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remake.yml
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packages:
- plant
- baad.data
- rmarkdown
- xtable
- RColorBrewer
- dplyr
- knitr
- parallel
- rstan
- grImport
- gridBase
sources:
- R
plot_options:
tall:
width: 4
height: 12
wide:
width: 12
height: 4
3x2:
width: 7.5
height: 5
square:
width: 6
height: 6
med_square:
width: 9
height: 9
large_square:
width: 12
height: 12
3x2small:
width: 6
height: 4
growth:
width: 8
height: 4
targets:
all:
depends:
- figures_plant
- figures_talk
# - figures_stan
- analysis.R
# A plain R version of this file (for those who don't like remake) -------------
analysis.R:
packages: remake
command: make_script(file=target_name)
# Data ------------------------
glopnet:
command: >
process_wright_2004("downloads/wright_2004.xls")
packages: readxl
downloads/wright_2004.xls:
download: http://www.nature.com/nature/journal/v428/n6985/extref/nature02403-s2.xls
cleanup_level: purge
check: exists
# Tables & figures (excluding those using stan) ------------------------
figures_plant:
depends:
- output/main/figure_conceptual.pdf
- output/main/lcp_schematic.pdf
- output/main/growth_light_height.pdf
- output/main/lcp_trait.pdf
- output/SI/growth_light_dia.pdf
- output/SI/growth_light_mass.pdf
- output/SI/growth_light_area.pdf
output/main/figure_conceptual.pdf:
command: latex_build("ms/figure_conceptual.tex", output=target_name, engine=I("xelatex"))
depends:
- output/conn/net_mass_production_dt_net_mass_production_dt.pdf
- output/conn/mass_total_dt_mass_total_dt.pdf
- output/conn/darea_leaf_dmass_live_darea_leaf_dmass_live.pdf
- output/conn/height_dt_height_dt.pdf
- output/conn/area_leaf_dt_area_leaf_dt.pdf
- output/conn/area_stem_dt_area_stem_dt.pdf
- output/conn/diameter_stem_dt_diameter_stem_dt.pdf
- output/main/mass_fraction.pdf
output/main/growth_light_height_grid.pdf:
command: figure_dY_dt_grid(height_dt_data_grid)
plot:
width: 10
height: 4
height_dt_data_grid:
command: figure_height_dt_data_grid()
output/main/growth_light_height.pdf:
command: figure_dY_dt(height_dt_data)
plot: 3x2
height_dt_data:
command: figure_height_dt_data()
output/SI/growth_light_dia.pdf:
command: figure_dY_dt(diameter_stem_dt_data)
plot: 3x2
diameter_stem_dt_data:
command: figure_diameter_stem_dt_data()
output/SI/growth_light_area.pdf:
command: figure_dY_dt(area_stem_dt_data)
plot: 3x2
area_stem_dt_data:
command: figure_area_stem_dt_data()
output/SI/growth_light_mass.pdf:
command: figure_dY_dt(mass_above_ground_dt_data)
plot: 3x2
mass_above_ground_dt_data:
command: figure_mass_above_ground_dt_data()
output/main/lcp_schematic.pdf:
command: figure_lcp_schematic()
plot:
width: 6
height: 4
output/main/lcp_trait.pdf:
command: figure_lcp_trait(lcp_trait_data)
plot:
width: 7.5
height: 2.5
lcp_trait_data:
command: figure_lcp_trait_data()
rate_vs_size_data:
command: figure_rate_vs_size_data()
output/main/mass_fraction.pdf:
command: figure_mass_fraction(rate_vs_size_data)
plot:
width: 10
height: 2.5
output/conn/net_mass_production_dt_net_mass_production_dt.pdf:
command: figure_rate_vs_size_panels(rate_vs_size_data, I("net_mass_production_dt"), I("output/conn"))
output/conn/mass_total_dt_mass_total_dt.pdf:
command: figure_rate_vs_size_panels(rate_vs_size_data, I("mass_total_dt"), I("output/conn"))
output/conn/darea_leaf_dmass_live_darea_leaf_dmass_live.pdf:
command: figure_rate_vs_size_panels(rate_vs_size_data, I("darea_leaf_dmass_live"), I("output/conn"))
output/conn/height_dt_height_dt.pdf:
command: figure_rate_vs_size_panels(rate_vs_size_data, I("height_dt"), I("output/conn"))
output/conn/area_leaf_dt_area_leaf_dt.pdf:
command: figure_rate_vs_size_panels(rate_vs_size_data, I("area_leaf_dt"), I("output/conn"))
output/conn/area_stem_dt_area_stem_dt.pdf:
command: figure_rate_vs_size_panels(rate_vs_size_data, I("area_stem_dt"), I("output/conn"))
output/conn/diameter_stem_dt_diameter_stem_dt.pdf:
command: figure_rate_vs_size_panels(rate_vs_size_data, I("diameter_stem_dt"), I("output/conn"))
# Figures (using stan) ------------------------
figures_stan:
depends:
- output/SI/assumptions.pdf
- output/SI/lma_tradeoff.pdf
output/SI/assumptions.pdf:
command: figure_assumptions(fit_a.lf_h.t, fit_a.lf_sap, fit_a.lf_m.rf, fit_h.t_msal)
plot: med_square
fit_a.lf_h.t:
command: fit_SMA_baad(I("a.lf"), I("h.t"))
check: exists
fit_a.lf_m.rf:
command: fit_SMA_baad(I("a.lf"), I("m.rf"))
check: exists
fit_a.lf_sap:
command: fit_SMA_baad(I("a.lf"), I("sap"))
check: exists
fit_h.t_msal:
command: fit_SMA_baad(I("h.t"), I("msal"))
check: exists
fit_lma_tradeoff:
command: fit_SMA_lma(glopnet)
check: exists
output/SI/lma_tradeoff.pdf:
command: figure_lma_tradeoff(glopnet, fit_lma_tradeoff)
plot: square
## Figures for a talk ----------------------------------------------
figures_talk:
depends:
# - output/talk/assumption_ht_1.pdf
# - output/talk/assumption_sap_1.pdf
# - output/talk/assumption_mrt_1.pdf
# - output/talk/assumption_ht_2.pdf
# - output/talk/assumption_sap_2.pdf
# - output/talk/assumption_mrt_2.pdf
- output/talk/growth_lma_1.pdf
- output/talk/growth_lma_2.pdf
- output/talk/growth_lma_3.pdf
- output/talk/growth_lma_4.pdf
- output/talk/growth_lma_5.pdf
- output/talk/growth_lma_6.pdf
- output/talk/growth_lma_7.pdf
- output/talk/growth_lma_8.pdf
- output/talk/growth_rho_1.pdf
- output/talk/growth_rho_2.pdf
- output/talk/growth_rho_3.pdf
- output/talk/growth_rho_4.pdf
- output/talk/growth_rho_5.pdf
- output/talk/growth_rho_6.pdf
- output/talk/growth_rho_7.pdf
- output/talk/growth_rho_8.pdf
- output/talk/growth_light_height.pdf
tree:
command: get.pic("data/tree.eps")
output/talk/assumption_ht_1.pdf:
command: figure_assumption_talk(fit_a.lf_h.t, FALSE)
plot: 3x2small
output/talk/assumption_sap_1.pdf:
command: figure_assumption_talk(fit_a.lf_sap, FALSE)
plot: 3x2small
output/talk/assumption_mrt_1.pdf:
command: figure_assumption_talk(fit_a.lf_m.rf, FALSE)
plot: 3x2small
output/talk/assumption_ht_2.pdf:
command: figure_assumption_talk(fit_a.lf_h.t, TRUE)
plot: 3x2small
output/talk/assumption_sap_2.pdf:
command: figure_assumption_talk(fit_a.lf_sap, TRUE)
plot: 3x2small
output/talk/assumption_mrt_2.pdf:
command: figure_assumption_talk(fit_a.lf_m.rf, TRUE)
plot: 3x2small
height_dt_data_talk:
command: figure_height_dt_data(sizes = I(c(0.25, 0.5, 1, 2, 5, 10, 15, 20)))
output/talk/growth_lma_1.pdf:
command: figure_dY_dt_talk(I("lma"), 1, height_dt_data_talk, tree)
plot: growth
output/talk/growth_lma_2.pdf:
command: figure_dY_dt_talk(I("lma"), 2, height_dt_data_talk, tree)
plot: growth
output/talk/growth_lma_3.pdf:
command: figure_dY_dt_talk(I("lma"), 3, height_dt_data_talk, tree)
plot: growth
output/talk/growth_lma_4.pdf:
command: figure_dY_dt_talk(I("lma"), 4, height_dt_data_talk, tree)
plot: growth
output/talk/growth_lma_5.pdf:
command: figure_dY_dt_talk(I("lma"), 5, height_dt_data_talk, tree)
plot: growth
output/talk/growth_lma_6.pdf:
command: figure_dY_dt_talk(I("lma"), 6, height_dt_data_talk, tree)
plot: growth
output/talk/growth_lma_7.pdf:
command: figure_dY_dt_talk(I("lma"), 7, height_dt_data_talk, tree)
plot: growth
output/talk/growth_lma_8.pdf:
command: figure_dY_dt_talk(I("lma"), 8, height_dt_data_talk, tree)
plot: growth
output/talk/growth_rho_1.pdf:
command: figure_dY_dt_talk(I("rho"), 1, height_dt_data_talk, tree)
plot: growth
output/talk/growth_rho_2.pdf:
command: figure_dY_dt_talk(I("rho"), 2, height_dt_data_talk, tree)
plot: growth
output/talk/growth_rho_3.pdf:
command: figure_dY_dt_talk(I("rho"), 3, height_dt_data_talk, tree)
plot: growth
output/talk/growth_rho_4.pdf:
command: figure_dY_dt_talk(I("rho"), 4, height_dt_data_talk, tree)
plot: growth
output/talk/growth_rho_5.pdf:
command: figure_dY_dt_talk(I("rho"), 5, height_dt_data_talk, tree)
plot: growth
output/talk/growth_rho_6.pdf:
command: figure_dY_dt_talk(I("rho"), 6, height_dt_data_talk, tree)
plot: growth
output/talk/growth_rho_7.pdf:
command: figure_dY_dt_talk(I("rho"), 7, height_dt_data_talk, tree)
plot: growth
output/talk/growth_rho_8.pdf:
command: figure_dY_dt_talk(I("rho"), 8, height_dt_data_talk, tree)
plot: growth
output/talk/growth_light_height.pdf:
command: figure_dY_dt_talk2(height_dt_data)
plot:
width: 8
height: 3