From 9e08e2c2fb5c79548b6261d09d4ed206fd22a883 Mon Sep 17 00:00:00 2001 From: Bethany Johnson Date: Tue, 5 Dec 2023 13:51:17 -0500 Subject: [PATCH] [v2.1.1] ecospat bug fix, add license, update maintainer --- DESCRIPTION | 4 ++-- NEWS.md | 6 ++++++ README.md | 4 ++-- inst/shiny/Rmd/text_about.Rmd | 2 +- inst/shiny/Rmd/text_intro_tab.Rmd | 2 +- inst/shiny/Rmd/userReport_intro.Rmd | 2 +- 6 files changed, 13 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index deb19314..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 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/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 5bc29eb4..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. 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.