inst/markdown/archive/README.md

In jae0/bio.snowcrab: Snow crab assessment suite using aegis* and associated projects and data streams.

Notes -- archived reports using rmarkdown (mostly)

The files in this directory are markdown (Rmarkdown) reports and script sequences to be used for the analysis of the snow crab data.

Viewing:

The can be viewed with a web-browser (some might require Markdown viewing extensions), or VScode's markdown preview or Rstudio's viewer.

Rendering

If you have GNU Make installed then it is as simple as running from the installation directory:

    make snowcrab_working_paper YR=2023 

This will copy relevant files to a temporary directory and run the rendering programs there. This is because modifying the source directory is unwise as it is a git repsitory or user write-permissions are usually constrained.

Add other options as required (eg, SOURCE (source directory), WK (work directory), etc... See inside the header of the Makefile for options.)

-- OR --

If you do not have GNU Make installed then you can run the commands inside the Makefile directly from a command prompt. But again the relevant file need to be copied or sym-linked to a working directory as there is usually write access is not permitted in the library directory. Copy or link also the markdown/media to the same work directory and then run the required commands.

Use the Makefile commands as hints. E.g. for snowcrab_presentation_methods.html :

    ln -sf ~/bio/bio.snowcrab/inst/markdown/media ~/bio.data/bio.snowcrab/assessments/media
    cp ~/bio/bio.snowcrab/inst/markdown/snowcrab_presentation_methods.rmd ~/bio.data/bio.snowcrab/assessments/

    Rscript -e "rmarkdown::render('~/bio.data/bio.snowcrab/assessments/snowcrab_presentation_methods.rmd', params=list( year.assessment=2023), media_loc='$(MEDIA)', debugging=FALSE , loc_dde='$(DDE)', output_dir='~/bio.data/bio.snowcrab/assessments/' ) " 

-- OR --

In Rstudio or MS VScode there looks to be funcationality to render these documents. For Rmarkdown copy the report file and rename extension to .Rmd or if Quarto, then .qmd. (In testing, the file name extension seems to required at least for Quarto). Configuration of the code editors are platform-specific and a moving target so check current online resources.

Do your tests with quick_test.md :

    make rmarkdown quick_test YR=2023 

jae0/bio.snowcrab documentation built on Nov. 6, 2024, 10:10 p.m.