In leppott/baytrends: Long Term Water Quality Trend Analysis

Helper code for creating library.

[e-mail] 2017-09-26

Copied from ContDataQC so some parts are not needed. 2017-12-04.

Package

Package related code.

Vignette

1. Need to run code below to add data to "vignette" directory so it will work.

# 1. change wd to vignettes
setwd(file.path("C:","Users","Erik.Leppo","OneDrive - Tetra Tech, Inc"
                ,"MyDocs_OneDrive","GitHub","ContDataQC","vignettes"))
#
# 2. Add data for vignette examples
# Parameters
Selection.Operation <- c("GetGageData","QCRaw", "Aggregate", "SummaryStats")
Selection.Type      <- c("Air","Water","AW","Gage","AWG","AG","WG")
Selection.SUB <- c("Data1_RAW","Data2_QC","Data3_Aggregated","Data4_Stats")
myDir.BASE <- getwd()
#
# Create data directories
myDir.create <- paste0("./",Selection.SUB[1])
  ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists")
myDir.create <- paste0("./",Selection.SUB[2])
  ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists")
myDir.create <- paste0("./",Selection.SUB[3])
  ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists")
myDir.create <- paste0("./",Selection.SUB[4])
  ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists")
#
# Save example data (assumes directory ./Data1_RAW/ exists)
myData <- data_raw_test2_AW_20130426_20130725
  write.csv(myData,paste0("./",Selection.SUB[1],"/test2_AW_20130426_20130725.csv"))
myData <- data_raw_test2_AW_20130725_20131015
  write.csv(myData,paste0("./",Selection.SUB[1],"/test2_AW_20130725_20131015.csv"))
myData <- data_raw_test2_AW_20140901_20140930
  write.csv(myData,paste0("./",Selection.SUB[1],"/test2_AW_20140901_20140930.csv"))
myData <- data_raw_test4_AW_20160418_20160726
  write.csv(myData,paste0("./",Selection.SUB[1],"/test4_AW_20160418_20160726.csv"))
myFile <- "config.TZ.Central.R"
  file.copy(file.path(path.package("ContDataQC"),"extdata",myFile)
            ,file.path(getwd(),Selection.SUB[1],myFile))

1. Knit the vignette in the vignette folder to ensure all of the code works and is properly displayed. This can take 2 to 5 min.

2. Use the code below to "build" the vignette and then use it in the pkg.

# generate Vignette
library(baytrends)
library(devtools)
devtools::build_vignettes()

# create vignette folder and default file
#devtools::use_vignette("ContDataQC_Vignette")

devtools::build() more useful and build_vignettes()

Create Package PDF reference manual

http://www.dominikschauer.com/how-to-create-an-r-package-including-documentation-vignettes-and-a-manual/

myLibrary <- "baytrends"
setwd(paste0("./", myLibrary))
system("R CMD Rd2pdf . --title=Package baytrends --output=./manual.pdf --force --no-clean --internals")

Create Package

Use the code below to create the package. Assumes you are in the development package directory

Delete Namespace, Collate section of DESCRIPTION, and \man\*

Need to remove end of line after Collate. Need first entry on the same line as "Collate:".

# Library Name
myLibrary <- "baytrends"
# Load Library
#library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# NEWS
#setwd(file.path(".", myLibrary))

# Render then Copy NEWS so picked up in help
rmarkdown::render("NEWS.rmd", "all")
file.copy("NEWS.md", "NEWS", overwrite = TRUE)
file.remove("NEWS.html")
#file.remove("NEWS.md")
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# # Library Name
# myLibrary <- "baytrends"
# # Load Library
# library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
#setwd(paste0("./", myLibrary))
devtools::document()
## Install New Package (locally)
#setwd("..") # return to root directory first
devtools::install(".", quick=FALSE, reload=TRUE, build_vignettes = TRUE)

# blank line above ensures no "updates" to packages.
# ## Reload library
# library(myLibrary, character.only = TRUE)
# change wd back to package
#setwd(file.path(".", myLibrary))
help(package=(myLibrary))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

After creating the package reload it after restarting R within RStudio (Ctrl + Shift + F10).

# Restart R within RStudio:  Ctrl + Shift + F10
library("baytrends")
help(package="baytrends")

Use pkgdown to build website. Will need to rebuild the package to include the new material.

Can use GitHub Actions to build instead of doing manually.

library(pkgdown)
pkgdown::build_site()

Downstream dependancies

# Downstream dependencies
devtools::revdep("baytrends")

URL check

urlchecker::url_check()

Check

# Check for errors (or press Cmd + Shift + E in RStudio)
#http://r-pkgs.had.co.nz/check.html
devtools::check()

If use RStudio, Build - Check Package, the output is easier to read.

Check failures (single vector so not very useful) but puts it all in one place. Have to run after using Check.

library(devtools)
# dir.check <- "C:\\Users\\Erik.Leppo\\OneDrive - Tetra Tech, Inc\\MyDocs_OneDrive\\GitHub\\baytrends.Rcheck"
dir.check <- file.path(dirname(getwd()), "baytrends.Rcheck")
#
check_failures(dir.check)
# 20240726, no longer a function

check on Linux

https://r-hub.github.io/rhub/index.html https://r-hub.github.io/rhub/articles/rhub.html

library(rhub)
# validate email
validate_email()
# run check (interactive for platform)
check()

# recommended prior to CRAN submission
check_for_cran() # win and linux

check_on_linux()

20240726, above no longer works since v2

Run all Examples.

# point to directory
devtools::run_examples(pkg = ".")

Alternate is testthat::test_examples() but is redundant with R CMD check.

code coverage

#library(covr)
covr::report()

Check functions and such

Index

Go straight to index.

help(package="baytrends")

Open Vignette

browseVignettes("baytrends")

Then click on "HTML" to open.

Run examples

example(analysisOrganizeData)

Test

Run all tests.

devtools::test()

Including Data

All data should have already been created.

Testings

https://testthat.r-lib.org/

https://r-pkgs.org/tests.html

Set up folders with devtools::test(). This is also the command to run tests.

Create test file usethis::use_test("name")

CI, Badges, Code Coverage, etc

• Continuous Integration with GitHub Actions (TravisCI shut down Dec 2020)
• Code Quality (CodeFactor)
  • CodeFactor.io
    • GitHub login
• Code Coverage (testing)
  • Codecov.io
    • GitHub login
    • After set up CI with GitHub Actions
• Package website (pkgdown and GitHub Action)
  • branch gh-pages, auto updates with each commit
  • Update in settings the location
• Badges; Maintained, Life Cycle, License, Issues, etc
  • https://github.com/GuangchuangYu/badger
    • Commands to create badges

badger package creates the text for pkg readme file.

Also https://shields.io/
https://github.com/badges/shields Can make some badges dynamic, static ones below

issues

release

downloads

pkg_GH <- "tetratech/baytrends"
pkg_lic <- "GPL-3"

# GitHub Action, CI
usethis::use_github_actions()
usethis::use_github_actions_badge()
# badger::badge_github_actions(pkg_GH)

# Code coverage
usethis::use_github_action("test-coverage")

# GitHub Action, pkgdown
usethis::use_github_action("pkgdown")

# Badges
# lifecycle
badger::badge_lifecycle("stable", "green") # stable/green, maturing/dormant/blue
# maintained
# license
badger::badge_license(pkg_lic)
# code quality
badger::badge_codefactor(pkg_GH)
# code testing coverage
badger::badge_codecov(pkg_GH)
# cmd check
badger::badge_github_actions(pkg_GH)

Test

Need to use testthat but not to that stage yet.

RStudio, Build - Test Package.

Other Stuff

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Upload to Github via GitHub Desktop utility
# 0. download from web via "clone or download" via "Open in Desktop" (GitHub Desktop) if not already in GitHub Desktop
# 1. Make changes in download/clone folder. (done above)
# 3. Open GH Desktop commit changes then sync.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# install from GitHub (via devtools)
devtools::install_github(paste0("leppott/",myLibrary))
#



#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# remove installed packages (if needed for troubleshooting)
search() # find
#detach(3) # remove by number
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


# to build package
#https://thepoliticalmethodologist.com/2014/08/14/building-and-maintaining-r-packages-with-devtools-and-roxygen2/
# To build the package as a compressed file in your working directory, run build(current.code, path=getwd()).

# to save internal data for examples
# example
#http://r-pkgs.had.co.nz/data.html#data-sysdata
# have to be at root directory (above package)
#devtools::use_data(NV.predictors,NV.bugs,pkg="MMIcalcNV",internal=TRUE,overwrite=TRUE)
## verify with data()

# To save RMD files
# http://stackoverflow.com/questions/30377213/how-to-include-rmarkdown-file-in-r-package
# /pkg/inst/rmd/
# system.file("rmd/file.Rmd", package="packagename")
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/
# Create Package
# create(myLibrary)

Test Stats only

# Parameters
Selection.Operation <- c("GetGageData","QCRaw", "Aggregate", "SummaryStats")
Selection.Type      <- c("Air","Water","AW","Gage","AWG","AG","WG")
Selection.SUB <- c("Data1_RAW","Data2_QC","Data3_Aggregated","Data4_Stats")
myDir.BASE <- getwd()
#
# Summary Stats, File
## Have to use "file" version.  
## Base version builds file name and expects "DATA" prefix

# Gage File + Other File
myData.Operation <- "SummaryStats" #Selection.Operation[4]
myFile <- c("Data4Stats_01187300_Gage_20130101_20141231.csv"
            ,"Data4Stats_test2_Aw_20130101_20141231.csv")
myDir.import <- file.path(".","data-raw")
myDir.export <- file.path(".","Data4_Stats")

#Leave off myReport.format and get default (docx).
ContDataQC(myData.Operation
           , fun.myDir.import=myDir.import
           , fun.myDir.export=myDir.export
           , fun.myFile=myFile)

SiteID, Date, Time, Date.Time, Parameters, Flag.Parameters

Only one flag per parameter. Do not need individual test flags.

"F" (fail) flags are changed to NA so they are dropped from the statistics that calculated.

Mocked up 2 files.

leppott/baytrends documentation built on July 29, 2024, 10:29 p.m.