diff --git a/DESCRIPTION b/DESCRIPTION index 9e81a0ec..8e6cf02e 100644 --- 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 index ff6ed81e..8fbf6be0 100644 --- 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 index 857a5bd8..66572b99 100644 --- 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 index 026d5266..f3248cb8 100644 --- 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 index 6119734e..fca05d85 100644 --- 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 index 521c67c5..9260d5d4 100644 --- a/man/DAISIE-package.Rd +++ b/man/DAISIE-package.Rd @@ -23,7 +23,9 @@ Cladogenesis and immigration rates can be dependent on diversity. \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 } } \seealso{