README.md

In misasa/chelyabinsk: Express geochemical datasets

r package -- chelyabinsk

R package for geochemical datasets

Description

R package for geochemical datasets. This package reads and processes geochemical datasets, downloads CASTEML from Medusa, processes IONML, and plots typical geochemical datasets.

See manual at `https://dream.misasa.okayama-u.ac.jp/documentation/chelyabinsk-manual.pdf'. See shiny project -- VisualAnalysis that refers to this package.

Dependency

gem package -- casteml

r package -- MedusaRClient

User's guide

To install this package issue following command.

R> install.packages('devtools')
R> devtools::install_github('misasa/chelyabinsk')
R> devtools::install_github('misasa/MedusaRClient')
R> library('chelyabinsk')
R> cbk.path("periodic-dflame0.csv")

Check a directory for packages ~/R/win-library/ when necessary. When you see message such like below, try following.

Error in curl::curl_fetch_disk(url, x$path, handle = handle) :   Problem with the SSL CA cert (path? access rights?

R> install.packages(c("curl", "httr"))

Examples to plot analyses related to a stone and its descendants are shown below. Issue following commands.

$ Rscript -e "chelyabinsk::cbk.plot(\"20130528105235-594267\", category=\"trace\")"

R> library(chelyabinsk)
R> pmlame <- cbk.read.casteml("20130528105235-594267")
R> cbk.plot.spider(pmlame,property="atomicnumber",reference="Wasson.1988")

Or write a Rscript with following lines.

#!/usr/bin/env Rscript
library(chelyabinsk)
rplotfile <- 'Rplots.pdf'; pdf(rplotfile)
cbk.plot("20130528105235-594267")
dev.off()

Developer's guide

1. Clone the project from GitHub and install appropriate packages.

https://github.com/misasa/chelyabinsk

$ cd ~/devel-godigo
$ git clone https://github.com/misasa/chelyabinsk.git
R> install.packages('testthat')
R> install.packages("roxygen2")

1. Locate your script with a function to directory "R". Write document with rule of Roxygen2. Do not use |#' | in main code besides the documentation in Roxygen2.

2. Update version number in ./DESCRIPTION and generate Rdoc by following commands.

$ cd ~/devel-godigo/chelyabinsk
$ Rscript -e "devtools::document()"

R> setwd(path.expand("~/devel-godigo/chelyabinsk"))
R> devtools::document()

1. Run test.

$ vi ./tests/testthat/test-mytest.R
$ R CMD check ../chelyabinsk

1. Update manual.

Copy manual automatically created by roxygen to https://dream.misasa.okayama-u.ac.jp/documentation/chelyabinsk-manual.pdf when necessary.

$ cp ./chelyabinsk.Rcheck/chelyabinsk-manual.pdf ~/devel-godigo/documentation/

1. Push to the server or build/install locally. An example of local installation is shown below.

$ R CMD build ../chelyabinsk
$ R CMD install chelyabinsk_1.0.tar.gz

Developer's TODO

1. Update R scripts in https://github.com/misasa/casteml/tree/master/template/plot
2. Write document in texinfo
3. Convert inst/extdata/periodic-table.csv to more handy format
4. Suppress Warnings on check

Developer's TODO (done)

1. Write document in each function by Roxygen2
2. Write test code
3. Write document in R/chelyabinsk-package.R
4. Have inst/extdata/ref.csv in casteml-dataframe format ref1.dataframe
5. Revise cbk.ref.R accordingly or create new function

misasa/chelyabinsk documentation built on Nov. 24, 2020, 5:47 a.m.