v1.0.2.9010

Revision for staged install, R v3.6.0, Issue #27 Some mods for shiny app (incomplete). Issue #22
leppott · May 3, 2019 · 9531fef · 9531fef
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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: 1.0.2.9009
+Version: 1.0.2.9010
 Authors@R: c(
   person("Erik W.", "Leppo", email="Erik.Leppo@tetratech.com", role=c("aut","cre")),
   person("Ann","Roseberry Lincoln", role="ctb"),
@@ -25,3 +25,4 @@ Suggests:
     XLConnect
 VignetteBuilder: knitr
 LazyData: true
+StagedInstall: no
diff --git a/NEWS b/NEWS
@@ -3,7 +3,16 @@ NEWS-MBSStools
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2019-05-01 11:32:11
+    #> Last Update: 2019-05-03 09:57:54
+
+# MBSStools v1.0.2.9010 (2019-05-01)
+
+  - Revise for staged install for R v3.6.0, Issue \#27
+      - DESCRIPTION
+          - StagedInstall: no
+      - Temporary fix. Still needs to be installed from a local file.
+  - Edits to Shiny App. Issue \#22.
+      - Incomplete.
 
 # MBSStools v1.0.2.9009 (2019-05-01)
 

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -17,6 +17,15 @@ knitr::opts_chunk$set(
 cat(paste0("Last Update: ",Sys.time()))
 ```
 
+MBSStools v1.0.2.9010 (2019-05-01)
+================
+
+* Revise for staged install for R v3.6.0, Issue #27
+    + DESCRIPTION
+        - StagedInstall: no
+    + Temporary fix.  Still needs to be installed from a local file.
+* Edits to Shiny App.  Issue #22.
+    + Incomplete.
 
 MBSStools v1.0.2.9009 (2019-05-01)
 ================

diff --git a/inst/shiny-examples/MBSStools/MetVal.csv b/inst/shiny-examples/MBSStools/MetVal.csv
@@ -0,0 +1,2 @@
+"","x"
+"1","df_import_DT"
diff --git a/inst/shiny-examples/MBSStools/global.R b/inst/shiny-examples/MBSStools/global.R
@@ -3,6 +3,7 @@
 # Packages
 library(shiny)
 library(MBSStools)
+library(DT)
 
 # Drop-down boxes
 #MMIs <- c("BIBI_genus", "BIBI_family", "FIBI")

diff --git a/inst/shiny-examples/MBSStools/server.R b/inst/shiny-examples/MBSStools/server.R
@@ -10,6 +10,7 @@
 # Packages
 library(shiny)
 library(MBSStools)
+library(DT)
 
 # Define server logic required to draw a histogram
 shinyServer(function(input, output) {
@@ -35,16 +36,37 @@ shinyServer(function(input, output) {
     #          sep = input$sep, quote = input$quote)
   })##output$df_import~END
 
+  output$df_import_DT <- renderDT({
+    # input$df_import will be NULL initially. After the user selects
+    # and uploads a file, it will be a data frame with 'name',
+    # 'size', 'type', and 'datapath' columns. The 'datapath'
+    # column will contain the local filenames where the data can
+    # be found.
+
+    inFile <- input$fn_input
+
+    if (is.null(inFile)){
+      return(NULL)
+    }
+
+    read.csv(inFile$datapath, header = input$header,
+             sep = input$sep, quote = input$quote, stringsAsFactors = FALSE)
+
+    # read.table(file = inFile$datapath, header = input$header,
+    #          sep = input$sep, quote = input$quote)
+
+  })##output$df_import_DT~END
+
   # b_CalcMetVal ####
   # Calculate IBI from df_import
   observeEvent(input$b_CalcMetVal, {
     #
-    df_data <- 'df_import'
+    df_data <- 'df_import_DT'
 
     if (is.null(df_data))
       return(NULL)
 
-    df_data$Person <- "Erik"
+    #df_data$Person <- "Erik"
 
     write.csv(df_data, "MetVal.csv")
 
@@ -53,12 +75,12 @@ shinyServer(function(input, output) {
 
     # myIndex <- input$MMI
     # thresh <- MBSStools::metrics_scoring
-    # myMetrics <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"Metric"])))
-    #
+    # myMetrics <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"MetricNames.Other"])))
+    # #
     # myCommunity <- Community[match(myIndex, MMIs)]
-    #
+    # #
     # myMetric.Values <- metric.values(df_data, myCommunity, myMetrics)
-    #
+    # #
     # return(myMetric.Values)
 
   })##observeEvent~b_CalcIBI~END
@@ -79,7 +101,7 @@ shinyServer(function(input, output) {
 
     myIndex <- input$MMI
     thresh <- MBSStools::metrics_scoring
-    myMetrics <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"Metric"])))
+    myMetrics <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"MetricName.Other"])))
 
     myCommunity <- Community[match(myIndex, MMIs)]
 
@@ -105,7 +127,7 @@ shinyServer(function(input, output) {
 
     myIndex <- input$MMI
     thresh <- MBSStools::metrics_scoring
-    myMetrics <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"Metric"])))
+    myMetrics <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"MetricName.Other"])))
 
     myCommunity <- Community[match(myIndex, MMIs)]
 
@@ -127,14 +149,24 @@ shinyServer(function(input, output) {
 
 
     filename = function() {
-      paste(input$dataset, "_", format(Sys.time(), "%Y%m%d_%H%M%S"), ".csv", sep = "")
+      paste(input$dataset, "_", format(Sys.time(), "%Y%m%d_%H%M%S"), ".zip", sep = "")
     },
-    content = function(file) {
-      write.csv(datasetInput(), file, row.names = FALSE)
-      # Save Values
-      # Save Scores
+    content = function(fname) {##content~START
+      tmpdir <- tempdir()
+      setwd(tempdir())
+      fs <- c("input.csv", "metval.csv", "metsc.csv")
+      file.copy(inFile$datapath, "input.csv")
+      file.copy(inFile$datapath, "metval.csv")
+      file.copy(inFile$datapath, "metsc.csv")
+      # write.csv(datasetInput(), file="input.csv", row.names = FALSE)
+      # write.csv(datasetInput(), file="metval.csv", row.names = FALSE)
+      # write.csv(datasetInput(), file="metsc.csv", row.names = FALSE)
+
       # Create Zip file
-    }
+      zip(zipfile = fname, files=fs)
+      if(file.exists(paste0(fname, ".zip"))) {file.rename(paste0(fname, ".zip"), fname)}
+    }##content~END
+    , contentType = "application/zip"
   )##downloadData~END
 
 })##shinyServer~END
diff --git a/inst/shiny-examples/MBSStools/ui.R b/inst/shiny-examples/MBSStools/ui.R
@@ -10,6 +10,7 @@
 # Packages
 library(shiny)
 library(MBSStools)
+library(DT)
 
 # Define UI for application that draws a histogram
 shinyUI(fluidPage(
@@ -20,7 +21,23 @@ shinyUI(fluidPage(
   # SideBar
   sidebarLayout(
     sidebarPanel(
-      h3("1. Load File")
+      # 0. Progress
+      h3("App Progress")
+      , p("1_LoadData, 2_CalcMetrics, 3_CalcIndex, 4_DownloadResults")
+      , h3("1. Load File")
+      , h4("Select file parameters")
+      , checkboxInput('header', 'Header', TRUE)
+      , radioButtons('sep', 'Separator',
+                     c(Comma=',',
+                       Semicolon=';',
+                       Tab='\t'),
+                     ',')
+      , radioButtons('quote', 'Quote',
+                     c(None='',
+                       'Double Quote'='"',
+                       'Single Quote'="'"),
+                     '"')
+      #, tags$hr()
       , fileInput('fn_input', 'Choose file to upload',
                 accept = c(
                   'text/csv',
@@ -31,19 +48,7 @@ shinyUI(fluidPage(
                   '.tsv'
                 )
       )##fileInput~END
-      , tags$hr()
-      , checkboxInput('header', 'Header', TRUE)
-      , radioButtons('sep', 'Separator',
-                   c(Comma=',',
-                     Semicolon=';',
-                     Tab='\t'),
-                   ',')
-      , radioButtons('quote', 'Quote',
-                   c(None='',
-                     'Double Quote'='"',
-                     'Single Quote'="'"),
-                   '"')
-      , tags$hr()
+      #, tags$hr()
       , h3("2. Calculate IBI")
       , selectInput("MMI", "Select an IBI to calculate:",
                     choices=MMIs)
@@ -57,12 +62,15 @@ shinyUI(fluidPage(
       , downloadButton("b_downloadData", "Download")
 
 
+
+
     )##sidebarPanel~END
     , mainPanel(
         tabsetPanel(type="tabs"
                     , tabPanel("Directions")
                     , tabPanel("Data, Import"
-                               , tableOutput('df_import'))
+                               #, tableOutput('df_import'))
+                               , dataTableOutput('df_import_DT'))
                     , tabPanel("Data, Metric Values"
                                , tableOutput('df_metric_values'))
                     , tabPanel("Data, Metric Scores"

diff --git a/man/MapTaxaObs.Rd b/man/MapTaxaObs.Rd