Merge pull request #205 from jread-usgs/master

v1.0.0

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: geoknife
 Type: Package
-Title: Geo-web processing of gridded data
-Version: 0.12.2
-Date: 2013-05-26
+Title: Web-processing of large gridded datasets
+Version: 1.0.0
+Date: 2015-10-02
 Authors@R: c( person("Jordan", "Read", role = c("aut","cre"),
     email = "[email protected]"),
     person("Jordan", "Walker", role = c("aut"),
@@ -15,19 +15,28 @@ Authors@R: c( person("Jordan", "Read", role = c("aut","cre"),
     email = "[email protected]"),
     person("Luke", "Winslow", role = c("aut"),
     email = "[email protected]"))
-Description: Methods for geo-web processing of gridded data via the Geo Data
-    Portal (cida.usgs.gov/gdp).
-License: file LICENSE
+Description: The geoknife R package processes gridded datasets found on the 
+  U.S. Geological Survey Geo Data Portal web application or elsewhere, 
+  using a web-enabled workflow that eliminates the need to download and store 
+  large datasets that are reliably hosted on the Internet. The package provides 
+  access to several data subset and summarization algorithms that are available 
+  on remote web processing servers.
+License: CC0
+URL: https://github.com/USGS-R/geoknife
+BugReports: https://github.com/USGS-R/geoknife/issues
 Copyright: This software is in the public domain because it contains materials
     that originally came from the United States Geological Survey, an agency of
     the United States Department of Interior. For more information, see the
     official USGS copyright policy at
     http://www.usgs.gov/visual-id/credit_usgs.html#copyright
+Depends:
+    R (>= 3.0)
 Imports:
     XML,
     methods,
     httr,
-    sp
+    sp,
+    utils
 Suggests:
     testthat,
     xtable,

NAMESPACE

@@ -91,3 +91,5 @@ importFrom(sp,Polygon)
 importFrom(sp,Polygons)
 importFrom(sp,SpatialPolygons)
 importFrom(sp,coordinates)
+importFrom(utils,packageVersion)
+importFrom(utils,read.table)

R/01-webdata-obj.R

@@ -1,7 +1,4 @@
 pkg.env <- new.env()
-.onAttach <- function(libname, pkgname) {
-  packageStartupMessage("This information is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The information has not received final approval by the U.S. Geological Survey (USGS) and is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the information. Although this software program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.")
-}
 .onLoad <- function(libname, pkgname){
   setJobState()
 }

R/03-geojob-obj.R

@@ -4,6 +4,7 @@
 #' @slot id job identifier
 #' @slot package.version the version of the geoknife package
 #' @slot algorithm.version the version of the algorithm used for processing
+#' @importFrom utils packageVersion
 #' @rdname geojob-class
 setClass(
   Class = "geojob",

R/parseTimeseries.R

@@ -11,6 +11,7 @@
 #'@keywords methods
 #'@author Luke A. Winslow, Jordan S. Read
 #'@export
+#'@importFrom utils read.table
 #'@examples
 #'local_file <- system.file('extdata','tsv_linear_ring.tsv', package = 'geoknife')
 #'output <- parseTimeseries(local_file, delim = '\t')

README.md

@@ -1,5 +1,5 @@
-`geoknife` package version 0.12.2
-=================================
+`geoknife` package version 1.0.0
+================================
 
 [![Build status](https://ci.appveyor.com/api/projects/status/0iacmg82mp50426o/branch/master)](https://ci.appveyor.com/project/jread-usgs/geoknife/branch/master) [![Build Status](https://travis-ci.org/USGS-R/geoknife.svg)](https://travis-ci.org/USGS-R/geoknife) [![Coverage Status](https://coveralls.io/repos/USGS-R/geoknife/badge.svg)](https://coveralls.io/r/USGS-R/geoknife) Tools for geo-web processing of gridded data via the [Geo Data Portal](http://cida.usgs.gov/gdp/ "Geo Data Portal"). `geoknife` slices up gridded data according to overlap with irregular features, such as watersheds, lakes, points, etc. The result is subsetted data in plain text, NetCDF, geotiff or other formats.
 <p align="center">
@@ -80,7 +80,7 @@ check(job)
     ## [1] "Process successful"
     ## 
     ## $URL
-    ## [1] "http://cida.usgs.gov:80/gdp/process/RetrieveResultServlet?id=e8677c0b-9e16-4b97-8bcb-645569750b0fOUTPUT"
+    ## [1] "http://cida.usgs.gov:80/gdp/process/RetrieveResultServlet?id=d5798a2e-0ea0-4ac2-89f2-c9cca72b41ccOUTPUT"
     ## 
     ## $statusType
     ## [1] "ProcessSucceeded"

inst/CITATION

@@ -0,0 +1,15 @@
+citHeader("To cite the geoknife package in publications use:")
+citEntry(entry = "Article", 
+    author = personList(
+        as.person("Jordan S. Read"), 
+        as.person("Jordan I. Walker"), 
+        as.person("Alison Appling"), 
+		as.person("David L. Blodgett"),
+		as.person("Emily K. Read"),
+		as.person("Luke A. Winslow")), 
+    title = "geoknife: Reproducible web-processing of large gridded datasets", 
+    journal = "Ecography", 
+    year = "in press", 
+    doi = "doi:10.1111/ecog.01880", 
+    url = "http://onlinelibrary.wiley.com/doi/10.1111/ecog.01880/abstract", 
+    textVersion = paste("Read JS, JI Walker, A Appling, DL Blodgett, EK Read, LA Winslow. in press. geoknife: Reproducible web-processing of large gridded datasets. Ecography. doi:10.1111/ecog.01880"))

inst/doc/geoknife.html

@@ -71,7 +71,7 @@
 <div id="header">
 <h1 class="title">geoknife package</h1>
 <h4 class="author"><em>Jordan Read</em></h4>
-<h4 class="date"><em>26 August, 2015</em></h4>
+<h4 class="date"><em>02 October, 2015</em></h4>
 </div>
 
 <div id="TOC">
@@ -364,32 +364,23 @@ <h3>query function for <code>webgeom</code></h3>
 <p>The <code>query</code> function on <code>webgeom</code> can be used to find possible inputs for each public field (other than <code>version</code> and <code>url</code> currently):</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">query</span>(stencil, <span class="st">'geoms'</span>)</code></pre></div>
 <pre><code>##  [1] &quot;sample:Alaska&quot;                  
-##  [2] &quot;sample:CONUS_Climate_Divisions&quot; 
-##  [3] &quot;derivative:CONUS_States&quot;        
-##  [4] &quot;sample:CONUS_states&quot;            
-##  [5] &quot;sample:CSC_Boundaries&quot;          
-##  [6] &quot;derivative:FWS_LCC&quot;             
-##  [7] &quot;sample:FWS_LCC&quot;                 
-##  [8] &quot;upload:HRU107_C2_copy1b&quot;        
-##  [9] &quot;derivative:wbdhu8_alb_simp&quot;     
-## [10] &quot;derivative:Level_III_Ecoregions&quot;
-## [11] &quot;derivative:NCA_Regions&quot;         
-## [12] &quot;upload:PheasBR_SubBasins_V04&quot;   
-## [13] &quot;draw:Pullman&quot;                   
-## [14] &quot;upload:STH113_SubBasins&quot;        
-## [15] &quot;upload:STH113_SubBasins_2&quot;      
-## [16] &quot;derivative:US_Counties&quot;         
-## [17] &quot;draw:UpperSkagit&quot;               
-## [18] &quot;upload:buff4dennis&quot;             
-## [19] &quot;upload:buff4dennis2&quot;            
-## [20] &quot;upload:buffy4dennis&quot;            
-## [21] &quot;draw:eFlowPoly&quot;                 
-## [22] &quot;draw:eflows&quot;                    
-## [23] &quot;sample:nps_boundary_2013&quot;       
-## [24] &quot;draw:ocean&quot;                     
-## [25] &quot;draw:ocean2&quot;                    
-## [26] &quot;sample:simplified_HUC8s&quot;        
-## [27] &quot;draw:western_us&quot;</code></pre>
+##  [2] &quot;upload:CIDA_TEST_&quot;              
+##  [3] &quot;sample:CONUS_Climate_Divisions&quot; 
+##  [4] &quot;derivative:CONUS_States&quot;        
+##  [5] &quot;sample:CONUS_states&quot;            
+##  [6] &quot;sample:CSC_Boundaries&quot;          
+##  [7] &quot;derivative:FWS_LCC&quot;             
+##  [8] &quot;sample:FWS_LCC&quot;                 
+##  [9] &quot;upload:GIS&quot;                     
+## [10] &quot;derivative:wbdhu8_alb_simp&quot;     
+## [11] &quot;upload:KS_RPA&quot;                  
+## [12] &quot;upload:KS_cnty&quot;                 
+## [13] &quot;derivative:Level_III_Ecoregions&quot;
+## [14] &quot;derivative:NCA_Regions&quot;         
+## [15] &quot;derivative:US_Counties&quot;         
+## [16] &quot;upload:dwr_regions&quot;             
+## [17] &quot;sample:nps_boundary_2013&quot;       
+## [18] &quot;sample:simplified_HUC8s&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">query</span>(stencil, <span class="st">'attributes'</span>)</code></pre></div>
 <pre><code>## [1] &quot;STATE&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">query</span>(stencil, <span class="st">'values'</span>)</code></pre></div>
@@ -674,7 +665,7 @@ <h3><code>cancel</code> geojob</h3>
 <p>The <code>geoknife</code> package currently limits the user processing requests to single-running processes, so as to avoid creating thousands of requests in error, which could overwhelm the processing resources. If there is a reason to support additional jobs at one time, please email the package maintainers with your query.</p>
 <p>To cancel and existing job: Cancel a running job but retain the details:</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">id</span>(job)</code></pre></div>
-<pre><code>## [1] &quot;http://cida.usgs.gov:80/gdp/process/RetrieveResultServlet?id=a722d5cd-9739-4268-89ff-e8efe1f9107f&quot;</code></pre>
+<pre><code>## [1] &quot;http://cida.usgs.gov:80/gdp/process/RetrieveResultServlet?id=b5b1a03c-a5ad-48c5-b6df-a50369abd0a8&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">job &lt;-<span class="st"> </span><span class="kw">cancel</span>(job)
 <span class="kw">id</span>(job)</code></pre></div>
 <pre><code>## [1] &quot;&lt;no active job&gt;&quot;</code></pre>