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RSCRIPT = Rscript
PLOT_SETTINGS = scripts/common/plot-settings.R
TEX_FILES = $(wildcard tex-input/*.tex) \
$(wildcard tex-input/*/*.tex) \
$(wildcard tex-input/*/*/*.tex)
MCMC_UTIL = scripts/common/mcmc-util.R
BIBLIOGRAPHY = bibliography/multi-phi-bib.bib
# useful compound make components
PLOTS = plots
RDS = rds
SCRIPTS = scripts
# ALL figures
ALL_PLOTS =
# if you wildcard the all-target, then nothing will happen if the target doesn't
# exist (no target). hard code the target.
# CHANGE THIS:
BASENAME = multiple-phi
WRITEUP = $(BASENAME).pdf
all : $(WRITEUP)
clean :
trash \
$(BASENAME).aux \
$(BASENAME).out \
$(BASENAME).pdf \
$(BASENAME).tex \
$(BASENAME).log \
Rplots.pdf
################################################################################
## Pooling visualisation tests
POOLING_TESTS = pooling-tests
POOLING_SCRIPTS = scripts/$(POOLING_TESTS)
POOLING_OUTPUTS = rds/$(POOLING_TESTS)
POOLING_PLOTS = plots/pooling-tests
POOLED_PLOT_2D = $(POOLING_PLOTS)/version-two.pdf
$(POOLING_SCRIPTS)/sub-plot-maker.R : $(POOLING_SCRIPTS)/density-functions.R
$(POOLED_PLOT_2D) : $(POOLING_SCRIPTS)/plot-pooled-priors.R $(PLOT_SETTINGS) $(POOLING_SCRIPTS)/sub-plot-maker.R
$(RSCRIPT) $<
ALL_PLOTS += $(POOLED_PLOT_2D)
################################################################################
## Owls example
OWLS_BASENAME = owls-example
OWLS_DATA = $(wildcard rds/owls-example/*-data.rds)
OWLS_SCRIPTS = $(SCRIPTS)/$(OWLS_BASENAME)
OWLS_RDS = $(RDS)/$(OWLS_BASENAME)
OWLS_PLOTS = $(PLOTS)/$(OWLS_BASENAME)
OWLS_POSTERIOR_SAMPLES = $(wildcard rds/owls-example/*-samples.rds)
OWLS_APPENDIX_TEX = tex-input/owls-example/appendix-info
$(OWLS_DATA) : $(OWLS_SCRIPTS)/load-and-write-data.R
$(RSCRIPT) $<
ORIG_IPM_SAMPLES = $(OWLS_RDS)/original-ipm-samples.rds
$(ORIG_IPM_SAMPLES) : $(OWLS_SCRIPTS)/fit-original-ipm.R $(OWLS_SCRIPTS)/models/original-ipm.bug $(OWLS_DATA)
$(RSCRIPT) $<
FECUNDITY_SUBPOSTERIOR = $(OWLS_RDS)/fecundity-subposterior-samples.rds
$(FECUNDITY_SUBPOSTERIOR) : $(OWLS_SCRIPTS)/fit-fecundity.R $(OWLS_SCRIPTS)/models/fecundity-model.stan $(FECUNDITY_DATA)
$(RSCRIPT) $<
CAPTURE_RECAPTURE_SUBPOSTERIOR = $(OWLS_RDS)/capture-recapture-subposterior-samples.rds
$(CAPTURE_RECAPTURE_SUBPOSTERIOR) : $(OWLS_SCRIPTS)/fit-capture-recapture.R $(OWLS_SCRIPTS)/models/capture-recapture.bug $(OWLS_DATA)
$(RSCRIPT) $<
FECUNDITY_DIAGNOSTIC_PLOT = $(OWLS_PLOTS)/stage-one-diagnostics-fecundity.png
$(FECUNDITY_DIAGNOSTIC_PLOT) : $(OWLS_SCRIPTS)/diagnostics-stage-one-fecundity-plot.R $(PLOT_SETTINGS) $(FECUNDITY_SUBPOSTERIOR)
$(RSCRIPT) $<
CAPTURE_RECAPTURE_DIAGNOSTIC_PLOT = $(OWLS_PLOTS)/stage-one-diagnostics-capture-recapture.png
$(CAPTURE_RECAPTURE_DIAGNOSTIC_PLOT) : $(OWLS_SCRIPTS)/diagnostics-stage-one-capture-recapture-plot.R $(PLOT_SETTINGS) $(CAPTURE_RECAPTURE_SUBPOSTERIOR)
$(RSCRIPT) $<
ALL_PLOTS += $(FECUNDITY_DIAGNOSTIC_PLOT) $(CAPTURE_RECAPTURE_DIAGNOSTIC_PLOT)
STAGE_ONE_DIAGNOSTIC_TABLE = $(OWLS_APPENDIX_TEX)/0010-stage-one-diagnostics.tex
$(STAGE_ONE_DIAGNOSTIC_TABLE) : $(OWLS_SCRIPTS)/diagnostics-stage-one-table.R $(FECUNDITY_SUBPOSTERIOR) $(CAPTURE_RECAPTURE_SUBPOSTERIOR)
$(RSCRIPT) $<
COUNT_DATA_SUBPOSTERIOR = $(OWLS_RDS)/count-data-subposterior-samples.rds
$(COUNT_DATA_SUBPOSTERIOR) : $(OWLS_SCRIPTS)/fit-count-data.R $(OWLS_SCRIPTS)/models/count-data.bug $(OWLS_DATA)
$(RSCRIPT) $<
COUNT_DATA_DIAGNOSTIC_PLOT = $(OWLS_PLOTS)/stage-one-diagnostics-population-count.png
$(COUNT_DATA_DIAGNOSTIC_PLOT) : $(OWLS_SCRIPTS)/diagnostics-stage-one-population-count-plot.R $(COUNT_DATA_SUBPOSTERIOR) $(MCMC_UTIL) $(PLOT_SETTINGS)
$(RSCRIPT) $<
ALL_PLOTS += $(COUNT_DATA_DIAGNOSTIC_PLOT)
NORMAL_APPROX_MELDED_POSTERIOR = $(OWLS_RDS)/melded-posterior-normal-approx-samples.rds
$(NORMAL_APPROX_MELDED_POSTERIOR) : $(OWLS_SCRIPTS)/fit-normal-approx.R $(CAPTURE_RECAPTURE_SUBPOSTERIOR) $(FECUNDITY_SUBPOSTERIOR) $(OWLS_DATA) $(OWLS_SCRIPTS)/models/count-data-normal-approx.bug
$(RSCRIPT) $<
MELDED_POSTERIOR = $(OWLS_RDS)/melded-posterior-samples.rds
$(MELDED_POSTERIOR) : $(OWLS_SCRIPTS)/mcmc-main-stage-two.R $(OWLS_SCRIPTS)/mcmc-nimble-functions.R $(FECUNDITY_SUBPOSTERIOR) $(CAPTURE_RECAPTURE_SUBPOSTERIOR) $(OWLS_DATA)
$(RSCRIPT) $<
MELDED_POSTERIOR_PHI_LOG_POOLING = $(OWLS_RDS)/melded-phi-samples-log-pooling.rds
$(MELDED_POSTERIOR_PHI_LOG_POOLING) : $(OWLS_SCRIPTS)/fit-chained-other-pooled-priors.R $(MCMC_UTIL) $(MELDED_POSTERIOR)
$(RSCRIPT) $<
MELDED_POSTERIOR_PHI_LIN_POOLING = $(OWLS_RDS)/melded-phi-samples-lin-pooling.rds
MELDED_POSTERIOR_INDICES_LOG_POOLING = $(OWLS_RDS)/melded-indices-log-pooling.rds
MELDED_POSTERIOR_INDICES_LIN_POOLING = $(OWLS_RDS)/melded-indices-lin-pooling.rds
$(MELDED_POSTERIOR_PHI_LIN_POOLING) : $(MELDED_POSTERIOR_PHI_LOG_POOLING)
$(MELDED_POSTERIOR_INDICES_LOG_POOLING) : $(MELDED_POSTERIOR_PHI_LOG_POOLING)
$(MELDED_POSTERIOR_INDICES_LIN_POOLING) : $(MELDED_POSTERIOR_PHI_LOG_POOLING)
SUBPOSTERIOR_PLOT = $(OWLS_PLOTS)/subposteriors.pdf
SUBPOSTERIOR_PLOT_MELDING_ONLY = $(OWLS_PLOTS)/subposteriors-melding-only.pdf
SUBPOSTERIOR_PLOT_PATCHWORK = $(OWLS_PLOTS)/subposteriors-both-patchwork.pdf
$(SUBPOSTERIOR_PLOT) \
$(SUBPOSTERIOR_PLOT_MELDING_ONLY) \
$(SUBPOSTERIOR_PLOT_PATCHWORK) &: \
$(OWLS_SCRIPTS)/plot-subposteriors.R \
$(PLOT_SETTINGS) \
$(MCMC_UTIL) \
$(ORIG_IPM_SAMPLES) \
$(FECUNDITY_SUBPOSTERIOR) \
$(CAPTURE_RECAPTURE_SUBPOSTERIOR) \
$(COUNT_DATA_SUBPOSTERIOR) \
$(MELDED_POSTERIOR) \
$(NORMAL_APPROX_MELDED_POSTERIOR) \
$(MELDED_POSTERIOR_PHI_LOG_POOLING) \
$(MELDED_POSTERIOR_PHI_LIN_POOLING)
$(RSCRIPT) $<
ALL_PLOTS += $(SUBPOSTERIOR_PLOT) $(SUBPOSTERIOR_PLOT_MELDING_ONLY) $(SUBPOSTERIOR_PLOT_PATCHWORK)
MELDED_DIAGNOSTIC_TABLE = tex-input/owls-example/appendix-info/0020-stage-two-diagnostics.tex
$(MELDED_DIAGNOSTIC_TABLE) : $(OWLS_SCRIPTS)/diagnostics-stage-two-table.R $(MELDED_POSTERIOR)
$(RSCRIPT) $<
MELDED_DIAGNOSTIC_PLOT = $(OWLS_PLOTS)/stage-two-diagnostics.png
$(MELDED_DIAGNOSTIC_PLOT) : $(OWLS_SCRIPTS)/diagnostics-stage-two-plot.R $(MELDED_POSTERIOR) $(PLOT_SETTINGS)
$(RSCRIPT) $<
MELDED_QQ_PLOT = $(OWLS_PLOTS)/orig-meld-qq-compare.pdf
$(MELDED_QQ_PLOT) : $(OWLS_SCRIPTS)/plot-qq-comparison.R $(MELDED_POSTERIOR) $(ORIG_IPM_SAMPLES) $(PLOT_SETTINGS)
$(RSCRIPT) $<
ALL_PLOTS += $(MELDED_DIAGNOSTIC_PLOT) $(MELDED_QQ_PLOT)
ORIGINAL_IPM_DIAGNOSTIC_PLOT = $(OWLS_PLOTS)/diagnostics-original-ipm.png
NORMAL_APPROXIMATION_DIAGNOSTIC_PLOT = $(OWLS_PLOTS)/stage-two-diagnostics-normal-approx.png
MELDED_LOG_DIAGNOSTIC_PLOT = $(OWLS_PLOTS)/stage-two-diagnostics-log-pooling.png
MELDED_LIN_DIAGNOSTIC_PLOT = $(OWLS_PLOTS)/stage-two-diagnostics-linear-pooling.png
OTHER_DIAGNOSTIC_SAMPLES = $(ORIG_IPM_SAMPLES) $(NORMAL_APPROX_MELDED_POSTERIOR) $(MELDED_POSTERIOR_INDICES_LOG_POOLING) $(MELDED_POSTERIOR_INDICES_LIN_POOLING)
$(MELDED_LOG_DIAGNOSTIC_PLOT) \
$(ORIGINAL_IPM_DIAGNOSTIC_PLOT) \
$(NORMAL_APPROXIMATION_DIAGNOSTIC_PLOT) \
$(MELDED_LIN_DIAGNOSTIC_PLOT) &: $(OWLS_SCRIPTS)/diagnostics-stage-two-non-poe-plot.R $(OTHER_DIAGNOSTIC_SAMPLES) $(PLOT_SETTINGS)
$(RSCRIPT) $<
ALL_PLOTS += $(MELDED_LIN_DIAGNOSTIC_PLOT) $(ORIGINAL_IPM_DIAGNOSTIC_PLOT) $(NORMAL_APPROXIMATION_DIAGNOSTIC_PLOT) $(MELDED_LOG_DIAGNOSTIC_PLOT)
OTHER_DIAGNOSTIC_TABLES = $(OWLS_APPENDIX_TEX)/0011-orig-ipm-diagnostics.tex \
$(OWLS_APPENDIX_TEX)/0021-stage-two-normal-approx-diagnostics.tex \
$(OWLS_APPENDIX_TEX)/0022-stage-two-log-pooling-diagnostics.tex \
$(OWLS_APPENDIX_TEX)/0023-stage-two-lin-pooling-diagnostics.tex
$(OTHER_DIAGNOSTIC_TABLES) : $(OWLS_SCRIPTS)/diagnostics-stage-two-non-poe-table.R $(OTHER_DIAGNOSTIC_SAMPLES) $(MCMC_UTIL)
$(RSCRIPT) $<
################################################################################
## surv-example
SURV_BASENAME = surv-example
SURV_SCRIPTS = $(SCRIPTS)/$(SURV_BASENAME)
SURV_RDS = $(RDS)/$(SURV_BASENAME)
SURV_PLOTS = $(PLOTS)/$(SURV_BASENAME)
SURV_MODELS = $(SURV_SCRIPTS)/models
SURV_TEX = tex-input/$(SURV_BASENAME)
SURV_GLOBAL_SETTINGS = $(SURV_SCRIPTS)/GLOBALS.R
### Submodel 1
SURV_SIMULATION_SETTINGS = $(SURV_RDS)/simulation-settings-and-joint-data.rds
$(SURV_SIMULATION_SETTINGS) : $(SURV_SCRIPTS)/simulation-settings-and-joint-data.R $(SURV_GLOBAL_SETTINGS)
$(RSCRIPT) $<
SURV_SUBMODEL_ONE_SIMULATED_DATA = $(SURV_RDS)/submodel-one-simulated-data.rds
$(SURV_SUBMODEL_ONE_SIMULATED_DATA) : $(SURV_SCRIPTS)/simulate-data-submodel-one.R $(SURV_SIMULATION_SETTINGS)
$(RSCRIPT) $<
SURV_SUMODEL_ONE = $(SURV_MODELS)/submodel-one.stan
SURV_SUBMODEL_ONE_OUTPUT = $(SURV_RDS)/submodel-one-output.rds
$(SURV_SUBMODEL_ONE_OUTPUT) : $(SURV_SCRIPTS)/fit-submodel-one.R $(SURV_SUBMODEL_ONE_SIMULATED_DATA) $(SURV_SUMODEL_ONE)
$(RSCRIPT) $<
SURV_ALL_SUBMODEL_ONE_INPUTS = $(SURV_SIMULATION_SETTINGS) $(SURV_SUBMODEL_ONE_SIMULATED_DATA) $(SURV_SUBMODEL_ONE_OUTPUT)
SURV_SUBMODEL_ONE_POSTERIOR_PLOT_DATA = $(SURV_RDS)/plot-submodel-1-data.rds
$(SURV_SUBMODEL_ONE_POSTERIOR_PLOT_DATA) : $(SURV_SCRIPTS)/prepare-submodel-one-plot-data.R $(MCMC_UTIL) $(SURV_ALL_SUBMODEL_ONE_INPUTS)
$(RSCRIPT) $<
SURV_SUBMODEL_ONE_POSTERIOR_PLOT = $(SURV_PLOTS)/submodel-one-posterior.pdf
$(SURV_SUBMODEL_ONE_POSTERIOR_PLOT) : $(SURV_SCRIPTS)/plot-submodel-one.R $(PLOT_SETTINGS) $(SURV_SUBMODEL_ONE_POSTERIOR_PLOT_DATA) $(SURV_SIMULATION_SETTINGS)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_SUBMODEL_ONE_POSTERIOR_PLOT)
SURV_SUBMODEL_ONE_DIAG_PLOT = $(SURV_PLOTS)/stage-one-submodel-one-diags.png
$(SURV_SUBMODEL_ONE_DIAG_PLOT) : $(SURV_SCRIPTS)/diagnose-submodel-one-plots.R $(PLOT_SETTINGS) $(MCMC_UTIL) $(SURV_SUBMODEL_ONE_OUTPUT)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_SUBMODEL_ONE_DIAG_PLOT)
SURV_SUBMODEL_ONE_DIAG_TABLE = $(SURV_TEX)/0080-submodel-one-numeric-diags.tex
$(SURV_SUBMODEL_ONE_DIAG_TABLE) : $(SURV_SCRIPTS)/diagnose-submodel-one-tables.R $(MCMC_UTIL) $(SURV_SUBMODEL_ONE_OUTPUT)
$(RSCRIPT) $<
TEX_FILES += $(SURV_SUBMODEL_ONE_DIAG_TABLE)
### Submodel 3
SURV_SUBMODEL_THREE_SIMULATED_DATA = $(SURV_RDS)/submodel-three-simulated-data.rds
$(SURV_SUBMODEL_THREE_SIMULATED_DATA) : $(SURV_SCRIPTS)/simulate-data-submodel-three.R $(SURV_SIMULATION_SETTINGS)
$(RSCRIPT) $<
SURV_SUMODEL_THREE = $(SURV_MODELS)/submodel-three.stan
SURV_SUBMODEL_THREE_OUTPUT = $(SURV_RDS)/submodel-three-output.rds
$(SURV_SUBMODEL_THREE_OUTPUT) : $(SURV_SCRIPTS)/fit-submodel-three.R $(SURV_SUBMODEL_THREE_SIMULATED_DATA) $(SURV_SUMODEL_THREE)
$(RSCRIPT) $<
SURV_ALL_SUBMODEL_THREE_INPUTS = $(SURV_SIMULATION_SETTINGS) $(SURV_SUBMODEL_THREE_SIMULATED_DATA) $(SURV_SUBMODEL_THREE_OUTPUT)
SURV_SUBMODEL_THREE_POSTERIOR_PLOT_DATA = $(SURV_RDS)/plot-submodel-3-data.rds
$(SURV_SUBMODEL_THREE_POSTERIOR_PLOT_DATA) : $(SURV_SCRIPTS)/prepare-submodel-three-plot-data.R $(MCMC_UTIL) $(SURV_ALL_SUBMODEL_THREE_INPUTS)
$(RSCRIPT) $<
SURV_SUBMODEL_THREE_POSTERIOR_PLOT = $(SURV_PLOTS)/submodel-three-posterior.pdf
$(SURV_SUBMODEL_THREE_POSTERIOR_PLOT) : $(SURV_SCRIPTS)/plot-submodel-three.R $(PLOT_SETTINGS) $(SURV_SUBMODEL_THREE_POSTERIOR_PLOT_DATA)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_SUBMODEL_THREE_POSTERIOR_PLOT)
SURV_SUBMODEL_THREE_DIAG_PLOT = $(SURV_PLOTS)/stage-one-submodel-three-diags.png
$(SURV_SUBMODEL_THREE_DIAG_PLOT) : $(SURV_SCRIPTS)/diagnose-submodel-three-plots.R $(PLOT_SETTINGS) $(MCMC_UTIL) $(SURV_SUBMODEL_THREE_OUTPUT)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_SUBMODEL_THREE_DIAG_PLOT)
SURV_SUBMODEL_THREE_DIAG_TABLE = $(SURV_TEX)/0081-submodel-three-numeric-diags.tex
$(SURV_SUBMODEL_THREE_DIAG_TABLE) : $(SURV_SCRIPTS)/diagnose-submodel-three-tables.R $(MCMC_UTIL) $(SURV_SUBMODEL_THREE_OUTPUT)
$(RSCRIPT) $<
TEX_FILES += $(SURV_SUBMODEL_THREE_DIAG_TABLE)
SURV_BOTH_LONGITUDINAL_PLOT = $(SURV_PLOTS)/both-longitudinal-submodels.pdf
$(SURV_BOTH_LONGITUDINAL_PLOT) : $(SURV_SCRIPTS)/plot-both-longitudinal-submodels.R $(PLOT_SETTINGS) $(SURV_SUBMODEL_ONE_POSTERIOR_PLOT_DATA) $(SURV_SUBMODEL_THREE_POSTERIOR_PLOT_DATA)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_BOTH_LONGITUDINAL_PLOT)
### Process stage one output
SURV_EXAMPLE_STAGE_ONE_PHI_12 = $(SURV_RDS)/stage-one-phi-12-samples.rds
SURV_EXAMPLE_STAGE_ONE_PHI_12_POST_MEDIAN = $(SURV_RDS)/stage-one-phi-12-posterior-median.rds
SURV_EXAMPLE_STAGE_ONE_PHI_23 = $(SURV_RDS)/stage-one-phi-23-samples.rds
SURV_EXAMPLE_STAGE_ONE_PHI_23_POST_MEDIAN = $(SURV_RDS)/stage-one-phi-23-posterior-median.rds
SURV_EXAMPLE_POST_MEDIANS = $(SURV_EXAMPLE_STAGE_ONE_PHI_12_POST_MEDIAN) $(SURV_EXAMPLE_STAGE_ONE_PHI_23_POST_MEDIAN)
$(SURV_EXAMPLE_STAGE_ONE_PHI_12) : $(SURV_SCRIPTS)/process-submodel-one.R $(SURV_SUBMODEL_ONE_OUTPUT)
$(RSCRIPT) $<
$(SURV_EXAMPLE_STAGE_ONE_PHI_23) : $(SURV_SCRIPTS)/process-submodel-three.R $(SURV_SUBMODEL_THREE_OUTPUT)
$(RSCRIPT) $<
$(SURV_EXAMPLE_STAGE_ONE_PHI_12_POST_MEDIAN) : $(SURV_EXAMPLE_STAGE_ONE_PHI_12)
$(SURV_EXAMPLE_STAGE_ONE_PHI_23_POST_MEDIAN) : $(SURV_EXAMPLE_STAGE_ONE_PHI_23)
### Stage 2
SURV_SUBMODEL_TWO_SIMULATED_DATA = $(SURV_RDS)/submodel-two-simulated-data.rds
$(SURV_SUBMODEL_TWO_SIMULATED_DATA) : $(SURV_SCRIPTS)/simulate-data-submodel-two.R $(SURV_GLOBAL_SETTINGS) $(SURV_SIMULATION_SETTINGS)
$(RSCRIPT) $<
### Stage 2 - sampling the melded posterior
SURV_SUBMODEL_TWO_PHI_STEP = $(SURV_MODELS)/submodel-two-phi-step.stan
SURV_SUBMODEL_TWO_PSI_STEP = $(SURV_MODELS)/submodel-two-psi-step.stan
SURV_STAGE_TWO_STAN_MODELS = $(SURV_SUBMODEL_TWO_PHI_STEP) $(SURV_SUBMODEL_TWO_PSI_STEP)
SURV_STAGE_TWO_PHI_12_SAMPLES = $(SURV_RDS)/stage-two-phi-12-samples.rds
SURV_STAGE_TWO_PHI_23_SAMPLES = $(SURV_RDS)/stage-two-phi-23-samples.rds
SURV_STAGE_TWO_PSI_2_SAMPLES = $(SURV_RDS)/stage-two-psi-2-samples.rds
SURV_STAGE_TWO_PSI_1_INDICES = $(SURV_RDS)/stage-two-psi-1-indices.rds
SURV_STAGE_TWO_PSI_3_INDICES = $(SURV_RDS)/stage-two-psi-3-indices.rds
$(SURV_STAGE_TWO_PHI_12_SAMPLES) : $(SURV_SCRIPTS)/fit-stage-two.R $(SURV_SUBMODEL_ONE_OUTPUT) $(SURV_SUBMODEL_THREE_OUTPUT) $(SURV_SUBMODEL_TWO_SIMULATED_DATA) $(SURV_STAGE_TWO_STAN_MODELS) $(SURV_GLOBAL_SETTINGS)
$(RSCRIPT) $<
$(SURV_STAGE_TWO_PHI_23_SAMPLES) : $(SURV_STAGE_TWO_PHI_12_SAMPLES)
$(SURV_STAGE_TWO_PSI_2_SAMPLES) : $(SURV_STAGE_TWO_PHI_12_SAMPLES)
$(SURV_STAGE_TWO_PSI_1_INDICES) : $(SURV_STAGE_TWO_PHI_12_SAMPLES)
$(SURV_STAGE_TWO_PSI_3_INDICES) : $(SURV_STAGE_TWO_PHI_12_SAMPLES)
### Stage 2 - diagnostics
#### This form of target definition + rule will make --dry-run report
#### incorrectly, but make will only run the relevant file once.
SURV_STAGE_TWO_DIAG_PLOTS = $(wildcard plots/surv-example/stage-two*-diags.png)
$(SURV_STAGE_TWO_DIAG_PLOTS) : $(SURV_SCRIPTS)/diagnose-stage-two-plots.R $(PLOT_SETTINGS) $(SURV_STAGE_TWO_PHI_12_SAMPLES) $(SURV_STAGE_TWO_PHI_23_SAMPLES) $(SURV_STAGE_TWO_PSI_2_SAMPLES)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_STAGE_TWO_DIAG_PLOTS)
#### The tables will be automatically picked up by TEX_FILES, under the
#### assumption that they exist first.
SURV_STAGE_TWO_DIAG_TABLES = $(wildcard tex-input/surv-example/009*-stage-two-**.tex)
$(SURV_STAGE_TWO_DIAG_TABLES) : $(SURV_SCRIPTS)/diagnose-stage-two-tables.R $(SURV_STAGE_TWO_PHI_12_SAMPLES) $(SURV_STAGE_TWO_PHI_23_SAMPLES) $(SURV_STAGE_TWO_PSI_2_SAMPLES) $(MCMC_UTIL)
$(RSCRIPT) $<
TEX_FILES += $(SURV_STAGE_TWO_DIAG_TABLES)
### Compositional step / plots
SURV_EXAMPLE_PHI_12_SRINKAGE_PLOT = $(SURV_PLOTS)/phi-12-inter-stage-comparison.pdf
$(SURV_EXAMPLE_PHI_12_SRINKAGE_PLOT) : $(SURV_SCRIPTS)/plot-event-time-shrinkage.R $(SURV_STAGE_TWO_PHI_12_SAMPLES) $(SURV_SUBMODEL_ONE_OUTPUT) $(SURV_SIMULATION_SETTINGS)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_EXAMPLE_PHI_12_SRINKAGE_PLOT)
SURV_EXAMPLE_PHI_23_SRINKAGE_PLOT = $(SURV_PLOTS)/phi-23-inter-stage-comparison.pdf
$(SURV_EXAMPLE_PHI_23_SRINKAGE_PLOT) : $(SURV_SCRIPTS)/plot-long-model-shrinkage.R $(SURV_STAGE_TWO_PHI_23_SAMPLES) $(SURV_SUBMODEL_THREE_OUTPUT) $(SURV_SIMULATION_SETTINGS)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_EXAMPLE_PHI_23_SRINKAGE_PLOT)
ALL_PHI = $(SURV_EXAMPLE_STAGE_ONE_PHI_12) $(SURV_EXAMPLE_STAGE_ONE_PHI_23) $(SURV_STAGE_TWO_PHI_12_SAMPLES) $(SURV_STAGE_TWO_PHI_23_SAMPLES)
SURV_EXAMPLE_CONTRACTION_PLOT = $(SURV_PLOTS)/phi-inter-stage-posterior-sd.pdf
$(SURV_EXAMPLE_CONTRACTION_PLOT) : $(SURV_SCRIPTS)/plot-contraction.R $(PLOT_SETTINGS) $(MCMC_UTIL) $(SURV_SIMULATION_SETTINGS) $(ALL_PHI)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_EXAMPLE_CONTRACTION_PLOT)
## point estimate comparison
SURV_EXAMPLE_POINT_EST_PSI_2_SAMPLES = $(SURV_RDS)/point-est-psi-2-samples.rds
$(SURV_EXAMPLE_POINT_EST_PSI_2_SAMPLES) : $(SURV_SCRIPTS)/fit-point-est-approx.R $(SURV_GLOBAL_SETTINGS) $(SURV_EXAMPLE_POST_MEDIANS) $(SURV_SUBMODEL_TWO_SIMULATED_DATA) $(SURV_EXAMPLE_STAGE_ONE_PHI_12) $(SURV_SUBMODEL_TWO_PSI_STEP)
$(RSCRIPT) $<
## Half way in between point estimates
SURV_EXAMPLE_POINT_EST_1_MELD_23_PSI_2_SAMPLES = $(SURV_RDS)/point-est-1-meld-23-psi-2-samples.rds
$(SURV_EXAMPLE_POINT_EST_1_MELD_23_PSI_2_SAMPLES) : $(SURV_SCRIPTS)/fit-point-est-1-meld-23.R $(SURV_SUBMODEL_ONE_OUTPUT) $(SURV_EXAMPLE_STAGE_ONE_PHI_12_POST_MEDIAN) $(SURV_SUBMODEL_THREE_OUTPUT) $(SURV_SUBMODEL_TWO_SIMULATED_DATA) $(SURV_STAGE_TWO_STAN_MODELS)
$(RSCRIPT) $<
SURV_EXAMPLE_POINT_EST_1_MELD_23_PHI_23_SAMPLES = $(SURV_RDS)/point-est-1-meld-23-phi-23-samples.rds
$(SURV_EXAMPLE_POINT_EST_1_MELD_23_PHI_23_SAMPLES) : $(SURV_EXAMPLE_POINT_EST_1_MELD_23_PSI_2_SAMPLES)
SURV_EXAMPLE_POINT_EST_1_MELD_23_PSI_3_INDICES = $(SURV_RDS)/point-est-1-meld-23-psi-3-indices.rds
$(SURV_EXAMPLE_POINT_EST_1_MELD_23_PSI_3_INDICES) : $(SURV_EXAMPLE_POINT_EST_1_MELD_23_PSI_2_SAMPLES)
## and the other war
SURV_EXAMPLE_POINT_EST_3_MELD_12_PSI_2_SAMPLES = $(SURV_RDS)/point-est-3-meld-12-psi-2-samples.rds
$(SURV_EXAMPLE_POINT_EST_3_MELD_12_PSI_2_SAMPLES) : $(SURV_SCRIPTS)/fit-point-est-3-meld-12.R $(SURV_SUBMODEL_ONE_OUTPUT) $(SURV_EXAMPLE_STAGE_ONE_PHI_23_POST_MEDIAN) $(SURV_SUBMODEL_TWO_SIMULATED_DATA) $(SURV_STAGE_TWO_STAN_MODELS)
$(RSCRIPT) $<
SURV_EXAMPLE_POINT_EST_3_MELD_12_PHI_23_SAMPLES = $(SURV_RDS)/point-est-3-meld-12-phi-23-samples.rds
$(SURV_EXAMPLE_POINT_EST_3_MELD_12_PHI_23_SAMPLES) : $(SURV_EXAMPLE_POINT_EST_3_MELD_12_PSI_2_SAMPLES)
SURV_EXAMPLE_POINT_EST_3_MELD_12_PSI_3_INDICES = $(SURV_RDS)/point-est-3-meld-12-psi-3-indices.rds
$(SURV_EXAMPLE_POINT_EST_3_MELD_12_PSI_3_INDICES) : $(SURV_EXAMPLE_POINT_EST_3_MELD_12_PSI_2_SAMPLES)
SURV_ALL_POINT_EST_PSI_2 = $(SURV_EXAMPLE_POINT_EST_PSI_2_SAMPLES) $(SURV_EXAMPLE_POINT_EST_1_MELD_23_PSI_2_SAMPLES) $(SURV_EXAMPLE_POINT_EST_3_MELD_12_PSI_2_SAMPLES)
## compare them all!
SURV_EXAMPLE_PSI_2_COMPARISON_PLOT = $(SURV_PLOTS)/psi-2-method-comparison.pdf
$(SURV_EXAMPLE_PSI_2_COMPARISON_PLOT) : $(SURV_SCRIPTS)/plot-psi-2-comparison.R $(PLOT_SETTINGS) $(MCMC_UTIL) $(SURV_STAGE_TWO_PHI_12_SAMPLES) $(SURV_ALL_POINT_EST_PSI_2)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_EXAMPLE_PSI_2_COMPARISON_PLOT)
# point estimate diagnostics
SURV_EXAMPLE_POINT_EST_DIAG_PLOT = $(SURV_PLOTS)/point-est-diags.png
SURV_EXAMPLE_POINT_EST_1_MELD_23_DIAG_PLOT = $(SURV_PLOTS)/point-est-1-meld-23-diags.png
SURV_EXAMPLE_POINT_EST_3_MELD_12_DIAG_PLOT = $(SURV_PLOTS)/point-est-3-meld-12-diags.png
SURV_EXAMPLE_POINT_EST_3_MELD_12_PHI_12_EVENT_ONLY_DIAG_PLOT = $(SURV_PLOTS)/point-est-3-meld-12-phi-12-event-only-diag.png
SURV_EXAMPLE_POINT_EST_1_MELD_23_PHI_23_EVENT_ONLY_DIAG_PLOT = $(SURV_PLOTS)/point-est-1-meld-23-phi-23-event-only-diag.png
$(SURV_EXAMPLE_POINT_EST_1_MELD_23_DIAG_PLOT) \
$(SURV_EXAMPLE_POINT_EST_3_MELD_12_DIAG_PLOT) \
$(SURV_EXAMPLE_POINT_EST_3_MELD_12_PHI_12_EVENT_ONLY_DIAG_PLOT) \
$(SURV_EXAMPLE_POINT_EST_1_MELD_23_PHI_23_EVENT_ONLY_DIAG_PLOT) \
$(SURV_EXAMPLE_POINT_EST_DIAG_PLOT) &: $(SURV_SCRIPTS)/diagnose-point-est-all-plots.R $(PLOT_SETTINGS) $(SURV_ALL_POINT_EST_PSI_2)
$(RSCRIPT) $<
ALL_PLOTS += $(SURV_EXAMPLE_POINT_EST_DIAG_PLOT) \
$(SURV_EXAMPLE_POINT_EST_1_MELD_23_DIAG_PLOT) \
$(SURV_EXAMPLE_POINT_EST_3_MELD_12_DIAG_PLOT) \
$(SURV_EXAMPLE_POINT_EST_3_MELD_12_PHI_12_EVENT_ONLY_DIAG_PLOT) \
$(SURV_EXAMPLE_POINT_EST_1_MELD_23_PHI_23_EVENT_ONLY_DIAG_PLOT)
SURV_EXAMPLE_POINT_EST_DIAG_TABLE = $(SURV_TEX)/0100-point-est-diag.tex
SURV_EXAMPLE_POINT_EST_1_MELD_23_DIAG_TABLE = $(SURV_TEX)/0101-point-est-1-meld-23-diag.tex
SURV_EXAMPLE_POINT_EST_3_MELD_12_DIAG_TABLE = $(SURV_TEX)/0102-point-est-3-meld-12-diag.tex
SURV_EXAMPLE_POINT_EST_1_MELD_23_PHI_23_DIAG_TABLE = $(SURV_TEX)/0104-point-est-1-meld-23-phi-23-diag.tex
SURV_EXAMPLE_POINT_EST_3_MELD_12_PHI_12_DIAG_TABLE = $(SURV_TEX)/0103-point-est-3-meld-12-phi-12-diag.tex
$(SURV_EXAMPLE_POINT_EST_1_MELD_23_DIAG_TABLE) \
$(SURV_EXAMPLE_POINT_EST_3_MELD_12_DIAG_TABLE) \
$(SURV_EXAMPLE_POINT_EST_1_MELD_23_PHI_23_DIAG_TABLE) \
$(SURV_EXAMPLE_POINT_EST_3_MELD_12_PHI_12_DIAG_TABLE) \
$(SURV_EXAMPLE_POINT_EST_DIAG_TABLE) &: $(SURV_SCRIPTS)/diagnose-point-est-all-tables.R $(MCMC_UTIL) $(SURV_ALL_POINT_EST_PSI_2)
$(RSCRIPT) $<
################################################################################
# MIMIC example
# bases
MIMIC_BASENAME = mimic-example
MIMIC_SCRIPTS = $(SCRIPTS)/$(MIMIC_BASENAME)
MIMIC_RDS = $(RDS)/$(MIMIC_BASENAME)
MIMIC_PLOTS = $(PLOTS)/$(MIMIC_BASENAME)
MIMIC_MODELS = $(MIMIC_SCRIPTS)/models
MIMIC_TEX = tex-input/$(MIMIC_BASENAME)
MIMIC_QUERIES = $(MIMIC_SCRIPTS)/queries
MIMIC_GLOBAL_SETTINGS = $(MIMIC_SCRIPTS)/GLOBALS.R
## fluid queries
MIMIC_INPUTS_CV = $(MIMIC_QUERIES)/inputs-cv.sql
MIMIC_INPUTS_MV = $(MIMIC_QUERIES)/inputs-mv.sql
MIMIC_OUTPUTS = $(MIMIC_QUERIES)/outputs.sql
MIMIC_RAW_FLUIDS = $(MIMIC_RDS)/raw-fluids-all-patients.rds
$(MIMIC_RAW_FLUIDS) : \
$(MIMIC_SCRIPTS)/get-raw-fluids.R \
$(MIMIC_INPUTS_CV) \
$(MIMIC_INPUTS_MV) \
$(MIMIC_OUTPUTS)
$(RSCRIPT) $< \
--inputs-cv-query $(MIMIC_INPUTS_CV) \
--inputs-mv-query $(MIMIC_INPUTS_MV) \
--outputs-query $(MIMIC_OUTPUTS) \
--output $@
## blood gasses
MIMIC_PF_COHORT = $(MIMIC_RDS)/pf-cohort-and-data.rds
MIMIC_PF_QUERY = $(MIMIC_QUERIES)/blood-gasses.sql
$(MIMIC_PF_COHORT) : \
$(MIMIC_SCRIPTS)/get-blood-gasses-and-define-pf-cohort.R \
$(MIMIC_PF_QUERY)
$(RSCRIPT) $< \
--blood-gasses-query $(MIMIC_PF_QUERY) \
--output $@
MIMIC_COMBINED_PF_RAW_FLUIDS = $(MIMIC_RDS)/combined-pf-and-raw-fluids.rds
$(MIMIC_COMBINED_PF_RAW_FLUIDS) : \
$(MIMIC_SCRIPTS)/refine-cohort-to-minimum-overlap.R \
$(MIMIC_RAW_FLUIDS) \
$(MIMIC_PF_COHORT)
$(RSCRIPT) $< \
--pf-cohort-and-data $(MIMIC_PF_COHORT) \
--raw-fluid-data $(MIMIC_RAW_FLUIDS) \
--output $@
MIMIC_COMBINED_PF_SUMMARISED_FLUIDS = $(MIMIC_RDS)/combined-pf-and-summarised-fluids.rds
$(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) : \
$(MIMIC_SCRIPTS)/refine-cohort-fluid-data.R \
$(MIMIC_COMBINED_PF_RAW_FLUIDS) \
$(MIMIC_GLOBAL_SETTINGS)
$(RSCRIPT) $< \
--combined-pf-and-raw-fluid-data $(MIMIC_COMBINED_PF_RAW_FLUIDS) \
--mimic-globals $(MIMIC_GLOBAL_SETTINGS) \
--output $@
MIMIC_DATA_PLOT = $(MIMIC_PLOTS)/pf-and-summarised-fluids-data.pdf
$(MIMIC_DATA_PLOT) : \
$(MIMIC_SCRIPTS)/plot-pf-and-summarised-fluid-data.R \
$(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
$(PLOT_SETTINGS)
$(RSCRIPT) $< \
--combined-pf-and-summarised-fluid-data $(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
--output $@
MIMIC_PF_SPLINE_MODEL_STAN = $(MIMIC_MODELS)/pf-bspline.stan
MIMIC_PF_DATA_STAN = $(MIMIC_RDS)/submodel-1-pf-data-stan-format.rds
MIMIC_PF_DATA_LIST = $(MIMIC_RDS)/submodel-1-pf-data-list-format.rds
$(MIMIC_PF_DATA_STAN) : \
$(MIMIC_SCRIPTS)/prepare-pf-stan-data.R \
$(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
$(MIMIC_GLOBAL_SETTINGS)
$(RSCRIPT) $< \
--combined-pf-and-summarised-fluid-data $(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
--mimic-globals $(MIMIC_GLOBAL_SETTINGS) \
--output $@
$(MIMIC_PF_DATA_LIST) : $(MIMIC_PF_DATA_STAN)
MIMIC_PF_MODEL_SAMPLES_LONG = $(MIMIC_RDS)/submodel-1-pf-samples-long.rds
MIMIC_PF_MODEL_SAMPLES_ARRAY = $(MIMIC_RDS)/submodel-1-pf-samples-array.rds
MIMIC_PF_MODEL_SAMPLES_PLOT_MU = $(MIMIC_RDS)/submodel-1-pf-samples-plot-mu.rds
$(MIMIC_PF_MODEL_SAMPLES_LONG) $(MIMIC_PF_MODEL_SAMPLES_ARRAY) $(MIMIC_PF_MODEL_SAMPLES_PLOT_MU) &: \
$(MIMIC_SCRIPTS)/fit-pf-spline-model.R \
$(MIMIC_PF_DATA_STAN) \
$(MIMIC_PF_SPLINE_MODEL_STAN) \
$(MIMIC_GLOBAL_SETTINGS)
$(RSCRIPT) $< \
--pf-submodel-stan-data $(MIMIC_PF_DATA_STAN) \
--pf-submodel-stan-model $(MIMIC_PF_SPLINE_MODEL_STAN) \
--mimic-globals $(MIMIC_GLOBAL_SETTINGS) \
--output-array $(MIMIC_PF_MODEL_SAMPLES_ARRAY) \
--output-plot-mu $(MIMIC_PF_MODEL_SAMPLES_PLOT_MU) \
--output $(MIMIC_PF_MODEL_SAMPLES_LONG)
MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY = $(MIMIC_RDS)/submodel-1-event-times-samples-array.rds
MIMIC_PF_EVENT_TIME_SAMPLES_LONG = $(MIMIC_RDS)/submodel-1-event-times-samples-long.rds
$(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY) $(MIMIC_PF_EVENT_TIME_SAMPLES_LONG) &: \
$(MIMIC_SCRIPTS)/process-pf-model-for-event-times.R \
$(MIMIC_PF_DATA_LIST) \
$(MIMIC_PF_MODEL_SAMPLES_LONG)
$(RSCRIPT) $< \
--pf-data-list-format $(MIMIC_PF_DATA_LIST) \
--pf-submodel-samples-long $(MIMIC_PF_MODEL_SAMPLES_LONG) \
--output-long $(MIMIC_PF_EVENT_TIME_SAMPLES_LONG) \
--output $(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY)
MIMIC_PF_FITTED_PLOT = $(MIMIC_PLOTS)/pf-data-and-bspline-fit.png
MIMIC_PF_FITTED_PLOT_TBL = $(MIMIC_RDS)/pf-data-and-bspline-plot-tbl.rds
$(MIMIC_PF_FITTED_PLOT) $(MIMIC_PF_FITTED_PLOT_TBL) &: \
$(MIMIC_SCRIPTS)/plot-pf-spline-fit.R \
$(MIMIC_PF_MODEL_SAMPLES_PLOT_MU) \
$(MIMIC_PF_DATA_LIST) \
$(MIMIC_PF_EVENT_TIME_SAMPLES_LONG) \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
$(PLOT_SETTINGS)
$(RSCRIPT) $< \
--mimic-pf-plot-mu $(MIMIC_PF_MODEL_SAMPLES_PLOT_MU) \
--mimic-pf-data-list $(MIMIC_PF_DATA_LIST) \
--mimic-pf-event-time-long $(MIMIC_PF_EVENT_TIME_SAMPLES_LONG) \
--mimic-globals $(MIMIC_GLOBAL_SETTINGS) \
--combined-pf-and-summarised-fluid-data $(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
--output-plot-tbl $(MIMIC_PF_FITTED_PLOT_TBL) \
--output $(MIMIC_PF_FITTED_PLOT)
MIMIC_DEMOGRAPHICS_QUERY = $(MIMIC_QUERIES)/demographics.sql
MIMIC_MEDIAN_FIRST_DAY_LABS_QUERY = $(MIMIC_QUERIES)/median-labs-first-day.sql
MIMIC_BASELINE_DATA = $(MIMIC_RDS)/baseline-covariate-data.rds
$(MIMIC_BASELINE_DATA) : \
$(MIMIC_SCRIPTS)/get-baseline-data.R \
$(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
$(MIMIC_DEMOGRAPHICS_QUERY) \
$(MIMIC_MEDIAN_FIRST_DAY_LABS_QUERY)
$(RSCRIPT) $< \
--combined-pf-and-summarised-fluid-data $(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
--demographics-query $(MIMIC_DEMOGRAPHICS_QUERY) \
--median-labs-query $(MIMIC_MEDIAN_FIRST_DAY_LABS_QUERY) \
--output $@
MIMIC_CUMULATIVE_FLUID_DATA = $(MIMIC_RDS)/cumulative-summarised-fluid-data.rds
MIMIC_FLUID_DATA_STAN = $(MIMIC_RDS)/submodel-3-fluid-data-stan-format.rds
$(MIMIC_FLUID_DATA_STAN) $(MIMIC_CUMULATIVE_FLUID_DATA) &: \
$(MIMIC_SCRIPTS)/prepare-fluid-stan-data.R \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS)
$(RSCRIPT) $< \
--combined-pf-and-summarised-fluid-data $(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
--mimic-globals $(MIMIC_GLOBAL_SETTINGS) \
--output-cumulative-fluid $(MIMIC_CUMULATIVE_FLUID_DATA) \
--output $(MIMIC_FLUID_DATA_STAN)
MIMIC_FLUID_MODEL_SAMPLES_LONG = $(MIMIC_RDS)/submodel-3-fluid-samples-long.rds
MIMIC_FLUID_MODEL_SAMPLES_ARRAY = $(MIMIC_RDS)/submodel-3-fluid-samples-array.rds
MIMIC_FLUID_MODEL_SAMPLES_PLOT_MU = $(MIMIC_RDS)/submodel-3-fluid-samples-plot-mu.rds
MIMIC_FLUID_PIECEWISE_MODEL_STAN = $(MIMIC_MODELS)/fluid-piecewise-linear.stan
$(MIMIC_FLUID_MODEL_SAMPLES_LONG) $(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) $(MIMIC_FLUID_MODEL_SAMPLES_PLOT_MU) &: \
$(MIMIC_SCRIPTS)/fit-fluid-piecewise-model.R \
$(MIMIC_FLUID_DATA_STAN) \
$(MIMIC_FLUID_PIECEWISE_MODEL_STAN) \
$(MIMIC_GLOBAL_SETTINGS)
$(RSCRIPT) $< \
--fluid-submodel-stan-data $(MIMIC_FLUID_DATA_STAN) \
--fluid-piecewise-stan-model $(MIMIC_FLUID_PIECEWISE_MODEL_STAN) \
--mimic-globals $(MIMIC_GLOBAL_SETTINGS) \
--output-array $(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) \
--output-plot-mu $(MIMIC_FLUID_MODEL_SAMPLES_PLOT_MU) \
--output $(MIMIC_FLUID_MODEL_SAMPLES_LONG)
MIMIC_FLUID_FITTED_PLOT = $(MIMIC_PLOTS)/fluid-data-and-piecewise-fit.png
MIMIC_FLUID_FITTED_PLOT_MU_TBL = $(MIMIC_RDS)/fluid-data-piecewise-plot-mu-tbl.rds
$(MIMIC_FLUID_FITTED_PLOT) $(MIMIC_FLUID_FITTED_PLOT_MU_TBL) &: \
$(MIMIC_SCRIPTS)/plot-fluid-piecewise-fit.R \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_CUMULATIVE_FLUID_DATA) \
$(MIMIC_FLUID_DATA_STAN) \
$(MIMIC_FLUID_MODEL_SAMPLES_PLOT_MU)
$(RSCRIPT) $< \
--mimic-globals $(MIMIC_GLOBAL_SETTINGS) \
--cumulative-fluid-data $(MIMIC_CUMULATIVE_FLUID_DATA) \
--fluid-stan-data $(MIMIC_FLUID_DATA_STAN) \
--fluid-plot-mu $(MIMIC_FLUID_MODEL_SAMPLES_PLOT_MU) \
--output-plot-tbl $(MIMIC_FLUID_FITTED_PLOT_MU_TBL) \
--output $(MIMIC_FLUID_FITTED_PLOT)
MIMIC_BOTH_FITTED_PLOT = $(MIMIC_PLOTS)/combined-pf-fluid-fit-plot.png
MIMIC_BOTH_FITTED_PLOT_SMALL = $(MIMIC_PLOTS)/combined-pf-fluid-fit-plot-small.pdf
$(MIMIC_BOTH_FITTED_PLOT) $(MIMIC_BOTH_FITTED_PLOT_SMALL) &: \
$(MIMIC_SCRIPTS)/plot-both-pf-and-fluid-fit.R \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_CUMULATIVE_FLUID_DATA) \
$(MIMIC_FLUID_FITTED_PLOT_MU_TBL) \
$(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
$(MIMIC_PF_FITTED_PLOT_TBL) \
$(MIMIC_PF_EVENT_TIME_SAMPLES_LONG)
$(RSCRIPT) $< \
--cumulative-fluid-data $(MIMIC_CUMULATIVE_FLUID_DATA) \
--fluid-plot-mu-tbl $(MIMIC_FLUID_FITTED_PLOT_MU_TBL) \
--pf-and-summarised-fluid-data $(MIMIC_COMBINED_PF_SUMMARISED_FLUIDS) \
--pf-plot-tbl $(MIMIC_PF_FITTED_PLOT_TBL) \
--pf-event-time-samples-long $(MIMIC_PF_EVENT_TIME_SAMPLES_LONG) \
--output-small $(MIMIC_BOTH_FITTED_PLOT_SMALL) \
--output $(MIMIC_BOTH_FITTED_PLOT)
ALL_PLOTS += $(MIMIC_BOTH_FITTED_PLOT)
# Start processing and fitting stage two with fixed subposterior median estimates.
MIMIC_SUBPOST_MEDIAN_EVENT_TIME = $(MIMIC_RDS)/median-event-time-data.rds
MIMIC_SUBPOST_MEAN_FLUID_FIT = $(MIMIC_RDS)/mean-fluid-fit-data.rds
$(MIMIC_SUBPOST_MEDIAN_EVENT_TIME) $(MIMIC_SUBPOST_MEAN_FLUID_FIT) &: \
$(MIMIC_SCRIPTS)/process-stage-one-outputs.R \
$(MIMIC_PF_EVENT_TIME_SAMPLES_LONG) \
$(MIMIC_FLUID_MODEL_SAMPLES_LONG)
$(RSCRIPT) $< \
--pf-event-time-samples-long $(MIMIC_PF_EVENT_TIME_SAMPLES_LONG) \
--fluid-model-samples-long $(MIMIC_FLUID_MODEL_SAMPLES_LONG) \
--output-fluid $(MIMIC_SUBPOST_MEAN_FLUID_FIT) \
--output $(MIMIC_SUBPOST_MEDIAN_EVENT_TIME)
MIMIC_BOTH_SUBPOST_MEDIAN_PSI_2_SAMPLES = $(MIMIC_RDS)/stage-two-median-inputs-psi-2-samples.rds
$(MIMIC_BOTH_SUBPOST_MEDIAN_PSI_2_SAMPLES) : \
$(MIMIC_SCRIPTS)/fit-stage-two-both-phi-median.R \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_SUBPOST_MEDIAN_EVENT_TIME) \
$(MIMIC_SUBPOST_MEAN_FLUID_FIT) \
$(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
$(MIMIC_BASELINE_DATA)
$(RSCRIPT) $< \
--pf-event-time-median $(MIMIC_SUBPOST_MEDIAN_EVENT_TIME) \
--fluid-model-mean $(MIMIC_SUBPOST_MEAN_FLUID_FIT) \
--baseline-data $(MIMIC_BASELINE_DATA) \
--psi-step-stan-model $(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
--output $@
MIMIC_PF_PRIOR_PLOT = $(MIMIC_PLOTS)/pf-prior-plot.png
MIMIC_PF_PRIOR_EST_PARAMS = $(MIMIC_RDS)/submodel-1-marginal-prior-parameter-estimates.rds
MIMIC_PF_PRIOR_STAN_MODEL = $(MIMIC_MODELS)/pf-prior-optimizer.stan
$(MIMIC_PF_PRIOR_PLOT) \
$(MIMIC_PF_PRIOR_EST_PARAMS) &: \
$(MIMIC_SCRIPTS)/sample-pf-model-prior-event-times.R \
$(PLOT_SETTINGS) \
$(MIMIC_GLOBAL_SETTINGS) \
$(MCMC_UTIL) \
$(MIMIC_PF_DATA_LIST) \
$(MIMIC_PF_PRIOR_STAN_MODEL)
$(RSCRIPT) $< \
--pf-data-list-format $(MIMIC_PF_DATA_LIST) \
--pf-prior-optim-stan-model $(MIMIC_PF_PRIOR_STAN_MODEL) \
--output-pf-prior-plot $(MIMIC_PF_PRIOR_PLOT) \
--output $(MIMIC_PF_PRIOR_EST_PARAMS)
MIMIC_SURV_PRIOR_PLOTS = $(wildcard plots/mimic-example/p3-prior-pairs/*.png)
MIMIC_SURV_PRIOR_EST_PARAMS = $(MIMIC_RDS)/submodel-2-marginal-prior-parameter-estimates.rds
MIMIC_SURV_PRIOR_PHI_12_MARGINAL_PLOT = $(MIMIC_PLOTS)/submodel-2-phi-12-marginal-fit-plot.png
MIMIC_SURV_PRIOR_PHI_12_MARGINAL_EST_PARAMS = $(MIMIC_RDS)/submodel-2-phi-12-marginal-prior-parameter-estimates.rds
MIMIC_SURV_PRIOR_STAN_MODEL = $(MIMIC_MODELS)/surv-prior-optimizer.stan
MIMIC_SURV_PRIOR_RAW_PRIOR_SAMPLES = $(MIMIC_RDS)/submodel-2-marignal-prior-raw-samples.rds
$(MIMIC_SURV_PRIOR_RAW_PRIOR_SAMPLES) \
$(MIMIC_SURV_PRIOR_EST_PARAMS) &: \
$(MIMIC_SCRIPTS)/sample-surv-submodel-prior.R \
$(PLOT_SETTINGS) \
$(MIMIC_FLUID_DATA_STAN) \
$(MIMIC_PF_DATA_LIST) \
$(MIMIC_BASELINE_DATA) \
$(MIMIC_SUBPOST_MEDIAN_EVENT_TIME) \
$(MIMIC_SURV_PRIOR_STAN_MODEL)
$(RSCRIPT) $< \
--fluid-stan-data $(MIMIC_FLUID_DATA_STAN) \
--pf-list-data $(MIMIC_PF_DATA_LIST) \
--baseline-covariate-data $(MIMIC_BASELINE_DATA) \
--submodel-one-median-both $(MIMIC_SUBPOST_MEDIAN_EVENT_TIME) \
--surv-prior-optim-stan-model $(MIMIC_SURV_PRIOR_STAN_MODEL) \
--output-raw-monte-carlo-prior-samples $(MIMIC_SURV_PRIOR_RAW_PRIOR_SAMPLES) \
--output $(MIMIC_SURV_PRIOR_EST_PARAMS)
$(MIMIC_SURV_PRIOR_PHI_12_MARGINAL_PLOT) \
$(MIMIC_SURV_PRIOR_PHI_12_MARGINAL_EST_PARAMS) &: \
$(MIMIC_SCRIPTS)/estimate-surv-submodel-event-time-marginal.R \
$(PLOT_SETTINGS) \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_SURV_PRIOR_RAW_PRIOR_SAMPLES) \
$(MIMIC_PF_DATA_LIST) \
$(MIMIC_PF_PRIOR_STAN_MODEL)
$(RSCRIPT) $< \
--surv-prior-samples-raw $(MIMIC_SURV_PRIOR_RAW_PRIOR_SAMPLES) \
--pf-data-list $(MIMIC_PF_DATA_LIST) \
--pf-prior-optim-stan-model $(MIMIC_PF_PRIOR_STAN_MODEL) \
--output-surv-event-time-only-prior-plot $(MIMIC_SURV_PRIOR_PHI_12_MARGINAL_PLOT) \
--output $(MIMIC_SURV_PRIOR_PHI_12_MARGINAL_EST_PARAMS)
$(MIMIC_SURV_PRIOR_PLOTS) &: \
$(MIMIC_SCRIPTS)/plot-surv-prior-est.R \
$(PLOT_SETTINGS) \
$(MIMIC_SURV_PRIOR_EST_PARAMS) \
$(MIMIC_SURV_PRIOR_RAW_PRIOR_SAMPLES)
$(RSCRIPT) $< \
--normal-approx-prior-estimates $(MIMIC_SURV_PRIOR_EST_PARAMS) \
--raw-monte-carlo-prior-samples $(MIMIC_SURV_PRIOR_RAW_PRIOR_SAMPLES) \
--output ''
# Fit stage two using parallel multi-stage sampler
# poe version
MIMIC_SURV_PSI_STEP_STAN_MODEL = $(MIMIC_MODELS)/surv-psi-step.stan
MIMIC_SURV_PHI_STEP_INDIV_MODEL = $(MIMIC_MODELS)/surv-phi-step-indiv.stan
MIMIC_STAGE_TWO_PSI_2_SAMPLES = $(MIMIC_RDS)/stage-two-poe-psi-2-samples.rds
MIMIC_STAGE_TWO_PHI_12_SAMPLES = $(MIMIC_RDS)/stage-two-poe-phi-12-samples.rds
MIMIC_STAGE_TWO_PHI_23_SAMPLES = $(MIMIC_RDS)/stage-two-poe-phi-23-samples.rds
MIMIC_STAGE_TWO_PSI_1_INDICES = $(MIMIC_RDS)/stage-two-poe-psi-1-indices.rds
MIMIC_STAGE_TWO_PSI_3_INDICES = $(MIMIC_RDS)/stage-two-poe-psi-3-indices.rds
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES) \
$(MIMIC_STAGE_TWO_PHI_12_SAMPLES) \
$(MIMIC_STAGE_TWO_PHI_23_SAMPLES) \
$(MIMIC_STAGE_TWO_PSI_1_INDICES) \
$(MIMIC_STAGE_TWO_PSI_3_INDICES) &: \
$(MIMIC_SCRIPTS)/fit-stage-two-poe.R \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY) \
$(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) \
$(MIMIC_BASELINE_DATA) \
$(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
$(MIMIC_SURV_PHI_STEP_INDIV_MODEL)
$(RSCRIPT) $< \
--pf-event-time-samples-array $(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY) \
--fluid-model-samples-array $(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) \
--fluid-model-stan-data $(MIMIC_FLUID_DATA_STAN) \
--baseline-data $(MIMIC_BASELINE_DATA) \
--psi-step-stan-model $(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
--phi-step-indiv-stan-model $(MIMIC_SURV_PHI_STEP_INDIV_MODEL) \
--output-phi-12-samples $(MIMIC_STAGE_TWO_PHI_12_SAMPLES) \
--output-phi-23-samples $(MIMIC_STAGE_TWO_PHI_23_SAMPLES) \
--output-psi-1-indices $(MIMIC_STAGE_TWO_PSI_1_INDICES) \
--output-psi-3-indices $(MIMIC_STAGE_TWO_PSI_3_INDICES) \
--output $(MIMIC_STAGE_TWO_PSI_2_SAMPLES)
MIMIC_POOLED_PRIOR_FUNCTIONS = $(MIMIC_SCRIPTS)/pooled-prior-functions.R
$(MIMIC_POOLED_PRIOR_FUNCTIONS) : $(MIMIC_PF_PRIOR_EST_PARAMS) $(MIMIC_SURV_PRIOR_EST_PARAMS) $(MIMIC_SURV_PRIOR_PHI_12_MARGINAL_EST_PARAMS)
MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC = $(MIMIC_RDS)/stage-two-log-psi-2-samples.rds
MIMIC_STAGE_TWO_PHI_12_SAMPLES_LOGARTHMIC = $(MIMIC_RDS)/stage-two-log-phi-12-samples.rds
MIMIC_STAGE_TWO_PHI_23_SAMPLES_LOGARTHMIC = $(MIMIC_RDS)/stage-two-log-phi-23-samples.rds
MIMIC_STAGE_TWO_PSI_1_INDICES_LOGARTHMIC = $(MIMIC_RDS)/stage-two-log-psi-1-indices.rds
MIMIC_STAGE_TWO_PSI_3_INDICES_LOGARTHMIC = $(MIMIC_RDS)/stage-two-log-psi-3-indices.rds
$(MIMIC_STAGE_TWO_PSI_3_INDICES_LOGARTHMIC) \
$(MIMIC_STAGE_TWO_PHI_12_SAMPLES_LOGARTHMIC) \
$(MIMIC_STAGE_TWO_PHI_23_SAMPLES_LOGARTHMIC) \
$(MIMIC_STAGE_TWO_PSI_1_INDICES_LOGARTHMIC) \
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC) &: \
$(MIMIC_SCRIPTS)/fit-stage-two-logarithmic.R \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY) \
$(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) \
$(MIMIC_BASELINE_DATA) \
$(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
$(MIMIC_SURV_PHI_STEP_INDIV_MODEL) \
$(MIMIC_POOLED_PRIOR_FUNCTIONS) \
$(MIMIC_PF_DATA_LIST) \
$(MIMIC_PF_PRIOR_EST_PARAMS) \
$(MIMIC_SURV_PRIOR_EST_PARAMS) \
$(MIMIC_FLUID_DATA_STAN)
$(RSCRIPT) $< \
--pf-event-time-samples-array $(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY) \
--fluid-model-samples-array $(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) \
--fluid-model-stan-data $(MIMIC_FLUID_DATA_STAN) \
--baseline-data $(MIMIC_BASELINE_DATA) \
--psi-step-stan-model $(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
--phi-step-indiv-stan-model $(MIMIC_SURV_PHI_STEP_INDIV_MODEL) \
--output-phi-12-samples $(MIMIC_STAGE_TWO_PHI_12_SAMPLES_LOGARTHMIC) \
--output-phi-23-samples $(MIMIC_STAGE_TWO_PHI_23_SAMPLES_LOGARTHMIC) \
--output-psi-1-indices $(MIMIC_STAGE_TWO_PSI_1_INDICES_LOGARTHMIC) \
--output-psi-3-indices $(MIMIC_STAGE_TWO_PSI_3_INDICES_LOGARTHMIC) \
--output $(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC)
# this is where the fixed phi_12 / phi_23 versions should go.
## 1: PoE, fix phi 12, meld phi 23
MIMIC_STAGE_TWO_PSI_2_SAMPLES_FIX_PHI_12_MELD_PHI_23 = $(MIMIC_RDS)/stage-two-poe-psi-2-samples-fix-phi-12-meld-phi-23.rds
MIMIC_STAGE_TWO_PHI_23_SAMPLES_FIX_PHI_12_MELD_PHI_23 = $(MIMIC_RDS)/stage-two-poe-phi-23-samples-fix-phi-12-meld-phi-23.rds
MIMIC_STAGE_TWO_PSI_3_INDICES_FIX_PHI_12_MELD_PHI_23 = $(MIMIC_RDS)/stage-two-poe-psi-3-indices-fix-phi-12-meld-phi-23.rds
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES_FIX_PHI_12_MELD_PHI_23) \
$(MIMIC_STAGE_TWO_PHI_23_SAMPLES_FIX_PHI_12_MELD_PHI_23) \
$(MIMIC_STAGE_TWO_PSI_3_INDICES_FIX_PHI_12_MELD_PHI_23) &: \
$(MIMIC_SCRIPTS)/fit-stage-two-poe-fix-phi-12-meld-phi-23.R \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_SUBPOST_MEDIAN_EVENT_TIME) \
$(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) \
$(MIMIC_BASELINE_DATA) \
$(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
$(MIMIC_SURV_PHI_STEP_INDIV_MODEL)
$(RSCRIPT) $< \
--pf-event-time-median-value $(MIMIC_SUBPOST_MEDIAN_EVENT_TIME) \
--fluid-model-samples-array $(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) \
--fluid-model-stan-data $(MIMIC_FLUID_DATA_STAN) \
--baseline-data $(MIMIC_BASELINE_DATA) \
--psi-step-stan-model $(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
--phi-step-indiv-stan-model $(MIMIC_SURV_PHI_STEP_INDIV_MODEL) \
--output-phi-23-samples $(MIMIC_STAGE_TWO_PHI_23_SAMPLES_FIX_PHI_12_MELD_PHI_23) \
--output-psi-3-indices $(MIMIC_STAGE_TWO_PSI_3_INDICES_FIX_PHI_12_MELD_PHI_23) \
--output $(MIMIC_STAGE_TWO_PSI_2_SAMPLES_FIX_PHI_12_MELD_PHI_23)
## 2: PoE, meld phi 12, fix phi 23
MIMIC_STAGE_TWO_PSI_2_SAMPLES_MELD_PHI_12_FIX_PHI_23 = $(MIMIC_RDS)/stage-two-poe-psi-2-samples-meld-phi-12-fix-phi-23.rds
MIMIC_STAGE_TWO_PHI_12_SAMPLES_MELD_PHI_12_FIX_PHI_23 = $(MIMIC_RDS)/stage-two-poe-phi-12-samples-meld-phi-12-fix-phi-23.rds
MIMIC_STAGE_TWO_PSI_1_INDICES_MELD_PHI_12_FIX_PHI_23 = $(MIMIC_RDS)/stage-two-poe-psi-1-indices-meld-phi-12-fix-phi-23.rds
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES_MELD_PHI_12_FIX_PHI_23) \
$(MIMIC_STAGE_TWO_PHI_12_SAMPLES_MELD_PHI_12_FIX_PHI_23) \
$(MIMIC_STAGE_TWO_PSI_1_INDICES_MELD_PHI_12_FIX_PHI_23) &: \
$(MIMIC_SCRIPTS)/fit-stage-two-poe-meld-phi-12-fix-phi-23.R \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY) \
$(MIMIC_SUBPOST_MEAN_FLUID_FIT) \
$(MIMIC_BASELINE_DATA) \
$(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
$(MIMIC_SURV_PHI_STEP_INDIV_MODEL)
$(RSCRIPT) $< \
--pf-event-time-samples-array $(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY) \
--fluid-model-median-value $(MIMIC_SUBPOST_MEAN_FLUID_FIT) \
--fluid-model-stan-data $(MIMIC_FLUID_DATA_STAN) \
--baseline-data $(MIMIC_BASELINE_DATA) \
--psi-step-stan-model $(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
--phi-step-indiv-stan-model $(MIMIC_SURV_PHI_STEP_INDIV_MODEL) \
--output-phi-12-samples $(MIMIC_STAGE_TWO_PHI_12_SAMPLES_MELD_PHI_12_FIX_PHI_23) \
--output-psi-1-indices $(MIMIC_STAGE_TWO_PSI_1_INDICES_MELD_PHI_12_FIX_PHI_23) \
--output $(MIMIC_STAGE_TWO_PSI_2_SAMPLES_MELD_PHI_12_FIX_PHI_23)
## 3: Log, fix phi 12, meld phi 23
MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23 = $(MIMIC_RDS)/stage-two-log-psi-2-samples-fix-phi-12-meld-phi-23.rds
MIMIC_STAGE_TWO_PHI_23_SAMPLES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23 = $(MIMIC_RDS)/stage-two-log-phi-23-samples-fix-phi-12-meld-phi-23.rds
MIMIC_STAGE_TWO_PSI_3_INDICES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23 = $(MIMIC_RDS)/stage-two-log-psi-3-indices-fix-phi-12-meld-phi-23.rds
$(MIMIC_STAGE_TWO_PSI_3_INDICES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23) \
$(MIMIC_STAGE_TWO_PHI_23_SAMPLES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23) \
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23) &: \
$(MIMIC_SCRIPTS)/fit-stage-two-logarithmic-fix-phi-12-meld-phi-23.R \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY) \
$(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) \
$(MIMIC_BASELINE_DATA) \
$(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
$(MIMIC_SURV_PHI_STEP_INDIV_MODEL) \
$(MIMIC_POOLED_PRIOR_FUNCTIONS) \
$(MIMIC_PF_DATA_LIST) \
$(MIMIC_PF_PRIOR_EST_PARAMS) \
$(MIMIC_SURV_PRIOR_EST_PARAMS) \
$(MIMIC_FLUID_DATA_STAN)
$(RSCRIPT) $< \
--pf-event-time-median-value $(MIMIC_SUBPOST_MEDIAN_EVENT_TIME) \
--fluid-model-samples-array $(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) \
--fluid-model-stan-data $(MIMIC_FLUID_DATA_STAN) \
--baseline-data $(MIMIC_BASELINE_DATA) \
--psi-step-stan-model $(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
--phi-step-indiv-stan-model $(MIMIC_SURV_PHI_STEP_INDIV_MODEL) \
--output-phi-23-samples $(MIMIC_STAGE_TWO_PHI_23_SAMPLES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23) \
--output-psi-3-indices $(MIMIC_STAGE_TWO_PSI_3_INDICES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23) \
--output $(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23)
## 4: Log, meld phi 12, fix phi 23
MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23 = $(MIMIC_RDS)/stage-two-log-psi-2-samples-meld-phi-12-fix-phi-23.rds
MIMIC_STAGE_TWO_PHI_12_SAMPLES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23 = $(MIMIC_RDS)/stage-two-log-phi-12-samples-meld-phi-12-fix-phi-23.rds
MIMIC_STAGE_TWO_PSI_1_INDICES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23 = $(MIMIC_RDS)/stage-two-log-psi-1-indices-meld-phi-12-fix-phi-23.rds
$(MIMIC_STAGE_TWO_PSI_1_INDICES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23) \
$(MIMIC_STAGE_TWO_PHI_12_SAMPLES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23) \
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23) &: \
$(MIMIC_SCRIPTS)/fit-stage-two-logarithmic-meld-phi-12-fix-phi-23.R \
$(MIMIC_GLOBAL_SETTINGS) \
$(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY) \
$(MIMIC_SUBPOST_MEAN_FLUID_FIT) \
$(MIMIC_BASELINE_DATA) \
$(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
$(MIMIC_SURV_PHI_STEP_INDIV_MODEL) \
$(MIMIC_POOLED_PRIOR_FUNCTIONS) \
$(MIMIC_PF_DATA_LIST) \
$(MIMIC_PF_PRIOR_EST_PARAMS) \
$(MIMIC_SURV_PRIOR_EST_PARAMS) \
$(MIMIC_FLUID_DATA_STAN)
$(RSCRIPT) $< \
--pf-event-time-samples-array $(MIMIC_PF_EVENT_TIME_SAMPLES_ARRAY) \
--fluid-model-median-value $(MIMIC_SUBPOST_MEAN_FLUID_FIT) \
--fluid-model-stan-data $(MIMIC_FLUID_DATA_STAN) \
--baseline-data $(MIMIC_BASELINE_DATA) \
--psi-step-stan-model $(MIMIC_SURV_PSI_STEP_STAN_MODEL) \
--phi-step-indiv-stan-model $(MIMIC_SURV_PHI_STEP_INDIV_MODEL) \
--output-phi-12-samples $(MIMIC_STAGE_TWO_PHI_12_SAMPLES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23) \
--output-psi-1-indices $(MIMIC_STAGE_TWO_PSI_1_INDICES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23) \
--output $(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23)
MIMIC_COMPARE_PSI_2_PLOT = $(MIMIC_PLOTS)/psi-2-method-comparison.pdf
MIMIC_COMPARE_PSI_2_PLOT_SMALL = $(MIMIC_PLOTS)/psi-2-method-comparison-small.pdf
MIMIC_COMPARE_PSI_2_ALPHA_ONLY = $(MIMIC_PLOTS)/psi-2-alpha-only-compare.pdf
$(MIMIC_COMPARE_PSI_2_PLOT) $(MIMIC_COMPARE_PSI_2_PLOT_SMALL) &: \
$(MIMIC_SCRIPTS)/plot-psi-2-comparison.R \
$(PLOT_SETTINGS) \
$(MCMC_UTIL) \
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES) \
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES_FIX_PHI_12_MELD_PHI_23) \
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES_MELD_PHI_12_FIX_PHI_23) \
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC) \
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23) \
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23) \
$(MIMIC_BOTH_SUBPOST_MEDIAN_PSI_2_SAMPLES) \
$(MIMIC_SUBPOST_MEDIAN_EVENT_TIME)
$(RSCRIPT) $< \
--full-melding-poe-psi-2-samples $(MIMIC_STAGE_TWO_PSI_2_SAMPLES) \
--melding-poe-fix-phi-12-meld-phi-23-psi-2-samples $(MIMIC_STAGE_TWO_PSI_2_SAMPLES_FIX_PHI_12_MELD_PHI_23) \
--melding-poe-meld-phi-12-fix-phi-23-psi-2-samples $(MIMIC_STAGE_TWO_PSI_2_SAMPLES_MELD_PHI_12_FIX_PHI_23) \
--full-melding-logarthmic-psi-2-samples $(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC) \
--melding-log-fix-phi-12-meld-phi-23-psi-2-samples $(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC_FIX_PHI_12_MELD_PHI_23) \
--melding-log-meld-phi-12-fix-phi-23-psi-2-samples $(MIMIC_STAGE_TWO_PSI_2_SAMPLES_LOGARTHMIC_MELD_PHI_12_FIX_PHI_23) \
--both-fixed-psi-2-samples $(MIMIC_BOTH_SUBPOST_MEDIAN_PSI_2_SAMPLES) \
--median-event-time-data $(MIMIC_SUBPOST_MEDIAN_EVENT_TIME) \
--output-small $(MIMIC_COMPARE_PSI_2_PLOT_SMALL) \
--output-alpha $(MIMIC_COMPARE_PSI_2_ALPHA_ONLY) \
--output $(MIMIC_COMPARE_PSI_2_PLOT)
ALL_PLOTS += $(MIMIC_COMPARE_PSI_2_PLOT_SMALL)
## some diagnostic plots
MIMIC_PF_SUBMODEL_DIAGNOSTIC_PLOT = $(MIMIC_PLOTS)/submodel-1-stage-1-diagnostics.png
$(MIMIC_PF_SUBMODEL_DIAGNOSTIC_PLOT) : \
$(MIMIC_SCRIPTS)/diagnostics-submodel-one-stage-one-plots.R \
$(PLOT_SETTINGS) \
$(MCMC_UTIL) \
$(MIMIC_PF_MODEL_SAMPLES_ARRAY)
$(RSCRIPT) $< \
--pf-submodel-samples-array $(MIMIC_PF_MODEL_SAMPLES_ARRAY) \
--output $@
ALL_PLOTS += $(MIMIC_PF_SUBMODEL_DIAGNOSTIC_PLOT)
MIMIC_FLUID_SUBMODEL_DIAGNOSTIC_PLOT = $(MIMIC_PLOTS)/submodel-3-stage-1-diagnostics.png
$(MIMIC_FLUID_SUBMODEL_DIAGNOSTIC_PLOT) : \
$(MIMIC_SCRIPTS)/diagnostics-submodel-three-stage-one-plots.R \
$(PLOT_SETTINGS) \
$(MCMC_UTIL) \
$(MIMIC_FLUID_MODEL_SAMPLES_ARRAY)
$(RSCRIPT) $< \
--fluid-submodel-samples-array $(MIMIC_FLUID_MODEL_SAMPLES_ARRAY) \
--output $@
ALL_PLOTS += $(MIMIC_FLUID_SUBMODEL_DIAGNOSTIC_PLOT)
MIMIC_FULL_MELDING_PHI_12_DIAGNOSTIC_PLOT = $(MIMIC_PLOTS)/phi-12-stage-2-diagnostics.png
MIMIC_FULL_MELDING_PHI_23_DIAGNOSTIC_PLOT = $(MIMIC_PLOTS)/phi-23-stage-2-diagnostics.png
MIMIC_FULL_MELDING_PSI_2_DIAGNOSTIC_PLOT = $(MIMIC_PLOTS)/psi-2-stage-2-diagnostics.png
MIMIC_FULL_MELDING_ALL_PHI_23_TRACE_PLOT = $(MIMIC_PLOTS)/full-stage-two-phi-23-trace.png
$(MIMIC_FULL_MELDING_PHI_12_DIAGNOSTIC_PLOT) \
$(MIMIC_FULL_MELDING_PHI_23_DIAGNOSTIC_PLOT) \
$(MIMIC_FULL_MELDING_ALL_PHI_23_TRACE_PLOT) \
$(MIMIC_FULL_MELDING_PSI_2_DIAGNOSTIC_PLOT) &: \
$(MIMIC_SCRIPTS)/diagnostics-full-melding-poe-stage-two-plots.R \
$(PLOT_SETTINGS) \
$(MCMC_UTIL) \
$(MIMIC_STAGE_TWO_PSI_2_SAMPLES) \
$(MIMIC_STAGE_TWO_PHI_12_SAMPLES) \
$(MIMIC_STAGE_TWO_PHI_23_SAMPLES)
$(RSCRIPT) $< \
--stage-two-phi-12-samples $(MIMIC_STAGE_TWO_PHI_12_SAMPLES) \
--stage-two-phi-23-samples $(MIMIC_STAGE_TWO_PHI_23_SAMPLES) \
--stage-two-psi-2-samples $(MIMIC_STAGE_TWO_PSI_2_SAMPLES) \
--phi-12-diagnostic-plot $(MIMIC_FULL_MELDING_PHI_12_DIAGNOSTIC_PLOT) \
--phi-23-diagnostic-plot $(MIMIC_FULL_MELDING_PHI_23_DIAGNOSTIC_PLOT) \
--output-full-phi-23-trace-plot $(MIMIC_FULL_MELDING_ALL_PHI_23_TRACE_PLOT) \
--output $(MIMIC_FULL_MELDING_PSI_2_DIAGNOSTIC_PLOT)