SSDM 0.2.1 CRAn release

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SSDM
 Type: Package
 Title: Stacked Species Distribution Modelling
-Version: 0.1.9040
+Version: 0.2.1
 Author: Sylvain Schmitt, Robin Pouteau, Dimitri Justeau, Philippe Birnbaum
 Maintainer: Sylvain Schmitt <[email protected]>
 URL: https://github.com/sylvainschmitt/SSDM

NEWS.Rmd

@@ -59,7 +59,7 @@ output: github_document
 - update in check args
 
 # SSDM 0.1.9031
-- `rgdal`issue on travis due to `test_load_vocc`
+- `rgdal`issue on travis due to `test_load_occ`
 
 # SSDM 0.1.9030
 - `rgdal`issue on travis due to `load_var`

R/Env.R

@@ -12,7 +12,7 @@
 #' @references R.J. Hijmans, C.H. &  Graham (2006) "The  ability  of climate
 #'   envelope  models  to  predict  the  effect  of  climate  change  on species
 #'   distributions." \emph{Global Change Biology} 12:2272-2281
-#'   \url{http://se-server.ethz.ch/staff/af/Fi159/H/Hi082_S.pdf}
+#'   \url{http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2486.2006.01256.x/full}
 #'
 #'   E. Fritsch (2012) "Les sols. Atlas de la Nouvelle-Caledonie (ed. by J.
 #'   Bonvallot, J.-C. Gay and E. Habert)" \emph{IRD-Congres de la

R/gui.R

@@ -6,6 +6,7 @@
 #'   \code{\link[shiny]{runApp}} for more details).
 #' @param host char. The IPv4 address that the application should listen on (see
 #'   \code{\link[shiny]{runApp}} for more details).
+#' @param working.directory char. Directory in which the application will run.
 #'
 #' @return Open a window with a shiny app to use the SSDM package with an
 #'   user-friendly interface.
@@ -20,13 +21,18 @@
 #' }
 #'
 #' @export
-gui <- function (port = getOption("shiny.port"), host = getOption("shiny.host", "127.0.0.1")) {
+gui <- function (port = getOption("shiny.port"),
+                 host = getOption("shiny.host", "127.0.0.1"),
+                 working.directory = getwd()) {
+
   appDir <- system.file("shiny", "gui", package = "SSDM")
   if (appDir == "") {
-    stop("Could not find example directory. Try re-installing `mypackage`.", call. = FALSE)
+    stop("Could not find shiny directory. Try re-installing `SSDM`.", call. = FALSE)
   }
-  assign("working.directory", getwd(), envir = .GlobalEnv)
-  shiny::runApp(appDir, display.mode = "normal", port = port, host = host)
-  ls()
-  rm(working.directory, envir = .GlobalEnv)
+
+  ui <- source(file.path(appDir, 'ui.R'))
+  serverWD <- source(file.path(appDir, 'server.R'))
+  shiny::runApp(shinyApp(ui = ui, server = serverWD(working.directory)),
+                         display.mode = "normal", port = port, host = host)
+  rm(ui, serverWD, envir = .GlobalEnv)
 }

README.Rmd

@@ -4,7 +4,8 @@ output: github_document
 ---
 
 [![Travis-CI Build Status](https://travis-ci.org/sylvainschmitt/SSDM.svg?branch=master)](https://travis-ci.org/sylvainschmitt/SSDM)
-[![CRAN](http://www.r-pkg.org/badges/version/SSDM)](http://cran.rstudio.com/package=SSDM) [![Downloads](http://cranlogs.r-pkg.org/badges/SSDM?color=brightgreen)](http://www.r-pkg.org/pkg/SSDM)
+[![CRAN](https://www.r-pkg.org/badges/version/SSDM)](https://CRAN.R-project.org/package=SSDM) 
+[![Downloads](http://cranlogs.r-pkg.org/badges/SSDM?color=brightgreen)](http://www.r-pkg.org/pkg/SSDM)
 [![Coverage Status](https://img.shields.io/codecov/c/github/sylvainschmitt/SSDM/master.svg)](https://codecov.io/github/sylvainschmitt/SSDM?branch=master)
 [![Research software impact](http://depsy.org/api/package/cran/SSDM/badge.svg)](http://depsy.org/package/r/SSDM)
 
@@ -41,7 +42,7 @@ install.packages("SSDM")
 After installing, **SSDM** package, you can launch the graphical user interface by typing gui() in the console.
 
 <center>[**Click to enlarge**](https://raw.githubusercontent.com/sylvainschmitt/SSDM/master/examples/SSDM.gif)<center>
-![Screenshot](examples/SSDM.gif)
+![Screenshot](https://raw.githubusercontent.com/sylvainschmitt/SSDM/master/examples/SSDM.gif)
 
 # Functionnalities
 

README.md

@@ -1,7 +1,7 @@
 SSDM: Stacked species distribution modelling
 ================
 
-[![Travis-CI Build Status](https://travis-ci.org/sylvainschmitt/SSDM.svg?branch=master)](https://travis-ci.org/sylvainschmitt/SSDM) [![CRAN](http://www.r-pkg.org/badges/version/SSDM)](http://cran.rstudio.com/package=SSDM) [![Downloads](http://cranlogs.r-pkg.org/badges/SSDM?color=brightgreen)](http://www.r-pkg.org/pkg/SSDM) [![Coverage Status](https://img.shields.io/codecov/c/github/sylvainschmitt/SSDM/master.svg)](https://codecov.io/github/sylvainschmitt/SSDM?branch=master) [![Research software impact](http://depsy.org/api/package/cran/SSDM/badge.svg)](http://depsy.org/package/r/SSDM)
+[![Travis-CI Build Status](https://travis-ci.org/sylvainschmitt/SSDM.svg?branch=master)](https://travis-ci.org/sylvainschmitt/SSDM) [![CRAN](https://www.r-pkg.org/badges/version/SSDM)](https://CRAN.R-project.org/package=SSDM) [![Downloads](http://cranlogs.r-pkg.org/badges/SSDM?color=brightgreen)](http://www.r-pkg.org/pkg/SSDM) [![Coverage Status](https://img.shields.io/codecov/c/github/sylvainschmitt/SSDM/master.svg)](https://codecov.io/github/sylvainschmitt/SSDM?branch=master) [![Research software impact](http://depsy.org/api/package/cran/SSDM/badge.svg)](http://depsy.org/package/r/SSDM)
 
 SSDM is a package to map species richness and endemism based on stacked species distribution models (SSDM). Individual SDMs can be created using a single or multiple algorithms (ensemble SDMs). For each species, an SDM can yield a habitat suitability map, a binary map, a between-algorithm variance map, and can assess variable importance, algorithm accuracy, and between-algorithm correlation. Methods to stack individual SDMs include summing individual probabilities and thresholding then summing. Thresholding can be based on a specific evaluation metric or by drawing repeatedly from a Bernouilli distribution. The SSDM package also provides a user-friendly interface `gui`.
 
@@ -41,7 +41,7 @@ After installing, **SSDM** package, you can launch the graphical user interface
 <center>
 [**Click to enlarge**](https://raw.githubusercontent.com/sylvainschmitt/SSDM/master/examples/SSDM.gif)
 <center>
-![Screenshot](examples/SSDM.gif)
+![Screenshot](https://raw.githubusercontent.com/sylvainschmitt/SSDM/master/examples/SSDM.gif)
 
 Functionnalities
 ================

cran-comment.md

@@ -4,15 +4,21 @@
 * win-builder (devel and release)
 
 ## R CMD check results
-There were no ERRORs, WARNINGs or NOTEs.
+There were no ERRORs or WARNINGs.
+
+There was one NOTE:
+Possibly mis-spelled words in DESCRIPTION:
+  SDM (11:73)
+  SDMs (10:53, 11:45, 14:56)
+  SSDM (10:34, 17:23)
+  Thresholding (15:61)
+  endemism (9:49)
+  thresholding (15:34)
+
+Those are scientific correctly spelled words of species distribution modelling field (SDM). It follows litterature included in pacakge documentation.
 
 ## Resubmission
 This is a resubmission. In this version I have:
 
-* Remove the term package in the first sentence of Description field in DESCRIPTION
-
-* Actualized Date field in DESCRIPTION to today
-
-* Import following functions in NAMESPACE : aggregate.data.frame arrows barplot cor glm glm.control heat.colors is.raster legend lsf.str rainbow rbinom read.csv read.csv2 runif sd tail terrain.colors var write.csv
-
-* Unactivated examples with an elapsed time > 5s
+* Fixed CRAN URL canonical form in README
+* Fixed reported bug on graphic user interface which was broken (on of the main functionality of the package) without assignment to global environment (following recommendations of Joe Chang https://github.com/rstudio/shiny/issues/237#issuecomment-288244875)