v3.2.0 release (#124)

* Add zenodo badge [skip ci] * Test cond on constant rate * test constant_rate_shift with cond * Add test sim_time_dependent * Add sim_trait_dependent cond test * Fix sim_constant_rate_shift cond test * Lint * More stringent constant_rate test * Better test title * fix constant_rate_shift test * Typo * More sim_time_dep cond test * More trait_dependent sim cond tests * test conditioning in relaxed rate * Remove duplicated tests * Add 2 type cond warning. Closes #123 * Fix cond relaxed rate gam test * Better warning text. Closes #123 * Lint * Move over tests from DAISIEtesting * No lintrbot * Increase travis wait time * Test warning of cond with 2 types * Split format_CS_sampled_stt and format_CS_trait files * abuse split-rate model with gamma = 0 * abuse time dependent model with gamma = 0 * Remove some input checks * Better tests sim_core_1_4a * test abuse and verbose DAISIE sim time dep * test abuse sim_core_trait_dependent * test no colonization happening returining 0 on stt * trait sims don't take nonoceanic pars * Delete DAISIE_single_branch * Add are_rates test * Better check format tests * Fix typo * Remove lingering nonoceanic pars in traits tests * Better is_simulation_outputs name checking * added higher subdivisions limit to integral_peak * added rel.tol to integral_peak * changed abs.tol to 1e-10 * changed integration to catch errors and return -Inf * changed rho to log gamma distribution and integrand to sum * removed if statement to catch integration errors * removed stop.on.error in integration * manual merge with 'hanno' Signed-off-by: Hanno <[email protected]> * builds,install & runs on Linux source package added Signed-off-by: Hanno <[email protected]> * Updated version and documentation * useDynLib in DAISIE-package.R, renewed documentation * useDynLib in DAISIE-package.R, renewed documentation * useDynLib in DAISIE-package.R, renewed documentation * No export pipe just import from magrittr * Correct appveyor.yml * logos and AppVeyor status in README * indent * lint * Progress correct brts ONEcolonist #125 * Only remove youngest_col if in vector. Progress #125 * Assert that youngest_col_time must be in btimes_all_clado_desc. Progress #125 * Format * Add comments and asserts. Remove else * Adjust refernce progress #125 * Add /pics to .Rbuildignore * Try adding col times, removing youngest. Progress #125 * Remove appveyor setup * Go GHA * GHA on onecolonist_fix * Switch to else if. Progress #125 * Fix references after testing. Progress #125 * Rename other_clades_same_ancestor to all_colonisations. Lint. Progress #125 * Better CI checks for testing * seq_along() not seq_len(). Progress #125 * Better doc. Progress #125 * Fix reference test CS_full_stt. Progress #125 * other_clades_same_ancestor -> all_colonisations. Progress #125 * other_clades_same_ancestor -> all_colonisations in core_1_4. Consider removing, changed to pass tests. Progress #125 * Better skips * Expand ONEcolonist hedge case coverage. Progress #125 * Comment temp code * Fix reference. Progress #125 * use NULL stt_table for testing. Progress #125 * Remove 1_4 and 1_5 functions and tests * Legacy functions removed from tests. Progress #126 * Remove more legacy code and tests. Progress #126 * V with single string w/ all times. Progress #125 * DAISIE_ONEcolonist returns all_event_times. Closes #125 * Update test-format_CS references. Progress #125 * Add $all_colonisations reference tests. Progress #125 * Add and rearrange ONEcolonist tests. Progress #125 * Remove unnecessary section. Close #125 * Sort all_colonisations from oldest to youngest. #125 * Expand tests and add test for 2 clado 1 nonendemic. #125 * Remove get_brts_mya(). Progress #126 * create_island() is internal. Progress #126 * Don't export DAISIE_make_global(). Progress #126 * Fix ONEcolonist documentation * Minor formatting * Use improved GHA yaml * Remove travis * Faster example in constant_rate * MinAge and better input support in DAISIE_dataprep * Fix table * Format pic * Try travis again * No roxygen doc on .Rproj * Travis in right place * Don't depend on Rcpp, RcppEigen, BH * Delete top level files * Buiild on Windows R4.0.2, Rtools40 Signed-off-by: Hanno <[email protected]> * Windows binary package added Signed-off-by: Hanno <[email protected]> * Linux: devtools::check pass Signed-off-by: Hanno <[email protected]> * Try Rcpp, RcppEigen, BH on imports * Rcpp, RcppEigen, BH on Imports * Don't run on PR. Install doMC on unix * Rcpp, RcppEigen, BH on Depends * still trying * R CMD check passes on Windows (R 3.6.3) R CMD check passes on Linux (R 3.6.3) Signed-off-by: Hanno <[email protected]> * Install ggtree * biocViews: to install ggtree instead * No longer use travis * date change * invoke_IW to test * Bug fix dopri5 and documentation * documentation * Solve Error: function 'enterRNGScope' not provided by package 'Rcpp' as outlined on https://github.com/immunogenomics/LISI/blob/master/NAMESPACE * Depend on specific setup-r tag See similar issue rsetienne/DDD#29 * GHA on macOS_fix * Use full SHA * Check if new test breaks covr * Add skip message * Don't define functions in tests * lint 2 integration tests * lint rate-shift and IW vs CS integration tests * Tweak time_dep ML WIP test * 2 type integration test lint * Remove redundant test-integration_tests * Informative comment on parallel test fix * Try loading Rcpp in tests * Avoid coverage check on solver test * Change flag location * Correct nocov flags * Split loglik_IW_solver and add to .covrignore * covr output in GHA output * Fix syntax * Remove Rcpp library call * skip_on_covr() and remove #nocov flags * Just run codecov * Delete wrong argument * Add @xieshu95's ORCID * Add @joshwlambert's ORCID * Add a NEWS.md file to track changes to the package * Add DAISIE_macOS instructions * Update NEWS.md to match v3.2.0 release notes * Add Big Sur note on README.md * Typo * setup-r@v1 again See Neves-P/DAISIErobustness/cb6ae80f545f01e8a2ebe0c134f915d8f804c7b4 * Add LICENSE file * arrows instead of = * Solving numerical problems with logcondprob * Improving numerical accuracy logcond * Modified test to conform to new logcond * cleaning up logcond * Improving logcond * bug fix * Resolving numerical issues near 0 in integration across parameters * passing mean and sd * fixed bug * Correctly format doi * relaxed rate in NEWS.md * Add note on logcondprob fix * Update date * updated relaxed_rate loglik * Use midpoint of function for better approximation * reduce approx threshold to 0.01 for relaxed-rate * Add @rscherrer's ORCID * Touch up references and authors * @HHildenbrandt is an author * changed approx threshold to 1 and change approximation to DAISIE_loglik * added tests for DAISIE_loglik_integrate * tidy DAISIE_loglik_integrate Co-authored-by: Pedro Neves <[email protected]> Co-authored-by: Neves-P <[email protected]> Co-authored-by: joshwlambert <[email protected]> Co-authored-by: rsetienne <[email protected]> Co-authored-by: = <=>
rsetienne · Mar 23, 2021 · dc62d86 · dc62d86
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,5 +1,6 @@
+^.*\.git$
+^.*\.github$
 ^.*\.Rproj$
-^\.Rproj\.user$
 ^\.travis\.yml$
 ^README\.md
 ^appveyor\.yml$
@@ -8,3 +9,12 @@
 ^CONTRIBUTING\.md$
 
 ^data-raw$
+^pics$
+^\.github$
+
+invoke_IW\.R
+test\.R
+test\.sh
+^\.Rproj\.user$
+^\.covrignore$
+^LICENSE$
diff --git a/.covrignore b/.covrignore
@@ -0,0 +1 @@
+tests/testthat/test-DAISIE_loglik_IW_solver.R
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,101 @@
+# 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
+on:
+  push:
+    branches:
+      - main
+      - master
+      - develop
+      - macOS_fix
+
+  # pull_request:
+  #   branches:
+  #     - main
+  #     - master
+  #     - develop
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@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: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+          if (.Platform$OS.type == "unix") remotes::install_cran("doMC")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Install covr and test coverage
+        if: matrix.config.r == 'devel'
+        run: |
+          remotes::install_cran("covr")
+          covr::codecov()
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
diff --git a/.gitignore b/.gitignore
@@ -15,5 +15,4 @@ src/*.gcda
 src/*.gcno
 **/.DS_Store
 **/Rplots.pdf
-doc
 Meta
diff --git a/.travis.yml b/.travis.yml
diff --git a/DAISIE.Rproj b/DAISIE.Rproj
@@ -18,4 +18,5 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace,vignette
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,11 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 3.1.0
-Date: 2020-09-27
+Version: 3.2.0
+Date: 2021-03-11
 Depends: R (>= 3.5.0)
 biocViews:
+SystemRequirements: C++14
 Imports: 
     deSolve,
     graphics,
@@ -19,7 +20,12 @@ Imports:
     foreach,
     doParallel,
     magrittr,
-    parallel
+    parallel,
+    Rcpp (>= 1.0.5)
+LinkingTo: 
+    Rcpp,
+    RcppEigen,
+    BH
 Suggests: 
     covr,
     testthat (>= 2.1.0),
@@ -58,7 +64,8 @@ Authors@R: c(
     person(given = "Joshua W.",
            family = "Lambert",
            role = c("aut"),
-           email = "[email protected]"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-5218-3046")),
     person(given = "Pedro",
            family = "Neves",
            role = c("aut"),
@@ -67,12 +74,17 @@ Authors@R: c(
     person(given = "Shu",
            family = "Xie",
            role = c("aut"),
-           email = "[email protected]"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-9594-946X")),
     person(given = "Richèl J.C.",
            family = "Bilderbeek",
            email = "[email protected]",
            role = c("aut"),
            comment = c(ORCID = "0000-0003-1107-7049")),
+    person(given = "Hanno",
+           family = "Hildenbrandt",
+           email = "[email protected]",
+           role = c("aut")),
     person(given = "Torsten",
            family = "Hauffe",
            email = "[email protected]",
@@ -91,7 +103,8 @@ Authors@R: c(
     person(given = "Raphael",
            family = "Scherrer",
            email = "[email protected]",
-           role = c("ctb")))
+           role = c("ctb"),
+           comment = c(ORCID = "0000-0002-1447-7630")))
 License: GPL-3
 Description: Simulates and computes the (maximum) likelihood of a dynamical 
     model of island biota assembly through speciation, immigration and