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30_analyze_data_series.yml
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30_analyze_data_series.yml
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target_default: 30_analyze_data
packages:
- EGRET
- EGRETci
- ggplot2
- dplyr
- cowplot
include:
- 29_analyze_data_source_tests.yml
sources:
- 30_analyze_data/code/plot_conc_flux.R
- 30_analyze_data/code/model_diagnostic_plots.R
- 30_analyze_data/code/create_four_panel_summary.R
targets:
30_analyze_data:
depends:
- figures/series/tp_conc_four_panel_plot.png
- figures/series/tp_flux_four_panel_plot.png
- figures/series/ss_conc_four_panel_plot.png
- figures/series/ss_flux_four_panel_plot.png
- figures/series/ortho_p_conc_four_panel_plot.png
- figures/series/ortho_p_flux_four_panel_plot.png
##############
# TP analysis
##############
# need to use the old modelEstimation in order to show residual plots. To do that, need to run
# modelEstimation, then runSeries using old surface. Should be the same as just doing runSeries.
tp_mest_eList:
command: modelEstimation(eList = tp_eList)
tp_wy_out_old:
command: runSeries(eList = tp_mest_eList, windowSide = I(7), paStart = I(10), paLong = I(12), oldSurface = I(TRUE))
# try narrowing the season window to remove monthly bias
tp_wy_out_ws1:
command: runSeries(eList = tp_mest_eList, windowSide = I(7), windowS = I(0.1), paStart = I(10), paLong = I(12), oldSurface = I(TRUE))
# output model residuals
figures/model_evaluation/tp_flux_bias_multi.pdf:
command: create_bias_plot(tp_wy_out_old, target_name)
figures/model_evaluation/tp_flux_bias_multi_ws1.pdf:
command: create_bias_plot(tp_wy_out_old, target_name)
# run series and bootstrap
tp_wy_out:
command: runSeries(eList = tp_eList, windowSide = I(7), paStart = I(10), paLong = I(12))
tp_wy_out_boot:
command: ciCalculations(eList = tp_wy_out, nBoot = I(100), blockLength = I(200), widthCI = I(90))
# run windowSide = 0 for comparison
tp_wy_out_stationary:
command: runSeries(eList = tp_eList, windowSide = I(0), paStart = I(10), paLong = I(12))
# four-panel plot from murphy paper
figures/series/tp_conc_four_panel_plot.png:
command: plot_four_panels(file_name = target_name, gen = tp_wy_out, fixed = tp_wy_out_stationary, conc = I(TRUE))
figures/series/tp_flux_four_panel_plot.png:
command: plot_four_panels(file_name = target_name, gen = tp_wy_out, fixed = tp_wy_out_stationary, conc = I(FALSE))
#######################
# suspended sediment #
#######################
ss_wy_out:
command: runSeries(eList = ss_eList, windowSide = I(7), paStart = 10, paLong = 12)
ss_wy_out_boot:
command: ciCalculations(eList = ss_wy_out, nBoot = I(100), blockLength = I(200), widthCI = I(90))
ss_wy_out_stationary:
command: runSeries(eList = ss_eList, windowSide = I(0), paStart = I(10), paLong = I(12))
ss_mest_eList:
command: modelEstimation(eList = ss_eList)
ss_wy_out_old:
command: runSeries(eList = ss_mest_eList, windowSide = I(7), paStart = I(10), paLong = I(12), oldSurface = I(TRUE))
# output model residuals
figures/model_evaluation/ss_flux_bias_multi.pdf:
command: create_bias_plot(ss_wy_out_old, target_name)
# other figs
figures/series/ss_conc_four_panel_plot.png:
command: plot_four_panels(file_name = target_name, gen = ss_wy_out, fixed = ss_wy_out_stationary, conc = I(TRUE))
figures/series/ss_flux_four_panel_plot.png:
command: plot_four_panels(file_name = target_name, gen = ss_wy_out, fixed = ss_wy_out_stationary, conc = I(FALSE))
############
# ortho P #
############
ortho_p_filt_wy_out:
command: runSeries(eList = ortho_p_filt_eList, windowSide = I(7), paStart = 10, paLong = 12, surfaceStart = I('1993-03-07'))
ortho_p_filt_wy_out_boot:
command: ciCalculations(eList = ortho_p_filt_wy_out, nBoot = I(100), blockLength = I(200), widthCI = I(90))
ortho_p_filt_wy_out_stationary:
command: runSeries(eList = ortho_p_filt_eList, windowSide = I(0), paStart = I(10), paLong = I(12))
ortho_p_filt_mest_eList:
command: modelEstimation(eList = ortho_p_filt_eList)
ortho_p_filt_wy_out_old:
command: runSeries(eList = ortho_p_filt_mest_eList, windowSide = I(7), paStart = I(10), paLong = I(12), oldSurface = I(TRUE))
# output model residuals
figures/model_evaluation/ortho_p_flux_bias_multi.pdf:
command: create_bias_plot(ortho_p_filt_wy_out_old, target_name)
# other figs
figures/series/ortho_p_conc_four_panel_plot.png:
command: plot_four_panels(file_name = target_name, gen = ortho_p_filt_wy_out, fixed = ortho_p_filt_wy_out_stationary, conc = I(TRUE))
figures/series/ortho_p_flux_four_panel_plot.png:
command: plot_four_panels(file_name = target_name, gen = ortho_p_filt_wy_out, fixed = ortho_p_filt_wy_out_stationary, conc = I(FALSE))