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remake.yml
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remake.yml
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## load packages
packages:
- dplyr
- magrittr
- lubridate
- tidyr
- ggplot2
- pryr
- rmarkdown
- readr
- gridExtra
- reshape2
- picante
- stargazer
- pander
- xtable
- vegan
- grid
- stringr
- rentrez
- knitcitations
- csvy
- rfigshare # github.com/ropensci/rfigshare/tree/sckott
- purrr
- broom
## source in R functions
sources:
- src/FUNCTIONS_predator_diversity.R
- src/FUNCTIONS_text.R
- src/CALC_pd_experiment_models.R
- src/FIGURE_themes.R
- src/FIG1.R
- src/FIG2.R
- src/FIG3.R
- src/DATA_summarize_randomization.R
- src/DATA_prop_eaten.R
- src/CALC_meta_dist.R
- src/CALC_dist_aic.R
- src/CALC_diet_aic.R
- src/CALC_diet_nlsconfint.R
- src/DATA_phylo_distance.R
- src/renew_rando.R
- src/mantel.R
- src/READING_data_published.R
- src/READING_data_published_zenodo.R
targets:
all:
depends:
- doc/predatordiversity.pdf
- doc/SuppMatt.pdf
## Figure themes
one_point:
command: makept()
cardoso08files:
command: read_published_zenodo(I("https://zenodo.org/record/168039/files/SrivastavaLab/cardoso2008-v1.0.0.zip"))
# occurrance data -- metabolic capacity
metabolic:
command: create_metabolic_matrix(cardoso08files)
# feeding trial data
#feeding_trials:
# command: read_csv("data/reorganized.feeding.trial.data.csv")
feeding_trials:
command: read_published_data(I("3978783"))
# experiment results
pd_raw:
command: read_published_data(I("3983964"))
predtree_timetree_ages:
#command: read.tree("data/predator_tree_time.newick")
command: read_published_newick(I("3980349"))
# Phylogenetic distance
phylogenetic_distance:
command: calc_phylogenetic_dist(predtree_timetree_ages)
## calculations -- data merging
## distribution
metabolic_distance:
command: make_metabolic_dist_pianka(metabolic)
metabolic_occur_phylo:
command: left_join(metabolic_distance, phylogenetic_distance)
meta_pd_mantel:
command: make_mantel_test(metabolic_distance, predtree_timetree_ages)
## feeding trials
prop_eaten:
command: calc_prop_eaten(feeding_trials)
diet_overlap:
command: make_prop_eaten_pianka(prop_eaten)
diet_overlap_phylo:
command: left_join(diet_overlap, phylogenetic_distance)
diet_pd_mantel:
command: make_mantel_test(diet_overlap, predtree_timetree_ages)
## analysis
## metabolic model fitting
distributional_similarity_AIC:
command: make_dist_sim_AIC(metabolic_occur_phylo)
## diet model fitting
diet_similarity_AIC:
command: make_diet_models(diet_overlap_phylo)
diet_predictions:
command: make_diet_predictions(diet_overlap_phylo)
## experiment models
pd_no_out:
command: drop_outlier(pd_raw)
pd_experiment_phylo_dist:
command: experiment_and_phylo(pd_no_out, phylogenetic_distance)
modlist:
command: make_modlist(pd_experiment_phylo_dist)
## bootstrap CI on differences
mean_diffs_boot_list:
command: make_nonadditive_bootCI(pd_no_out)
mean_diffs_boot:
command: extract_obs_ci(mean_diffs_boot_list)
rando_pvals:
command: make_rando_pvals(mean_diffs_boot_list)
nonadd_effect:
command: relevel_nonadd_boot(mean_diffs_boot)
nonadd_effect_pd:
command: left_join(nonadd_effect, phylogenetic_distance)
doc/predatordiversity.md:
depends:
- rando_pvals
- pd_no_out
- feeding_trials
- metabolic
- metabolic_occur_phylo
- diet_overlap_phylo
- experiment_phylo
- diet_pd_mantel
- meta_pd_mantel
- modlist
- cardoso08files
knitr: true
# doc/predatordiversity.pdf:
# depends:
# - Figures/FIG_1.pdf
# - Figures/FIG_2.pdf
# - Figures/FIG_3.pdf
# command: render("doc/predatordiversity.md")
experiment_phylo:
command: pd_exper_responses(pd_no_out, phylogenetic_distance)
Figures/FIG_1.png:
command: make_fig_1(metabolic_occur_phylo, diet_overlap_phylo, experiment_phylo, diet_predictions)
plot:
width: 500
height: 500
Figures/FIG_2.png:
command: make_fig_2(pd_no_out, one_point)
plot:
width: 500
height: 500
Figures/FIG_3.png:
command: make_fig_3(nonadd_effect_pd)
plot:
width: 500
height: 500
### PDF versions
Figures/FIG_1.pdf:
command: make_fig_1(metabolic_occur_phylo, diet_overlap_phylo, experiment_phylo, diet_predictions)
plot: true
Figures/FIG_2.pdf:
command: make_fig_2(pd_no_out, one_point)
plot: true
Figures/FIG_3.pdf:
command: make_fig_3(nonadd_effect_pd)
plot: true
doc/predatordiversity.docx:
depends:
- Figures/FIG_1.png
- Figures/FIG_2.png
- Figures/FIG_3.png
- doc/formatting/pdef.bib
command: render("doc/predatordiversity.md", output_format = I("word_document"))
doc/predatordiversity.pdf:
depends:
- Figures/FIG_1.pdf
- Figures/FIG_2.pdf
- Figures/FIG_3.pdf
- doc/formatting/pdef.bib
command: render("doc/predatordiversity.md", output_format = I("pdf_document"))
#### supplementary materials
doc/SuppMatt.md:
knitr:
chdir: true
depends:
- predtree_timetree_ages
- distributional_similarity_AIC
- prop_eaten
- diet_similarity_AIC
- pd_no_out
doc/SuppMatt.pdf:
command: render("doc/SuppMatt.md", output_format = I("pdf_document"))