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Makefile
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#####################################
# name: Makefile
# author: Dylan Morris <[email protected]>
#
# Makefile to generate analyses
# for Fischer et al study of N95
# mask decontamination for SARS-CoV-2
####################################
#####################################
# Directory structure
####################################
default: all
SRC := src
OUTPUT := out
DATA := dat
RAW := $(DATA)/raw
CLEANED := $(DATA)/cleaned
PARAMS := $(SRC)/parameters
MCMC_CHAINS := $(OUTPUT)/mcmc_chains
FIGURE_DIR = $(OUTPUT)/figures
TABLE_DIR = $(OUTPUT)/tables
#####################################
# File extensions and the like
####################################
CHAINS_SUFFIX = _chains.Rds
PRIOR_CHECK_NAME = _prior_check
#####################################
# Expected bash settings
#
# Check these vs your local
# machine setup if you are having
# difficulty reproducing the
# analysis
#####################################
CXX := g++-8
MKDIR := @mkdir -p
RM := rm -rf
R_OPTIONS = --vanilla
R_COMMAND := Rscript $(R_OPTIONS)
# R creates a blank Rplots.pdf when run
# from the command line. This removes it.
FIG_CLEANUP = @$(RM) Rplots.pdf
#####################################
# Installation / dependencies
#
# Rules for prepping analysis
#####################################
.PHONY: depend
depend:
$(R_COMMAND) $(SRC)/install_needed_packages.R
#####################################
# data locations
#####################################
DECON_DATAFILE = decon_data.csv
MASK_DATAFILE = mask_fit_data.csv
RAW_DECON_DATA = $(RAW)/$(DECON_DATAFILE)
CLEANED_DECON_DATA = $(CLEANED)/$(DECON_DATAFILE)
RAW_MASK_DATA = $(RAW)/$(MASK_DATAFILE)
CLEANED_MASK_DATA = $(CLEANED)/$(MASK_DATAFILE)
CLEANED_DATA = $(CLEANED_DECON_DATA) $(CLEANED_MASK_DATA)
## use corrected titer data
DECON_DATA = $(CLEANED_DECON_DATA)
MASK_DATA = $(CLEANED_MASK_DATA)
#####################################
# code locations
#####################################
CLEANING_SCRIPT = $(SRC)/clean_data.R
MASK_CLEANING_SCRIPT = $(SRC)/clean_mask_data.R
FITTING_SCRIPT = $(SRC)/fit_stan_model.R
MASK_FITTING_SCRIPT = $(SRC)/fit_mask_model.R
MASK_PRIOR_CHECK_SCRIPT = $(SRC)/fit_mask_model_prior_check.R
DIAGNOSTIC_SCRIPT = $(SRC)/chain_diagnostics.R
SPLINE_MODEL_SRC = decon_decay_spline.stan
MASK_MODEL_SRC = mask_fit_nonlinear.stan
INFER_TITER_MODEL_SRC = well_titer_estimates.stan
TITER_MEAN_MODEL_SRC = well_titer_means.stan
#####################################
# parameter locations
#####################################
PLOT_PARAMS = $(PARAMS)/plotting_style.R
## paths to hyperparameters
MASK_HYPERS = $(PARAMS)/mask_hyperparams.R
DECON_HYPERS = $(PARAMS)/decon_hyperparams.R
INFER_TITER_HYPERS = $(PARAMS)/well_titer_estimates_hyperparams.R
INFER_MEAN_HYPERS = $(PARAMS)/well_titer_means_hyperparams.R
#####################################
# model names and output locations
#####################################
WELL_MODEL_NAME = well
DECON_MODEL_NAME = decon
DECON_CHAINS = $(MCMC_CHAINS)/$(DECON_MODEL_NAME)$(CHAINS_SUFFIX)
DECON_TITER_NAME = inferred_decon_titers
DECON_TITER_CHAINS = $(MCMC_CHAINS)/$(DECON_TITER_NAME)$(CHAINS_SUFFIX)
DECON_MEANS_NAME = inferred_decon_means
DECON_MEANS_CHAINS = $(MCMC_CHAINS)/$(DECON_MEANS_NAME)$(CHAINS_SUFFIX)
MASK_MODEL_NAME = mask
MASK_CHAINS = $(MCMC_CHAINS)/$(MASK_MODEL_NAME)$(CHAINS_SUFFIX)
MASK_PRIOR_CHECK_CHAINS = $(MCMC_CHAINS)/$(MASK_MODEL_NAME)$(PRIOR_CHECK_NAME)$(CHAINS_SUFFIX)
MODELS = $(WELL_MODEL_NAME) $(DECON_MODEL_NAME) $(MASK_MODEL_NAME)
CHAIN_PATHS = $(DECON_CHAINS) $(MASK_CHAINS) $(DECON_MEANS_CHAINS) $(MASK_PRIOR_CHECK_CHAINS)
CHAIN_DIAGNOSTICS = $(OUTPUT)/chain_diagnostics.csv
DECON_FIGURES = figure_decon_main.pdf figure_decon_controls.pdf figure_mask_posterior_check.pdf figure_mask_prior_check.pdf figure_decon_masks.pdf figure_decon_dmem.pdf
FIGURES = $(DECON_FIGURES)
FIGURE_PATHS = $(addprefix $(FIGURE_DIR)/, $(FIGURES))
TABLES = table_decon.docx
TABLE_PATHS = $(addprefix $(TABLE_DIR)/, $(TABLES))
#####################################
# Rules
#
# definition of dependency
# tree and specification of
# rules for doing stuff
#####################################
##########################
# rules for data cleaning
##########################
$(CLEANED)/%.csv: $(RAW)/%.csv $(CLEANING_SCRIPT)
$(MKDIR) $(CLEANED)
$(R_COMMAND) $(CLEANING_SCRIPT) $< $@
$(CLEANED_MASK_DATA): $(MASK_CLEANING_SCRIPT) $(RAW_MASK_DATA)
$(MKDIR) $(CLEANED)
$(R_COMMAND) $^ $@
#####################################
# rules for model fitting and post-processing
#####################################
$(DECON_TITER_CHAINS): $(FITTING_SCRIPT) $(SRC)/$(INFER_TITER_MODEL_SRC) $(DECON_DATA) $(INFER_TITER_HYPERS)
$(MKDIR) $(MCMC_CHAINS)
$(R_COMMAND) $^ $@
$(DECON_MEANS_CHAINS): $(FITTING_SCRIPT) $(SRC)/$(TITER_MEAN_MODEL_SRC) $(DECON_DATA) $(INFER_MEAN_HYPERS)
$(MKDIR) $(MCMC_CHAINS)
$(R_COMMAND) $^ $@
$(DECON_CHAINS): $(FITTING_SCRIPT) $(SRC)/$(SPLINE_MODEL_SRC) $(DECON_DATA) $(DECON_HYPERS)
$(MKDIR) $(MCMC_CHAINS)
$(R_COMMAND) $^ $@
$(MASK_CHAINS): $(MASK_FITTING_SCRIPT) $(SRC)/$(MASK_MODEL_SRC) $(MASK_DATA) $(MASK_HYPERS)
$(MKDIR) $(MCMC_CHAINS)
$(R_COMMAND) $^ $@
$(MASK_PRIOR_CHECK_CHAINS): $(MASK_PRIOR_CHECK_SCRIPT) $(SRC)/$(MASK_MODEL_SRC) $(MASK_DATA) $(MASK_HYPERS)
$(MKDIR) $(MCMC_CHAINS)
$(R_COMMAND) $^ $@
$(CHAIN_DIAGNOSTICS): $(DIAGNOSTIC_SCRIPT) $(CHAIN_PATHS)
$(MKDIR) $(OUTPUT)
$(R_COMMAND) $^ $@
#####################################
# rules for table generation
#####################################
$(TABLE_DIR)/table_decon.docx: $(SRC)/table_decon.R $(DECON_DATA) $(DECON_CHAINS) $(PLOT_PARAMS)
$(MKDIR) $(TABLE_DIR)
$(R_COMMAND) $^ $@
#####################################
# rules for figure generation
#####################################
$(FIGURE_DIR)/figure_decon_main.%: $(SRC)/figure_decon_main.R $(DECON_DATA) $(MASK_DATA) $(DECON_CHAINS) $(DECON_MEANS_CHAINS) $(MASK_CHAINS) $(PLOT_PARAMS)
$(MKDIR) $(FIGURE_DIR)
$(R_COMMAND) $^ $@
$(FIG_CLEANUP)
$(FIGURE_DIR)/figure_decon_controls.%: $(SRC)/figure_decon_controls.R $(DECON_DATA) $(MASK_DATA) $(DECON_CHAINS) $(DECON_MEANS_CHAINS) $(MASK_CHAINS) $(PLOT_PARAMS)
$(MKDIR) $(FIGURE_DIR)
$(R_COMMAND) $^ $@
$(FIG_CLEANUP)
$(FIGURE_DIR)/figure_decon_dmem.%: $(SRC)/figure_decon_dmem.R $(DECON_DATA) $(DECON_CHAINS) $(DECON_MEANS_CHAINS) $(PLOT_PARAMS)
$(MKDIR) $(FIGURE_DIR)
$(R_COMMAND) $^ $@
$(FIG_CLEANUP)
$(FIGURE_DIR)/figure_decon_masks.%: $(SRC)/figure_decon_masks.R $(MASK_DATA) $(MASK_CHAINS) $(PLOT_PARAMS)
$(MKDIR) $(FIGURE_DIR)
$(R_COMMAND) $^ $@
$(FIG_CLEANUP)
$(FIGURE_DIR)/figure_mask_posterior_check.%: $(SRC)/figure_mask_pp_check.R $(MASK_DATA) $(MASK_CHAINS) $(PLOT_PARAMS)
$(MKDIR) $(FIGURE_DIR)
$(R_COMMAND) $^ $@
$(FIG_CLEANUP)
$(FIGURE_DIR)/figure_mask_prior_check.%: $(SRC)/figure_mask_pp_check.R $(MASK_DATA) $(MASK_PRIOR_CHECK_CHAINS) $(PLOT_PARAMS)
$(MKDIR) $(FIGURE_DIR)
$(R_COMMAND) $^ $@
$(FIG_CLEANUP)
#####################################
# convenience rules for making
# various quantities
#####################################
.PHONY: data
data: $(CLEANED_DATA)
.PHONY: chains
chains: $(CHAIN_PATHS)
.PHONY: diagnostics
diagnostics: $(CHAIN_DIAGNOSTICS)
.PHONY: figures
figures: $(FIGURE_PATHS)
.PHONY: tables
tables: $(TABLE_PATHS)
.PHONY: echo_figures echo_chains
echo_figures:
echo $(FIGURE_PATHS)
echo_chains:
echo $(CHAIN_PATHS)
## remove emacs tempfiles, etc.
.PHONY deltemp:
$(RM) $(SRC)/*~*
$(RM) $(SRC)/*#*
$(RM) $(PARAMS)/*~*
$(RM) $(PARAMS)/*#*
.PHONY: clean
clean: deltemp
$(RM) $(OUTPUT)
$(RM) $(CLEANED)
all: depend data chains diagnostics figures tables