diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..42a2a3d --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,7 @@ +^.*\.Rproj$ +^\.Rproj\.user$ +^CONDUCT\.md$ + +README.Rmd +README.md +README_cache diff --git a/.gitignore b/.gitignore index 1b65020..2ecf144 100644 --- a/.gitignore +++ b/.gitignore @@ -24,3 +24,6 @@ r_kehra.Rproj data/* images/* *.tar.gz + +README_cache +kehra.Rproj diff --git a/CONDUCT.md b/CONDUCT.md new file mode 100644 index 0000000..52a673e --- /dev/null +++ b/CONDUCT.md @@ -0,0 +1,25 @@ +# Contributor Code of Conduct + +As contributors and maintainers of this project, we pledge to respect all people who +contribute through reporting issues, posting feature requests, updating documentation, +submitting pull requests or patches, and other activities. + +We are committed to making participation in this project a harassment-free experience for +everyone, regardless of level of experience, gender, gender identity and expression, +sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion. + +Examples of unacceptable behavior by participants include the use of sexual language or +imagery, derogatory comments or personal attacks, trolling, public or private harassment, +insults, or other unprofessional conduct. + +Project maintainers have the right and responsibility to remove, edit, or reject comments, +commits, code, wiki edits, issues, and other contributions that are not aligned to this +Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed +from the project team. + +Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by +opening an issue or contacting one or more of the project maintainers. + +This Code of Conduct is adapted from the Contributor Covenant +(http:contributor-covenant.org), version 1.0.0, available at +http://contributor-covenant.org/version/1/0/0/ diff --git a/kehra/DESCRIPTION b/DESCRIPTION similarity index 98% rename from kehra/DESCRIPTION rename to DESCRIPTION index 9f55210..331c853 100644 --- a/kehra/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: kehra Type: Package Title: Collect, Assemble and Model Air Pollution, Weather and Health Data -Version: 0.1 +Version: 0.3 Date: 2016-06-09 Author: Claudia Vitolo [aut, cre], Allan Tucker [aut], Andrew Russell [aut] Maintainer: Claudia Vitolo diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 9cecc1d..0000000 --- a/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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It is safest -to attach them to the start of each source file to most effectively -state the exclusion of warranty; and each file should have at least -the "copyright" line and a pointer to where the full notice is found. - - {one line to give the program's name and a brief idea of what it does.} - Copyright (C) {year} {name of author} - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - {project} Copyright (C) {year} {fullname} - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/kehra/NAMESPACE b/NAMESPACE similarity index 100% rename from kehra/NAMESPACE rename to NAMESPACE diff --git a/kehra/R/fillMissingValues.R b/R/fillMissingValues.R similarity index 100% rename from kehra/R/fillMissingValues.R rename to R/fillMissingValues.R diff --git a/kehra/R/getSeason.R b/R/getSeason.R similarity index 100% rename from kehra/R/getSeason.R rename to R/getSeason.R diff --git a/kehra/R/pointInspection.R b/R/pointInspection.R similarity index 100% rename from kehra/R/pointInspection.R rename to R/pointInspection.R diff --git a/kehra/R/windDirection.R b/R/windDirection.R similarity index 100% rename from kehra/R/windDirection.R rename to R/windDirection.R diff --git a/kehra/R/windSpeed.R b/R/windSpeed.R similarity index 100% rename from kehra/R/windSpeed.R rename to R/windSpeed.R diff --git a/README.Rmd b/README.Rmd new file mode 100644 index 0000000..2f1786b --- /dev/null +++ b/README.Rmd @@ -0,0 +1,64 @@ +--- +output: + github_document +--- + + + +kehra: an R package to collect, assemble and model air pollution, weather and health data +============================================================== + +```{r echo=FALSE} +knitr::opts_chunk$set( + comment = '#>', + collapse = TRUE, + warning = FALSE, + message = FALSE, + eval = FALSE, + cache = TRUE +) +``` + +[![CRAN Status Badge](http://www.r-pkg.org/badges/version/kehra)](http://cran.r-project.org/web/packages/kehra) +[![CRAN Total Downloads](http://cranlogs.r-pkg.org/badges/grand-total/kehra)](http://cran.rstudio.com/web/packages/kehra/index.html) +[![CRAN Monthly Downloads](http://cranlogs.r-pkg.org/badges/kehra)](http://cran.rstudio.com/web/packages/kehra/index.html) + +The package [kehra](https://cran.r-project.org/package=kehra) allows to collect, assemble and model air pollution, weather and health data. The package is being developed as part of the British Council's funded KEHRA project and builds upon other R packages such as [rdefra](https://cran.r-project.org/package=rdefra) to retrieve pollution data from the UK-AIR database hosted by the UK Department for Enviornment, Food and Rural Affairs, and the [bnlearn](https://cran.r-project.org/package=bnlearn) to model the assembled database using Bayesian Networks. + +## Dependencies + +The kehra package depends on the Geospatial Data Abstraction Library (gdal) and some additional CRAN packages. Check for missing dependencies and install them using the commands below: + +```{r} +packs <- c('Hmisc', 'raster', 'reshape2', 'stringr', 'sp', 'xts', 'zoo', + 'devtools', 'rgdal') +new.packages <- packs[!(packs %in% installed.packages()[,'Package'])] +if(length(new.packages)) install.packages(new.packages) +``` + +## Installation + +Get the released version from CRAN: + +```{r} +install.packages('kehra') +``` + +Or the development version from github using [devtools](https://github.com/hadley/devtools): + +```{r} +devtools::install_github('kehraProject/kehra') +``` + +Load the kehra package: + +```{r, eval = TRUE} +library('kehra') +``` + +## Meta + +* Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms. +* Please [report any issues or bugs](https://github.com/kehraProject/kehra/issues). +* License: [GPL-3](https://opensource.org/licenses/GPL-3.0) +* Get citation information for `kehra` in R doing `citation(package = 'kehra')` diff --git a/kehra/inst/AirPollutionBNinEngland.R b/inst/AirPollutionBNinEngland.R similarity index 100% rename from kehra/inst/AirPollutionBNinEngland.R rename to inst/AirPollutionBNinEngland.R diff --git a/kehra/inst/SetUpDesktop.sh b/inst/SetUpDesktop.sh similarity index 100% rename from kehra/inst/SetUpDesktop.sh rename to inst/SetUpDesktop.sh diff --git a/kehra/inst/SetUpServer.sh b/inst/SetUpServer.sh similarity index 100% rename from kehra/inst/SetUpServer.sh rename to inst/SetUpServer.sh diff --git a/kehra/inst/cmip5.sh b/inst/cmip5.sh similarity index 100% rename from kehra/inst/cmip5.sh rename to inst/cmip5.sh diff --git a/kehra/inst/ecmwf.py b/inst/ecmwf.py similarity index 100% rename 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