smartell / CatchMSY

Integrated Catch MSY method for data poor stock assessment.

Installing the catchMSY package from github.

First you need to install the devtools package

Mac and Linux:

install.packages("devtools")

Window:

library(devtools)
build_github_devtools()

#### Restart R before continuing ####
install.packages("devtools.zip", repos = NULL, type = "source")

# Remove the package after installation
unlink("devtools.zip")

Once devtools is installed you can install the catchMSY package directly from github:

devtools::install_github("smartell/catchMSY",build_vignettes=TRUE)

Vignettes

You can build all vignettes from the console with devtools::build() to create a package bundle with the vignettes included. RStudio’s “Build & reload” does not build vignettes to save time. Similarly, devtools::install_github() (and friends) will not build vignettes by default because they’re time consuming and may require additional packages. You can force building with devtools::install_github(build_vignettes = TRUE). This will also install all suggested packages.

You can also build the vignettes using "devtools::build_vignettes()" in R.

Workflow for building the catchMSY package

Using the makefile

From the terminal navigate to the directory containg the catchMSY pacakge.

make clean
make 
make install

Using the devtools package for building the catchMSY package.

devtools::load_all()

---

To do

• fix non-linear search routine
• Create S3 ploting routines for sID class
  • biomass plot
  • fishing mortality rate plot
  • depletion
  • pairs plot for posterior samples
• Summary function for sid class.
  • non-linear search summary.
  • importance sample summary.
• Add nll for average weight.
• add nll for change in mean length.
• add the importance function for statistical SIR
• life-hisotry: specifically sequential hermaphrodites (protogynous Scarids–Parrot fish)

---