Update README

Signed-off-by: Yuan Tang <[email protected]>

.Rbuildignore

@@ -2,7 +2,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.travis\.yml$
-^README\.rst$
+^README\.md$
 ^vignettes/rsconnect/.*$
 ^\.httr-oauth$
 ^cran-comments\.md$

R/fortify_surv.R

@@ -39,7 +39,7 @@ fortify.survfit <- function(model, data = NULL, surv.connect = FALSE,
       varying.names <- c('n.risk', 'n.event', 'pstate', 'std.err', 'upper', 'lower')
       varying.i <- lapply(varying.names, function(x) which(startsWith(colnames(d), x)))
       d <- reshape(d, varying = varying.i, v.names = varying.names, timevar = NULL, direction = 'long')
-      d <- subset(d, select = -c(id))
+      d <- suppressWarnings(subset(d, select = -c(id)))
       rownames(d) <- NULL
 
       if (length(model$states) > 1) {

README.md

@@ -0,0 +1,122 @@
+**Note**: This package has been maintained by [@terrytangyuan](https://github.com/terrytangyuan) since 2015. Please [consider sponsoring](https://github.com/sponsors/terrytangyuan)!
+
+[![cran](http://www.r-pkg.org/badges/version/ggfortify)](https://CRAN.R-project.org/package=ggfortify)
+[![download](https://cranlogs.r-pkg.org/badges/grand-total/ggfortify)](https://CRAN.R-project.org/package=ggfortify)
+
+# ggfortify
+
+This package offers ``fortify`` and ``autoplot`` functions to allow automatic ``ggplot2`` to visualize statistical result of popular R packages. Check out our [R Journal paper] (https://journal.r-project.org/archive/2016-2/tang-horikoshi-li.pdf) for more details on the overall architecture design and a gallery of visualizations created with this package. Also check out [autoplotly package](https://github.com/terrytangyuan/autoplotly) that could automatically generate interactive visualizations with [plotly.js](https://plot.ly/) style based on ``ggfortify``. The generated visualizations can also be easily extended using ``ggplot2`` syntax while staying interactive.
+
+
+## Installation
+
+- Install the latest stable release from CRAN:
+```
+install.packages('ggfortify')
+```
+
+- Install the development version from Github:
+```
+if (!require("remotes")) install.packages("remotes")
+  remotes::install_github('sinhrks/ggfortify')
+```
+
+## Examples
+
+* [Concepts and Basics of ggfortify](https://cran.r-project.org/web/packages/ggfortify/vignettes/basics.html)
+* [Plotting Diagnostics for LM and GLM with ggplot2 and ggfortify](https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_lm.html)
+* [Plotting Time Series with ggplot2 and ggfortify](https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_ts.html)
+* [Plotting PCA, clustering, LFDA and MDS](https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_pca.html)
+* [Plotting Survival Curves using ggplot2 and ggfortify](https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_surv.html)
+* [Plotting Probability Distributions with ggplot2 and ggfortify](https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_dist.html)
+* [Automatic Generation of Interactive Visualizations in ggplot2 and plotly Styles](https://terrytangyuan.github.io/2018/02/12/autoplotly-intro/)
+* [一行R代码实现繁琐的可视化](http://terrytangyuan.github.io/2015/11/24/ggfortify-intro/)
+
+## Reference/Citation
+
+To cite ggfortify in publications, please use (available via ``citation("ggfortify")``):
+```
+  Yuan Tang, Masaaki Horikoshi, and Wenxuan Li (2016). ggfortify: Unified Interface to Visualize
+  Statistical Result of Popular R Packages. The R Journal, 8.2, 478-489.
+
+  Masaaki Horikoshi and Yuan Tang (2016). ggfortify: Data Visualization Tools for Statistical
+  Analysis Results. https://CRAN.R-project.org/package=ggfortify
+```
+
+## Coverage
+
+This covers following classes:
+
+- ``base::matrix``
+- ``base::table`` (supports ``fortify`` only)
+- ``cluster::clara``
+- ``cluster::fanny``
+- ``cluster::pam``
+- ``cluster::silhouette``
+- ``changepoint::cpt``
+- ``fGarch::fGARCH``
+- ``forecast::bats``
+- ``forecast::forecast``
+- ``forecast::ets``
+- ``forecast::nnetar``
+- ``fracdiff::fracdiff``
+- ``glmnet::cv.glmnet``
+- ``glmnet::glmnet``
+- ``KFAS::KFS``
+- ``KFAS::signal`` (inference)
+- ``lfda::lfda``
+- ``lfda::klfda``
+- ``lfda::self``
+- ``maps::map``
+- ``MASS::isoMDS`` (inference)
+- ``MASS::sammon`` (inference)
+- ``raster::RasterBrick``
+- ``raster::RasterCommon``
+- ``raster::RasterLayer``
+- ``raster::RasterStack``
+- ``ROCR::performance``
+- ``sp::Line``
+- ``sp::Lines``
+- ``sp::Polygon``
+- ``sp::Polygons``
+- ``sp::SpatialLines``
+- ``sp::SpatialLinesDataFrame``
+- ``sp::SpatialPoints``
+- ``sp::SpatialPointsDataFrame``
+- ``sp::SpatialPolygons``
+- ``sp::SpatialPolygonsDataFrame``
+- ``splines::basis``
+- ``stats::acf``
+- ``stats::ar``
+- ``stats::Arima``
+- ``stats::cmdscale`` (inference)
+- ``stats::decomposed.ts``
+- ``stats::density``
+- ``stats::factanal``
+- ``stats::glm``
+- ``stats::HoltWinters``
+- ``stats::kmeans``
+- ``stats::lm``
+- ``stats::prcomp``
+- ``stats::princomp``
+- ``stats::spec``
+- ``stats::stepfun``
+- ``stats::stl``
+- ``stats::ts``
+- ``survival::survfit``
+- ``survival::survfit.cox``
+- ``survival::survfitms``
+- ``strucchange::breakpoints``
+- ``strucchange::breakpointsfull``
+- ``timeSeries::timeSeries``
+- ``tseries::irts``
+- ``vars::varprd``
+- ``xts::xts``
+- ``zoo::zooreg``
+
+## Helper Functions
+
+- ``ggdistribution`` to plot PDF/CDF
+- ``ggcpgram`` to plot ``cpgram``
+- ``ggtsdiag`` to plot ``tsdiag``
+- ``ggfreqplot`` to generalize ``monthplot``