simplified diagram

README.md

@@ -21,16 +21,13 @@ For information on how to get dat access, see https://www.center-tbi.eu/data.
 The workflow assumes a linux command line.
 To facilitate reproducibility, a 
 [docker container](https://cloud.docker.com/u/kkmann/repository/docker/kkmann/gose-6mo-imputation)
-container with all software dependencies
-(R packages etc.) is provided [here]().
+container with all software dependencies (R packages etc.) is provided.
 The workflow itself is automated using [snakemake]() 5.2.1.
-
 To fully leverage the container and snakemake workflow, the following software
 dependencies must be available:
 
-* [python](https://www.python.org/download/releases/3.5.1/) 3.5.1 (higher versions might work as well) 
-* [snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) version 5.2.1 (higher versions will work as well)
-* [singularity](https://www.sylabs.io/guides/2.6/user-guide/index.html) 2.6.0 (higher versions might work as well)
+* [snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) version 5.2.1+; requires [python](https://www.python.org/download/releases/3.5.1/) 3.5.1+
+* [singularity](https://www.sylabs.io/guides/2.6/user-guide/index.html) 2.6.0+
 
 
 

Snakefile

-singularity: "docker://kkmann/gose-6mo-imputation@sha256:7c431eddca0933b09efce89a353c0abdf54aa07e601b31cb5b0535e4895091cd"
+singularity: "docker://kkmann/gose-6mo-imputation@sha256:85724229d8f4243aaebd6228e5cc7833474577ac107f9719b00016765f9ee342"
 
 configfile: "config.yml"
 

docker/dockerfile

@@ -6,9 +6,10 @@ MAINTAINER Kevin Kunzmann kevin.kunzmann@mrc-bsu.cam.ac.uk
 RUN sudo apt-get update
 
 # install prerequisits
-RUN sudo apt-get -y install libcurl4-openssl-dev curl
+RUN sudo apt-get -y install libcurl4-openssl-dev curl bzip2
 
 # install required R packages
+RUN R -e "install.packages('diagram')"
 RUN R -e "install.packages('rstan')"
 RUN R -e "install.packages('brms')"
 RUN R -e "install.packages('mice')"
@@ -18,5 +19,4 @@ RUN R -e "install.packages('e1071')"
 RUN R -e "install.packages('msm')"
 RUN R -e "install.packages('cowplot')"
 RUN R -e "install.packages('pander')"
-RUN R -e "install.packages('DiagrammeR')"
 RUN R -e "devtools::install_github('kkmann/describr')"

manuscript/manuscript.Rmd

@@ -296,7 +296,7 @@ Baseline covariates are added as linear fixed effects to to the
 population mean.
 The model was fitted using Bayesian statistics via the BRMS 
 package @brms2017, @brms2018 for the R environment for statistical 
-computing @r2016 and the Stan modelling language @stan2017. 
+computing @R2016 and the Stan modelling language @stan2017. 
 Non-informative priors were used for the model parameters.
 
 
@@ -360,29 +360,35 @@ This model class assumes that the transitions between adjacent GOSe
 states can be modeled as a Markov process and the transition 
 intensities between adjacent states are fitted to the observed data.
 
-```{r diagram, echo=FALSE, fig.cap="Structural diagram of allowed transitions between GOSe states for the proposed multi-state model.", fig.width=3.5, fig.height=2}
-DiagrammeR::grViz("
-digraph boxes_and_circles {
-
-  # a 'graph' statement
-  graph [layout = dot, rankdir = LR, overlap = false, fontsize = 10]
-
-  # several 'node' statements
-  node [shape = circle,
-        fixedsize = true,
-        width = 0.9] // sets as circles
-  1; 2; 3; 4; 5; 6; 7; 8
-
-  # several 'edge' statements
-  2->1 2->3
-  3->1 3->2 3->4
-  4->1 4->3 4->5
-  5->1 5->4 5->6
-  6->1 6->5 6->7
-  7->1 7->6 7->8
-  8->1 8->7
+```{r diagram, echo=FALSE, fig.cap="Structural diagram of allowed transitions between GOSe states for the proposed multi-state model.", fig.width=8, fig.height=4}
+# define transition matrix
+Q <- matrix(0, nrow = 8, ncol = 8)
+for (i in 1:8) {
+  for (j in 1:8) {
+    if (i == j - 1 & i != 1) {
+      Q[i, j] <- 1
+    }
+    if (i == j + 1) {
+      Q[i, j] <- 1
+    }
+  }
 }
-")
+Q[2:8, 1] <- 1 # allow instantaneous deaths
+Q <- t(Q)
+curvature <- Q / 5
+curvature[1, ] <- 0
+diagram::plotmat(
+  Q, 
+  relsize = 1, 
+  shadow.size = 0, 
+  pos = c(1, 7), 
+  box.size = .033, 
+  arr.pos = .55, 
+  arr.length = .33, 
+  arr.type = "triangle", 
+  cex.txt = 0, 
+  curve = curvature
+)
 ```
 
 To account for the fact that state-transitions might be more frequent 

manuscript/references.bib

@@ -9,7 +9,7 @@ title = {{Multi-State Models for Panel Data: The msm Package for R}},
 volume = {38},
 year = {2011}
 }
-@article{r2016,
+@article{R2016,
 archivePrefix = {arXiv},
 arxivId = {arXiv:1011.1669v3},
 author = {Team, R Development Core and {R Development Core Team}, R},