v2.0.6.9025

2022-06-07 - fix: Modify config.R for salinity, Issue #138 - Update other copies in package - feature: Begin adding miniDOT to shiny, Issue #141
leppott · Jun 7, 2022 · 2a39ce6 · 2a39ce6
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ContDataQC
 Title: Quality Control (QC) of Continous Monitoring Data
-Version: 2.0.6.9024
+Version: 2.0.6.9025
 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
@@ -3,10 +3,17 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2022-05-31 12:48:48
+    #> Last Update: 2022-06-07 09:47:51
 
 # Version History
 
+## v2.0.6.9025
+
+2022-06-07
+
+-   fix: Modify config.R for salinity, Issue #138
+    -   Update other copies in package
+
 ## v2.0.6.9024
 
 2022-05-31

diff --git a/NEWS.md b/NEWS.md
@@ -3,10 +3,17 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2022-05-31 12:48:48
+    #> Last Update: 2022-06-07 09:47:51
 
 # Version History
 
+## v2.0.6.9025
+
+2022-06-07
+
+-   fix: Modify config.R for salinity, Issue #138
+    -   Update other copies in package
+
 ## v2.0.6.9024
 
 2022-05-31

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -21,6 +21,12 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## v2.0.6.9025
+2022-06-07
+
+* fix: Modify config.R for salinity, Issue #138
+    + Update other copies in package
+
 ## v2.0.6.9024
 2022-05-31
 

diff --git a/R/config.R b/R/config.R
@@ -293,6 +293,7 @@ ContData.env$myNames.DataFields <- c(ContData.env$myName.WaterTemp
                                      , ContData.env$myName.Turbidity
                                      , ContData.env$myName.Chlorophylla
                                      , ContData.env$myName.WaterLevel
+									                   , ContData.env$myName.Salinity
                                      , ContData.env$myName.Discrete.WaterTemp
                                      , ContData.env$myName.Discrete.AirTemp
                                      , ContData.env$myName.Discrete.WaterP
@@ -323,6 +324,7 @@ ContData.env$myNames.DataFields.Lab <- c(ContData.env$myLab.WaterTemp
                                          , ContData.env$myLab.Turbidity
                                          , ContData.env$myLab.Chlorophylla
                                          , ContData.env$myLab.WaterLevel
+                                         , ContData.env$myLab.Salinity
                                          , ContData.env$myLab.Discrete.WaterTemp
                                          , ContData.env$myLab.Discrete.AirTemp
                                          , ContData.env$myLab.Discrete.WaterP
@@ -365,6 +367,7 @@ ContData.env$myNames.Order <- c(ContData.env$myName.SiteID
                                 , ContData.env$myName.Turbidity
                                 , ContData.env$myName.Chlorophylla
                                 , ContData.env$myName.WaterLevel
+                                , ContData.env$myName.Salinity
                                 , ContData.env$myName.LoggerID.Water
                                 , ContData.env$myName.RowID.Water
                                 , ContData.env$myName.Discrete.WaterTemp

diff --git a/data-raw/ProcessFileCopy_Config.R b/data-raw/ProcessFileCopy_Config.R
@@ -20,6 +20,11 @@ config.from <- file.path(".", "R", "config.R")
 config.to.template <- file.path(".", "inst", "shiny-examples", "ContDataQC"
                                , "www", "Config_Template.R")
 file.copy(config.from, config.to.template, overwrite = TRUE)
+#
+config.from <- file.path(".", "R", "config.R")
+config.to.template <- file.path(".", "inst", "shiny-examples", "ContDataQC"
+                                , "www", "Config_Default.R")
+file.copy(config.from, config.to.template, overwrite = TRUE)
 
 # 3. Copy to extdata
 config.from <- file.path(".", "R", "config.R")

diff --git a/data-raw/ProcessRMD_ShinyHTML.R b/data-raw/ProcessRMD_ShinyHTML.R
@@ -0,0 +1,53 @@
+# Create HTML files for use with Shiny app
+# Erik.Leppo@tetratech.com
+# 2022-06-01
+#~~~~~~~~~~~~~~
+
+
+# Packages
+# libary(rmarkdown)
+
+# # Files
+# path_rmd <- "data-raw/rmd"
+# myFiles <- list.files(path = path_rmd
+#                       , pattern = "^App_.+\\.Rmd$"
+#                       , full.names = TRUE)
+# #myFiles <- myFiles[!myFiles %in% "data-raw/RMD/ShinyHTML_About.Rmd"]
+#
+# # Loop over files
+#
+#
+# # Render as HTML
+# path_shiny_www <- file.path("inst", "shiny-examples", "ContDataQC", "www")
+#
+#
+# for(i in myFiles) {
+#   # file name w/o extension
+#   #i_fn <- tools::file_path_sans_ext(basename(i))
+#   # save to HTML
+#   rmarkdown::render(input = i
+#                     , output_dir = path_shiny_www
+#                 #, output_format = rmarkdown::html_fragment(df_print = "kable")
+#                 )
+# }## FOR ~ i
+#
+# shell.exec(normalizePath(path_shiny_www))
+
+#______________________________
+# Knit to HTML manually
+
+path_rmd <- "data-raw/rmd"
+path_shiny_www <- file.path("inst", "shiny-examples", "ContDataQC", "www")
+
+# open folder
+shell.exec(normalizePath(path_rmd))
+
+# Copy
+myFile <- list.files(path = path_rmd
+                     , pattern = "^App_.+\\.html$"
+                     , full.names = TRUE)
+file.copy(myFile
+          , file.path(path_shiny_www, basename(myFile))
+          , overwrite = TRUE)
+# Delete
+unlink(myFile)
diff --git a/data-raw/rmd/App_2eDataPrep.Rmd b/data-raw/rmd/App_2eDataPrep.Rmd
@@ -0,0 +1,28 @@
+---
+title: "DataPrep_miniDOT_Cat"
+output: html_fragment
+---
+```{r setup, include=FALSE}
+# ---
+# title: "DataPrep_miniDOT_Cat"
+# date: '2022-06-01'
+# ---
+knitr::opts_chunk$set(echo = FALSE)
+```
+
+# miniDOT Concatenate
+
+This function compiles Dissolved Oxygen data files downloaded from PME miniDot 
+DO loggers. Use if the data where not compiled using the PME java app on the 
+logger.
+
+All files uploaded will be merged into a single multi-column CSV file.
+
+## Examples
+
+Example images of before and and after performing reformat.
+
+![Raw miniDOT file](miniDOT_1raw.png)
+
+
+![Concatenated miniDOT file](miniDOT_2cat.png)
diff --git a/data-raw/rmd/App_2fDataPrep.Rmd b/data-raw/rmd/App_2fDataPrep.Rmd
@@ -0,0 +1,43 @@
+---
+title: "DataPrep_miniDOT_Reformat"
+output: html_fragment
+---
+```{r setup, include=FALSE}
+# ---
+# title: "DataPrep_miniDOT_Reformat"
+# date: '2022-06-01'
+# ---
+knitr::opts_chunk$set(echo = FALSE)
+```
+
+# miniDOT Reformat
+
+The miniDOT reformat function will convert the concatenated miniDOT file to the standard expected input for use with ContDataQC.
+
+The CSV output of this function should be placed in the Data0_Original folder.
+
+## Instructions
+
+* Click the ‘Browse’ button and select the input file(s). You can run multiple files at once. The status bar will tell you when the upload is complete.
+
+* Click the ‘Reformat miniDOT file(s)’ button; a status bar will appear in the lower right corner.
+
+* After the function is done running, a ‘Download’ button will appear. Click this button.
+
+* Save the zipped file in the Data1_RAW folder
+
+* Your files are now ready to be run through the QC function!
+
+## Common errors -
+
+* DO percent saturation values of all NA.  This is caused by the miniDOT cat program when no inputs are provided to calculate DO percent saturation.  All NA values will cause no statistics to be generated for this parameter later in the QC process.
+
+## Examples
+
+Example images of before and and after performing reformat.
+
+![Concatenated miniDOT file](miniDOT_2cat.png)
+
+
+![Reformated miniDOT file](miniDOT_3reformat.png)
+
diff --git a/data-raw/rmd/miniDOT_1raw.png b/data-raw/rmd/miniDOT_1raw.png
diff --git a/data-raw/rmd/miniDOT_2cat.png b/data-raw/rmd/miniDOT_2cat.png
diff --git a/data-raw/rmd/miniDOT_3reformat.png b/data-raw/rmd/miniDOT_3reformat.png
diff --git a/inst/extdata/config.ORIG.R b/inst/extdata/config.ORIG.R
@@ -293,6 +293,7 @@ ContData.env$myNames.DataFields <- c(ContData.env$myName.WaterTemp
                                      , ContData.env$myName.Turbidity
                                      , ContData.env$myName.Chlorophylla
                                      , ContData.env$myName.WaterLevel
+									                   , ContData.env$myName.Salinity
                                      , ContData.env$myName.Discrete.WaterTemp
                                      , ContData.env$myName.Discrete.AirTemp
                                      , ContData.env$myName.Discrete.WaterP
@@ -323,6 +324,7 @@ ContData.env$myNames.DataFields.Lab <- c(ContData.env$myLab.WaterTemp
                                          , ContData.env$myLab.Turbidity
                                          , ContData.env$myLab.Chlorophylla
                                          , ContData.env$myLab.WaterLevel
+                                         , ContData.env$myLab.Salinity
                                          , ContData.env$myLab.Discrete.WaterTemp
                                          , ContData.env$myLab.Discrete.AirTemp
                                          , ContData.env$myLab.Discrete.WaterP
@@ -365,6 +367,7 @@ ContData.env$myNames.Order <- c(ContData.env$myName.SiteID
                                 , ContData.env$myName.Turbidity
                                 , ContData.env$myName.Chlorophylla
                                 , ContData.env$myName.WaterLevel
+                                , ContData.env$myName.Salinity
                                 , ContData.env$myName.LoggerID.Water
                                 , ContData.env$myName.RowID.Water
                                 , ContData.env$myName.Discrete.WaterTemp

diff --git a/inst/shiny-examples/ContDataQC/external/tab_2DataPrep.R b/inst/shiny-examples/ContDataQC/external/tab_2DataPrep.R
@@ -53,7 +53,59 @@ function() {
                                               , height = 600, width = 1000)
                                       ) ## mainPanel ~ END
                                     )# sidebarLayout~ END
-                         )## tabPanel  ~ END
+                         )## tabPanel ~ HOBO ~ END
+                         , tabPanel("miniDOT Concatenate"
+                                    , sidebarLayout(
+                                      sidebarPanel(
+                                        tags$div(title = "Select one miniDOT csv files to upload here"
+                                                 , fileInput("selectedFiles_miniDOT"
+                                                             , label = "Choose files"
+                                                             , multiple = TRUE
+                                                             , accept = ".csv"
+                                                             , width = "600px") # same as HOBO
+                                        )##tags$div ~ END
+                                        #Only shows the "Run operation" button after data are uploaded
+                                        ,tags$div(title="Click to run selected operation (miniDOT reformat)"
+                                                  ,uiOutput('ui.runProcess_miniDOT')
+                                        )# tags$div ~ END
+                                        , br()
+                                        #Only shows the "Download" button after the process has run
+                                        ,tags$div(title="Click to download your data"
+                                                  ,uiOutput('ui.downloadData_miniDOT')
+                                        )# tags$div ~ END
+                                      )# sidebarPanel~ END
+                                      , mainPanel(
+                                        includeHTML("www/App_2eDataPrep.html")
+
+                                      ) ## mainPanel ~ END
+                                    )# sidebarLayout~ END
+                         )## tabPanel ~ miniDOT cat ~ END
+                         , tabPanel("miniDOT Reformat"
+                                    , sidebarLayout(
+                                      sidebarPanel(
+                                        tags$div(title = "Select one miniDOT csv files to upload here"
+                                                 , fileInput("selectedFiles_miniDOT"
+                                                             , label = "Choose files"
+                                                             , multiple = TRUE
+                                                             , accept = ".csv"
+                                                             , width = "600px") # same as HOBO
+                                                 )##tags$div ~ END
+                                        #Only shows the "Run operation" button after data are uploaded
+                                        ,tags$div(title="Click to run selected operation (miniDOT reformat)"
+                                                  ,uiOutput('ui.runProcess_miniDOT')
+                                        )# tags$div ~ END
+                                        , br()
+                                        #Only shows the "Download" button after the process has run
+                                        ,tags$div(title="Click to download your data"
+                                                  ,uiOutput('ui.downloadData_miniDOT')
+                                        )# tags$div ~ END
+                                      )# sidebarPanel~ END
+                                      , mainPanel(
+                                        includeHTML("www/App_2fDataPrep.html")
+
+                                      ) ## mainPanel ~ END
+                                    )# sidebarLayout~ END
+                         )## tabPanel ~ miniDOT reformat ~ END
              )## tabsetPanel ~ END
            )## mainPanel ~ END
   ) ## tabPanel ~ Config ~ END