diff --git a/.Rbuildignore b/.Rbuildignore index b24da460..689873b2 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -12,3 +12,4 @@ cmip5* # worldclim files ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^LICENSE$ diff --git a/DESCRIPTION b/DESCRIPTION index ea48ba86..71785f98 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: wallace -Version: 2.1.0 -Date: 2023-09-25 +Version: 2.1.1 +Date: 2023-12-05 Title: A Modular Platform for Reproducible Modeling of Species Niches and Distributions Description: The 'shiny' application Wallace is a modular platform for @@ -13,14 +13,14 @@ Description: The 'shiny' application Wallace is a modular platform for website: . Authors@R: c(person("Jamie M.", "Kass", email = "jamie.kass@oist.jp", role = "aut"), - person("Gonzalo E.", "Pinilla-Buitrago", email = "gepinillab@gmail.com", role = c("aut", "cre")), + person("Gonzalo E.", "Pinilla-Buitrago", email = "gepinillab@gmail.com", role = "aut"), person("Andrea", "Paz", email = "paz.andreita@gmail.com", role = "aut"), person("Bethany A.", "Johnson", email = "bjohnso005@citymail.cuny.edu", role = "aut"), person("Valentina", "Grisales-Betancur", email = "vgrisale@eafit.edu.co", role = "aut"), person("Dean", "Attali", email = "daattali@gmail.com", role = "aut"), person("Matthew E.", "Aiello-Lammens", email = "matt.lammens@gmail.com", role = "aut"), person("Cory", "Merow", email = "corymerow@gmail.com", role = "aut"), - person("Mary E.", "Blair", email = "mblair1@amnh.org", role = "aut"), + person("Mary E.", "Blair", email = "mblair1@amnh.org", role = c("aut", "cre")), person("Robert P.", "Anderson", email = "randerson@ccny.cuny.edu", role = "aut"), person("Sarah I.", "Meenan", email = "sarah.meenan@gmail.com", role = "ctb"), person("Olivier", "Broennimann", email = "olivier.broennimann@unil.ch", role = "ctb"), diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..f288702d --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/NAMESPACE b/NAMESPACE index 27b427c1..074f9abb 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,6 +4,7 @@ export(clearAll) export(create_module) export(ecoClimate_getdata) export(ecoClimate_select) +export(ecospat.plot.nicheDEV) export(envs_ecoClimate) export(envs_userEnvs) export(envs_worldclim) diff --git a/NEWS.md b/NEWS.md index 316d2669..15bec38d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +wallace 2.1.1 +============= +- Fixed bug in occ density grid & niche overlap +- Updated licensing +- Updated developers & pkg maintainer + wallace 2.1.0 ============= - Removed `rgeos` (package expiring) diff --git a/R/espace_nicheOv.R b/R/espace_nicheOv.R index 5e0824d1..bae7422a 100644 --- a/R/espace_nicheOv.R +++ b/R/espace_nicheOv.R @@ -54,7 +54,7 @@ #' } #' #' @return A list of 4 elements if all is set to TRUE. Elements are overlap -#' (Schoener's D), USE (ecopstat.niche.dyn.index), equiv and simil. +#' (Schoener's D), USE (ecospat.niche.dyn.index), equiv and simil. #' @author Jamie Kass #' @author Olivier Broennimann #' @seealso \code{\link{espace_pca}} \code{\link{espace_occDens}} @@ -80,7 +80,7 @@ espace_nicheOv <- function(z1, z2, iter = 100, equivalency = FALSE, if (equivalency == TRUE) { smartProgress(logger, message = "Calculating niche equivalency...", { nicheOv$equiv <- ecospat::ecospat.niche.equivalency.test( - z1, z2, iter, overlap.alternative = "higher" + z1, z2, rep = 100, overlap.alternative = "higher" ) }) } @@ -88,7 +88,7 @@ espace_nicheOv <- function(z1, z2, iter = 100, equivalency = FALSE, if (similarity == TRUE) { smartProgress(logger, message = "Calculating niche similarity", { nicheOv$simil <- ecospat::ecospat.niche.similarity.test( - z1, z2, iter, overlap.alternative = "higher", rand.type = 1 + z1, z2, rep = 100, overlap.alternative = "higher", rand.type = 1 ) }) } diff --git a/R/espace_occDens.R b/R/espace_occDens.R index ff4ea0b6..528b03b2 100644 --- a/R/espace_occDens.R +++ b/R/espace_occDens.R @@ -48,7 +48,7 @@ #' } #' #' @return Returns a list of 2 lists (one for each species). Each list is an -#' ecospat noche object that contains 10 species specific slots with +#' ecospat niche object that contains 10 species specific slots with #' information outputed by ecospat::grid.clim.dyn. z.uncor is the density of #' occurrence of the species and z.cor the occupancy of the environment by #' the species. It has the input parameters as individual slots. diff --git a/R/helper_functions.R b/R/helper_functions.R index 9faa257f..518771de 100644 --- a/R/helper_functions.R +++ b/R/helper_functions.R @@ -311,6 +311,50 @@ remEnvsValsNA <- function(occs, occsEnvsVals, spN, logger) { }) } +####################### # +# ESPACE # +####################### # +#' @title ecospat.plot.nicheDEV +#' @description For internal use. Plot occ density +#' @param z A gridclim object for the species distribution created by ecospat.grid.clim.dyn()/espace_occDens(). +#' @param title A title for the plot. +#' @param name.axis1 A label for the first axis. +#' @param name.axis2 A label for the second axis. +#' @param cor Correct the occurrence densities of the species by the prevalence of the environments in its range (TRUE = yes, FALSE = no). +#' @keywords internal +#' @export +ecospat.plot.nicheDEV <- function(z, title = "", name.axis1 = "Axis 1", name.axis2 = "Axis 2", cor = FALSE) { + if (is.null(z$y)) { + R <- length(z$x) + x <- z$x + xx <- sort(rep(1:length(x), 2)) + if (cor == FALSE) + y1 <- z$z.uncor/max(z$z.uncor) + if (cor == TRUE) + y1 <- z$z.cor/max(z$z.cor) + Y1 <- z$Z/max(z$Z) + yy1 <- sort(rep(1:length(y1), 2))[-c(1:2, length(y1) * 2)] + YY1 <- sort(rep(1:length(Y1), 2))[-c(1:2, length(Y1) * 2)] + plot(x, y1, type = "n", xlab = name.axis1, ylab = "density of occurrence") + graphics::polygon(x[xx], c(0, y1[yy1], 0, 0), col = "grey") + graphics::lines(x[xx], c(0, Y1[YY1], 0, 0)) + } + if (!is.null(z$y)) { + if (cor == FALSE) + terra::plot(z$z.uncor,col=grDevices::gray(100:0 / 100),legend=FALSE, xlab = name.axis1, + ylab = name.axis2,mar = c(3.1,3.1,2.1,3.1)) + if (cor == TRUE) + terra::plot(z$z.cor,col=grDevices::gray(100:0 / 100),legend=FALSE, xlab = name.axis1, + ylab = name.axis2,mar = c(3.1,3.1,2.1,3.1)) + terra::contour( + z$Z, add = TRUE, levels = stats::quantile(z$Z[z$Z > 0], c(0, 0.5)), + drawlabels = FALSE, lty = c(1, 2) + ) + } + title(title) +} +# end of espace. BAJ added 10/31/2023 after ecospat.plot.niche() from ecospat 4.0.0 wasn't working + ####################### # # VISUALIZE & TRANSFER # ####################### # diff --git a/R/penvs_bgExtent.R b/R/penvs_bgExtent.R index 79b31ad9..d96a7d2d 100644 --- a/R/penvs_bgExtent.R +++ b/R/penvs_bgExtent.R @@ -29,6 +29,7 @@ #' @return A SpatialPolygons object that contains all occurrences from occs #' @author Jamie Kass #' @author Gonzalo E. Pinilla-Buitrago +#' @author Bethany A. Johnson # @note #' @seealso \code{\link{penvs_userBgExtent}}, \code{\link{penvs_drawBgExtent}}, diff --git a/R/penvs_drawBgExtent.R b/R/penvs_drawBgExtent.R index 75c3935e..5adafa74 100644 --- a/R/penvs_drawBgExtent.R +++ b/R/penvs_drawBgExtent.R @@ -42,6 +42,7 @@ #' @author Jamie Kass #' @author Gonzalo E. Pinilla-Buitrago +#' @author Bethany A. Johnson # @note #' @seealso \code{\link{penvs_userBgExtent}}, \code{\link{penvs_bgExtent}}, #' \code{\link{penvs_bgMask}} , \code{\link{penvs_bgSample}} diff --git a/R/penvs_userBgExtent.R b/R/penvs_userBgExtent.R index 32184233..1c9ecc36 100644 --- a/R/penvs_userBgExtent.R +++ b/R/penvs_userBgExtent.R @@ -39,6 +39,7 @@ #' @author Jamie Kass #' @author Gonzalo E. Pinilla-Buitrago #' @author Andrea Paz +#' @author Bethany A. Johnson # @note #' @seealso \code{\link{penvs_drawBgExtent}}, \code{\link{penvs_bgExtent}}, diff --git a/R/xfer_draw.R b/R/xfer_draw.R index c0819750..be98e58b 100644 --- a/R/xfer_draw.R +++ b/R/xfer_draw.R @@ -34,6 +34,7 @@ #' larger than specified if drawBgBuf > 0. #' @author Gonzalo Pinilla +#' @author Bethany A. Johnson # @note #' @seealso \code{\link{xfer_userEnvs}} #' @export diff --git a/R/xfer_userExtent.R b/R/xfer_userExtent.R index fa8dd66d..08fd5e00 100644 --- a/R/xfer_userExtent.R +++ b/R/xfer_userExtent.R @@ -33,6 +33,7 @@ #' @author Jamie Kass #' @author Gonzalo E. Pinilla-Buitrago #' @author Andrea Paz +#' @author Bethany A. Johnson #' @seealso \code{\link{penvs_drawBgExtent}}, \code{\link{penvs_bgExtent}}, #' \code{\link{penvs_bgMask}} , \code{\link{penvs_bgSample}} #' @export diff --git a/README.md b/README.md index fbeab92d..468332ea 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ [![R-CMD-check](https://github.com/wallaceEcoMod/wallace/workflows/R-CMD-check/badge.svg)](https://github.com/wallaceEcoMod/wallace/actions) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![CRAN version](http://www.r-pkg.org/badges/version/wallace)](https://CRAN.R-project.org/package=wallace) [![downloads](https://cranlogs.r-pkg.org:443/badges/grand-total/wallace?color=orange)](https://cranlogs.r-pkg.org:443/badges/grand-total/wallace?color=orange) -# Wallace (v2.1.0) +# Wallace (v2.1.1) *Wallace* is a modular platform for reproducible modeling of species niches and distributions, written in R. The application guides users through a complete analysis, from the acquisition of data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface. @@ -27,7 +27,7 @@ run_wallace() Please make sure you have installed the latest versions of both R (Mac OS, Windows) and RStudio (Mac OS / Windows: choose the free version). #### How to run Maxent with maxent.jar -*Wallace* v2.1.0 includes two options to run Maxent models: maxnet and maxent.jar. The former, which is an R implementation and fits the model with the package `glmnet`, is now the default and does not require the package `rJava` (see Phillips et al. 2017). The latter, which is the Java implementation, runs the `maxent()` function in the package `dismo`. This function requires the user to place the `maxent.jar` file in the `/java` directory of the `dismo` package root folder. You can download Maxent here, and locate `maxent.jar`, which is the Maxent program itself, in the downloaded folder. You can find the directory path to `dismo/java` by running `system.file('java', package="dismo")` at the R console. Simply copy `maxent.jar` and paste it into this folder. If you try to run Maxent in *Wallace* without the file in place, you will get a warning message in the log window and Maxent will not run. +*Wallace* v2.1.1 includes two options to run Maxent models: maxnet and maxent.jar. The former, which is an R implementation and fits the model with the package `glmnet`, is now the default and does not require the package `rJava` (see Phillips et al. 2017). The latter, which is the Java implementation, runs the `maxent()` function in the package `dismo`. This function requires the user to place the `maxent.jar` file in the `/java` directory of the `dismo` package root folder. You can download Maxent here, and locate `maxent.jar`, which is the Maxent program itself, in the downloaded folder. You can find the directory path to `dismo/java` by running `system.file('java', package="dismo")` at the R console. Simply copy `maxent.jar` and paste it into this folder. If you try to run Maxent in *Wallace* without the file in place, you will get a warning message in the log window and Maxent will not run. ### Potential Issues diff --git a/inst/shiny/Rmd/text_about.Rmd b/inst/shiny/Rmd/text_about.Rmd index d8c89ba4..55384603 100644 --- a/inst/shiny/Rmd/text_about.Rmd +++ b/inst/shiny/Rmd/text_about.Rmd @@ -7,7 +7,7 @@ output: html_document logo -Welcome to *Wallace*, a flexible application for reproducible ecological modeling, built for community expansion. The current version of *Wallace* (v2.1.0) steps the user through a full niche/distribution modeling analysis, from data acquisition to visualizing results. +Welcome to *Wallace*, a flexible application for reproducible ecological modeling, built for community expansion. The current version of *Wallace* (v2.1.1) steps the user through a full niche/distribution modeling analysis, from data acquisition to visualizing results. The application is written in `R` with the web app development package `shiny`. Please find the stable version of *Wallace* on CRAN, and the development version on Github. We also maintain a *Wallace* website that has some basic info, links, and will be updated with tutorial materials in the near future. @@ -47,15 +47,17 @@ For more information and relevant links see our ENM 2020.* -Kass, J.M. and G.E. Pinilla-Buitrago. 18 May 2020. “Wallace Ecological Modeling Application: flexible and reproducible modeling of species’ niches and distributions built for community expansion.” ENM 2020: Online course in ecological niche modeling (Peterson, A. T. editor), Week 19, Talk 2. Watch on YouTube. +Kass, J.M. and G.E. Pinilla-Buitrago. 18 May 2020. “Wallace Ecological Modeling Application: flexible and reproducible modeling of species’ niches and distributions built for community expansion.” ENM 2020: Online course in ecological niche modeling (Peterson, A. T. editor), Week 19, Talk 2. *The following webinar was the "37th Global Online Biodiversity Informatics Seminar" in the Biodiversity Informatics Training Curriculum organized by Town Peterson.* -Kass, J. M. 9 May 2018. "WALLACE: A flexible platform for reproducible modeling of species niches and distributions built for community expansion." Broadcast from the City College of New York, City University of New York. Watch on YouTube. +Kass, J. M. 9 May 2018. "WALLACE: A flexible platform for reproducible modeling of species niches and distributions built for community expansion." Broadcast from the City College of New York, City University of New York. Global Online Seminar #37 - Wallace. -*The following webinar was part of the "Modelado de Distribuciones Potenciales" series, organized by Angela Cuervo.* +*Para seminarios en español, los siguientes seminarios fueron organizados por Angela Cuervo como parte de la serie Modelado de Distribuciones Potenciales y Analisis Espaciales.* -Anderson, R. P. 21 May 2018. "El software Wallace para modelar nichos y distribuciones: Un coche con motor R, volante de ratón y cerebro de humano." Broadcast from the City College of New York, City University of New York. Watch on YouTube. +Paz, A. 3 October 2023. "Wallace EcoMod: Nuevas funcionalidades para aplicaciones en conservación". Seminarios 2023 - Wallace EcoMod + +Anderson, R. P. 21 May 2018. "El software Wallace para modelar nichos y distribuciones: Un coche con motor R, volante de ratón y cerebro de humano." Broadcast from the City College of New York, City University of New York. Analisis espaciales: 2017 - El software Wallace. *For more videos, check out the Wallace EcoMod YouTube channel.* diff --git a/inst/shiny/Rmd/text_intro_tab.Rmd b/inst/shiny/Rmd/text_intro_tab.Rmd index 4d1cd6f5..d8f64e53 100644 --- a/inst/shiny/Rmd/text_intro_tab.Rmd +++ b/inst/shiny/Rmd/text_intro_tab.Rmd @@ -5,7 +5,7 @@ output: html_document #### WORKFLOW -*Wallace* (v2.1.0) currently includes ten components, or steps of a possible workflow. Each component includes two or more modules, which are possible analyses for that step. +*Wallace* (v2.1.1) currently includes ten components, or steps of a possible workflow. Each component includes two or more modules, which are possible analyses for that step. **Components:** diff --git a/inst/shiny/Rmd/userReport_intro.Rmd b/inst/shiny/Rmd/userReport_intro.Rmd index 0db7bac5..06373e82 100644 --- a/inst/shiny/Rmd/userReport_intro.Rmd +++ b/inst/shiny/Rmd/userReport_intro.Rmd @@ -10,7 +10,7 @@ knit_engines$set(asis = function(options) { knitr::opts_chunk$set(message = FALSE, warning = FALSE, eval = FALSE) ``` -Please find below the R code history from your *Wallace* v2.1.0 session. +Please find below the R code history from your *Wallace* v2.1.1 session. You can reproduce your session results by running this R Markdown file in RStudio. diff --git a/inst/shiny/modules/espace_occDens.R b/inst/shiny/modules/espace_occDens.R index 94d47d50..fb517ff6 100644 --- a/inst/shiny/modules/espace_occDens.R +++ b/inst/shiny/modules/espace_occDens.R @@ -66,8 +66,8 @@ espace_occDens_module_server <- function(input, output, session, common) { mSp <- curSp() } req(spp[[mSp]]$occDens) - ecospat::ecospat.plot.niche(spp[[mSp]]$occDens[[sp1]], title = spName(sp1)) - ecospat::ecospat.plot.niche(spp[[mSp]]$occDens[[sp2]], title = spName(sp2)) + ecospat.plot.nicheDEV(spp[[mSp]]$occDens[[sp1]], title = spName(sp1)) + ecospat.plot.nicheDEV(spp[[mSp]]$occDens[[sp2]], title = spName(sp2)) }) } diff --git a/inst/shiny/modules/espace_occDens.Rmd b/inst/shiny/modules/espace_occDens.Rmd index b6c83e40..948e3f7e 100644 --- a/inst/shiny/modules/espace_occDens.Rmd +++ b/inst/shiny/modules/espace_occDens.Rmd @@ -11,8 +11,8 @@ espace_occDens_{{multAbr}} <- espace_occDens( pca = espace_pca_{{multAbr}}) # Plots graphics::par(mfrow = c(1,2)) -ecospat::ecospat.plot.niche(espace_occDens_{{multAbr}}[["{{spName1}}"]], +ecospat.plot.nicheDEV(espace_occDens_{{multAbr}}[["{{spName1}}"]], title = "{{spName1}}") -ecospat::ecospat.plot.niche(espace_occDens_{{multAbr}}[["{{spName2}}"]], +ecospat.plot.nicheDEV(espace_occDens_{{multAbr}}[["{{spName2}}"]], title = "{{spName2}}") ``` diff --git a/inst/shiny/modules/penvs_bgExtent.yml b/inst/shiny/modules/penvs_bgExtent.yml index 5a483838..44b1aa9e 100644 --- a/inst/shiny/modules/penvs_bgExtent.yml +++ b/inst/shiny/modules/penvs_bgExtent.yml @@ -1,5 +1,5 @@ component: "penvs" short_name: "Select Study Region" long_name: "Select Study Region by Extent" -authors: "Jamie M. Kass, Bruno Vilela, Robert P. Anderson" +authors: "Jamie M. Kass, Bruno Vilela, Bethany A. Johnson, Robert P. Anderson" package: [sp, sf] diff --git a/inst/shiny/modules/penvs_drawBgExtent.yml b/inst/shiny/modules/penvs_drawBgExtent.yml index 582f1c05..802718ba 100644 --- a/inst/shiny/modules/penvs_drawBgExtent.yml +++ b/inst/shiny/modules/penvs_drawBgExtent.yml @@ -1,5 +1,5 @@ component: "penvs" short_name: "Draw Study Region" long_name: "Draw Study Region" -authors: "Gonzalo E. Pinilla-Buitrago, Jamie M. Kass, Bruno Vilela, Robert P. Anderson" +authors: "Gonzalo E. Pinilla-Buitrago, Jamie M. Kass, Bruno Vilela, Bethany A. Johnson, Robert P. Anderson" package: [] diff --git a/inst/shiny/modules/penvs_userBgExtent.yml b/inst/shiny/modules/penvs_userBgExtent.yml index 721f1664..bf604d1a 100644 --- a/inst/shiny/modules/penvs_userBgExtent.yml +++ b/inst/shiny/modules/penvs_userBgExtent.yml @@ -1,5 +1,5 @@ component: "penvs" short_name: "User-specified Study Region" long_name: "User-specified Study Region" -authors: "Jamie M. Kass, Bruno Vilela, Robert P. Anderson" +authors: "Jamie M. Kass, Bruno Vilela, Bethany A. Johnson, Robert P. Anderson" package: [] diff --git a/inst/shiny/modules/xfer_area.yml b/inst/shiny/modules/xfer_area.yml index eda4ecb8..fda7610b 100644 --- a/inst/shiny/modules/xfer_area.yml +++ b/inst/shiny/modules/xfer_area.yml @@ -1,5 +1,5 @@ component: "xfer" short_name: "Transfer to New Extent" long_name: "Transfer to New Extent" -authors: "Jamie M. Kass, Bruno Vilela, Gonzalo E. Pinilla-Buitrago, Robert P. Anderson" +authors: "Jamie M. Kass, Bruno Vilela, Gonzalo E. Pinilla-Buitrago, Bethany A. Johnson, Robert P. Anderson" package: [dismo] diff --git a/inst/shiny/modules/xfer_time.yml b/inst/shiny/modules/xfer_time.yml index d1bd5797..9408ed7c 100644 --- a/inst/shiny/modules/xfer_time.yml +++ b/inst/shiny/modules/xfer_time.yml @@ -1,5 +1,5 @@ component: "xfer" short_name: "Transfer to New Time" long_name: "Transfer to New Time" -authors: "Jamie M. Kass, Bruno Vilela, Gonzalo E. Pinilla-Buitrago, Robert P. Anderson" +authors: "Jamie M. Kass, Bruno Vilela, Gonzalo E. Pinilla-Buitrago, Bethany A. Johnson, Robert P. Anderson" package: [dismo] diff --git a/inst/shiny/modules/xfer_user.yml b/inst/shiny/modules/xfer_user.yml index e0b6c7c9..c6e7017a 100644 --- a/inst/shiny/modules/xfer_user.yml +++ b/inst/shiny/modules/xfer_user.yml @@ -1,5 +1,5 @@ component: "xfer" short_name: "Transfer to User Environments" long_name: "Transfer to User Environments" -authors: "Gonzalo E. Pinilla-Buitrago, Jamie M. Kass, Robert P. Anderson" +authors: "Gonzalo E. Pinilla-Buitrago, Jamie M. Kass, Bethany A. Johnson, Robert P. Anderson" package: [dismo] diff --git a/inst/shiny/server.R b/inst/shiny/server.R index bbdd4dfc..81b6be86 100644 --- a/inst/shiny/server.R +++ b/inst/shiny/server.R @@ -521,8 +521,8 @@ function(input, output, session) { mSp <- curSp() } req(spp[[mSp]]$occDens) - ecospat::ecospat.plot.niche(spp[[mSp]]$occDens[[sp1]], title = spName(sp1)) - ecospat::ecospat.plot.niche(spp[[mSp]]$occDens[[sp2]], title = spName(sp2)) + ecospat.plot.nicheDEV(spp[[mSp]]$occDens[[sp1]], title = spName(sp1)) + ecospat.plot.nicheDEV(spp[[mSp]]$occDens[[sp2]], title = spName(sp2)) dev.off() } ) diff --git a/man/ecospat.plot.nicheDEV.Rd b/man/ecospat.plot.nicheDEV.Rd new file mode 100644 index 00000000..dd6470ef --- /dev/null +++ b/man/ecospat.plot.nicheDEV.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/helper_functions.R +\name{ecospat.plot.nicheDEV} +\alias{ecospat.plot.nicheDEV} +\title{ecospat.plot.nicheDEV} +\usage{ +ecospat.plot.nicheDEV( + z, + title = "", + name.axis1 = "Axis 1", + name.axis2 = "Axis 2", + cor = FALSE +) +} +\arguments{ +\item{z}{A gridclim object for the species distribution created by ecospat.grid.clim.dyn()/espace_occDens().} + +\item{title}{A title for the plot.} + +\item{name.axis1}{A label for the first axis.} + +\item{name.axis2}{A label for the second axis.} + +\item{cor}{Correct the occurrence densities of the species by the prevalence of the environments in its range (TRUE = yes, FALSE = no).} +} +\description{ +For internal use. Plot occ density +} +\keyword{internal} diff --git a/man/espace_nicheOv.Rd b/man/espace_nicheOv.Rd index aca88242..6e905998 100644 --- a/man/espace_nicheOv.Rd +++ b/man/espace_nicheOv.Rd @@ -30,7 +30,7 @@ shiny, otherwise leave the default NULL.} } \value{ A list of 4 elements if all is set to TRUE. Elements are overlap - (Schoener's D), USE (ecopstat.niche.dyn.index), equiv and simil. + (Schoener's D), USE (ecospat.niche.dyn.index), equiv and simil. } \description{ Function evaluates niche overlap between the two species for diff --git a/man/espace_occDens.Rd b/man/espace_occDens.Rd index 31e50444..e686cd2b 100644 --- a/man/espace_occDens.Rd +++ b/man/espace_occDens.Rd @@ -19,7 +19,7 @@ shiny, otherwise leave the default NULL.} } \value{ Returns a list of 2 lists (one for each species). Each list is an - ecospat noche object that contains 10 species specific slots with + ecospat niche object that contains 10 species specific slots with information outputed by ecospat::grid.clim.dyn. z.uncor is the density of occurrence of the species and z.cor the occupancy of the environment by the species. It has the input parameters as individual slots. diff --git a/man/penvs_bgExtent.Rd b/man/penvs_bgExtent.Rd index b0c62ac7..dae0893f 100644 --- a/man/penvs_bgExtent.Rd +++ b/man/penvs_bgExtent.Rd @@ -52,4 +52,6 @@ bgExt <- penvs_bgExtent(occs, bgSel = 'bounding box', bgBuf = 0.5) Jamie Kass Gonzalo E. Pinilla-Buitrago + +Bethany A. Johnson } diff --git a/man/penvs_drawBgExtent.Rd b/man/penvs_drawBgExtent.Rd index 11a311ae..80e84b6d 100644 --- a/man/penvs_drawBgExtent.Rd +++ b/man/penvs_drawBgExtent.Rd @@ -71,4 +71,6 @@ drawBgBf <- penvs_drawBgExtent(polyExtXY = expertDrawPoly, polyExtID = 1, Jamie Kass Gonzalo E. Pinilla-Buitrago + +Bethany A. Johnson } diff --git a/man/penvs_userBgExtent.Rd b/man/penvs_userBgExtent.Rd index f7c27b6a..1de10e7a 100644 --- a/man/penvs_userBgExtent.Rd +++ b/man/penvs_userBgExtent.Rd @@ -71,4 +71,6 @@ Jamie Kass Gonzalo E. Pinilla-Buitrago Andrea Paz + +Bethany A. Johnson } diff --git a/man/xfer_draw.Rd b/man/xfer_draw.Rd index 23eabf69..460debb8 100644 --- a/man/xfer_draw.Rd +++ b/man/xfer_draw.Rd @@ -54,4 +54,6 @@ polygonTest <- xfer_draw(polyXfXY = userDrawPoly, polyXfID, } \author{ Gonzalo Pinilla + +Bethany A. Johnson } diff --git a/man/xfer_userExtent.Rd b/man/xfer_userExtent.Rd index 561d1b17..d4266e8f 100644 --- a/man/xfer_userExtent.Rd +++ b/man/xfer_userExtent.Rd @@ -57,4 +57,6 @@ Jamie Kass Gonzalo E. Pinilla-Buitrago Andrea Paz + +Bethany A. Johnson } diff --git a/tests/testthat/test_espace_occDens.R b/tests/testthat/test_espace_occDens.R index e4719f15..6ed2b0e9 100644 --- a/tests/testthat/test_espace_occDens.R +++ b/tests/testthat/test_espace_occDens.R @@ -52,17 +52,17 @@ test_that("output checks", { ## Test that all outputs but x and y and inputs (including occupancy, density ## and weights) are all raster layers #sp1 - expect_is(TestOccDens[[sp.name1]]$z,'RasterLayer') - expect_is(TestOccDens[[sp.name1]]$Z,'RasterLayer') - expect_is(TestOccDens[[sp.name1]]$z.uncor,'RasterLayer') - expect_is(TestOccDens[[sp.name1]]$z.cor,'RasterLayer') - expect_is(TestOccDens[[sp.name1]]$w,'RasterLayer') + expect_is(TestOccDens[[sp.name1]]$z,'SpatRaster') + expect_is(TestOccDens[[sp.name1]]$Z,'SpatRaster') + expect_is(TestOccDens[[sp.name1]]$z.uncor,'SpatRaster') + expect_is(TestOccDens[[sp.name1]]$z.cor,'SpatRaster') + expect_is(TestOccDens[[sp.name1]]$w,'SpatRaster') #sp2 - expect_is(TestOccDens[[sp.name2]]$z,'RasterLayer') - expect_is(TestOccDens[[sp.name2]]$Z,'RasterLayer') - expect_is(TestOccDens[[sp.name2]]$z.uncor,'RasterLayer') - expect_is(TestOccDens[[sp.name2]]$z.cor,'RasterLayer') - expect_is(TestOccDens[[sp.name2]]$w,'RasterLayer') + expect_is(TestOccDens[[sp.name2]]$z,'SpatRaster') + expect_is(TestOccDens[[sp.name2]]$Z,'SpatRaster') + expect_is(TestOccDens[[sp.name2]]$z.uncor,'SpatRaster') + expect_is(TestOccDens[[sp.name2]]$z.cor,'SpatRaster') + expect_is(TestOccDens[[sp.name2]]$w,'SpatRaster') }) diff --git a/wallace b/wallace new file mode 100644 index 00000000..e69de29b