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40_pesticide_figs.yml
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40_pesticide_figs.yml
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target_default: 40_pesticide_figs
include:
- 30_reports.yml
packages:
- knitr
- rmarkdown
- toxEval
- dplyr
- tidyr
- ggplot2
- yaml
- viridis
- lubridate
sources:
- 40_pesticide_figs/src/combo_graph_function.R
- 40_pesticide_figs/src/fig1_combo_graph.R
- 40_pesticide_figs/src/plot_tox_endpoints_manuscript.R
- 40_pesticide_figs/src/endpoint_graph.R
- 40_pesticide_figs/src/summary_figures.R
- 40_pesticide_figs/src/unique_chem_figs.R
- 40_pesticide_figs/src/generate_site_info_table.R
targets:
40_pesticide_figs:
depends:
- figure/tox_bench_conc.png
- figure/tox_bench.png
- figure/endpoint.png
# - summary figs by site, time, total conc. etc - #
summary_figs:
depends:
- figure/sum_conc_by_site.png
- figure/sum_conc_by_site_detects.png
- figure/sum_conc_by_site_month.png
- figure/sum_conc_through_time_by_site.png
- figure/sum_conc_by_month_site.png
- figure/ndetect_by_site_month.png
- figure/ndetect_by_month_site.png
- figure/ndetect_through_time_by_site.png
#- figure/nchems_bysitedate.png
- figure/cumulative_chems_time_bysite.png
- figure/new_chems_time_bysite.png
- figure/site_table.csv
- figure/tox_bench_conc_deg.png
- figure/tox_bench_hbs.png
sum_conc:
command: sum_pest_conc(reduced_dat, chems_missing_cas)
unique_chems:
command: get_n_unique_chems(reduced_dat, sites)
sums:
command: combine_dat(parent_sums, sites)
figures/ms_figures/site_table.csv:
command: gather_site_info(target_name, sites, sum_conc, unique_chems)
# still need to classify chems with no chem Class
# also need to get everything in same units
figures/ms_supplement_figures/chem_table.csv:
command: gather_chem_info(target_name, chem_dls, chemicalSummary_conc, chem_info, parents = chem_crosswalk)
# figures/ms_supplement_figures/site_chem_table.csv:
# command: gather_chem_info(target_name, chem_dls, chemicalSummary_conc, chem_info, parents = chem_crosswalk)
figure/cumulative_chems_time_bysite.png:
command: plot_unique_chems(target_name, unique_chems, type = I('cumulative'))
figure/new_chems_time_bysite.png:
command: plot_unique_chems(target_name, unique_chems, type = I('new'))
figure/sum_conc_by_site.png:
command: boxplot_bysite(sum_conc, target_name, detect_only = FALSE)
figure/sum_conc_by_site_detects.png:
command: boxplot_bysite(sum_conc, target_name, detect_only = TRUE)
figure/sum_conc_by_site_month.png:
command: boxplot_bysite_month(sum_conc, target_name, site_info)
figure/sum_conc_through_time_by_site.png:
command: plot_throughtime_bysite(sum_conc, target_name)
figure/sum_conc_by_month_site.png:
command: boxplot_bymonth_site(sum_conc, target_name, site_info)
figure/ndetect_by_site_month.png:
command: boxplot_ndetect_bysite_month(sum_conc, target_name, site_info)
figure/ndetect_by_month_site.png:
command: boxplot_ndetect_bymonth_site(sum_conc, target_name, site_info)
figure/ndetect_through_time_by_site.png:
command: plot_nchem_throughtime_bysite(sum_conc, target_name, site_info)
#figure/nchems_bysitedate.png:
# command: plot_nchem_bysitedate(reduced_dat, target_name)
pesticide_sum_concentration_figs:
command: plot_sum_concentration()
graph_data_tox:
command: graph_chem_data(chemicalSummary)
graph_data_wq:
command: graph_chem_data(chemicalSummary_bench, sum_logic = FALSE)
graph_data_conc:
command: graph_chem_data(chemicalSummary_conc)
graph_data_tox_deg:
command: graph_chem_data(chemicalSummary_deg_meto)
graph_data_hbs:
command: graph_chem_data(chemicalSummary_bench_hbs, sum_logic = FALSE)
figure/tox_bench_conc.png:
command: graphData_combos(graph_data_tox, graph_data_wq, graph_data_conc, target_name)
figure/tox_bench_conc_deg.png:
command: graphData_combos(graph_data_tox_deg, graph_data_wq, graph_data_conc, target_name)
figure/tox_bench_hbs.png:
command: graphData_combos(graph_data_tox, graph_data_wq, graph_data_hbs, target_name)
figure/tox_bench.png:
command: graphData_wq_tox(graph_data_tox, graph_data_wq, target_name)
figure/endpoint.png:
command: endpoint_graph(target_name, chemicalSummary, AOP, I(0.001), I(10))
figure/tox_eval_dls.png:
command: plot_dls_tox(chem_dls, chemicalSummary_dls, pCodeInfo, target_name)