v1.1.0.9023

Rebuild vignette with taxa distribution map as image; Issue #33
leppott · Jul 9, 2020 · 8a3d23e · 8a3d23e
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Showing 7 changed files with 23 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,7 +4,7 @@ Description: Suite of tools for data manipulation and calculations for Maryland
     DNR MBSS program.  Includes functions for calculating FIBI, BIBI (MBSS 
     genus), BIBI (MSW family), PHI, flow sums, ion contributions, and taxa 
     distribution maps.
-Version: 1.1.0.9022
+Version: 1.1.0.9023
 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 b/NEWS
@@ -3,7 +3,11 @@ NEWS-MBSStools
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2020-07-09 10:55:39
+    #> Last Update: 2020-07-09 12:04:57
+
+# MBSStools v1.1.0.9023 (2020-07-09)
+
+  - Rebuild vignette with taxa distribution map as image; Issue \#33
 
 # MBSStools v1.1.0.9022 (2020-07-09)
 

diff --git a/NEWS.md b/NEWS.md
@@ -3,7 +3,11 @@ NEWS-MBSStools
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2020-07-09 10:55:39
+    #> Last Update: 2020-07-09 12:04:57
+
+# MBSStools v1.1.0.9023 (2020-07-09)
+
+  - Rebuild vignette with taxa distribution map as image; Issue \#33
 
 # MBSStools v1.1.0.9022 (2020-07-09)
 

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -16,6 +16,10 @@ knitr::opts_chunk$set(
 ```{r, echo = FALSE}
 cat(paste0("Last Update: ",Sys.time()))
 ```
+MBSStools v1.1.0.9023 (2020-07-09)
+================
+* Rebuild vignette with taxa distribution map as image; Issue #33
+
 MBSStools v1.1.0.9022 (2020-07-09)
 ================
 * Shiny app, ensure download button is not active until create zip file; Issue #32 

diff --git a/inst/shiny-examples/MBSStools/ui.R b/inst/shiny-examples/MBSStools/ui.R
@@ -19,7 +19,7 @@ library(shinyjs) # used for togglestate of download button
 shinyUI(fluidPage(
 
   # Application title
-  titlePanel("MBSStools, IBI Calculator, v1.1.0.9022"),
+  titlePanel("MBSStools, IBI Calculator, v1.1.0.9023"),
 
   # SideBar
   sidebarLayout(

diff --git a/vignettes/MBSStools_vignette.Rmd b/vignettes/MBSStools_vignette.Rmd
@@ -291,11 +291,15 @@ wd <- getwd()
 MapTaxaObs(Obs, XWalk, wd, onlymatches = FALSE)
 ```
 
-The intent behind this function was to recreate the fish taxa distribution maps.  But the data inputs are not specific to fish and can be used for benthic macroinvertebrate data.
+The intent behind this function was to recreate the fish taxa distribution maps on the MBSS website.  
+
+http://eyesonthebay.dnr.maryland.gov/mbss/fishes.cfm
+
+The data inputs are not specific to fish and can be used for benthic macroinvertebrate data or any other presence/absence data.
 
 The taxa distribution map for brown trout is shown below.
 
-```{r TaxaMap Brown Trout, echo=FALSE, results="hide", fig.show='hold', warnings=FALSE, eval=TRUE}
+```{r TaxaMap_BrownTrout, echo=FALSE, results="hide", fig.show='hold', warnings=FALSE, eval=FALSE}
 # example map.
 # include only brown trout
 # brntrout.png
@@ -322,8 +326,6 @@ file.copy(file.path(path.package("MBSStools"),"extdata",myFiles),file.path(wd,"D
 ### GIS
 unzip(file.path(path.package("MBSStools"),"extdata","MD_GIS.zip"),exdir=file.path(wd,"GIS"))
 
-
-
 # data files
 obs <- "AllFish_95to16.xls"
 xWalk <- "TaxaMapsCrossWalk20170731.xlsx"
@@ -402,6 +404,7 @@ taxon <- as.character(map.taxa$CommonName[i])
  #reset old working directory
  #setwd <- oldwd
 ```
+![Taxa distribution for Brown Trout.](map_BrownTrout.png)
 
 ## Stream Discharge
 Calculate stream discharge based on field measurements.  Side channels that are properly identified in the data will be included.

diff --git a/vignettes/map_BrownTrout.png b/vignettes/map_BrownTrout.png