Merge pull request #141 from rsetienne/develop

v4.1.1
rsetienne · Apr 20, 2022 · 3667412 · 3667412
2 parents a207782 + 2a374d1
commit 3667412
Show file tree

Hide file tree

Showing 6 changed files with 14 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 4.1.0
-Date: 2022-04-13
+Version: 4.1.1
+Date: 2022-04-14
 Depends: R (>= 3.5.0)
 biocViews:
 SystemRequirements: C++14

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# DAISIE 4.1.1
+
+* Correctly use `is.data.frame()` rather than `class(foo) == "data.frame"` to satisfy CRAN note.
+
 # DAISIE 4.1.0
 
 * Rework IW simulation code to:

diff --git a/R/DAISIE-package.R b/R/DAISIE-package.R
@@ -14,7 +14,9 @@
 #' \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. (2021).The robustness of a simple dynamic model of island biodiversity to geological and eustatic change. bioRxiv 2021.07.26.453064. \doi{10.1101/2021.07.26.453064}.\cr
+#' \item Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2021).The robustness of a simple dynamic model of island biodiversity to geological and eustatic change. bioRxiv. \doi{10.1101/2021.07.26.453064}.\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. (2022). A simple island biodiversity model is robust to trait dependence in diversification and colonization rates. biRrxiv. \doi{10.1101/2022.01.01.474685}.\cr
 #' }
 #' @keywords internal
 #' @import Rcpp

diff --git a/R/DAISIE_plot_age_diversity.R b/R/DAISIE_plot_age_diversity.R
@@ -33,7 +33,7 @@ DAISIE_plot_age_diversity <- function(
   island,
   title = "Clade age vs clade diversity",
   island_age = NA) {
-  if (class(island) == "data.frame") {
+  if (is.data.frame(island)) {
     if (is.na(island_age)) {
       stop("Island age must be specified if the input file is a table")
       }

diff --git a/R/DAISIE_plot_island.R b/R/DAISIE_plot_island.R
@@ -34,7 +34,7 @@
 #'
 #' @export DAISIE_plot_island
 DAISIE_plot_island <- function (island, island_age = NA) {
-  if (class(island) == "data.frame") {
+  if (is.data.frame(island)) {
     if (is.na(island_age)) {
       stop("Island age must be specified if the input file is a table")
       }

diff --git a/man/DAISIE-package.Rd b/man/DAISIE-package.Rd