Merge pull request #398 from bjohnso005/biomodelos

v2.0.4 merge Biomodelos

NEWS.md

@@ -1,3 +1,9 @@
+wallace 2.0.4
+=============
+- Added Spanish translation of vignette
+- Updates to v2 vignette
+- `skip_on_cran()` added to several tests
+
 wallace 2.0.3
 =============
 - Fix conditional in test for occs_queryDB

README.md

@@ -43,7 +43,7 @@ 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.

_pkgdown.yml

@@ -11,12 +11,11 @@ navbar:
     menu:
     - text: Tutorial Vignette v2
       href: articles/tutorial-v2.html
+    - text: Tutorial Vignette v2 (ESP)
+      href: articles/tutorial-v2-esp.html
     - text: Module addition
       href: articles/module-addition.html
     - text: -------
-    - text: "Beta Testing"
-    - text: Install instructions
-      href: articles/beta-testing.html
     - text: "Archive"
     - text: Tutorial Vignette v1
       href: articles/tutorial-v1.html

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>")
 )

inst/shiny/Rmd/text_how_to_use.Rmd

@@ -4,7 +4,9 @@ output: html_document
 ---
 
 ### **Overview of** ***Wallace***
-This information is designed to orient the user to the *Wallace* interface. For detailed instructions and a sample walkthrough, please consult the <a href="" target="_blank">vignette</a>.  
+This information is designed to orient the user to the *Wallace* interface. For detailed instructions and a sample walkthrough, please consult the <a href="https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html" target="_blank">vignette</a>.  
+
+*Para obtener instrucciones detalladas y un tutorial de muestra en español, consulte <a href="https://wallaceecomod.github.io/wallace/articles/tutorial-v2-esp.html" target="_blank">la viñeta en español</a>.*
 
 #### **Components and Modules**
 *Wallace* is composed of **Components** – discrete steps in the workflow. Navigate through the components by clicking on the names in the top orange navigation panel. Components need to be run consecutively, but a few are optional (e.g., **Env Space**).  
@@ -38,17 +40,17 @@ Closing the browser window will terminate the Wallace analysis, but R will remai
 #### **References**
 Anderson, R. P. (2015). El modelado de nichos y distribuciones: no es simplemente "clic, clic, clic." [With English and French translations: Modeling niches and distributions: it's not just "click, click, click" and La modélisation de niche et de distributions: ce n'est pas juste "clic, clic, clic"]. *Biogeografía*, 8, 4-27. <a href="https://2278aec0-37af-4634-a250-8bb191f1aab7.filesusr.com/ugd/e41566_e8acb6f9c20c44fa9cd729161582857d.pdf" target="_blank">pdf</a>
 
-Anderson, R.P. (2012). Harnessing the world's biodiversity data: promise and peril in ecological niche modeling of species distributions. *Annals of the New York Academy of Sciences*, 1260(1), 66-80. <a href="https://doi.org/10.1111/j.1749-6632.2011.06440.x" target="_blank">https://doi.org/10.1111/j.1749-6632.2011.06440.x</a>
+Anderson, R.P. (2012). Harnessing the world's biodiversity data: promise and peril in ecological niche modeling of species distributions. *Annals of the New York Academy of Sciences*, 1260(1), 66-80. <a href="https://doi.org/10.1111/j.1749-6632.2011.06440.x" target="_blank">DOI:10.1111/j.1749-6632.2011.06440.x</a>
 
-Franklin, J. (2010). *Mapping species distributions*. Cambridge University Press. <a href="https://doi.org/10.1017/CBO9780511810602" target="_blank">https://doi.org/10.1017/CBO9780511810602</a> 
+Franklin, J. (2010). *Mapping species distributions*. Cambridge University Press. <a href="https://doi.org/10.1017/CBO9780511810602" target="_blank">DOI:10.1017/CBO9780511810602</a> 
 
-Guisan, A., Thuiller, W., & Zimmermann, N. E. (2017). Habitat suitability and distribution models: With applications in R. Cambridge University Press. <a href="https://doi.org/10.1017/9781139028271" target="_blank">https://doi.org/10.1017/9781139028271</a>
+Guisan, A., Thuiller, W., & Zimmermann, N. E. (2017). Habitat suitability and distribution models: With applications in R. Cambridge University Press. <a href="https://doi.org/10.1017/9781139028271" target="_blank">DOI:10.1017/9781139028271</a>
 
-Kass, J.M., Vilela, B., Aiello-Lammens, M.E., Muscarella, R., Merow, C., & Anderson, R.P. (2018). Wallace: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. *Methods in Ecology and Evolution*, 9(4), 1151-1156. <a href="https://doi.org/10.1111/2041-210X.12945" target="_blank">https://doi.org/10.1111/2041-210X.12945</a>
+Kass, J.M., Vilela, B., Aiello-Lammens, M.E., Muscarella, R., Merow, C., & Anderson, R.P. (2018). Wallace: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. *Methods in Ecology and Evolution*, 9(4), 1151-1156. <a href="https://doi.org/10.1111/2041-210X.12945" target="_blank">DOI:10.1111/2041-210X.12945</a>
 
-Peterson, A. T. et al. (2022). ENM2020: A Free Online Course and Set of Resources on Modeling Species’ Niches and Distributions. *Biodiversity Informatics*, 17. <a href="https://doi.org/10.17161/bi.v17i.15016" target="_blank">https://doi.org/10.17161/bi.v17i.15016</a> 
+Peterson, A. T. et al. (2022). ENM2020: A Free Online Course and Set of Resources on Modeling Species’ Niches and Distributions. *Biodiversity Informatics*, 17. <a href="https://doi.org/10.17161/bi.v17i.15016" target="_blank">DOI:10.17161/bi.v17i.15016</a> 
 
 Peterson, A. T., Soberón, J., Pearson, R. G., Anderson, R. P., Martínez-Meyer, E., Nakamura, M., & Araújo, M. B. (2011). *Ecological niches and geographic distributions* (MPB-49). Princeton University Press. <a href="https://press.princeton.edu/books/paperback/9780691136882/ecological-niches-and-geographic-distributions-mpb-49" target="_blank">Princeton University Press</a> 
 
-Zurell, D., Franklin, J., König, C., Bouchet, P.J., Dormann, C.F., Elith, J., Fandos, G., Feng, X., Guillera-Arroita, G., Guisan, A., Lahoz-Monfort, J.J., Leitão, P.J., Park, D.S., Peterson, A.T., Rapacciuolo, G., Schmatz, D.R., Schröder, B., Serra-Diaz, J.M., Thuiller, W., Yates, K.L., Zimmermann,N.E., & Merow, C. (2020). A standard protocol for reporting species distribution models. *Ecography*, 43(9), 1261-1277. <a href="https://doi.org/10.1111/ecog.04960" target="_blank">https://doi.org/10.1111/ecog.04960</a> 
+Zurell, D., Franklin, J., König, C., Bouchet, P.J., Dormann, C.F., Elith, J., Fandos, G., Feng, X., Guillera-Arroita, G., Guisan, A., Lahoz-Monfort, J.J., Leitão, P.J., Park, D.S., Peterson, A.T., Rapacciuolo, G., Schmatz, D.R., Schröder, B., Serra-Diaz, J.M., Thuiller, W., Yates, K.L., Zimmermann,N.E., & Merow, C. (2020). A standard protocol for reporting species distribution models. *Ecography*, 43(9), 1261-1277. <a href="https://doi.org/10.1111/ecog.04960" target="_blank">DOI:10.1111/ecog.04960</a> 
 

tests/testthat/test_envs_ecoClimate.R

@@ -19,6 +19,8 @@ bcScenarioFail='Present'
 
 ##start testing
 test_that('error_checks', {
+  # skip on CRAN
+  skip_on_cran()
   # Skip if cannot download
   skip_if(class(varsEcoClimate) == "try-error")
   ##wrong AOGCM
@@ -40,6 +42,8 @@ test_that('error_checks', {
   })
 
 test_that('output_checks', {
+  # skip on CRAN
+  skip_on_cran()
   # Skip if cannot download
   skip_if(class(varsEcoClimate) == "try-error")
   #output is a rasterstack

tests/testthat/test_envs_worldclim.R

@@ -21,6 +21,8 @@ test_that("error checks", {
 
 ### test output features
 test_that("output type checks", {
+  # skip on CRAN
+  skip_on_cran()
   # the output is a RasterBrick
   expect_is(arcmin10, "RasterStack")
   # the number of layer is the same as specified in the selected variables list

tests/testthat/test_occs_paleoDb.R

@@ -8,7 +8,7 @@ context("paleoDb")
 spName <- "Didelphis virginiana"
 spNameError <- "Panthera onc"
 genus <- "panthera"
-#maximum number of occurences to download
+#maximum number of occurrences to download
 occNum <- 100
 # For PaleobioDB only Holocene is allowed.
 timeInterval <- "Holocene"
@@ -19,7 +19,7 @@ if (Sys.info()['sysname'] != "Windows") {
 }
 
 
-###Test that erorrs check
+###Test that errors check
   ### test if the error messages appear when they are supposed to
 test_that("error checks", {
   # paleobioDB failing in Windows
@@ -56,6 +56,8 @@ test_that("error checks", {
 test_that("output type checks", {
   # paleobioDB failing in Windows
   skip_on_os("windows")
+  # skip on CRAN
+  skip_on_cran()
   #output is a list
   expect_is(occsPaleo, "list")
   #List has two elements
@@ -64,6 +66,8 @@ test_that("output type checks", {
 test_that("output data checks", {
   # paleobioDB failing in Windows
   skip_on_os("windows")
+  # skip on CRAN
+  skip_on_cran()
   # if the original database has records without coordinates OR duplicates:
   if ((TRUE %in% duplicated(occsPaleo$orig[,c('longitude','latitude')]) == TRUE) |
       (NA %in% occsPaleo$orig[,c('longitude','latitude')]) == TRUE){
@@ -93,7 +97,7 @@ test_that("headers check", {
   skip_on_os("windows")
   #
   expect_false('FALSE' %in%  (keyPaleoHeaders %in% names(occsPaleo$orig)))
-  # the headers in the claned table are the ones specified in the function
+  # the headers in the cleaned table are the ones specified in the function
   expect_equal(names(occsPaleo$cleaned),c(keyPaleoHeaders,"pop"))
 })
 

tests/testthat/test_occs_queryDb.R

@@ -124,7 +124,7 @@ test_that("GBIF headers", {
   skip_if(class(out.gbif) == "try-error")
   # the original headers haven't changed
   expect_false('FALSE' %in% (headersGBIF %in% names(out.gbif[[i]]$orig)))
-  # the headers in the claned table are the ones specified in the function
+  # the headers in the cleaned table are the ones specified in the function
   expect_equal(names(out.gbif[[i]]$cleaned),
                c("occID", "scientific_name", "longitude", "latitude", "country",
                  "state_province", "locality", "year", "record_type",
@@ -242,7 +242,7 @@ for (i in 1:length(spNames)) {
 # test_that("Bison headers", {
 #   # the original headers haven't changed
 #   expect_false('FALSE' %in%  (headersBison %in% names(out.bison[[i]]$orig)))
-#   # the headers in the claned table are the ones specified in the function
+#   # the headers in the cleaned table are the ones specified in the function
 #   expect_equal(names(out.bison[[i]]$cleaned),
 #                c("occID", "scientific_name", "longitude", "latitude", "country",
 #                  "state_province", "locality", "year", "record_type","catalog_number",
@@ -295,7 +295,7 @@ headersBien <- c("scrubbed_species_binomial", "longitude", "latitude",
 # test_that("Bien headers", {
 #   # the original headers haven't changed
 #   expect_false('FALSE' %in%  (headersBien %in% names(out.bien[[i]]$orig)))
-#   # the headers in the claned table are the ones specified in the function
+#   # the headers in the cleaned table are the ones specified in the function
 #   expect_equal(names(out.bien[[i]]$cleaned),
 #                c("occID", "scientific_name", "longitude", "latitude", "country",
 #           "state_province", "locality", "year", "record_type", "catalog_number",