0000-0003-4325-1275")),
+  			 person("Mark", "Puttick",     role = c("aut", "cph")),
+  			 person("Jack", "Hatfield",    role = c("aut", "cph"))
+  			 )
 Maintainer: Thomas Guillerme <[email protected]>
-Version: 1.7.0
-Date: 2022-08-08
+Version: 1.8
+Date: 2023-12-11
 Description: A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
 Depends:
     R (>= 3.6.0),
@@ -16,6 +20,7 @@ Imports:
 	Claddis,
 	ellipse,
 	geometry,
+	GET,
 	graphics,
 	grDevices,
 	MASS,
@@ -24,17 +29,16 @@ Imports:
 	parallel,
 	phangorn,
 	phyclust,
+	phylolm,
 	utils,
 	vegan,
 	scales,
-	spptest,
+	zoo,
 License: GPL-3 | file LICENSE
-Remotes:
-    github::myllym/spptest@no_fastdepth
 Suggests:
 	MCMCglmm,
     geoscale,
     testthat,
     knitr
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 URL: https://github.com/TGuillerme/dispRity

NAMESPACE

@@ -10,16 +10,18 @@ importFrom("geometry", "convhulln", "dot")
 importFrom("graphics", "abline", "axis", "boxplot", "hist", "image", "lines", "mtext", "par", "plot", "points", "polygon", "text", "layout", "legend", "barplot")
 importFrom("grDevices", "colorRampPalette", "grey", "hcl", "heat.colors", "adjustcolor")
 importFrom("MASS", "mvrnorm")
-importFrom("methods", "hasArg", "formalArgs")#, "is")
+importFrom("methods", "hasArg", "formalArgs", "is")
 importFrom("mnormt", "dmnorm", "rmnorm")
 # importFrom("paleotree", "timeSliceTree")
 importFrom("phangorn", "dist.hamming", "NJ", "RF.dist", "CI", "RI", "optim.parsimony", "parsimony")
 importFrom("phyclust", "gen.seq.HKY")
+importFrom("phylolm", "phylolm")
 importFrom("utils", "combn", "data", "capture.output", "tail")
-importFrom("vegan", "adonis", "vegdist")
+importFrom("vegan", "adonis2", "vegdist")
 importFrom("scales", "rescale")
-importFrom("spptest", "create_curve_set", "rank_envelope")
+importFrom("GET", "create_curve_set", "rank_envelope")
 importFrom("parallel", "parLapply", "detectCores", "makeCluster", "clusterExport", "stopCluster")
+importFrom("zoo", "rollmean")
 # importFrom("geomorph", "gpagen")
 # importFrom("RCurl", "getURL", "url.exists")
 
@@ -61,7 +63,8 @@ export(dimension.level2.fun)
 export(dimension.level3.fun)
 export(disalignment)
 export(displacements)
-export(ellipse.volume)
+export(ellipse.volume) # alias for ellipsoid.volume
+export(ellipsoid.volume)
 export(edge.length.tree)
 export(func.div)
 export(func.eve)
@@ -77,6 +80,7 @@ export(projections.tree)
 export(quantiles)
 export(radius)
 export(ranges)
+export(roundness)
 export(span.tree.length)
 export(variances)
 
@@ -88,6 +92,7 @@ export(model.test)
 export(model.test.sim)
 export(model.test.wrapper)
 export(null.test)
+export(pgls.dispRity)
 export(randtest.dispRity)
 # export(sequential.test)
 
@@ -103,7 +108,9 @@ export(get.subsets)
 export(get.covar)
 export(n.subsets)
 export(make.dispRity)
-export(rescale.dispRity)
+export(name.subsets)
+export(rescale.dispRity) # alias for scale
+export(scale.dispRity)
 export(size.subsets)
 export(sort.dispRity)
 export(add.tree)
@@ -120,9 +127,10 @@ export(MCMCglmm.traits)
 export(MCMCglmm.levels)
 export(MCMCglmm.sample)
 export(MCMCglmm.covars)
+export(MCMCglmm.variance)
 export(pair.plot)
 export(random.circle)
-export(randtest.dist)
+export(distance.randtest)
 export(reduce.matrix)
 export(reduce.space)
 export(remove.zero.brlen)
@@ -140,8 +148,8 @@ export(get.contrast.matrix)
 export(sim.morpho)
 export(multi.ace)
 
-##S3 
-S3method(adonis, dispRity)
+##S3
+S3method(scale, dispRity)
 S3method(matrix, dispRity)
 S3method(plot, char.diff)
 S3method(plot, dispRity)

NEWS.md

@@ -1,27 +1,52 @@
-<!-- 
-dispRity 0.2.0 (2016-04-01)
+dispRity v1.8 (2023-12-11) *dispRity.multi*
 =========================
 
 ### NEW FEATURES
 
-  * Blabla
+ * Added the _dispRity.multi_ internal architecture now allowing users to work with different matrices **and** different trees as inputs for `custom.subsets`, `chrono.subsets`, `boot.matrix` and `dispRity`. This change is not affecting the user level appart from now allowing to bypass some error messages (thanks to Mario Corio for that obvious suggestion).
+ * *New utility function*: `name.subsets` for directly accessing the subsets names of a `dispRity` object (basically doing `names(my_dispRity$subsets)`).
+ * *New utility function*: `MCMCglmm.variance` for calculating the variance for specific terms in a `"MCMCglmm"` model.
+ * *New* statistical test: `pgls.dispRity` to run PGLS test on a `dispRity` object with a level-2 metric and a tree (using excellent [`phylolm`](https://CRAN.R-project.org/package=phylolm) algorithm). The new test comes with its own S3 print, summary and plot functions if the input `dispRity` data contains multiple trees or multiple matrices (running and handling the output of multiple `phylolm`).
+ * *New* options to `get.tree` utility function to get the trees in each subsets (thanks to Jack Hadfield for this suggestion and help with implementation).
+ * *New vignette* compiling resources for developers to help people (and future me) to edit the package. 
+ * *New metric*: `roundness` to measure the roundness of a variance-covariance matrix. 
 
 ### MINOR IMPROVEMENTS
 
-  * Blabla
+ * **CHANGE IN DEFAULT ARGUMENTS** for the `custom.subsets`, `chrono.subsets`, `boot.matrix` and `dispRity` functions: the `tree`, `FADLAD`, `prob` and `dimensions` arguments is now `NULL` by default (instead of missing).
+ * **CHANGE IN DEFAULT ARGUMENTS** for the `projections` function. The defaults are now `scale = TRUE`, `centre = FALSE` (previously `TRUE`) and `abs = FALSE` (previously `TRUE`). The default arguments for `dispRity.covar.projections` remain unchanged though (`scale = TRUE`, `centre = TRUE`, `abs = TRUE`).
+ * `randtest.dispRity` function's `subsets` argument now can take a list of arguments of subsets to compare is `data` is a `dispRity` object. The call message has also been updated to be much more verbose and clear of what has been tested.
+ * optimised internal logic for all the `projections.*` functions for speed.
+ * `test.metric` now also adds the slope coefficient if the option `model` is used.
+ * the default legends/row names when using `plot`/`summary` on `test.metric` results are now more easy to interpret.
+ * `reduce.space` has now 25 times less chances to be stuck on a local optimum.
+ * `match.tip.edges` now also works on nodes and on `"multiPhylo"` objects and has a added an option `use.parsimony` (default is `TRUE`) to propagate the matching down the tree (i.e. if two nodes have the same unique ancestor and variable value, the ancestor is consider to have that variable value as well).
+ * Improved margins handling in `covar.plot`.
+ * Updated test coverage here and there.
+ * `clean.data` can now also handle a list of `"phylo"` objects as `tree` input (i.e. it does not need to be specifically classed as `"multiPhylo"`).
+ * Changed dependencies to [`spptest`](https://github.com/myllym/spptest) to [`GET`](https://github.com/myllym/GET).
+ * `space.maker` can now generate specific row names and be replicated to generate a bunch of spaces (via the new optional arguments `elements.names` and `replicates` respectively).
+ * The `add.tree` utility function now has an optional argument to override any existing trees (`replace = TRUE`) or not (`replace = FALSE`; which remains the default previous behaviour). 
+ * `print.dispRity` now recognises and highlights simulated data from the [`treats`](https://github.com/tguillerme/treats) package.
+ * Improved `NA` management for `S3` functions.
+ * Improved automatic centering and scaling for `covar.plot` making the figures more aesthetic.
+ * `remove.zero.brlen` now also removes negative branch lengths and works on `"multiPhylo"` objects (thanks to Thomas Johnson for this suggestion).
+ * `fill.dispRity` has now an extra argument `check` to toggle the data checking on and off (more for developers).
+ * `multi.ace` is now described in details in the manual.
+ * `slice.tree` has now a `keep.all.ancestors` option to do exactly that.
 
 ### BUG FIXES
-
-  * Blabla
+
+ * The correct types of changes are now plotted in legend when plotting the results of `test.metric`.
+ * `get.disparity` now correctly concatenates one dimensional results into a `"numeric"` (rather than a `"matrix"`).
+ * `make.metric` now internally handles `covar` object correctly (i.e. as distance matrices).
+ * Calculating disparity for multiple matrices and customised subsets now works as expected for all metric levels.
 
 ### DEPRECATED AND DEFUNCT
 
-  * Blabla
- -->
-
-<!--   * `dtt.dispRity` now works with any tree (including non-ultrametric ones and fossils only ones). -->
-<!--   * `dtt.dispRity` now works with time-slicing. -->
-
+ * `ellipse.volume` has been changed to `ellipsoid.volume` to more accurately reflect what it is measuring.
+ * `rescale.dispRity` has been changed to `scale.dispRity` and correctly registered as a S3 method.
+ * `randtest.dist` has been changed to `distance.randtest` to avoid conflict with `*.dist` S3 methods.
 
 dispRity v1.7 (2022-08-08) *MacMacGlimm*
 =========================
@@ -73,7 +98,7 @@ dispRity v1.7 (2022-08-08) *MacMacGlimm*
  * `standardGeneric` functions are now correctly interpreted as functions throughout the package.
  * Fixed bug when plotting level 1 disparity metric results without bootstrapped (`observed = TRUE` is now used as the default).
  * Fixed bug when plotting `test.metric` plots with `save.steps` options with more than two types of shifts.
- * Fixed bug with `null.test` which is now correctly managing the number of dimensions inherited from `dispRity` objects (thanks to [Alex Slavenko](https://alexslavenko.weebly.com/) for spotting this one and the two above).
+ * Fixed bug with `null.test` which is now correctly managing the number of dimensions inherited from `dispRity` objects (thanks to Alex Slavenko for spotting this one and the two above).
  * Fixed bug when using level 2 dimension metrics on unidimensional data (the metric is now detected as a level 2 correctly; thanks to Catherine Klein and [Rachel Warnock](https://www.gzn.nat.fau.de/palaeontologie/team/professors/rachel-warnock/) for noticing that one).
  * Update internal use of `is(data, c("array", "matrix"))` to `is.array(data)` for R 4.1.2.
 
@@ -92,7 +117,7 @@ dispRity v1.6.0 (2021-04-16) *dispRitree*
  * You can now save the shifts results in `test.metric` with `save.steps` and then visualise them with `plot.dispRity` along side the disparity metric test results.
  * *New* utility function `n.subsets` to directly get the number of subsets in a `dispRity` object.
  * *New* statistical test: `randtest.dispRity` that is a wrapper for `ade4::randtest` applied to `dispRity` objects (not dissimilar from `null.test`).
- * Six more demo datasets have been added to the package! These datasets are the ones used in [Guillerme et al. 2020](https://scholar.google.co.uk/scholar?hl=en&as_sdt=0%2C5&q=Shifting+spaces%3A+Which+disparity+or+dissimilarity+measurement+best+summarize+occupancy+in+multidimensional+spaces%3F&btnG=) and published originally in [Beck & Lee 2014](https://royalsocietypublishing.org/doi/full/10.1098/rspb.2014.1278) (that one was originally the only demo dataset in the package), [Wright 2017](https://www.cambridge.org/core/journals/journal-of-paleontology/article/bayesian-estimation-of-fossil-phylogenies-and-the-evolution-of-early-to-middle-paleozoic-crinoids-echinodermata/E37972902541CD0995AAD08A1122BD54), [Marcy et al. 2016](https://link.springer.com/article/10.1186/s12862-016-0782-1), [Hopkins & Pearson 2016](https://pdfs.semanticscholar.org/a3f0/50944d2aefa1df811ea94a3eea630d82c24f.pdf)), [Jones et al. 2015](https://scholar.google.co.uk/scholar?hl=en&as_sdt=0%2C5&q=Dispersal+mode+mediates+the+effect+of+patch+size+and+patch+connectivity+on+metacommunity+diversity&btnG=), [Healy et al. 2019](https://www.nature.com/articles/s41559-019-0938-7). Thanks to all these authors for their open science work!
+ * Six more demo datasets have been added to the package! These datasets are the ones used in [Guillerme et al. 2020](https://scholar.google.co.uk/scholar?hl=en&as_sdt=0%2C5&q=Shifting+spaces%3A+Which+disparity+or+dissimilarity+measurement+best+summarize+occupancy+in+multidimensional+spaces%3F&btnG=) and published originally in [Beck & Lee 2014](https://doi.org/10.1098/rspb.2014.1278) (that one was originally the only demo dataset in the package), [Wright 2017](https://www.cambridge.org/core/journals/journal-of-paleontology/article/bayesian-estimation-of-fossil-phylogenies-and-the-evolution-of-early-to-middle-paleozoic-crinoids-echinodermata/E37972902541CD0995AAD08A1122BD54), [Marcy et al. 2016](https://link.springer.com/article/10.1186/s12862-016-0782-1), [Hopkins & Pearson 2016](https://pdfs.semanticscholar.org/a3f0/50944d2aefa1df811ea94a3eea630d82c24f.pdf)), [Jones et al. 2015](https://scholar.google.co.uk/scholar?hl=en&as_sdt=0%2C5&q=Dispersal+mode+mediates+the+effect+of+patch+size+and+patch+connectivity+on+metacommunity+diversity&btnG=), [Healy et al. 2019](https://www.nature.com/articles/s41559-019-0938-7). Thanks to all these authors for their open science work!
  * `dispRity` objects now have a reserved `$tree` component that contain any number of trees attached to the data. This allows any function to use the reserved argument name `tree` to extract directly the relevant tree from the `dispRity` object, for functions like `chrono.subsets` or metrics like `ancestral.dist`! To help manipulate the `tree` component of the `dispRity` object, you can now use the new utility functions `add.tree`, `get.tree` and `remove.tree`.
 
 ### MINOR IMPROVEMENT
@@ -390,7 +415,7 @@ dispRity v0.3 (2017-01-25) *dispRity lite*
 
 ### NEW FEATURES
 
-  * Complete change of the `dispRity` object architecture (see more [here](https://github.com/TGuillerme/dispRity/blob/master/disparity_object.md)).
+  * Complete change of the `dispRity` object architecture.
 
 ### MINOR IMPROVEMENTS