v2.0.7.9026

- refactor: Move version number from title to about, Issue \#161
- refactor: Add file identifiers to download links, Issue \#160

Author: leppott

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ContDataQC
 Title: Quality Control (QC) of Continous Monitoring Data
-Version: 2.0.7.9025
+Version: 2.0.7.9026
 Authors@R: c(
 	person("Erik W", "Leppo", email="[email protected]",role=c("aut","cre")),
 	person("Ann","Roseberry Lincoln", role="ctb"),
@@ -42,5 +42,5 @@ Remotes:
     tsangyp/StreamThermal,
     jasonelaw/iha
 StagedInstall: no
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Config/testthat/edition: 3

NEWS

@@ -3,10 +3,17 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-01-25 12:04:12.540163
+    #> Last Update: 2024-01-31 14:12:04.111378
 
 # Version History
 
+## v2.0.7.9026
+
+2024-01-31
+
+- refactor: Move version number from title to about, Issue \#161
+- refactor: Add file identifiers to download links, Issue \#160
+
 ## v2.0.7.9025
 
 2024-01-25

NEWS.md

@@ -3,10 +3,17 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-01-25 12:04:12.540163
+    #> Last Update: 2024-01-31 14:12:04.111378
 
 # Version History
 
+## v2.0.7.9026
+
+2024-01-31
+
+- refactor: Move version number from title to about, Issue \#161
+- refactor: Add file identifiers to download links, Issue \#160
+
 ## v2.0.7.9025
 
 2024-01-25

NEWS.rmd

@@ -21,6 +21,12 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## v2.0.7.9026
+2024-01-31
+
+* refactor: Move version number from title to about, Issue #161
+* refactor: Add file identifiers to download links, Issue #160
+
 ## v2.0.7.9025
 2024-01-25
 

data-raw/ProcessRMD_Gibbs_ShinyHTML.R

@@ -4,10 +4,68 @@
 # 2022-09-16
 #~~~~~~~~~~~~~~
 
+# AUTO, RMD 2 HTML ----
+# EWL, 2024-01-31
+# Render RMD to HTML and move to www
 
 # Packages
 # libary(rmarkdown)
 
+# Files
+myFiles <- list.files(path = "inst/shiny-examples/ContDataQC/rmd"
+                      , pattern = "^App_"
+                      , full.names = TRUE)
+
+# Loop over files
+
+
+# Render as HTML
+path_shiny_www <- file.path("inst"
+                            , "shiny-examples"
+                            , "ContDataQC"
+                            , "www"
+                            , "RMD_HTML")
+
+
+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)
+}## FOR ~ i
+
+shell.exec(normalizePath(path_shiny_www))
+
+
+# MANUAL, Move Knitted HTML ----
+# Knit to HTML manually
+# Move those HTML files to www
+
+path_rmd <- file.path("inst", "shiny-examples", "ContDataQC", "rmd")
+path_shiny_www <- file.path("inst", "shiny-examples", "ContDataQC", "www", "RMD_HTML")
+
+# open folder
+shell.exec(normalizePath(path_rmd))
+
+# Copy
+myFile <- list.files(path = path_rmd
+                     , pattern = "^App_.+\\.html$"
+                     , full.names = TRUE)
+file.copy(myFile
+          , file.path(path_shiny_www, basename(myFile))
+          , overwrite = TRUE)
+# Delete
+unlink(myFile)
+
+
+
+
+# OLD code ----
+#
+# Packages
+# libary(rmarkdown)
+
 # # Files
 # path_rmd <- "data-raw/rmd"
 # myFiles <- list.files(path = path_rmd
@@ -33,23 +91,3 @@
 # }## FOR ~ i
 #
 # shell.exec(normalizePath(path_shiny_www))
-
-#______________________________
-# Knit to HTML manually
-
-path_rmd <- file.path("inst", "shiny-examples", "ContDataQC", "rmd")
-path_shiny_www <- file.path("inst", "shiny-examples", "ContDataQC", "www", "RMD_HTML")
-
-# open folder
-shell.exec(normalizePath(path_rmd))
-
-# Copy
-myFile <- list.files(path = path_rmd
-                     , pattern = "^App_.+\\.html$"
-                     , full.names = TRUE)
-file.copy(myFile
-          , file.path(path_shiny_www, basename(myFile))
-          , overwrite = TRUE)
-# Delete
-unlink(myFile)
-

inst/shiny-examples/ContDataQC/external/tab_1_About.R

@@ -7,6 +7,7 @@ function() {
              tabsetPanel(type = "tabs"
 
                          , tabPanel("Overview"
+                                    , p(paste0("Version ", version, "."))
                                     , includeHTML("www/RMD_HTML/App_1a_Overview.html")
                          )## tabPanel ~ END
 

inst/shiny-examples/ContDataQC/global.R

@@ -21,6 +21,9 @@ library(shinyjs)
 # #access Window's zipping abilities
 # Sys.setenv(PATH = paste(Sys.getenv("PATH"), "C:\\Rtools\\bin", sep = ";"))
 
+# Version Number
+version <- "2.0.7.9026"
+
 #Maximum individual file size that can be uploaded is 70 MB
 options(shiny.maxRequestSize = 70 * 1024^2)
 

inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.rmd

@@ -33,7 +33,7 @@ The ContDataQC R package and Shiny app were developed with the following objecti
 
 The figure below lays out the general workflow for using the ContDataQC R tools. Items in bold blue text show functions that can be performed with ContDataQC.
 
-Want to try it yourself? Click [here](Custom_QC_Config_ECO66G20_test1.R) to 
+Want to try it yourself? Click [here](Custom_QC_Config_ECO66G20_test1.R) [R] to 
 download test files.
 
 ![ContDataQC Shiny App workflow](RMD_Images/1.1_Fig1_About_20230828.jpg){width=95%}

inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd

@@ -23,7 +23,7 @@ if(boo_DEBUG==TRUE){
 There are two sets of test files, one from Onset HOBO U20 water level loggers (non-vented pressure transducers) and one from a miniDOT DO sensor. We are happy to add more test data to this website. If you have example files that you would like to contribute, please send them to Jen Stamp ([Jen.Stamp\@tetratech.com](mailto:[email protected]){.email}).
 
 # Onset HOBO
-The Onset HOBO U20 files can be downloaded [here](TestData_HOBOU20_20220822.zip).
+The Onset HOBO U20 files can be downloaded [here](TestData_HOBOU20_20220822.zip) [ZIP].
 The test data consist of two comma-separated values (CSV) files. The files are from the same site but cover two different time periods. 
 
 * **Test**
@@ -36,7 +36,7 @@ The test data consist of two comma-separated values (CSV) files. The files are f
 
 # miniDOT DO Sensors
 
-The miniDOT DO test files can be downloaded [here](TestData_miniDOT.zip).
+The miniDOT DO test files can be downloaded [here](TestData_miniDOT.zip) [ZIP].
 They are from one site and one deployment period.
 You’ll see two sets of folders. Within each folder are example input and output files.
 

inst/shiny-examples/ContDataQC/rmd/App_1d_Tips.rmd

@@ -40,21 +40,21 @@ people using the data decide whether to remove questionable measurements from
 their analysis. 
 
 *	Document that you checked each point flagged as ‘F’ and ‘S’ by adding a data 
-qualifier to the Comment column. Click [here](DataQualifiers_20220210.xlsx) to 
+qualifier to the Comment column. Click [here](DataQualifiers_20220210.xlsx) [XLSX] to 
 download the list of data qualifiers currently being used by RMN partners.
 
 *	Leave missing data cells blank.
 
 ## Workflow
 
-Click [here](Workflow_QC_report_20220824.pdf) for recommendations on a workflow
+Click [here](Workflow_QC_report_20220824.pdf) [PDF] for recommendations on a workflow
 for reviewing the QC reports.
 
 If you have a backlog of data files from multiple deployments and are wondering 
-how to most efficiently QC the files, [here](Workflow_DataPileup_20220824.pdf) 
+how to most efficiently QC the files, [here](Workflow_DataPileup_20220824.pdf) [PDF] 
 is a recommended workflow.
 
-Click [here](SiteVisitChecklist.zip) for a site visit checklist to help ensure 
+Click [here](SiteVisitChecklist.zip) [ZIP] for a site visit checklist to help ensure 
 that you do not forget to document information that is important for the data QC
 process.
 
@@ -64,12 +64,12 @@ Some people have had problems with air and water sensors being out of sync (
 e.g., one records at 11:00 and the other records at 11:07). If you are deploying
 air and water sensors at a site, make sure they are recording at the same time. 
 This will make data processing faster and easier. If you are using Onset HOBO 
-sensors, click [here](HOBO_ConfigLaunch_20170803.pdf) for tips on configuring 
+sensors, click [here](HOBO_ConfigLaunch_20170803.pdf) [PDF] for tips on configuring 
 them in a way that ensures they will record at the same time. 
 
 Another issue that sometimes occurs is data overlap (where more than one file 
 has measurements covering part of the same time periods). If you are using Onset
-HOBO sensors, click [here](HOBO_DataDownload_20170823.pdf) for procedures to 
+HOBO sensors, click [here](HOBO_DataDownload_20170823.pdf) [PDF] for procedures to 
 follow during data download to clear sensor memory and avoid overlapping data.
 
 ## Accuracy checks
@@ -79,20 +79,20 @@ lab and/or in the field with sensor measurements from the closest date/time. The
 sensor measurement should be within the accuracy quoted by the manufacturer (
 e.g., ±0.2°C if you are using the Onset HOBO proV2 sensor). Accuracy checks are 
 used to validate your data, and in some cases, correct for sensor drift. Click 
-[here](EXAMPLE_AccuracyCheckWkst.xlsx) to download an example of an accuracy 
+[here](EXAMPLE_AccuracyCheckWkst.xlsx) [XLSX] to download an example of an accuracy 
 check worksheet being kept by an RMN partner. 
 
 ## Visual checks of time series plots
 
 Visual checks of time series plots are an important part of the QC process. 
-Click [here](PlotQC_WatchList_20220824.pdf) to see a compilation of patterns to 
+Click [here](PlotQC_WatchList_20220824.pdf) [PDF] to see a compilation of patterns to 
 watch for when interpreting the plots. They include ice cover, beaver activity, 
 leaf packs, dewatering, and dead batteries. We will continue to add slides to 
 this as we receive materials.
 
 ## Checking sensor data against other data sources
 
-This is optional but encouraged if time permits. Click [here](Daymet_Wx_Gage.zip) for instructional 
+This is optional but encouraged if time permits. Click [here](Daymet_Wx_Gage.zip) [ZIP] for instructional 
 materials from David Smith (Kentucky Division of Water) on how he has been 
 downloading data from nearby weather stations and USGS gages, as well as modeled
 air temperature and precipitation data from Daymet (