update Rbuildignore

get rid of dependencies
fix minor things
update man file to e.g., use the right structure in return sections
fix offset error in particle filter
remove test_utils file from R directory

.Rbuildignore

@@ -3,24 +3,18 @@
 \.log$
 ^\.git
 ^\.Rprofile
-
 ^\.commit$
-^\.sandbox
 
 \.o$
 \.txt$
 Rplots\.pdf$
 dynamichazard\.dll$
-useful_scripts$
-testfuture\.R$
 ^\.travis\.yml$
-pbc_data\.Rmd$
-Sim_study_with_logit\.Rmd$
 release_questions\.R$
 cran-comments\.md$
-revdep/
 
 ^README
+^README_cache
 
 vignettes/\.jss
 vignettes/figure
@@ -32,10 +26,8 @@ vignettes/Diagnostics/Rossi_ex\.html
 vignettes/Diagnostics/Rossi_source\.url
 vignettes/Diagnostics/Rossi\.txt
 
-Examples
-sandbox
-speedtest
+^\.sandbox
+^speedtest
 tests/testthat/previous_results/local_tests
-README_cache
 data-raw
 TODO

.gitignore

@@ -8,9 +8,6 @@ src/**/*.o
 src/**/*.so
 src/**/*.dll
 *.log
-
-vignettes/figures
-revdep
 .commit
 
 **/*.log
@@ -19,6 +16,7 @@ revdep
 **/tex2pdf*/
 **/Rplots.pdf
 
+vignettes/*.md
 vignettes/*_cache/
 vignettes/Prebuild/*_cache/
 vignettes/pandoc*.pdf
@@ -33,7 +31,7 @@ vignettes/Prebuild/Particle_filtering/*
 !vignettes/Prebuild/Particle_filtering/Particle_filtering.pdf
 !vignettes/Prebuild/Particle_filtering/Particle_filtering.tex
 
-sandbox/*
+.sandbox/*
 **/Rprof.out
 **/Sweave.sty
 README_cache

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dynamichazard
 Type: Package
 Title: Dynamic Hazard Models using State Space Models
-Version: 0.5.1
+Version: 0.5.2
 Authors@R: c(person("Benjamin", "Christoffersen", 
                     email = "[email protected]", 
                     role = c("cre", "aut")),
@@ -22,8 +22,8 @@ Description: Contains functions that lets you fit dynamic hazard models using
 License: GPL-2
 LazyData: TRUE
 LinkingTo: Rcpp, RcppArmadillo
-Imports: parallel, Rcpp (>= 0.12.6), boot, stringr, data.table
-Depends: R (>= 3.3.2), stats, graphics, utils, survival
+Imports: parallel, Rcpp (>= 0.12.6), boot
+Depends: R (>= 3.3.0), stats, graphics, utils, survival
 RoxygenNote: 6.0.1
 Suggests: testthat, knitr, rmarkdown, timereg, captioner, biglm, httr, mgcv, shiny, formatR, R.rsp, speedglm, dichromat, colorspace
 VignetteBuilder: knitr, R.rsp