v1.2.0.9001

* fix: Update examples and vignette to not use droplevels() + Revised thresholds no longer has levels
leppott · Apr 8, 2024 · be09e1f · be09e1f
1 parent 4b7023f
commit be09e1f
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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: 1.2.0
+Version: 1.2.0.9001
 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 +3,12 @@ NEWS-MBSStools
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-04-05 16:00:44.873446
+    #> Last Update: 2024-04-08 12:38:08.080495
+
+# MBSStools v1.2.0.9001 (2024-04-08)
+
+- fix: Update examples and vignette to not use droplevels()
+  - Revised thresholds no longer has levels
 
 # MBSStools v1.2.0 (2024-04-05)
 

diff --git a/NEWS.md b/NEWS.md
@@ -3,7 +3,12 @@ NEWS-MBSStools
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-04-05 16:00:44.873446
+    #> Last Update: 2024-04-08 12:38:08.080495
+
+# MBSStools v1.2.0.9001 (2024-04-08)
+
+- fix: Update examples and vignette to not use droplevels()
+  - Revised thresholds no longer has levels
 
 # MBSStools v1.2.0 (2024-04-05)
 

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -17,6 +17,11 @@ knitr::opts_chunk$set(
 cat(paste0("Last Update: ",Sys.time()))
 ```
 
+MBSStools v1.2.0.9001 (2024-04-08)
+================
+* fix: Update examples and vignette to not use droplevels()
+    + Revised thresholds no longer has levels
+
 MBSStools v1.2.0 (2024-04-05)
 ================
 * refactor: Bump version number for fix in previous commit

diff --git a/R/metric.scores.R b/R/metric.scores.R
@@ -31,8 +31,8 @@
 #' # Thresholds
 #' thresh <- metrics_scoring
 #' # get metric names for myIndex
-#' (myMetrics.Fish <- as.character(droplevels(unique(thresh[thresh[,
-#' "Index.Name"]==myIndex,"MetricName.Other"]))))
+#' (myMetrics.Fish <- as.character(unique(thresh[thresh[,
+#' "Index.Name"] == myIndex,"MetricName.Other"])))
 #' # Taxa Data
 #' myDF.Fish <- taxa_fish
 #' myMetric.Values.Fish <- metric.values(myDF.Fish, "fish", myMetrics.Fish,
@@ -61,8 +61,8 @@
 #' # Thresholds
 #' thresh <- metrics_scoring
 #' # get metric names for myIndex
-#' (myMetrics.Bugs.MBSS <- as.character(droplevels(unique(thresh[thresh[,
-#' "Index.Name"]==myIndex,"MetricName.Other"]))))
+#' (myMetrics.Bugs.MBSS <- as.character(unique(thresh[thresh[,
+#' "Index.Name"] == myIndex,"MetricName.Other"])))
 #' # Taxa Data
 #' myDF.Bugs.MBSS <- taxa_bugs_genus
 #' myMetric.Values.Bugs.MBSS <- metric.values(myDF.Bugs.MBSS, "bugs",
@@ -102,8 +102,8 @@
 #' # Thresholds
 #' thresh <- metrics_scoring
 #' # get metric names for myIndex
-#' (myMetrics.Bugs.MSW <- as.character(droplevels(unique(thresh[thresh[,
-#' "Index.Name"]==myIndex,"MetricName.Other"]))))
+#' (myMetrics.Bugs.MSW <- as.character(unique(thresh[thresh[,
+#' "Index.Name"] == myIndex,"MetricName.Other"])))
 #' # Taxa Data
 #' myDF.Bugs.MSW <- taxa_bugs_family
 #' myMetric.Values.Bugs.MSW <- metric.values(myDF.Bugs.MSW, "bugs",

diff --git a/R/metric.values.R b/R/metric.values.R
@@ -97,8 +97,8 @@
 #' # Thresholds
 #' thresh <- metrics_scoring
 #' # get metric names for myIndex
-#' (myMetrics.Fish <- as.character(droplevels(unique(thresh[thresh[,
-#' "Index.Name"]==myIndex,"MetricName.Other"]))))
+#' (myMetrics.Fish <- as.character(unique(thresh[thresh[,
+#' "Index.Name"] == myIndex,"MetricName.Other"])))
 #' # Taxa Data
 #' myDF.Fish <- taxa_fish
 #' myMetric.Values.Fish <- metric.values(myDF.Fish, "fish", myMetrics.Fish)
@@ -110,8 +110,8 @@
 #' # Thresholds
 #' thresh <- metrics_scoring
 #' # get metric names for myIndex
-#' (myMetrics.Bugs.MBSS <- as.character(droplevels(unique(thresh[thresh[,
-#' "Index.Name"]==myIndex,"MetricName.Other"]))))
+#' (myMetrics.Bugs.MBSS <- as.character(unique(thresh[thresh[,
+#' "Index.Name"] == myIndex,"MetricName.Other"])))
 #' # Taxa Data
 #' myDF.Bugs.MBSS <- taxa_bugs_genus
 #' myMetric.Values.Bugs.MBSS <- metric.values(myDF.Bugs.MBSS, "bugs",
@@ -123,8 +123,8 @@
 #' # Thresholds
 #' thresh <- metrics_scoring
 #' # get metric names for myIndex
-#' (myMetrics.Bugs.MSW <- as.character(droplevels(unique(thresh[thresh[,
-#' "Index.Name"]==myIndex,"MetricName.Other"]))))
+#' (myMetrics.Bugs.MSW <- as.character(unique(thresh[thresh[,
+#' "Index.Name"] == myIndex,"MetricName.Other"])))
 #' # Taxa Data
 #' myDF.Bugs.MSW <- taxa_bugs_family
 #' myMetric.Values.Bugs.MSW <- metric.values(myDF.Bugs.MSW, "bugs",
@@ -136,8 +136,7 @@
 # myIndex <- "MBSS.2005.Fish"
 # thresh <- metrics_scoring
 # (myMetrics.Fish <- as.character(
-#   droplevels(unique(thresh[thresh[,"Index.Name"]==
-#                                              myIndex,"MetricName.Other"]))))
+#   unique(thresh[thresh[,"Index.Name"] == myIndex,"MetricName.Other"])))
 # myDF <- taxa_fish # myDF.Fish
 # # myMetric.Values.Fish <- metric.values(myDF, "SampleID", "fish",
 # #                                       myMetrics.Fish, TRUE)

diff --git a/doc/MBSStools_vignette.R b/doc/MBSStools_vignette.R
@@ -14,7 +14,7 @@ myIndex <- "MBSS.2005.Fish"
 # Thresholds
 thresh <- metrics_scoring
 # get metric names for myIndex
-(myMetrics.Fish <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"MetricName.Other"]))))
+(myMetrics.Fish <- as.character(unique(thresh[thresh[,"Index.Name"] == myIndex,"MetricName.Other"])))
 # Taxa Data
 myDF.Fish <- taxa_fish
 myMetric.Values.Fish <- metric.values(myDF.Fish, "fish", myMetrics.Fish, TRUE)
@@ -31,7 +31,7 @@ myIndex <- "MBSS.2005.Bugs"
 # Thresholds
 thresh <- metrics_scoring
 # get metric names for myIndex
-(myMetrics.Bugs.MBSS <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"MetricName.Other"]))))
+(myMetrics.Bugs.MBSS <- as.character(unique(thresh[thresh[,"Index.Name"] == myIndex,"MetricName.Other"])))
 # Taxa Data
 myDF.Bugs.MBSS <- taxa_bugs_genus
 myMetric.Values.Bugs.MBSS <- metric.values(myDF.Bugs.MBSS, "bugs", myMetrics.Bugs.MBSS)
@@ -54,7 +54,7 @@ myIndex <- "MSW.1999.Bugs"
 # Thresholds
 thresh <- metrics_scoring
 # get metric names for myIndex
-(myMetrics.Bugs.MSW <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"MetricName.Other"]))))
+(myMetrics.Bugs.MSW <- as.character(unique(thresh[thresh[,"Index.Name"] == myIndex,"MetricName.Other"])))
 # Taxa Data
 myDF.Bugs.MSW <- taxa_bugs_family
 myMetric.Values.Bugs.MSW <- metric.values(myDF.Bugs.MSW, "bugs", myMetrics.Bugs.MSW)
@@ -126,12 +126,12 @@ head(df.lu.taxa)
 ## ----TaxaMaps Example Code, eval=FALSE----------------------------------------
 #  # Set Working Directory
 #  wd <- getwd()
-#  
+#
 #  # Inputs
 #  Obs <- "AllFish_95to16.xls"
 #  XWalk <- "TaxaMapsCrossWalk20170731.xlsx"
 #  wd <- getwd()
-#  
+#
 #  # Create maps
 #  MapTaxaObs(Obs, XWalk, wd, onlymatches = FALSE)
 
@@ -170,7 +170,7 @@ xWalk <- "TaxaMapsCrossWalk20170731.xlsx"
 
 oldwd <- getwd()
 setwd("..") #resets to vignette dir when run as code chunk
-dirMain <- getwd()  
+dirMain <- getwd()
 dirData = "Data"
 dirGIS = "GIS"
 verbose = TRUE
@@ -228,7 +228,7 @@ taxon <- as.character(map.taxa$CommonName[i])
   df.taxon.sites <- subset(df.taxa.obs, df.taxa.obs[,"CommonName"]==taxon)
   df.taxon.sites <- subset(df.taxon.sites, !is.na(df.taxon.sites["Latitude83"]))
 
-  
+
   plot(state, col="white", border="gray")
     plot(coastline, add = TRUE, col="light blue", border=FALSE)
     plot(counties, add = TRUE, col="white", border="darkslategray", lwd=0.5)
@@ -237,8 +237,8 @@ taxon <- as.character(map.taxa$CommonName[i])
                           "+proj=lcc +lat_1=39.45 +lat_2=38.3 +lat_0=37.66666666666666 +lon_0=-77
             +x_0=400000 +y_0=0 +datum=NAD83 +units=m +no_defs")
     points(proj.sites[,1], proj.sites[,2], pch=21, col="black", bg="green", cex=1.0)
-        
-        
+
+
  #reset old working directory
  #setwd <- oldwd
 

diff --git a/inst/shiny-examples/MBSStools/rsconnect/shinyapps.io/tetratech-wtr-wne/MBSStools.dcf b/inst/shiny-examples/MBSStools/rsconnect/shinyapps.io/tetratech-wtr-wne/MBSStools.dcf
@@ -5,9 +5,7 @@ account: tetratech-wtr-wne
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 2566633
-bundleId: 4773852
+bundleId:
 url: https://tetratech-wtr-wne.shinyapps.io/MBSStools/
-when: 1625071889.94754
-lastSyncTime: 1625071889.94754
 asMultiple: FALSE
 asStatic: FALSE
diff --git a/inst/shiny-examples/MBSStools/server.R b/inst/shiny-examples/MBSStools/server.R
@@ -162,8 +162,8 @@ shinyServer(function(input, output) {
 
       #myIndex <- input$MMI
       thresh <- MBSStools::metrics_scoring
-      myMetrics <- as.character(droplevels(unique(thresh[thresh[
-        ,"Index.Name"]==myIndex,"MetricName.Other"])))
+      myMetrics <- as.character(unique(thresh[thresh[
+        ,"Index.Name"] == myIndex,"MetricName.Other"]))
       #
      # myCommunity <- Community[match(myIndex, MMIs)]
       myCol_Strata <- col_Strata[match(myIndex, MMIs)]

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, v1.2.0"),
+  titlePanel("MBSStools, IBI Calculator, v1.2.0.9001"),
 
   # SideBar
   sidebarLayout(

diff --git a/man/metric.scores.Rd b/man/metric.scores.Rd
diff --git a/man/metric.values.Rd b/man/metric.values.Rd