ALSFRS.Rnw

\documentclass{article}
\usepackage[left=20mm, right=15mm, top=15mm, bottom=20mm]{geometry}

\begin{document}
%\VignetteEngine{knitr::knitr}
<<setup, cache=FALSE>>=
library("knitr")
opts_chunk$set(cache = FALSE, echo = TRUE,  
               fig.show='hold', message=FALSE, warning=FALSE)

ca <- FALSE

library("ggplot2")
theme_set(theme_bw(base_size = 18))
library("partykit")
library("sandwich")
library("gridExtra")
library("plyr")
source("ALSFRS_basis.R")
source("basis/personalised_models.R")
source("basis/pruning.R")
source("basis/variable_importance.R")

read_chunk('ALSFRS_R.R')
@



<<data, cache = TRUE>>=
@


\section{Fitting function}
<<fittingfunction, cache = TRUE>>=
@


\section{Compute random forest}
<<forest, cache = TRUE, dependson = c("data", "fittingfunction")>>=
@


\section{Obtain personalised models}
<<pm, out.width = "0.66\\textwidth", out.height = "0.33\\textwidth", fig.width=8, fig.height=4, cache = FALSE>>=
@


\section{Variable importance}
<<varimp, fig.height=11, cache = FALSE>>=
@


\section{Obtain log-Likelihoods}
<<logLiks, cache = TRUE, dependson = "forest">>=
@


<<bootstrapLogliks, cache = FALSE>>=
@


<<sessionInfo>>=
sessionInfo()
@

\end{document}