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remake.yml
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212 lines (179 loc) · 5.32 KB
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sources: remake/
packages:
- ape
- XML
- geiger
- dplyr
- arbutus
- diversitree
- parallel
- reshape2
- ggplot2
- grid
- gridExtra
- sowsear
- markdown
targets:
all:
depends:
- figures
- tables
- model-adequacy.html
data:
depends:
- leaf_n
- seed_mass
- sla
fits:
depends:
- fits_ml
- fits_bayes
figures:
depends:
- output/figs/aic-support.pdf
- output/figs/dic-support.pdf
- output/figs/pval-hist-ml.pdf
- output/figs/pval-hist-bayes.pdf
- output/figs/ad-aic.pdf
- output/figs/ad-dic.pdf
- output/figs/ad-size-ml.pdf
- output/figs/ad-size-bayes.pdf
- output/figs/ad-age-ml.pdf
- output/figs/ad-age-bayes.pdf
- output/figs/two-clades.pdf
tables:
depends:
- output/results-ml.csv
- output/results-bayes.csv
data_subsets:
depends: [leaf_n_subsets, seed_mass_subsets, sla_subsets]
data/wright_2004.xls:
command: download_wright_2004(target_name)
cleanup_level: purge
wright_2004:
command: process_wright_2004("data/wright_2004.xls")
packages: xlsx
kew:
command: kew_build()
cleanup_level: never
check: exists
data/leda.txt:
command: download_leda(target_name)
cleanup_level: purge
leda:
command: process_leda("data/leda.txt")
data/zae/PhylogeneticResources.zip:
command: download_zae_trees(target_name)
cleanup_level: purge
check: exists
data/zae/Spermatophyta_Genera.csv:
command: download_zae_genera(target_name)
cleanup_level: purge
vascular_plant_phylogeny:
command: unpack_tree("data/zae/PhylogeneticResources.zip")
## This will prevent the expensive re-hashing of
## PhylogeneticResources.zip
check: code
genus_order_lookup:
command: unpack_genus_order_lookup("data/zae/Spermatophyta_Genera.csv")
synonyms:
command: make_synonyms("data/spermatophyta_synonyms_PLANTLIST.csv", vascular_plant_phylogeny)
## Also avoids expensive hash
check: code
corrections:
command: make_corrections("data/names-tr.txt", vascular_plant_phylogeny)
species_leaf_n:
command: make_species_leaf_n(wright_2004, synonyms, corrections)
species_seed_mass:
command: make_species_seed_mass(kew, synonyms, corrections)
species_sla:
command: make_species_sla(wright_2004, leda, synonyms, corrections)
leaf_n:
command: build_data(species_leaf_n, vascular_plant_phylogeny)
seed_mass:
command: build_data(species_seed_mass, vascular_plant_phylogeny)
sla:
command: build_data(species_sla, vascular_plant_phylogeny)
## These are the partitioned data sets. There's repetition here
## because I'm not yet supporting templating of target types.
leaf_n_subsets:
command: make_data_subsets(leaf_n)
seed_mass_subsets:
command: make_data_subsets(seed_mass)
sla_subsets:
command: make_data_subsets(sla)
fits_ml_leaf_n:
command: run_model_ad_ml(leaf_n_subsets)
fits_ml_seed_mass:
command: run_model_ad_ml(seed_mass_subsets)
fits_ml_sla:
command: run_model_ad_ml(sla_subsets)
fits_ml:
command: combine_fits(fits_ml_leaf_n, fits_ml_seed_mass, fits_ml_sla)
fits_bayes_leaf_n:
command: run_model_ad_bayes(leaf_n_subsets)
fits_bayes_seed_mass:
command: run_model_ad_bayes(seed_mass_subsets)
fits_bayes_sla:
command: run_model_ad_bayes(sla_subsets)
fits_bayes:
command: combine_fits(fits_bayes_leaf_n, fits_bayes_seed_mass, fits_bayes_sla)
fits_ml_best:
command: prune_dataset_best(fits_ml)
fits_bayes_best:
command: prune_dataset_best(fits_bayes)
example_fits:
command: extract_example_fits(fits_ml_seed_mass)
output/figs/aic-support.pdf:
plot: {width: 9, height: 6}
command: fig_model_support_ic(fits_ml)
output/figs/dic-support.pdf:
plot: {width: 9, height: 6}
command: fig_model_support_ic(fits_bayes)
output/figs/pval-hist-ml.pdf:
plot: {width: 9, height: 5}
command: fig_pval_histogram(fits_ml_best)
output/figs/pval-hist-bayes.pdf:
plot: {width: 9, height: 5}
command: fig_pval_histogram(fits_bayes_best)
output/figs/ad-aic.pdf:
plot: {width: 7, height: 6}
command: fig_modelad_ic(fits_ml)
output/figs/ad-dic.pdf:
plot: {width: 7, height: 6}
command: fig_modelad_ic(fits_bayes)
output/figs/ad-size-ml.pdf:
plot: {width: 7, height: 6}
command: fig_modelad_size(fits_ml_best)
output/figs/ad-size-bayes.pdf:
plot: {width: 7, height: 6}
command: fig_modelad_size(fits_bayes_best)
output/figs/ad-age-ml.pdf:
plot: {width: 7, height: 6}
command: fig_modelad_age(fits_ml_best)
output/figs/ad-age-bayes.pdf:
plot: {width: 7, height: 6}
command: fig_modelad_age(fits_bayes_best)
output/figs/two-clades.pdf:
plot: {width: 9, height: 5}
command: fig_two_clades(example_fits)
output/results-ml.csv:
command: write_csv(fits_ml, target_name)
output/results-bayes.csv:
command: write_csv(fits_bayes, target_name)
model-adequacy.Rmd:
command: sowsear("./model-adequacy.R", output=target_name)
model-adequacy.md:
knitr: true
depends:
- species_sla
- species_leaf_n
- species_seed_mass
- fits_ml
- fits_ml_best
- fits_bayes
- fits_bayes_best
- example_fits
- vascular_plant_phylogeny
model-adequacy.html:
command: md2html("model-adequacy.md")