v0.0.0.9018

leppott · leppott · commit bd116be17a91 · 2017-09-24T16:52:50.000-04:00
Final clean up before v1.  Vignette, Readme, fixes to get examples in
Vignette working.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MBSStools
 Title: MBSS tool suite for calculations and data manipulation.
-Version: 0.0.0.9016
+Version: 0.0.0.9018
 Authors@R: c(
   person("Erik W.", "Leppo", email="Erik.Leppo@tetratech.com", role=c("aut","cre")),
   person("Ann","Roseberry Lincoln", role="ctb"),
diff --git a/NEWS.md b/NEWS.md
@@ -2,7 +2,7 @@ NEWS-MBSStools
 ================
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
-    #> Last Update: 2017-09-19 13:26:34
+    #> Last Update: 2017-09-24 16:49:46
 
 Version history.
 
@@ -11,6 +11,32 @@ Planned Updates
 
 -   Documentation (vignette).
 
+v0.0.0.9018
+===========
+
+2017-09-24
+
+-   Add install guide notebook.
+
+-   Tweak vignette.
+
+-   Update Readme.
+
+-   Final version before going to v1.0.0.
+
+-   IonContrib, ensure data input is a data frame.
+
+-   PHI, ensure data input is a data frame.
+
+v0.0.0.9017
+===========
+
+2017-09-20
+
+-   Update vignette.
+
+-   Fixed example for fish metrics in metric.values(). 20170920.
+
 v0.0.0.9016
 ===========
 
diff --git a/NEWS.rmd b/NEWS.rmd
@@ -25,6 +25,28 @@ Version history.
 
 * Documentation (vignette).
 
+# v0.0.0.9018
+2017-09-24
+
+* Add install guide notebook.
+
+* Tweak vignette.
+
+* Update Readme.
+
+* Final version before going to v1.0.0.
+
+* IonContrib, ensure data input is a data frame.
+
+* PHI, ensure data input is a data frame.
+
+# v0.0.0.9017
+2017-09-20
+
+* Update vignette.  
+
+* Fixed example for fish metrics in metric.values().  20170920.
+
 # v0.0.0.9016
 2017-09-19
 
diff --git a/R/IonContrib.R b/R/IonContrib.R
@@ -53,12 +53,13 @@
 #' @export
 IonContrib <- function(ion.data, ion.ref=MBSS.Ion.Ref, col.Cond="") {##FUNCTION.IonContrib.START
   #
-  # # QC
+  # # # QC
   # ion.data <- MBSS.Ion.Data
   # ion.ref <- MBSS.Ion.Ref
   # col.Cond <- ""
   # 0. Rename Data
-  data.calc <- ion.data
+  data.calc <- as.data.frame(ion.data)
+  ion.ref <- as.data.frame(ion.ref)
   # 1. Get Ion List
   myIons <- ion.ref$Name[ion.ref$Name %in% colnames(data.calc)]
   #print(myIons)
diff --git a/R/PHIcalc.R b/R/PHIcalc.R
@@ -55,6 +55,7 @@ PHIcalc <- function(fun.df,fun.names=c("SampID"
                                         , "Erosn_SevL_03"
                                         , "RoadDist_m")){
   # 0. QC ####
+  fun.df <- as.data.frame(fun.df)
   # 0.1. QC column names
   # Define dataframe names
   names.default <- c("SampID"
diff --git a/R/metric.values.R b/R/metric.values.R
@@ -76,7 +76,7 @@
 #' (myMetrics.Fish <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"Metric"]))))
 #' # Taxa Data
 #' myDF.Fish <- taxa_fish
-#' myMetric.Values.Fish <- metric.values(myDF.Fish, "SampleID", "fish", myMetrics.Fish, TRUE)
+#' myMetric.Values.Fish <- metric.values(myDF.Fish, "SampleID", "fish", myMetrics.Fish)
 #' View(myMetric.Values.Fish)
 #'
 #' # Metrics, Index, Benthic Macroinvertebrates, genus
diff --git a/README.Rmd b/README.Rmd
@@ -31,9 +31,9 @@ To aid MBSS staff with calculations and data manipulations.
 
 Status
 ------------
-Development stage.  
+Final. 
 
 
 Usage
 ------------
-
+By MBSS staff or those using MBSS data.
diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@ README-MBSStools
 ================
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-    #> Last Update: 2017-03-27 15:12:26
+    #> Last Update: 2017-09-24 16:50:00
 
 Suite of tools for data manipulation and calculations for Maryland DNR MBSS program.
 
@@ -21,7 +21,9 @@ To aid MBSS staff with calculations and data manipulations.
 Status
 ------
 
-Development stage.
+Final.
 
 Usage
 -----
+
+By MBSS staff or those using MBSS data.
diff --git a/inst/extdata/MBSS Install Guide.pdf b/inst/extdata/MBSS Install Guide.pdf
diff --git a/inst/extdata/MBSStools_Install_Guide.Rmd b/inst/extdata/MBSStools_Install_Guide.Rmd
@@ -0,0 +1,26 @@
+---
+title: "MBSS Install Guide"
+output: html_notebook
+---
+
+`MBSStools` is an R library with functions to perform various analyses by MBSS staff and those working with MBSS data.  An installed copy of R is required.  A copy of RStudio is recommended.
+
+#Installation
+The code for MBSStools is hosted on GitHub at https://github.com/leppott/MBSStools and can be installed within R but the library `devtools` is required.  To install devtools use the code below.
+
+```{r, eval=FALSE}
+install.packages("devtools")
+```
+
+Once `devtools` is installed the code below will install `MBSStools`.
+
+```{r, eval=FALSE}
+library(devtools)
+install_github("leppott/MBSStools")
+```
+
+Alternatively, a zip file containing the R library can be downloaded from GitHub (https://github.com/leppott/MBSStools) and installed manually from R's menu bar (Packages - Install package(s) from local zip files).
+
+#GitHub
+GitHub is a code sharing website.  `MBSStools` is hosted on this site for ease of updating and distribution.  There is also issue tracking on the website.  The most current vesion of the package will always be installed with the code above.
+
diff --git a/inst/extdata/MBSStools_Install_Guide.nb.html b/inst/extdata/MBSStools_Install_Guide.nb.html
diff --git a/inst/extdata/Notebook_MBSStools.Rmd b/inst/extdata/Notebook_MBSStools.Rmd
@@ -0,0 +1,72 @@
+---
+title: "Notebook, MBSStools"
+output: html_notebook
+---
+
+This is an [R Markdown](http://rmarkdown.rstudio.com) Notebook. When you execute code within the notebook, the results appear beneath the code. 
+
+Execute chunks by clicking the *Run* button within the chunk or by placing your cursor inside it and pressing *Ctrl+Shift+Enter*. 
+
+# Package
+
+Package related code.
+
+## Vignette
+```{r, eval=FALSE}
+# generate Vignette
+library(MBSStools)
+library(devtools)
+devtools::build_vignettes()
+```
+devtools::build() more useful and build_vignettes()
+
+## Create Package
+Use the code below to create the package.  Assumes you are in the development package directory
+
+```{r, eval=FALSE}
+# Library Name
+myLibrary <- "MBSStools" # "ContDataQC","MMIcalc","MMIcalcNV","MBSStools","XC95"
+# Load Library
+library(devtools)
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# Create Package
+# create(myLibrary)
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# files to library folder
+# file.copy("metric.values.R","./Library/MMIcalc/R/metric.values.R",overwrite=TRUE)
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# Document, Install, and Reload Library
+## Generate Documentation
+setwd(paste0("./",myLibrary))
+devtools::document()
+## Install New Package (locally)
+setwd("..") # return to root directory first
+devtools::install(myLibrary)
+## Reload library
+library(myLibrary,character.only = TRUE)
+# change wd back to package
+setwd(paste0("./",myLibrary))
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+```
+
+After creating the package reload it after restarting R within RStudio (Control+Shift+F10).
+
+```{r, eval=FALSE}
+# Restart R within RStudio:  Ctrl + Shift + F10
+library(MBSStools)
+?metric.scores  
+```
+
+## Including Data
+All data should have already been created.
+
+## Error Checking
+Need to use testthat but not to that stage yet.
+```{r, eval=FALSE}
+# Check for errors (or press Cmd + Shift + E in RStudio)
+devtools::check()
+```
+
+
diff --git a/inst/extdata/Notebook_MBSStools.nb.html b/inst/extdata/Notebook_MBSStools.nb.html
@@ -177,6 +177,20 @@ <h1 class="title toc-ignore">Notebook, MBSStools</h1>
 <div id="package" class="section level1">
 <h1>Package</h1>
 <p>Package related code.</p>
+<div id="vignette" class="section level2">
+<h2>Vignette</h2>
+<!-- rnb-text-end -->
+<!-- rnb-chunk-begin -->
+<!-- rnb-source-begin eyJkYXRhIjpbIiMgZ2VuZXJhdGUgVmlnbmV0dGUiLCJsaWJyYXJ5KE1CU1N0b29scykiLCJsaWJyYXJ5KGRldnRvb2xzKSIsImRldnRvb2xzOjpidWlsZF92aWduZXR0ZXMoKSJdfQ== -->
+<pre class="r"><code># generate Vignette
+library(MBSStools)
+library(devtools)
+devtools::build_vignettes()</code></pre>
+<!-- rnb-source-end -->
+<!-- rnb-chunk-end -->
+<!-- rnb-text-begin -->
+<p>devtools::build() more useful and build_vignettes()</p>
+</div>
 <div id="create-package" class="section level2">
 <h2>Create Package</h2>
 <p>Use the code below to create the package. Assumes you are in the development package directory</p>
@@ -211,7 +225,7 @@ <h2>Create Package</h2>
 <!-- rnb-source-end -->
 <!-- rnb-chunk-end -->
 <!-- rnb-text-begin -->
-<p>After creating the package reload it after restarting R within RStudio.</p>
+<p>After creating the package reload it after restarting R within RStudio (Control+Shift+F10).</p>
 <!-- rnb-text-end -->
 <!-- rnb-chunk-begin -->
 <!-- rnb-source-begin eyJkYXRhIjpbIiMgUmVzdGFydCBSIHdpdGhpbiBSU3R1ZGlvOiAgQ3RybCArIFNoaWZ0ICsgRjEwIiwibGlicmFyeShNQlNTdG9vbHMpIiwiP21ldHJpYy5zY29yZXMgICJdfQ== -->
@@ -224,6 +238,7 @@ <h2>Create Package</h2>
 </div>
 <div id="including-data" class="section level2">
 <h2>Including Data</h2>
+<p>All data should have already been created.</p>
 </div>
 <div id="error-checking" class="section level2">
 <h2>Error Checking</h2>
@@ -236,19 +251,11 @@ <h2>Error Checking</h2>
 <!-- rnb-source-end -->
 <!-- rnb-chunk-end -->
 <!-- rnb-text-begin -->
-</div>
-</div>
-<div id="items-to-do" class="section level1">
-<h1>Items to Do</h1>
-<ol style="list-style-type: decimal">
-<li><p>IBI - calculate metrics - B, F, and MSW</p></li>
-<li><p>Score metrics</p></li>
-<li><p>QC</p></li>
-</ol>
 <!-- rnb-text-end -->
 </div>
+</div>
 
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diff --git a/man/metric.values.Rd b/man/metric.values.Rd
diff --git a/vignettes/MBSStools_vignette.Rmd b/vignettes/MBSStools_vignette.Rmd
