merged folders

Author: eduardszoecs

mesocosm/prc/.gitignore

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+.Rproj.user
+.Rhistory
+.RData

mesocosm/prc/prc.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes

mesocosm/prc/server.R

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+library(shiny)
+library(vegan)
+data(pyrifos)
+time <- gl(11, 12, labels=c(-4, -1, 0.1, 1, 2, 4, 8, 12, 15, 19, 24))
+treatment <- factor(rep(c(0.1, 0, 0, 0.9, 0, 44, 6, 0.1, 44, 0.9, 0, 6), 11))
+replicate <- gl(12, 1, length=132)
+envdata <- data.frame(replicate, treatment, time)
+
+
+shinyServer(function(input, output){
+  abu <- reactive({
+      abufile <- input$abufile
+      if (input$example == TRUE & is.null(abufile)) {
+        pyrifos
+      } else {
+        if (input$example == FALSE & !is.null(abufile)) {
+          read.csv(
+            file = abufile$datapath,
+            header = input$header,
+            sep = input$sep,
+            quote = input$quote
+            )
+        }	
+      }
+      })
+
+  env <- reactive({
+    envfile <- input$envfile
+    if (input$example == TRUE & is.null(envfile)) {
+      envdata
+    } else {
+      if (input$example == FALSE & !is.null(envfile)) {
+        read.csv(
+          file = envfile$datapath,
+          header = input$header,
+          sep = input$sep,
+          quote = input$quote
+        )
+      }  
+    }
+  })
+  
+  
+  output$abutable <- renderTable({
+    abu()[1:10 , 1:10]
+    })
+  
+  output$envtable <- renderTable({
+    env()[1:10, ]
+  })
+})

mesocosm/prc/ui.R

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+#runApp('C:\\Users\\pbuttigi\\Documents\\Revolution\\EATME\\RDA', launch.browser = FALSE)
+
+library(shiny)
+library(markdown)
+
+shinyUI(
+  navbarPage("PRC",
+             tabPanel('Data'),
+             sidebarLayout(
+                sidebarPanel(
+                  tabsetPanel(
+                    tabPanel("Example data", 
+                            h4("Use example data"),
+                            p("Tick the box below if you'd like to use the chlorpyrifos' dataset:"),
+                            checkboxInput('example', 'Use Chlorpyrifos dataset', FALSE),
+                            h4("Download example data"),
+                            p("Alternatively, you can download both data files here and upload them in the next tab.")
+                            ),
+                    tabPanel("Data Upload",
+                              h3("Upload data in csv format"),
+                              h4("CSV settings:"),
+                              h5(strong("Header")),
+                              checkboxInput('header', 'first row contains column names', TRUE),
+                              radioButtons(
+                                inputId = 'sep',
+                                label = 'Separator',
+                                choices = c(
+                                  Comma = ',',
+                                  Semicolon = ';',
+                                  Tab = '\t'
+                                  )
+                                ),
+                              radioButtons(
+                                inputId = 'quote',
+                                label = 'Quotes',
+                                choices = c(
+                                  'Double quotes' = '"',
+                                  'Single quotes' = "'",
+                                  'None' = ''
+                                )
+                              ), 
+                            h5(strong("Abundance data")),
+                            fileInput(
+                              inputId = 'abufile', 
+                              label = 'Select a CSV file with samples as rows and species as columns.',
+                              accept = c('text/csv','text/comma-separated-values','.csv')
+                            ),
+                            h5(strong("Explanatory data")),
+                            fileInput(
+                              'envfile', 
+                              'Select a CSV file with three columns: time, treatment and replicat. ',
+                              accept = c('text/csv','text/comma-separated-values','.csv')
+                              )
+                            )
+                    )
+                  ),
+                mainPanel(
+                  h3("Abundance data"),
+                  p("Displaying first 10 species, and rows"),
+                  tableOutput("abutable"),
+                  h3("Env data"),
+                  p("Displaying first 10 rows"),
+                  tableOutput("envtable")
+                  ),
+                ),
+             tabPanel('Transformations'),
+             tabPanel('Plot'),
+             tabPanel('Summary'),
+             tabPanel('Population level statistics')
+             ))

power_ecotox

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+Subproject commit b262ed268700ec29f4e5fbdfd5d10227772d131f