[Mboost-commits] r779 - / www www/img www_src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jul 22 15:45:16 CEST 2014
Author: thothorn
Date: 2014-07-22 15:45:16 +0200 (Tue, 22 Jul 2014)
New Revision: 779
Added:
www/img/
www/img/anonymous.png
www/img/benjamin_hofner.jpg
www/img/matthias_schmid.jpg
www/img/peter_buehlmann.jpg
www/img/thomas_kneib.jpg
www/img/torsten_hothorn.jpg
www_src/
www_src/03_getting_started.Rmd
www_src/04_publications.Rmd
www_src/README.txt
www_src/_config.yml
www_src/authors.yml
www_src/config.R
www_src/mboost.bib
www_src/publish.R
www_src/setup.R
www_src/site.css
Log:
start webpage
Added: www/img/anonymous.png
===================================================================
(Binary files differ)
Property changes on: www/img/anonymous.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: www/img/benjamin_hofner.jpg
===================================================================
(Binary files differ)
Property changes on: www/img/benjamin_hofner.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: www/img/matthias_schmid.jpg
===================================================================
(Binary files differ)
Property changes on: www/img/matthias_schmid.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: www/img/peter_buehlmann.jpg
===================================================================
(Binary files differ)
Property changes on: www/img/peter_buehlmann.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: www/img/thomas_kneib.jpg
===================================================================
(Binary files differ)
Property changes on: www/img/thomas_kneib.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: www/img/torsten_hothorn.jpg
===================================================================
(Binary files differ)
Property changes on: www/img/torsten_hothorn.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: www_src/03_getting_started.Rmd
===================================================================
--- www_src/03_getting_started.Rmd (rev 0)
+++ www_src/03_getting_started.Rmd 2014-07-22 13:45:16 UTC (rev 779)
@@ -0,0 +1,56 @@
+---
+layout: page
+title: Getting Started
+permalink: /getting_started/
+---
+
+Your first regression tree
+========================================================
+
+First, install and fire-up R on your computer. Within R, one needs to
+install the mboost package by typing
+
+```{r eval=FALSE}
+install.packages("mboost")
+```
+
+and hitting the ENTER key. Once the package is installed, you can
+load it using
+
+```{r results: hide}
+library("mboost")
+```
+
+Now all mboost functions are ready to be used, for example the mboost()
+function for fitting an additive regression model to the bodyfat data
+
+```{r}
+data("bodyfat", package = "TH.data")
+
+### formula interface: additive Gaussian model with
+### a non-linear step-function in `age', a linear function in `waistcirc'
+### and a smooth non-linear smooth function in `hipcirc'
+mod <- mboost(DEXfat ~ btree(age) + bols(waistcirc) + bbs(hipcirc),
+ data = bodyfat)
+```
+
+The model can be plotted
+
+```{r fig.width=9, fig.height=6}
+layout(matrix(1:3, nc = 3, byrow = TRUE))
+plot(mod, ask = FALSE, main = "formula")
+
+```
+
+or used for computing predictions
+
+```{r}
+summary(predict(mod))
+```
+
+which can be compared to the actual response values:
+
+```{r fig.width=6, fig.height=6}
+plot(bodyfat$DEXfat, predict(mod))
+abline(a = 0, b = 1)
+```
Added: www_src/04_publications.Rmd
===================================================================
--- www_src/04_publications.Rmd (rev 0)
+++ www_src/04_publications.Rmd 2014-07-22 13:45:16 UTC (rev 779)
@@ -0,0 +1,53 @@
+---
+layout: page
+title: Publications
+permalink: /publications/
+---
+
+Scholary papers describing the methodology
+========================================================
+
+```{r setup, include = FALSE, cache = FALSE}
+library("RefManageR")
+bib <- ReadBib("TH.bib", check = FALSE)
+BibOptions(check.entries = FALSE, style = "html", cite.style = "authoryear",
+ bib.style = "numeric")
+```
+The mboost package implements componentwise functional gradient descent
+boosting, originally invented by `r Citet(bib, "Buehlmann_Yu_2003")`.
+The theory and package are described in the review by
+`r Citet(bib, "Buehlmann:2008:StatSci")`, an overview about the implementation
+is given in `r Citet(bib, "Hothorn+Buehlmann+Kneib+Schmid+Hofner_2010")`
+and `r Citet(bib, "Hothorn:2006:Bioinformatics:16940323")`.
+
+Applications in survival analysis are described in
+`r Citet(bib, "Hothorn:2006:Biostatistics:16344280")` and
+`r Citet(bib, "Schmid+Hothorn:2008a")`.
+
+Geoadditive models have been dealt with by
+`r Citet(bib, "Kneib+Hothorn+Tutz:2009")` and
+`r Citet(bib, "Hothorn+Mueller+Schroeder_2011")`.
+
+Boosted quantile regression models were introduced by
+`r Citet(bib, "Fenske+Kneib+Hothorn_2011")` and later extended
+to longitudinal data by `r Citet(bib, "Fenske_Fahrmeir_Hothorn_2013")`
+and to the derivation of prediction intervals by
+`r Citet(bib, "Mayr_Hothorn_Fenske_2012")`.
+
+The application of P-spline base-learners was discussed by
+`r Citet(bib, "Schmid+Hothorn:2008b")`. Unbiased model selection
+was implemented as described by `r Citet(bib, "Hofner+Hothorn+Kneib_2011")`.
+An approach to non-linear time series can be found in
+`r Citet(bib, "Robinzonov_Tutz_Hothorn_2012")`.
+Boosted classifiers based on a direct optimisation of the partial AUC were
+introduced by `r Citet(bib, "Schmid_Hothorn_Krause_2012")`.
+
+`r Citet(bib, "Hothorn_Kneib_Buehlmann_2014")` used componentwise array
+boosting to fit a novel class of conditional transformation models;
+some simplifications are given by `r Citet(bib, "Moest_Schmid_Faschingbauer_2014")`.
+
+**References**
+
+```{r results = "asis", echo = FALSE}
+PrintBibliography(bib, .opts = list(check.entries = FALSE, sorting = "ynt"))
+```
Added: www_src/README.txt
===================================================================
--- www_src/README.txt (rev 0)
+++ www_src/README.txt 2014-07-22 13:45:16 UTC (rev 779)
@@ -0,0 +1,17 @@
+
+Update the web page:
+
+(1) install pkg2html from R-forge
+
+(2) install jekyll from http://jekyllrb.com/
+
+(3) run setup.R in www_src
+
+(4) in the newly created dir html, run
+
+ html> jekyll serve --watch
+
+ and point you web browser to localhost:4000
+
+(5) if everything is OK, run publish.R in www_src
+ and commit changes in www
Added: www_src/_config.yml
===================================================================
--- www_src/_config.yml (rev 0)
+++ www_src/_config.yml 2014-07-22 13:45:16 UTC (rev 779)
@@ -0,0 +1,6 @@
+# Site settings
+baseurl: ""
+
+# Build settings
+markdown: kramdown
+permalink: pretty
Added: www_src/authors.yml
===================================================================
--- www_src/authors.yml (rev 0)
+++ www_src/authors.yml 2014-07-22 13:45:16 UTC (rev 779)
@@ -0,0 +1,42 @@
+- name: Torsten Hothorn
+ given: Torsten
+ family: Hothorn
+ role:
+ - aut
+ - cre
+ email: Torsten.Hothorn_ at _R-project.org
+ url: http://user.math.uzh.ch/hothorn/
+ image: /img/torsten_hothorn.jpg
+ comment: ~
+- name: Peter Bühlmann
+ given: Peter
+ family: Bühlmann
+ role: aut
+ email: ~
+ comment: ~
+ url: http://stat.ethz.ch/~buhlmann/
+ image: /img/peter_buehlmann.jpg
+- name: Thomas Kneib
+ given: Thomas
+ family: Kneib
+ role: aut
+ email: ~
+ comment: ~
+ url: http://www.uni-goettingen.de/de/264255.html
+ image: /img/thomas_kneib.jpg
+- name: Matthias Schmid
+ given: Matthias
+ family: Schmid
+ role: aut
+ email: ~
+ comment: ~
+ url: https://www3.uni-bonn.de/imbie
+ image: /img/matthias_schmid.jpg
+- name: Benjamin Hofner
+ given: Benjamin
+ family: Hofner
+ role: aut
+ email: ~
+ comment: ~
+ url: http://benjaminhofner.de/
+ image: /img/benjamin_hofner.jpg
Added: www_src/config.R
===================================================================
--- www_src/config.R (rev 0)
+++ www_src/config.R 2014-07-22 13:45:16 UTC (rev 779)
@@ -0,0 +1,8 @@
+
+pkg <- "mboost"
+dest <- "html"
+publish <- "../www"
+
+download.file("http://user.math.uzh.ch/hothorn/TH.bib", dest = "TH.bib")
+system("cat mboost.bib >> TH.bib")
+bib <- "TH.bib"
\ No newline at end of file
Added: www_src/mboost.bib
===================================================================
--- www_src/mboost.bib (rev 0)
+++ www_src/mboost.bib 2014-07-22 13:45:16 UTC (rev 779)
@@ -0,0 +1,12 @@
+
+ at article{Buehlmann_Yu_2003,
+ author = {Peter B{\"u}hlmann and Bin Yu},
+ title = {Boosting with {$L_2$} Loss: Regression and
+ Classification},
+ journal = {Journal of the American Statistical
+ Association},
+ pages = {324-338},
+ year = {2003},
+ volume = {98},
+ number = {462}
+}
Added: www_src/publish.R
===================================================================
--- www_src/publish.R (rev 0)
+++ www_src/publish.R 2014-07-22 13:45:16 UTC (rev 779)
@@ -0,0 +1,16 @@
+
+source("config.R")
+
+x <- readLines("_config.yml")
+x[grep("^baseurl", x)] <- paste("baseurl: http://", pkg, ".r-forge.r-project.org", sep = "")
+
+writeLines(x, file.path(dest, "_config.yml"))
+
+wd <- setwd(dest)
+
+system("jekyll build")
+
+setwd(wd)
+
+system(paste("cp -ra", file.path(dest, "_site/*"), publish))
+
Added: www_src/setup.R
===================================================================
--- www_src/setup.R (rev 0)
+++ www_src/setup.R 2014-07-22 13:45:16 UTC (rev 779)
@@ -0,0 +1,60 @@
+
+library("pkg2html")
+library("markdown")
+
+source("config.R")
+
+if (!file.exists(dest))
+ dir.create(dest)
+
+stopifnot(file.exists(dest))
+
+template <- system.file("template", package = "pkg2html")
+
+system(paste("cp -ra", file.path(template, "*"), dest, sep = " "))
+
+wd <- setwd(file.path(dest, "_data"))
+R2yaml(pkg)
+writeLines(bib2yaml(file.path(wd, bib),
+ c("Buehlmann:2008:StatSci",
+"Hothorn+Buehlmann+Kneib+Schmid+Hofner_2010",
+"Hothorn:2006:Bioinformatics:16940323",
+"Hothorn:2006:Biostatistics:16344280",
+"Schmid+Hothorn:2008a",
+"Kneib+Hothorn+Tutz:2009",
+"Hothorn+Mueller+Schroeder_2011",
+"Fenske+Kneib+Hothorn_2011",
+"Fenske_Fahrmeir_Hothorn_2013",
+"Mayr_Hothorn_Fenske_2012",
+"Schmid+Hothorn:2008b",
+"Hofner+Hothorn+Kneib_2011",
+"Schmid_Hothorn_Krause_2012",
+"Hothorn_Kneib_Buehlmann_2014",
+"Moest_Schmid_Faschingbauer_2014")),
+ con = "cites.yml")
+
+setwd(wd)
+setwd(file.path(dest, "_posts"))
+NEWS2md(pkg)
+
+setwd(wd)
+
+Rmd <- list.files(pattern = "Rmd$")
+
+for (f in Rmd)
+ writeLines(Rmd2html(f), con = file.path(dest, gsub("Rmd$", "html", f)))
+
+x <- readLines(file.path(dest, "_data", "pkg.yml"))
+x <- c(x, paste("headpic: /img/", pkg, ".png", sep = ""))
+writeLines(x, con = file.path(dest, "_data", "pkg.yml"))
+
+file.copy("_config.yml", dest, overwrite = TRUE)
+
+yml <- list.files(pattern = "yml$")
+yml <- yml[-grep("^_", yml)]
+sapply(yml, function(f) file.copy(f, file.path(dest, "_data"), overwrite = TRUE))
+
+system(paste("cat site.css >> ", file.path(dest, "css", "main.css")))
+
+system(paste("cp ", file.path(publish, "img", "*"), file.path(dest, "img")))
+
Added: www_src/site.css
===================================================================
--- www_src/site.css (rev 0)
+++ www_src/site.css 2014-07-22 13:45:16 UTC (rev 779)
@@ -0,0 +1,3 @@
+a { color: #a7b057; text-decoration: none; }
+a:visited { color: #b9615f; }
+
More information about the Mboost-commits
mailing list