[v2.0.4+] Changes for CRAN

README.md

@@ -44,7 +44,7 @@ If PDF downloading of session code is not working for you, please follow the fol
      - Step 3: To set this path variable run: `Sys.setenv(PATH=paste(Sys.getenv("PATH"),"C:/Program Files/MiKTeX 2.9/miktex/bin/x64/",sep=";"))`.
 
 #### Windows Users: Only for Github installation
-If you are using Windows, please download and install <a href="https://cran.r-project.org/bin/windows/Rtools/" target="_blank">RTools</a> before installing the `devtools` package. After you install RTools, please make sure you add "C:\Rtools\bin" to your PATH variable (instructions <a href="https://stackoverflow.com/a/29480538/1274346" target="_blank">here</a>). Additionally, when using `devtools` on Windows machines, there is a known <a href="https://github.com/r-lib/devtools/issues/1298" target="_blank">bug</a> that sometimes results in the inability to download all package dependencies. If this happens to you, please install the packages and their dependencies directly from CRAN.
+If you are using Windows, please download and install <a href="https://cran.r-project.org/bin/windows/Rtools/" target="_blank">RTools</a> before installing the `devtools` package. After you install RTools, please make sure you add "C:\Rtools\bin" to your PATH variable (instructions <a href="https://stackoverflow.com/questions/29129681/create-zip-file-error-running-command-had-status-127/29480538#29480538" target="_blank">here</a>). Additionally, when using `devtools` on Windows machines, there is a known <a href="https://github.com/r-lib/devtools/issues/1298" target="_blank">bug</a> that sometimes results in the inability to download all package dependencies. If this happens to you, please install the packages and their dependencies directly from CRAN.
 
 #### Any other problems with install_github()
 Although the recommended way to install is through CRAN, if you are trying to install the Github version and are having problems, follow these steps.

inst/CITATION

@@ -1,32 +1,32 @@
 citHeader("To cite wallace in publications use:")
 
-citEntry(
-  entry    = "Article",
+bibentry(
+  bibtype    = "Article",
   title    = "wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions",
-  author   = personList(
-    as.person("J. M. Kass"),
-    as.person("G. E. Pinilla-Buitrago"),
-    as.person("A. Paz"),
-    as.person("B. A. Johnson"),
-    as.person("V. Grisales-Betancur"),
-    as.person("S. I. Meenan"),
-    as.person("D. Attali"),
-    as.person("O. Broennimann"),
-    as.person("P. J. Galante"),
-    as.person("B. S. Maitner"),
-    as.person("H. L. Owens"),
-    as.person("S. Varela"),
-    as.person("M. E. Aiello-Lammens"),
-    as.person("C. Merow"),
-    as.person("M. E. Blair"),
-    as.person("R. P. Anderson")
+  author   = c(
+    person("J. M. Kass"),
+    person("G. E. Pinilla-Buitrago"),
+    person("A. Paz"),
+    person("B. A. Johnson"),
+    person("V. Grisales-Betancur"),
+    person("S. I. Meenan"),
+    person("D. Attali"),
+    person("O. Broennimann"),
+    person("P. J. Galante"),
+    person("B. S. Maitner"),
+    person("H. L. Owens"),
+    person("S. Varela"),
+    person("M. E. Aiello-Lammens"),
+    person("C. Merow"),
+    person("M. E. Blair"),
+    person("R. P. Anderson")
   ),
   journal  = "Ecography",
-  year     = "2022",
-  volume   = "",
+  year     = "2023",
+  volume   = "2023(3)",
   number   = "e06547",
-  pages    = "",
-  url      = "",
+  pages    = "1-9",
+  url      = "https://onlinelibrary.wiley.com/doi/full/10.1111/ecog.06547",
   textVersion =
-  paste("Kass, J.M., Pinilla-Buitrago, G.E., Paz, A., Johnson, B.A., Grisales-Betancur, V., Meenan, S.I., Attali, D., Broennimann, O., Galante, P.J., Maitner, B.S., Owens, H., Varela, S., Aiello-Lammens, Merow, C., M.E., Blair, M.E. & Anderson, R.P. (2022). wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions. Ecography, e06547. <https://doi.org/10.1111/ecog.06547>")
+  paste("Kass, J.M., Pinilla-Buitrago, G.E., Paz, A., Johnson, B.A., Grisales-Betancur, V., Meenan, S.I., Attali, D., Broennimann, O., Galante, P.J., Maitner, B.S., Owens, H., Varela, S., Aiello-Lammens, Merow, C., M.E., Blair, M.E. & Anderson, R.P. (2023). wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions. Ecography, e06547. <https://doi.org/10.1111/ecog.06547>")
 )

vignettes/tutorial-v2-esp.Rmd

@@ -3,7 +3,7 @@ title: "Tutorial de Wallace Aplicación de modelado Ecológico v2.0"
 author: 
 - Bethany A. Johnson, Gonzalo E. Pinilla-Buitrago, Andrea Paz, Jamie M. Kass, Sarah I. Meenan, Robert P. Anderson
 - Traducción al español por Andrea Paz y Bethany Johnson
-date: "11 March 2023"
+date: "2023-03-11"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Tutorial de Wallace Aplicación de modelado Ecológico v2.0}

vignettes/tutorial-v2.Rmd

@@ -1,7 +1,7 @@
 ---
 title: "Wallace Ecological Modeling Application v2.0 Vignette"
 author: Bethany A. Johnson, Gonzalo E. Pinilla-Buitrago, Andrea Paz, Jamie M. Kass, Sarah I. Meenan, Robert P. Anderson
-date: "4/18/2022; updated 03/11/2023"
+date: "2022-04-18; updated 2023-03-11"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Wallace Ecological Modeling Application v2.0 Vignette}
@@ -101,7 +101,7 @@ knitr::include_graphics("vignette_img/orientation_2.png")
 
 (**1**) These are the components. You will be stepping sequentially through them. *Wallace v2* now includes a Support button (**1a**), which links to the Google Group, email, website, and the Github page to report issues, as well as the quit button (**1b**), which will end the session.\
 (**2**) This is the toolbar with all the user interface controls, such as buttons, text inputs, etc. You can see that the module *Query Database (Present)* is currently selected. You'll see that two other modules exist for this component: *Query Database (Paleo)* and *User-specified*. This last module lets you upload your own occurrence data. Try choosing it instead and notice that the toolbar changes, then click back to *Query Database (Present)*.\
-Both the **Component** and *Module* have queestion mark buttons (?) next to the title text. Clicking these will link to the respective guidance texts.\
+Both the **Component** and *Module* have question mark buttons (?) next to the title text. Clicking these will link to the respective guidance texts.\
 Within this toolbar, you can find the module name and the `R` packages it uses (**2a**), as well as the control panel for the selected module (**2b**). Modules can be contributed by other researchers and the developers; CRAN links and documentation are at the bottom.\
 (**3**) The right side is the visualization space. Any functions performed will trigger a message in the log window (**3a**). This window will also display any error messages. *Wallace v2.0.4* now allows the user to load multiple species. If multiple species are loaded, toggle and select between species using the species drop-down menu (**3b**).\
 The visualization space includes several tabs (**3c**), including an interactive map, occurrence records table, results window, model and component guidance text windows, and a tab for saving outputs and the current session.\