diff --git a/README.Rmd b/README.Rmd new file mode 100644 index 0000000000000000000000000000000000000000..0945fd17f7a16ffe01e9782788b694f0428b6ca1 --- /dev/null +++ b/README.Rmd @@ -0,0 +1,131 @@ +```{r, echo=FALSE, include=FALSE} +## Get VERSION and create file names +ver <- sub(x=grep(x=readLines("DESCRIPTION"), pattern="^Version: ", + value=TRUE), + pattern="^Version: ", replacement="") +pkg.name <- "mcglm_" +pkg.source <- paste0(pkg.name, ver, ".tar.gz") +pkg.win <- paste0(pkg.name, ver, ".zip") +``` + +# mcglm `r ver` + +<!-- [](http://git.leg.ufpr.br/ci/projects/1?ref=master) --> +<!-- Build status for the stable version (`master` branch) --> +<!-- --> +<!-- [](http://git.leg.ufpr.br/ci/projects/1?ref=devel) --> +<!-- Build status for the development version (`devel` branch) --> + +The `mcglm` package fit multivariate covariance generalized linear models +(Bonat and Jorgensen, 2015). + +## Introduction + +`mcglm` fit multivariate covariance generalized linear models. It allows +use a different linear predictor for each response variable of a +multivariate response. The response variable can be continous or +dicrete, like counts and binary and also limited continuos ou +discrete/continuous inflated responses. The most important and relevant +feature is that many covariance structures can be used to model the +relations among variables. + +This package is part of the Thesis of the first author. + +## Download and install + +### Linux/Mac + +Use the `devtools` package (available from +[CRAN](http://cran-r.c3sl.ufpr.br/web/packages/devtools/index.html)) to +install automatically from this GitLab repository: + +```{r, eval=FALSE} +library(devtools) +install_git("http://git.leg.ufpr.br/wbonat/mcglm.git") +``` + +Alternatively, download the package tarball: [`r pkg.source`][] +and run from a UNIX terminal (make sure you are on the container file +directory): + +```{r, echo=FALSE, comment=NA} +cmd <- paste("R CMD INSTALL -l /path/to/your/R/library", pkg.source) +cat(cmd, sep = "\n") +``` + +Or, inside an `R` session: + +```{r, echo=FALSE, comment=NA} +inst <- paste0("install.packages(", "\"", pkg.source, "\"", ", repos = NULL,\n", + " lib.loc = \"/path/to/your/R/library\",\n", + " dependencies = TRUE)") +cat(inst, sep = "\n") +``` + +Note that `-l /path/to/your/R/library` in the former and `lib.loc = +"/path/to/your/R/library"` in the latter are optional. Only use it if +you want to install in a personal library, other than the standard R +library. + +### Windows + +Download Windows binary version: [`r pkg.win`][] (**do not unzip +it under Windows**), put the file in your working directory, and from +inside `R`: + +```{r, echo=FALSE, comment=NA} +instw <- paste0("install.packages(", "\"", pkg.win, "\"", ", repos = NULL,\n", + " dependencies = TRUE)") +cat(instw, sep = "\n") +``` + +### Development version + +By default, if you use `devtools::install_git()`, or download any of the +package tarball or Windows binary version, it will install the stable +version of the package (from the `master` branch of this repository). + +If you want to install the development version, you can use + +```r +library(devtools) +install_git("http://git.leg.ufpr.br/wbonat/mcglm.git", branch = "devel") +``` + +Note that the development version can contain bugs and other unknown +features, so use it at your own risk! + +## Documentation + +The reference manual in PDF can be found here: [mcglm-manual.pdf][] + +## Contributing + +This R package is develop using [`roxygen2`][] for documentation and +[`devtools`] to check and build. Also, we adopt the [Gitflow worflow][] +in this repository. Please, see the +[instructions for contributing](./contributing.md) to collaborate. + +## License + +This package is released under the +[GNU General Public License (GPL) v3.0][]. + +See [LICENSE](./LICENSE) + +<!-- links --> + +```{r, echo=FALSE, include=FALSE} +pkg.source.link <- paste0("http://www.leg.ufpr.br/~fernandomayer/mcglm/", + pkg.source) +pkg.win.link <- paste0("http://www.leg.ufpr.br/~fernandomayer/mcglm/", + pkg.win) +``` + +[GNU General Public License (GPL) v3.0]: http://www.gnu.org/licenses/gpl-3.0.html +[`roxygen2`]: https://github.com/klutometis/roxygen +[`devtools`]: https://github.com/hadley/devtools +[`r pkg.source`]: `r pkg.source.link` +[`r pkg.win`]: `r pkg.win.link` +[mcglm-manual.pdf]: http://www.leg.ufpr.br/~leg/mcglm/source/mcglm-manual.pdf +[Gitflow worflow]: http://nvie.com/posts/a-successful-git-branching-model/ diff --git a/README.md b/README.md index a26fa2279a4c8fdaeb5c22fe6baffe7e1cbe47ba..8802ba07de393eda0da186498ad4e817787ce306 100644 --- a/README.md +++ b/README.md @@ -1 +1,119 @@ -The mcglm package fit multivariate covariance generalized linear models (Bonat and Jorgensen, 2015). \ No newline at end of file + + +# mcglm 0.0.1 + +<!-- [](http://git.leg.ufpr.br/ci/projects/1?ref=master) --> +<!-- Build status for the stable version (`master` branch) --> +<!-- --> +<!-- [](http://git.leg.ufpr.br/ci/projects/1?ref=devel) --> +<!-- Build status for the development version (`devel` branch) --> + +The `mcglm` package fit multivariate covariance generalized linear models +(Bonat and Jorgensen, 2015). + +## Introduction + +`mcglm` fit multivariate covariance generalized linear models. It allows +use a different linear predictor for each response variable of a +multivariate response. The response variable can be continous or +dicrete, like counts and binary and also limited continuos ou +discrete/continuous inflated responses. The most important and relevant +feature is that many covariance structures can be used to model the +relations among variables. + +This package is part of the Thesis of the first author. + +## Download and install + +### Linux/Mac + +Use the `devtools` package (available from +[CRAN](http://cran-r.c3sl.ufpr.br/web/packages/devtools/index.html)) to +install automatically from this GitLab repository: + + +```r +library(devtools) +install_git("http://git.leg.ufpr.br/wbonat/mcglm.git") +``` + +Alternatively, download the package tarball: [mcglm_0.0.1.tar.gz][] +and run from a UNIX terminal (make sure you are on the container file +directory): + + +``` +R CMD INSTALL -l /path/to/your/R/library mcglm_0.0.1.tar.gz +``` + +Or, inside an `R` session: + + +``` +install.packages("mcglm_0.0.1.tar.gz", repos = NULL, + lib.loc = "/path/to/your/R/library", + dependencies = TRUE) +``` + +Note that `-l /path/to/your/R/library` in the former and `lib.loc = +"/path/to/your/R/library"` in the latter are optional. Only use it if +you want to install in a personal library, other than the standard R +library. + +### Windows + +Download Windows binary version: [mcglm_0.0.1.zip][] (**do not unzip +it under Windows**), put the file in your working directory, and from +inside `R`: + + +``` +install.packages("mcglm_0.0.1.zip", repos = NULL, + dependencies = TRUE) +``` + +### Development version + +By default, if you use `devtools::install_git()`, or download any of the +package tarball or Windows binary version, it will install the stable +version of the package (from the `master` branch of this repository). + +If you want to install the development version, you can use + +```r +library(devtools) +install_git("http://git.leg.ufpr.br/wbonat/mcglm.git", branch = "devel") +``` + +Note that the development version can contain bugs and other unknown +features, so use it at your own risk! + +## Documentation + +The reference manual in PDF can be found here: [mcglm-manual.pdf][] + +## Contributing + +This R package is develop using [`roxygen2`][] for documentation and +[`devtools`] to check and build. Also, we adopt the [Gitflow worflow][] +in this repository. Please, see the +[instructions for contributing](./contributing.md) to collaborate. + +## License + +This package is released under the +[GNU General Public License (GPL) v3.0][]. + +See [LICENSE](./LICENSE) + +<!-- links --> + + + +[GNU General Public License (GPL) v3.0]: http://www.gnu.org/licenses/gpl-3.0.html +[`roxygen2`]: https://github.com/klutometis/roxygen +[`devtools`]: https://github.com/hadley/devtools +[mcglm_0.0.1.tar.gz]: http://www.leg.ufpr.br/~fernandomayer/mcglm/mcglm_0.0.1.tar.gz +[mcglm_0.0.1.zip]: http://www.leg.ufpr.br/~fernandomayer/mcglm/mcglm_0.0.1.zip +[mcglm-manual.pdf]: http://www.leg.ufpr.br/~leg/mcglm/source/mcglm-manual.pdf +[Gitflow worflow]: http://nvie.com/posts/a-successful-git-branching-model/