Merge pull request #73 from goldingn/master

inline with modules, and tied to a specific version, ready to be tagged
zoonproject · Aug 14, 2015 · 50f39bd · 50f39bd
2 parents 1b77474 + d2a9bea
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,10 +2,9 @@ Package: zoon
 Type: Package
 Title: Reproducible, accessible & shareable species distribution modelling
     in R.
-Version: 0.3
-Date: 2014-08-04
-Author: Tim Lucas, Nick Golding, Greg McInerny, Emiel van Loon
-Maintainer: Tim Lucas <[email protected]>
+Version: 0.3.1
+Author: Tim Lucas, Nick Golding, Tom August, Greg McInerny, Emiel van Loon
+Maintainer: Tom August <[email protected]>
 Description: A package for reproducible species distribution modelling. The
     package reads user submitted modules from an online repository, runs full
     SDM workflows and returns output that is fully reproducible.
@@ -18,7 +17,8 @@ Imports:
     httpuv,
     dismo
 Depends:
-    raster
+    raster,
+    R (>= 3.2.0)
 Suggests:
     knitr,
     testthat

diff --git a/R/DataDocumentation.R b/R/DataDocumentation.R
@@ -28,3 +28,32 @@ NULL
 
 NULL
 
+
+
+#' @name CWBZim
+#' @title Presence/absence of the coffee white stem borer in Zimbabwe 2003
+#' @description This is an example presence/absence dataset for the 
+#' coffee white stem borer \emph{Monochamus leuconotus} P. taken from an
+#' open access dataset on the Dryad data repository.
+#' The data are made available by those authors under a Creative Commons CC0
+#' These data are used in the module CWBZimbabwe which can be used for running
+#' toy presence/absence species distribution models.
+#' @docType data
+#' @format data.frame with five columns, longitude, latitude, value (1 for 
+#'    presence), type (presence) and a column of 1s indicating this is 
+#'    training data not external validation data.
+#' @source Original publication:
+#' Kutywayo D, Chemura A, Kusena W, Chidoko P, Mahoya C (2013) The impact of
+#'  climate change on the potential distribution of agricultural pests: the case
+#'   of the coffee white stem borer (\emph{Monochamus leuconotus} P.) in
+#'    Zimbabwe. PLoS ONE 8(8): e73432.
+#'    Dryad data package:
+#'    Kutywayo D, Chemura A, Kusena W, Chidoko P, Mahoya C (2013) Data from:
+#'    The impact of climate change on the potential distribution of agricultural
+#'     pests: the case of the coffee white stem borer (\emph{Monochamus
+#'      leuconotus} P.) in Zimbabwe. Dryad Digital Repository.
+#'    \url{http://dx.doi.org/10.1371/journal.pone.0073432}
+#' 
+#' @author Nick Golding August 2015
+
+NULL
diff --git a/R/SearchFunctions.R b/R/SearchFunctions.R
@@ -61,7 +61,17 @@ make_url <- function(owner, repo, sha) {
 gh_list_files <- function(owner, repo, ...) {
   token <- github_auth(appname = "zoonproject", key = "945195231bd7edd336c9", secret = 'd43d121439b081db59e5f0852e25712294128e2f')
 
-  sha <- FindNewestCommit(owner, rep, token)
+  # if this is a dev version, find the most recent version of modules
+  if (.sha == 'master') {
+
+    sha <- FindNewestCommit(owner, rep, token)
+
+  } else {
+
+    # otherwise use the target sha for modules
+    sha <- .sha
+
+  }    
 
   req <- GET(make_url(owner, repo, sha), config = list(token = token))
   out <- content(req)

diff --git a/R/zoon.R b/R/zoon.R
@@ -12,6 +12,15 @@
 # A PROTOTYPE FOR REPRODUCIBLE, ACCESSIBLE & SHAREABLE SCIENTIFIC OUTPUTS IN R
 
 
+
+
+# name a specific sha for an state of the modules repo, for tagged
+# versions of zoon, or 'master' for non-tagged versions
+.sha <- 'b1544fbadaa21c41b4b51922ae73e44923b890ed'
+#.sha <- 'master'
+
+
+
 #'Zoon: A package for comparing multple SDM models, good model diagnostics
 #'      and better reproducibility
 #'@name zoon

diff --git a/R/zoonHelpers.R b/R/zoonHelpers.R
@@ -19,9 +19,11 @@ LoadModule <- function(module){
   module <- gsub('"', '', module)
 
   # Create url that matches zoon repo
+  # .sha will vary based on whether this is pegged to a specific version of
+  # modules
   zoonURL <- 
-    paste0('https://raw.githubusercontent.com/zoonproject/modules/master/R/',
-           module, '.R')
+    sprintf('https://raw.githubusercontent.com/zoonproject/modules/%s/R/%s.R',
+            .sha, module)
 
   # If module is a path, load module
   if (file.exists(module)){

diff --git a/README.md b/README.md
@@ -14,23 +14,35 @@ You'll need to be using R version 3.2.0 or higher.
 On Windows:
 
 ```r
-# install the raster package first
-install.packages('raster')
-
 # install the Windows binary of the latest release
-install.packages('https://github.com/zoonproject/zoon/releases/download/0.3/zoon_0.3.zip',
+install.packages('https://github.com/zoonproject/zoon/releases/download/0.3.1/zoon_0.3.1.zip',
                 repos = NULL, method = 'libcurl')
+
+# install dependencies
+install.packages(pkgDepends('zoon')$Depends)
+
+# install imports
+install.packages(unlist(strsplit(gsub(',', '', installed.packages(fields = c('imports'))['zoon','Imports']), '\n'))[-1])
+
+# load zoon
+library(zoon)
 ```
 
 and on OSX or Linux:
 
 ```r
-# install the raster package first
-install.packages('raster')
-
 # install the Windows binary of the latest release
-install.packages('https://github.com/zoonproject/zoon/releases/download/0.3/zoon_0.3.tar.gz',
+install.packages('https://github.com/zoonproject/zoon/releases/download/0.3.1/zoon_0.3.1.tar.gz',
                 repos = NULL, method = 'libcurl')
+
+# install dependencies
+install.packages(pkgDepends('zoon')$Depends)
+
+# install imports
+install.packages(unlist(strsplit(gsub(',', '', installed.packages(fields = c('imports'))['zoon','Imports']), '\n'))[-1])
+
+# load zoon
+library(zoon)
 ```
 
 

diff --git a/data/CWBZim.RData b/data/CWBZim.RData
diff --git a/man/CWBZim.Rd b/man/CWBZim.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/DataDocumentation.R
+\docType{data}
+\name{CWBZim}
+\alias{CWBZim}
+\title{Presence/absence of the coffee white stem borer in Zimbabwe 2003}
+\format{data.frame with five columns, longitude, latitude, value (1 for
+   presence), type (presence) and a column of 1s indicating this is
+   training data not external validation data.}
+\source{
+Original publication:
+Kutywayo D, Chemura A, Kusena W, Chidoko P, Mahoya C (2013) The impact of
+ climate change on the potential distribution of agricultural pests: the case
+  of the coffee white stem borer (\emph{Monochamus leuconotus} P.) in
+   Zimbabwe. PLoS ONE 8(8): e73432.
+   Dryad data package:
+   Kutywayo D, Chemura A, Kusena W, Chidoko P, Mahoya C (2013) Data from:
+   The impact of climate change on the potential distribution of agricultural
+    pests: the case of the coffee white stem borer (\emph{Monochamus
+     leuconotus} P.) in Zimbabwe. Dryad Digital Repository.
+   \url{http://dx.doi.org/10.1371/journal.pone.0073432}
+}
+\description{
+This is an example presence/absence dataset for the
+coffee white stem borer \emph{Monochamus leuconotus} P. taken from an
+open access dataset on the Dryad data repository.
+The data are made available by those authors under a Creative Commons CC0
+These data are used in the module CWBZimbabwe which can be used for running
+toy presence/absence species distribution models.
+}
+\author{
+Nick Golding August 2015
+}
+