final updates

Author: florianhartig

BayesianTools/.Rbuildignore

@@ -3,4 +3,6 @@ _pkgdown\.yml$
 ^CRAN.md
 tests/testthat/Rplots.pdf
 vignettes/*.R
-vignettes/*.html
+vignettes/*.html
+^doc$
+^Meta$

BayesianTools/.gitignore

@@ -1,3 +1,5 @@
 .Rproj.user
 .Rhistory
 .RData
+/doc/
+/Meta/

BayesianTools/R/BayesianTools.R

@@ -1,6 +1,6 @@
 #' @keywords internal
 #' @references 
-#' vignette("Manual for the BayesianTools R package", package="BayesianTools")
+#' To access the vignettes, type vignette(package="BayesianTools")
 #' @details A package with  general-purpose MCMC and SMC samplers, as well as plots and diagnostic functions for Bayesian statistics, particularly for process-based models. 
 #' 
 #' The package contains 2 central functions, \code{\link{createBayesianSetup}}, which creates a standardized Bayesian setup with likelihood and priors, and \code{\link{runMCMC}}, which allows to run various MCMC and SMC samplers.

BayesianTools/man/BayesianTools-package.Rd

@@ -1,13 +1,14 @@
 ---
-title: "Bayesian Tools - General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics"
+title: "Reference Manual for the BayesianTools R package"
 output: 
   rmarkdown::html_vignette:
     toc: true
 vignette: >
-  %\VignetteIndexEntry{Manual for the BayesianTools R package}
-  \usepackage[utf8]{inputenc}
+  %\VignetteIndexEntry{Reference Manual for the BayesianTools R package}
   %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 abstract: "The BayesianTools (BT) package supports model analysis (including sensitivity analysis and uncertainty analysis), Bayesian model calibration, as well as model selection and multi-model inference techniques for system models." 
+date: "`r format(Sys.time(), '%d %B, %Y')`"
 editor_options: 
   markdown: 
     wrap: 72

BayesianTools/man/WAIC.Rd

@@ -5,9 +5,10 @@ output:
     toc: true
 vignette: >
   %\VignetteIndexEntry{Interfacing your model with R}
-  \usepackage[utf8]{inputenc}
   %\VignetteEngine{knitr::rmarkdown}
-abstract: "This tutorial discusses how to interface models written in other programming languages with R, so that they can be fit with BayesianTools"  
+  %\VignetteEncoding{UTF-8}
+abstract: "This tutorial discusses how to interface models written in other programming languages with R, so that they can be fit with BayesianTools <br>"  
+date: "`r format(Sys.time(), '%d %B, %Y')`"
 author: Florian Hartig
 editor_options: 
   chunk_output_type: console

BayesianTools/vignettes/BayesianTools.Rmd

@@ -1,21 +1,21 @@
 ---
-title: "Fitting standard statistical models with the BayesianTools Package"
+title: "Practical examples fitting models with Bayesian Tools"
 output: 
   rmarkdown::html_vignette:
     toc: true
 vignette: >
-  %\VignetteIndexEntry{Statistical Models with the BayesianTools Package}
-  \usepackage[utf8]{inputenc}
+  %\VignetteIndexEntry{Practical examples fitting models with Bayesian Tools}
   %\VignetteEngine{knitr::rmarkdown}
-abstract: "This vignette shows how to fit standard statistical models with the BayesianTools package" 
+  %\VignetteEncoding{UTF-8}
+abstract: "This vignette shows how to fit standard statistical models with the BayesianTools package"  
 author: Florian Hartig
+date: "`r format(Sys.time(), '%d %B, %Y')`"
 editor_options: 
   chunk_output_type: console
 ---
 
-
 ```{r global_options, include=FALSE}
-knitr::opts_chunk$set(fig.width=5, fig.height=5, warning=FALSE, cache = F)
+knitr::opts_chunk$set(fig.width=7, fig.height=7, warning=FALSE, cache = F)
 ```
 
 ```{r, echo = F, message = F}
@@ -52,7 +52,7 @@ likelihood(par)
 
 Creating the BayesianSetup by combining likelihood with uniform (flat) priors
 
-```{r, message=F}
+```{r}
 library(BayesianTools)
 setup <- createBayesianSetup(likelihood = likelihood, 
                              lower = c(-100,-100,0), 
@@ -62,8 +62,8 @@ setup <- createBayesianSetup(likelihood = likelihood,
 
 Creating required setup for wrapper function runMCMC to start MCMCs
 
-```{r}
-settings <- list(iterations = 10000, nrChains = 2)
+```{r, message=F}
+settings <- list(iterations = 10000, nrChains = 2, message = F)
 res <- runMCMC(bayesianSetup = setup, settings = settings)
 ```
 
@@ -133,13 +133,13 @@ likelihood(c(4,10,6,20,rep(0,11)))
 
 Estimating the model
 
-```{r, message=F}
+```{r}
 library(BayesianTools)
 setup <- createBayesianSetup(likelihood = likelihood, 
                              lower = c(-20,-50,0,0,rep(-100,11)), 
                              upper = c(20,50,50,100,rep(100,11)),
                              names = c("a", "b", "err-sd", "RE-sd", 1:11))
-settings <- list(iterations = 30000, nrChains = 2)
+settings <- list(iterations = 30000, nrChains = 2, message = F)
 
 res <- runMCMC(bayesianSetup = setup, settings = settings)
 ```