v0.3.0.9018

Fixes for R v3.6.0, Issue #18 Updated badges in ReadMe.
leppott · May 17, 2019 · 9594d7a · 9594d7a
1 parent f8c909f
commit 9594d7a
Show file tree

Hide file tree

Showing 19 changed files with 247 additions and 3,157 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -2,3 +2,5 @@
 ^\.Rproj\.user$
 ^\.travis\.yml$
 _test/
+^doc$
+^Meta$
diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,5 @@
 .Ruserdata
 _test/
 
+doc
+Meta
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BioMonTools
 Type: Package
 Title: Tools for Biomonitoring and Bioassessment
-Version: 0.3.0.9017
+Version: 0.3.0.9018
 Author: c(
 	person("Erik W.", "Leppo", email="Erik.Leppo@tetratech.com",role=c("aut","cre")), 
 	person("Jen", "Stamp", role="ctb"),
@@ -29,5 +29,4 @@ Suggests:
     rmarkdown,
     XLConnect
 VignetteBuilder: knitr
-StagedInstall: no
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
diff --git a/NEWS b/NEWS
@@ -4,7 +4,7 @@ NEWS
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2019-05-08 10:03:00
+    #> Last Update: 2019-05-17 11:01:28
 
 # Planned Updates
 
@@ -22,6 +22,16 @@ NEWS
 
 # Version History
 
+## Changes in Version 0.3.0.9018 (2019-05-17)
+
+  - Fixes for R v3.6.0, Issue \#18
+      - DESCRIPTION
+          - Remove StagedInstall: no
+      - README
+          - Add directions for fix for devtools.
+  - README
+      - Update badges.
+
 ## Changes in Version 0.3.0.9017 (2019-05-08)
 
   - Metric names, fix those added in previous update, Issue \#3

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -32,6 +32,16 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## Changes in Version 0.3.0.9018 (2019-05-17)
+
+* Fixes for R v3.6.0, Issue #18
+    + DESCRIPTION
+        - Remove StagedInstall: no
+    + README
+        - Add directions for fix for devtools.
+* README
+    + Update badges.
+
 ## Changes in Version 0.3.0.9017 (2019-05-08)
 
 * Metric names, fix those added in previous update, Issue #3

diff --git a/README.Rmd b/README.Rmd
@@ -21,21 +21,22 @@ Suite of functions and tools for bioassessment and biomonitoring.
 
 Badges
 -----------
+[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://GitHub.com/leppott/BioMonTools/graphs/commit-activity)
+[![GitHub license](https://img.shields.io/github/license/leppott/BioMonTools.svg)](https://github.com/leppott/BioMonTools/blob/master/LICENSE)
 [![Travis-CI Build Status](https://travis-ci.org/leppott/BioMonTools.svg?branch=master)](https://travis-ci.org/leppott/BioMonTools)
-[![GitHub license](https://img.shields.io/github/license/Naereen/StrapDown.js.svg)](https://github.com/leppott/BioMonTools/blob/master/LICENSE)
-[![GitHub release](https://img.shields.io/github/release/Naereen/StrapDown.js.svg)](https://GitHub.com/leppott/BioMonTools/releases/)
-[![Github all releases](https://img.shields.io/github/downloads/Naereen/StrapDown.js/total.svg)](https://GitHub.com/leppott/BioMonTools/releases/)
-[![GitHub issues](https://img.shields.io/github/issues/Naereen/StrapDown.js.svg)](https://GitHub.com/leppott/BioMonTools/issues/)
+[![GitHub issues](https://img.shields.io/github/issues/leppott/BioMonTools.svg)](https://GitHub.com/leppott/BioMonTools/issues/)
+
+[![GitHub release](https://img.shields.io/github/release/leppott/BioMonTools.svg)](https://GitHub.com/leppott/BioMonTools/releases/)
+[![Github all releases](https://img.shields.io/github/downloads/leppott/BioMonTools/total.svg)](https://GitHub.com/leppott/BioMonTools/releases/)
 
 Installation
 ------------
-library(devtools)  #install if needed
-
-install_github("leppott/BioMonTools")
-
-To get vignettes need to use the following.
 
+```{r, eval=FALSE}
+library(devtools)  #install if needed
+Sys.setenv("TAR" = "internal")  # needed for R v3.6.0
 install_github("leppott/BioMonTools", force=TRUE, build_vignettes=TRUE)
+```
 
 Purpose
 ------------
@@ -54,4 +55,8 @@ the same database or spreadsheet.  Only need to format data for use with these t
 
 Documentation
 ------------
-Vignette and install guide are planned for the future.
+Vignette and install guide udpates are planned for the future.
+
+Issues
+------------
+https://github.com/leppott/BioMonTools/issues
diff --git a/README.md b/README.md
@@ -3,28 +3,33 @@ README-BioMonTools
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-    #> Last Update: 2018-12-03 08:42:47
+    #> Last Update: 2019-05-17 10:58:28
 
-Suite of functions and tools for bioassessment and biomonitoring.
+Suite of functions and tools for bioassessment and
+biomonitoring.
 
 ## Badges
 
+[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://GitHub.com/leppott/BioMonTools/graphs/commit-activity)
+[![GitHub
+license](https://img.shields.io/github/license/leppott/BioMonTools.svg)](https://github.com/leppott/BioMonTools/blob/master/LICENSE)
 [![Travis-CI Build
 Status](https://travis-ci.org/leppott/BioMonTools.svg?branch=master)](https://travis-ci.org/leppott/BioMonTools)
 [![GitHub
-license](https://img.shields.io/github/license/Naereen/StrapDown.js.svg)](https://github.com/leppott/BioMonTools/blob/master/LICENSE)
+issues](https://img.shields.io/github/issues/leppott/BioMonTools.svg)](https://GitHub.com/leppott/BioMonTools/issues/)
+
 [![GitHub
-release](https://img.shields.io/github/release/Naereen/StrapDown.js.svg)](https://GitHub.com/leppott/BioMonTools/releases/)
+release](https://img.shields.io/github/release/leppott/BioMonTools.svg)](https://GitHub.com/leppott/BioMonTools/releases/)
 [![Github all
-releases](https://img.shields.io/github/downloads/Naereen/StrapDown.js/total.svg)](https://GitHub.com/leppott/BioMonTools/releases/)
-[![GitHub
-issues](https://img.shields.io/github/issues/Naereen/StrapDown.js.svg)](https://GitHub.com/leppott/BioMonTools/issues/)
+releases](https://img.shields.io/github/downloads/leppott/BioMonTools/total.svg)](https://GitHub.com/leppott/BioMonTools/releases/)
 
 ## Installation
 
-library(devtools) \#install if needed
-
-install\_github(“leppott/BioMonTools”)
+``` r
+library(devtools)  #install if needed
+Sys.setenv("TAR" = "internal")  # needed for R v3.6.0
+install_github("leppott/BioMonTools", force=TRUE, build_vignettes=TRUE)
+```
 
 ## Purpose
 
@@ -46,4 +51,8 @@ data for use with these tools.
 
 ## Documentation
 
-Vignette and install guide are planned for the future.
+Vignette and install guide udpates are planned for the future.
+
+## Issues
+
+<https://github.com/leppott/BioMonTools/issues>
diff --git a/doc/vignette_BioMonTools.html b/doc/vignette_BioMonTools.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Erik.Leppo@tetratech.com" />
 
-<meta name="date" content="2019-01-14" />
+<meta name="date" content="2019-05-17" />
 
 <title>Vignette, BioMonTools</title>
 
@@ -293,6 +293,9 @@
 code > span.fu { color: #900; font-weight: bold; }  code > span.er { color: #a61717; background-color: #e3d2d2; } 
 </style>
 
+
+
+
 </head>
 
 <body>
@@ -301,8 +304,8 @@
 
 
 <h1 class="title toc-ignore">Vignette, BioMonTools</h1>
-<h4 class="author"><em><a href="mailto:Erik.Leppo@tetratech.com">Erik.Leppo@tetratech.com</a></em></h4>
-<h4 class="date"><em>2019-01-14</em></h4>
+<h4 class="author"><a href="mailto:Erik.Leppo@tetratech.com">Erik.Leppo@tetratech.com</a></h4>
+<h4 class="date">2019-05-17</h4>
 
 
 
@@ -479,13 +482,13 @@ <h3>Data Preparation</h3>
 <td align="right">9</td>
 <td align="right">7</td>
 <td align="right">0.0000000</td>
-<td align="right">0.4023769</td>
-<td align="right">0.2071307</td>
-<td align="right">0.1188455</td>
-<td align="right">0.0000000</td>
-<td align="right">0.0370370</td>
-<td align="right">0.3333333</td>
-<td align="right">0.2592593</td>
+<td align="right">40.237691</td>
+<td align="right">20.713073</td>
+<td align="right">11.884550</td>
+<td align="right">0.000000</td>
+<td align="right">3.703704</td>
+<td align="right">33.333333</td>
+<td align="right">25.925926</td>
 </tr>
 <tr class="even">
 <td align="left">02087REF_Bug_2002-08-22_0</td>
@@ -501,14 +504,14 @@ <h3>Data Preparation</h3>
 <td align="right">21</td>
 <td align="right">7</td>
 <td align="right">1</td>
-<td align="right">0.0313653</td>
-<td align="right">0.1512915</td>
-<td align="right">0.0553506</td>
-<td align="right">0.6402214</td>
-<td align="right">0.0526316</td>
-<td align="right">0.5526316</td>
-<td align="right">0.1842105</td>
-<td align="right">0.0263158</td>
+<td align="right">3.1365314</td>
+<td align="right">15.129151</td>
+<td align="right">5.535055</td>
+<td align="right">64.022140</td>
+<td align="right">5.263158</td>
+<td align="right">55.263158</td>
+<td align="right">18.421053</td>
+<td align="right">2.631579</td>
 </tr>
 <tr class="odd">
 <td align="left">03013CSR_Bug_2003-07-01_0</td>
@@ -525,13 +528,13 @@ <h3>Data Preparation</h3>
 <td align="right">2</td>
 <td align="right">4</td>
 <td align="right">0.0000000</td>
-<td align="right">0.0295858</td>
-<td align="right">0.1025641</td>
-<td align="right">0.6015779</td>
-<td align="right">0.0000000</td>
-<td align="right">0.1875000</td>
-<td align="right">0.1250000</td>
-<td align="right">0.2500000</td>
+<td align="right">2.958580</td>
+<td align="right">10.256410</td>
+<td align="right">60.157791</td>
+<td align="right">0.000000</td>
+<td align="right">18.750000</td>
+<td align="right">12.500000</td>
+<td align="right">25.000000</td>
 </tr>
 <tr class="even">
 <td align="left">03053CSR_Bug_2003-08-14_0</td>
@@ -547,14 +550,14 @@ <h3>Data Preparation</h3>
 <td align="right">18</td>
 <td align="right">6</td>
 <td align="right">3</td>
-<td align="right">0.0331588</td>
-<td align="right">0.4275742</td>
-<td align="right">0.1570681</td>
-<td align="right">0.0907504</td>
-<td align="right">0.0277778</td>
-<td align="right">0.5000000</td>
-<td align="right">0.1666667</td>
-<td align="right">0.0833333</td>
+<td align="right">3.3158813</td>
+<td align="right">42.757417</td>
+<td align="right">15.706806</td>
+<td align="right">9.075044</td>
+<td align="right">2.777778</td>
+<td align="right">50.000000</td>
+<td align="right">16.666667</td>
+<td align="right">8.333333</td>
 </tr>
 <tr class="odd">
 <td align="left">03054CSR_Bug_2003-08-18_0</td>
@@ -570,14 +573,14 @@ <h3>Data Preparation</h3>
 <td align="right">3</td>
 <td align="right">1</td>
 <td align="right">3</td>
-<td align="right">0.0053763</td>
-<td align="right">0.0645161</td>
-<td align="right">0.0537634</td>
-<td align="right">0.7491039</td>
-<td align="right">0.0769231</td>
-<td align="right">0.2307692</td>
-<td align="right">0.0769231</td>
-<td align="right">0.2307692</td>
+<td align="right">0.5376344</td>
+<td align="right">6.451613</td>
+<td align="right">5.376344</td>
+<td align="right">74.910394</td>
+<td align="right">7.692308</td>
+<td align="right">23.076923</td>
+<td align="right">7.692308</td>
+<td align="right">23.076923</td>
 </tr>
 <tr class="even">
 <td align="left">06012CSR_Bug_2006-09-05_0</td>
@@ -593,14 +596,14 @@ <h3>Data Preparation</h3>
 <td align="right">17</td>
 <td align="right">11</td>
 <td align="right">4</td>
-<td align="right">0.0110092</td>
-<td align="right">0.3284404</td>
-<td align="right">0.4311927</td>
-<td align="right">0.1853211</td>
-<td align="right">0.0250000</td>
-<td align="right">0.4250000</td>
-<td align="right">0.2750000</td>
-<td align="right">0.1000000</td>
+<td align="right">1.1009174</td>
+<td align="right">32.844037</td>
+<td align="right">43.119266</td>
+<td align="right">18.532110</td>
+<td align="right">2.500000</td>
+<td align="right">42.500000</td>
+<td align="right">27.500000</td>
+<td align="right">10.000000</td>
 </tr>
 </tbody>
 </table>
@@ -1104,7 +1107,7 @@ <h2>rarify</h2>
 <a class="sourceLine" id="cb10-17" data-line-number="17">                     ,<span class="dt">abund=</span><span class="st">&quot;N_Taxa&quot;</span>,<span class="dt">subsiz=</span>mySize, <span class="dt">mySeed=</span>Seed_US)</a>
 <a class="sourceLine" id="cb10-18" data-line-number="18"><span class="co">#&gt; Rarify of samples complete. </span></a>
 <a class="sourceLine" id="cb10-19" data-line-number="19"><span class="co">#&gt;  Number of samples =  12 </span></a>
-<a class="sourceLine" id="cb10-20" data-line-number="20"><span class="co">#&gt;  Execution time (sec) =  0.0200000000000031</span></a>
+<a class="sourceLine" id="cb10-20" data-line-number="20"><span class="co">#&gt;  Execution time (sec) =  0</span></a>
 <a class="sourceLine" id="cb10-21" data-line-number="21"></a>
 <a class="sourceLine" id="cb10-22" data-line-number="22"><span class="co"># view results</span></a>
 <a class="sourceLine" id="cb10-23" data-line-number="23"><span class="co">#dim(bugs_mysize)</span></a>
@@ -1292,8 +1295,8 @@ <h3>Flags</h3>
 </tr>
 <tr class="even">
 <td>individuals, small</td>
-<td align="right">75</td>
-<td align="right">603</td>
+<td align="right">80</td>
+<td align="right">598</td>
 </tr>
 <tr class="odd">
 <td>Low density (ft2)</td>