R package for VRAP rewrite
library(devtools)
#tell devtools build only for your machine: 32- or 64-bit
#needed because C++ code in the VRAP 2.0 package
options(devtools.install.args = "--no-multiarch")
#VRAP 2.0
install_github("eeholmes/VRAPCpp")
#VRAP 1.0
install_github("eeholmes/VRAP")
The vignettes in the package are not built by default as that would take a long time. If you want them built add build_vignettes = TRUE
to the install_github
call. However, the normal procedure for a package is for the package developer to build the vignettes locally and then put the Rmd and html (from knit) files in the inst/doc
folder which will then get uploaded to github.
To build all the vignettes in the vignette
folder in the package and put the files into inst/doc
. Use
#note "." must be the base level of the package for this to work.
require(devtools)
build_vignettes()
Or knit the vignette and manually move the html file and Rmd file into the inst/doc
folder.
The package has vignettes that discuss the background of VRAP and show how to use it. To view the vignettes available use:
browseVignettes(package="VRAPS")
You can open a vignette rmarkdown file using
vignette_rmd_file = "Background.Rmd"
fpath <- system.file("doc", vignette_rmd_file, package="VRAPS")
file.open(fpath)
Martin: Add totAEQmort to RunSims2C(). I have defined at top. But simFish() needs to be altered to return it. See changes to RunSims2R().
I did not do the BYHR SummaryStats. I wasn't sure anyone used them and didn't want to add a bunch more code.
setwd("vignette_files")
out = Main.VRAP1("tmp.rav")
out = Main.VRAP1("tmp.rav", version="C")
That will run tmp.rav
through Main.VRAP1() and make all the VRAP 1.0 output files. Note, Martin needs to add totAEQmort to simFish()
before this will run.
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