Merge pull request #153 from rsetienne/develop

v4.3.1
rsetienne · Feb 12, 2023 · 7d62c63 · 7d62c63
2 parents d0ed3df + 4e9323c
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diff --git a/.zenodo.json b/.zenodo.json
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,11 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 4.3.0
-Date: 2023-12-26
-Depends: R (>= 3.5.0)
+Version: 4.3.1
+Date: 2023-02-10
+Depends: R (>= 4.1.0)
 biocViews:
-SystemRequirements: C++14
+SystemRequirements: C++17
 Imports: 
     deSolve,
     graphics,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# DAISIE 4.3.1
+
+* Fix issue that prevented 'covr' from running correctly.
+* Depend on R >= 4.1.0, C++17.
+* Tests of `DAISIE_ML_*()` and integration tests don't run on CRAN due to too long runtime.
+
 # DAISIE 4.3.0
 
 * Due to recent changes in CRAN policy that result in warnings due to the use of Rcpp related packages that link to libraries that use `sprintf` ('Rcpp' and 'BH'), 'DAISIE' now requires Rcpp v(>= 1.0.10) and BH v(>= 1.81.0-1). See https://github.com/RcppCore/Rcpp/pull/1236 and https://github.com/eddelbuettel/bh/pull/90 respectively. Also require package 'DDD' v(>= 5.0.0).

diff --git a/R/DAISIE-package.R b/R/DAISIE-package.R
@@ -14,9 +14,10 @@
 #' \item Valente, L., Phillimore, A. B., Melo, M., Warren, B. H., Clegg, S. M., Havenstein, K., & Etienne, R. S. (2020). A simple dynamic model explains the diversity of island birds worldwide. Nature 579: 92-96. \doi{10.1038/s41586-020-2022-5}.\cr
 #' \item Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal of Biogeography 47: 1849–1860. \doi{10.1111/jbi.13914}.\cr
 #' \item Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. EcoEvoRxiv. \doi{10.32942/osf.io/w5ntf}.\cr
-#' \item Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography. \doi{10.1111/jbi.14519}.\cr
+#' \item Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography 49: 2091-2104. \doi{10.1111/jbi.14519}.\cr
 #' \item Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. \doi{10.1101/2022.01.13.476210}.\cr
 #' \item Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? Evolution. \doi{10.1093/evolut/qpad006}.\cr
+#' \item Michielsen, N. M., Goodman, S. M., Soarimalala, V., van der Geer, A. A. E., Dávalos, L. M., Saville, G. I., Upham, N., Valente, L. (2023). The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar. Nature Communications 14 (14).\doi{10.1038/s41467-022-35215-3}.\cr
 #' }
 #' @keywords internal
 #' @import Rcpp

diff --git a/R/DAISIE_loglik_CS.R b/R/DAISIE_loglik_CS.R
@@ -1230,7 +1230,11 @@ DAISIE_integrate_const <- function(initprobs,tvec,rhs_func,pars,rtol,atol,method
   # Use a regular expression to extract if the part that we are interested
   # in is present
   function_as_text <- as.character(body(rhs_func)[2])
-  if (function_as_text == 'rhs <- 0')
+  do_fun_1 <- grepl(pattern = "rhs <- 0", x = function_as_text)
+  do_fun_2 <- grepl(pattern = "rhs <- 1", x = function_as_text)
+  do_fun_3 <- grepl(pattern = "rhs <- 2", x = function_as_text)
+
+  if (do_fun_1)
   {
     lx <- (length(initprobs) - 1)/2
     parsvec <- c(DAISIE_loglik_rhs_precomp(pars,lx))
@@ -1252,7 +1256,7 @@ DAISIE_integrate_const <- function(initprobs,tvec,rhs_func,pars,rtol,atol,method
     #    atol = atol,
     #    method = method
     #  )[2, -1]
-  } else if (function_as_text == 'rhs <- 1')
+  } else if (do_fun_2)
   {
     lx <- (length(initprobs))/4
     parsvec <- c(DAISIE_loglik_rhs_precomp(pars,lx))
@@ -1264,7 +1268,7 @@ DAISIE_integrate_const <- function(initprobs,tvec,rhs_func,pars,rtol,atol,method
                        method,
                        runmod = "daisie_runmod1")
 
-  } else if (function_as_text == 'rhs <- 2')
+  } else if (do_fun_3)
   {
     lx <- (length(initprobs))/3
     parsvec <- c(DAISIE_loglik_rhs_precomp(pars,lx))

diff --git a/README.md b/README.md
@@ -75,10 +75,10 @@ Remotes:
 
 For feature requests or bug-reports or other matters, please submit an [issue](https://github.com/rsetienne/DAISIE/issues/new).
 
-## `git` branching workflow
+## Feature branches
 
  * `master`: build should always pass. [@rsetienne](https://github.com/rsetienne) has control over `develop` to `master` merges.
- * `develop`: merge of topic branches, merge with `master` by [@rsetienne](https://github.com/rsetienne) iff build passes.
+ * `develop`: merge of feature branches, merge with `master` by [@rsetienne](https://github.com/rsetienne) iff build passes.
 
 ## Contributors
 
@@ -106,8 +106,10 @@ For feature requests or bug-reports or other matters, please submit an [issue](h
 
 * Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. https://doi.org/10.32942/osf.io/w5ntf
 
-* Santos Neves, P.\*, Lambert, J. W.\*, Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography. https://doi.org/10.1111/jbi.14519
+* Santos Neves, P.\*, Lambert, J. W.\*, Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography 49: 2091-2104. https://doi.org/10.1111/jbi.14519
 
 * Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. https://doi.org/10.1101/2022.01.13.476210
 
-* Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? Evolution. https://doi.org/10.1093/evolut/qpad006.
+* Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? Evolution. https://doi.org/10.1093/evolut/qpad006
+
+* Michielsen, N. M., Goodman, S. M., Soarimalala, V., van der Geer, A. A. E., Dávalos, L. M., Saville, G. I., Upham, N., Valente, L. (2023). The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar. Nature Communications 14 (14). https://doi.org/10.1038/s41467-022-35215-3
diff --git a/man/DAISIE-package.Rd b/man/DAISIE-package.Rd
diff --git a/src/DAISIE_CS.cpp b/src/DAISIE_CS.cpp
@@ -1,4 +1,4 @@
-// [[Rcpp::plugins(cpp14)]]
+// [[Rcpp::plugins(cpp17)]]
 // [[Rcpp::depends(BH)]]
 
 

diff --git a/src/DAISIE_IW.cpp b/src/DAISIE_IW.cpp
@@ -1,5 +1,6 @@
 //' @export daisie_odeint_iw
 
+// [[Rcpp::plugins(cpp17)]]
 // [[Rcpp::plugins(openmp)]]
 // [[Rcpp::depends(RcppEigen)]]
 

diff --git a/tests/testthat/test-DAISIE_ML1.R b/tests/testthat/test-DAISIE_ML1.R
@@ -2,7 +2,7 @@ context("DAISIE_ML1")
 
 test_that("use", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
-
+  skip_on_cran()
   data(Galapagos_datalist)
   datalist <- Galapagos_datalist
   initparsopt <- c(2.5, 2.7, 20, 0.009, 1.01)
@@ -39,6 +39,7 @@ test_that("use", {
 
 test_that("abuse", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
+  skip_on_cran()
   utils::data(Galapagos_datalist)
   datalist <- Galapagos_datalist
   initparsopt <- c(2.5, 2.7, 20, 0.009, 1.01)

diff --git a/tests/testthat/test-DAISIE_ML2.R b/tests/testthat/test-DAISIE_ML2.R
@@ -1,6 +1,6 @@
 test_that("use", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
-
+  skip_on_cran()
   utils::data(Macaronesia_datalist, package = "DAISIE")
   invisible(capture.output(
     tested_MLE <- DAISIE_ML2(
@@ -59,6 +59,7 @@ test_that("use", {
 
 test_that("abuse", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
+  skip_on_cran()
   expect_error(tested_MLE <- DAISIE:::DAISIE_ML2(
     datalist = "nonsense",
     initparsopt = c(

diff --git a/tests/testthat/test-DAISIE_ML4.R b/tests/testthat/test-DAISIE_ML4.R
@@ -19,6 +19,7 @@ test_that("DAISIE_ML4 is silent and produces correct output", {
 test_that("DAISIE_loglik_all_choosepar4 is silent and produces correct output", {
   utils::data(Galapagos_datalist)
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
+  skip_on_cran()
   # Throws warnings and DLSODES output
   invisible(capture.output(suppressWarnings(
     output <- DAISIE_loglik_all_choosepar4(

diff --git a/tests/testthat/test-DAISIE_MW_ML.R b/tests/testthat/test-DAISIE_MW_ML.R
@@ -1,7 +1,7 @@
 test_that("DAISIE_MW_ML produces correct output", {
 
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
-
+  skip_on_cran()
 
 
   utils::data(archipelagos41)

diff --git a/tests/testthat/test-DAISIE_loglik_CS.R b/tests/testthat/test-DAISIE_loglik_CS.R
@@ -1,5 +1,6 @@
 test_that("DAISIE_loglik_CS_choice produces correct output for CS_version 1", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
+  skip_on_cran()
   pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010)
   pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA, 0.0e+00, 1.0e-04,
              1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01)
@@ -21,6 +22,7 @@ test_that("DAISIE_loglik_CS_choice produces correct output for CS_version 1", {
 test_that("DAISIE_loglik_CS_choice produces correct output for relaxed-rate
           model (CS_version = 2)", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
+  skip_on_cran()
   pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010)
   pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA, 0.0e+00, 1.0e-04,
              1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01)
@@ -46,7 +48,7 @@ test_that("DAISIE_loglik_CS_choice produces correct output for relaxed-rate
 
 test_that("DAISIE_loglik_CS_choice produces same output for CS_version = 0
           (with M = 1) and CS_version = 1 ", {
-
+  skip_on_cran()
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
   pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010)
   pars2 <- c(100, 11, 0, 0, NA, 0.0e+00, 1.0e-04,
@@ -77,6 +79,7 @@ test_that("DAISIE_loglik_CS_choice produces same output for CS_version = 0
 
 test_that("DAISIE_loglik_all produces correct output for relaxed-rate model", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
+  skip_on_cran()
   utils::data(Galapagos_datalist)
   invisible(capture.output(suppressWarnings(
     loglik <- DAISIE::DAISIE_loglik_all(
@@ -98,6 +101,7 @@ test_that("DAISIE_loglik_all produces correct output for relaxed-rate model", {
 
 test_that("DAISIE_loglik produces correct output", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
+  skip_on_cran()
   output <- DAISIE_loglik(pars1 = c(2.061154e-09, 2.683455e+00, 1.000000e+01,
                                     9.332070e-03, 1.010073e+00),
                           pars2 = c(100, 0, 0, 0, NA),
@@ -115,7 +119,7 @@ test_that("DAISIE_loglik produces correct output", {
 test_that("DAISIE_loglik_all produces same output for CS_version 0 and 1 with
           and without conditioning", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
-
+  skip_on_cran()
   utils::data(Galapagos_datalist)
   Galapagos_datalist2 <- Galapagos_datalist
   for(i in 2:9) {
@@ -162,6 +166,7 @@ test_that("DAISIE_loglik_all produces same output for CS_version 0 and 1 with
 test_that("DAISIE_loglik_CS_choice produces equivalent output for ODEINT RKCK54
           and deSolve lsodes", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
+  skip_on_cran()
   pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010)
   pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA, 0.0e+00, 1.0e-04,
              1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01)

diff --git a/tests/testthat/test-DAISIE_loglik_IW_solver.R b/tests/testthat/test-DAISIE_loglik_IW_solver.R
@@ -1,6 +1,6 @@
 test_that("IW and CS loglik is same when K = Inf", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
-
+  skip_on_cran()
   utils::data(Galapagos_datalist, package = "DAISIE")
   pars1 <- c(0.35, 0.3, Inf, 0.001, 0.3)
   pars2 <- c(120, 11, 0, 1)
@@ -51,7 +51,7 @@ test_that("loglik IW various solver options give similar results", {
   # Test is not included in coverage due to issue with running loglik_IW
   # code from covr::package_coverage()
   testthat::skip_on_covr()
-
+  skip_on_cran()
   utils::data(frogs_datalist, package = "DAISIE")
   pars1 <- c(0.2, 0.1, 1000.1, 0.001, 0.3)
   pars2 <- c(40, 11, 0, 0)

diff --git a/tests/testthat/test-integration_DAISIE.R b/tests/testthat/test-integration_DAISIE.R
@@ -63,6 +63,7 @@ test_that("clade specific rate-shift loglik works", {
 test_that("IW and CS loglik is same when K = Inf", {
   skip_if(Sys.getenv("CI") == "" && !(Sys.getenv("USERNAME") == "rampa"),
           message = "Run only on CI")
+  skip_on_cran()
   data(Galapagos_datalist, package = "DAISIE")
   pars1 <- c(0.35, 0.3, Inf, 0.001, 0.3)
   pars2 <- c(80, 11, 1, 0)
@@ -103,6 +104,7 @@ test_that("IW and CS loglik is same when K = Inf", {
 test_that("DAISIE_ML simple case works", {
   skip_if(Sys.getenv("CI") == "" && !(Sys.getenv("USERNAME") == "rampa"),
           message = "Run only on CI")
+  skip_on_cran()
   expected_mle <- data.frame(
     lambda_c = 2.583731356303842,
     mu = 2.708828027514834,
@@ -131,6 +133,7 @@ test_that("DAISIE_ML simple case works", {
 test_that("DAISIE_ML simple case works with zero probability of initial presence", {
   skip_if(Sys.getenv("CI") == "" && !(Sys.getenv("USERNAME") == "rampa"),
           message = "Run only on CI")
+  skip_on_cran()
   expected_mle <- data.frame(
     lambda_c = 2.583731356303842,
     mu = 2.708828027514834,
@@ -190,6 +193,7 @@ test_that("DAISIE_ML simple case works with estimating probability of initial
           presence", {
   skip_if(Sys.getenv("CI") == "" && !(Sys.getenv("USERNAME") == "rampa"),
           message = "Run only on CI")
+  skip_on_cran()
 
   expected_mle <- data.frame(
     lambda_c = 2.54079308283855,