/
remake.yml
101 lines (90 loc) · 2.61 KB
/
remake.yml
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sources:
- R
packages:
- ape
- grid
- diversitree
- phyndr
- sowsear
- knitr
- rmarkdown
- taxonlookup
- rncl
- rotl
- taxize
- readxl
knitr_options:
vignette:
auto_figure_prefix: true
chdir: true
targets:
all:
depends:
- ms/phyndr-ms.pdf
- vignette/vignette.html
ms:
depends:
- ms/phyndr-ms.pdf
ms/phyndr-ms.pdf:
command: latex_build("ms/phyndr-ms.tex", "ms/phyndr.bib", clean=TRUE)
depends:
- ms/figs/venn.pdf
- ms/figs/phyndr-eg-magallon.pdf
- ms/numbers.tex
ms/figs/venn.pdf:
command: venn()
plot:
width: 6
height: 4
vignette:
depends:
- vignette/vignette.html
## Manuscript
source_data/magallon_tree.nex:
download: http://datadryad.org/bitstream/handle/10255/dryad.76144/Magallon_etal_PL_ML.nex?sequence=1
magallon_tree:
command: load_magallon_tree("source_data/magallon_tree.nex")
magallon_tree_modified:
command: clean_magallon_tiplabel(magallon_tree)
source_data/woody_data.csv:
download: http://datadryad.org/bitstream/handle/10255/dryad.59002/GlobalWoodinessDatabase.csv?sequence=1
woody_data:
command: load_woody_data("source_data/woody_data.csv")
phyndr_magallon:
command: phyndr_taxonomy_wrap(magallon_tree_modified, woody_data)
ms/figs/phyndr-eg-magallon.pdf:
command: fig_tree_single(phyndr_magallon)
plot:
width: 6
height: 6
## Vignette
vignette/vignette.html:
command: render("vignette/vignette.md", quiet=TRUE)
vignette/vignette.md:
knitr: vignette
depends:
- source_data/magallon.tre
- source_data/wood.csv
- source_data/meredith.tre
- source_data/bmr.csv
- source_data/zanne.tre
vignette/vignette.Rmd:
command: sowsear("vignette/vignette.R")
## Write objects used in main text to file
source_data/magallon.tre:
command: write_mag_tree(magallon_tree_modified)
source_data/wood.csv:
command: write_woody_dat(woody_data)
## Write vignette-specific files
source_data/bmr_data_test.xls:
download: http://www.nature.com/nature/journal/v464/n7289/extref/nature08920-s2.xls
source_data/bmr.csv:
command: build_bmr_dat("source_data/bmr_data_test.xls")
source_data/meredith_mammal.tre:
download: http://datadryad.org/bitstream/handle/10255/dryad.56186/Mammalia.tre?sequence=1
source_data/meredith.tre:
command: build_meredith_tree("source_data/meredith_mammal.tre")
source_data/zae_tree.zip:
download: http://datadryad.org/bitstream/handle/10255/dryad.55548/PhylogeneticResources.zip?sequence=1
source_data/zanne.tre:
command: build_zae_tree("source_data/zae_tree.zip")