TRANSDATA_BIO=$(HRSDIR)/hrs113r_transition_bio.dta
SASBIO = $(CURDIR)/run.sas_bio.sh

## Biomarker Make Rules
biomarkers: $(DATADIR)/nhanes_analytic.dta $(ESTIMATES)/nhanes_biomarkers/nhanes_ldl.ster $(DATADIR)/new51s_status_quo_bio.dta $(DATADIR)/stock_hrs_2010_bio.dta $(HRSDIR)/hrs113r_transition_bio.dta

$(DATADIR)/nhanes_analytic.dta: fem_env.do FEM_Stata/Makedata/NHANES/gen_nhanes_biomarkers.do
	cd FEM_Stata/Makedata/NHANES && $(STATA) gen_nhanes_biomarkers.do
$(ESTIMATES)/nhanes_biomarkers/nhanes_ldl.ster: fem_env.do FEM_Stata/Makedata/NHANES/nhanes_impute_ldl.do $(DATADIR)/nhanes_analytic.dta
	cd FEM_Stata/Makedata/NHANES && $(STATA) nhanes_impute_ldl.do
$(HRSDIR)/bio_hrs_recoded.dta: fem_env.do FEM_Stata/Makedata/HRS/gen_biomarkers.do $(DATADIR)/hrs_analytic_recoded.dta $(ESTIMATES)/nhanes_biomarkers/nhanes_ldl.ster
	cd FEM_Stata/Makedata/HRS && $(STATA) gen_biomarkers.do
$(HRSDIR)/bio_hrs_recoded_prepimp.dta: $(HRSDIR)/bio_hrs_recoded.dta fem_env.do FEM_Stata/Makedata/HRS/biomarker_impute_prep_1.do
	cd FEM_Stata/Makedata/HRS && $(STATA) biomarker_impute_prep_1.do
$(HRSDIR)/bio_imp20tiles_wide.dta: $(HRSDIR)/bio_hrs_recoded_prepimp.dta fem_env.do FEM_Stata/Makedata/HRS/biomarker_impute_prep_2.do
	cd FEM_Stata/Makedata/HRS && $(STATA) biomarker_impute_prep_2.do
$(HRSDIR)/bio_imp_all.sas7bdat: $(HRSDIR)/bio_imp20tiles_wide.dta $(HRSDIR)/bio_hrs_recoded_prepimp_v1.dta fem_env.sas FEM_Sas/HRS/Biomarkers/bio_pct_impute.sas 
	cd FEM_Sas/HRS/Biomarkers/ && $(SASBIO) bio_pct_impute.sas 

## Conversion to Stata
$(HRSDIR)/bio_imp_all.dta: $(HRSDIR)/bio_imp_all.sas7bdat
	cd FEM_Sas/utilities && FILEPATH=$< $(SAS) export_stata.sas

$(HRSDIR)/bio_hrs_recoded_impfinal.dta: $(HRSDIR)/bio_imp_all.dta fem_env.do FEM_Stata/Makedata/HRS/biomarker_impute_final.do $(ESTIMATES)/nhanes_biomarkers/nhanes_ldl.ster
	cd FEM_Stata/Makedata/HRS && $(STATA) biomarker_impute_final.do
	

$(DATADIR)/new51s_status_quo_bio.dta: $(HRSDIR)/bio_hrs_recoded_impfinal.dta $(COMMON) FEM_Stata/Makedata/HRS/new51_simulate.do $(DATADIR)/pop5152_projection_2150.dta $(DATADIR)/age5055_hrs1992.dta $(DATADIR)/age5055_hrs2004.dta $(DATADIR)/trend_all_status_quo.dta $(BASEDIR)/incoming_vcmatrix.dta $(BASEDIR)/incoming_means_econ_tos.dta $(BASEDIR)/incoming_means.dta $(BASEDIR)/incoming_means_econ.dta $(UTILITIES)/_getestimates.mo $(INIT_EST) $(RESTIMATES)/minit_logtenure $(DATADIR)/minit_deprsymp $(DATADIR)/sinit_deprsymp $(DATADIR)/new51_painstat.ster $(DATADIR)/new51_adlstat.ster $(DATADIR)/new51_iadlstat.ster $(DATADIR)/incoming_base.dta  FEM_Stata/Makedata/HRS/new51_simulate.do  $(BASEDIR)/incoming_cut_points.dta $(UTILITIES)/calc_cut_point.ado $(UTILITIES)/calc_cut_point_ml.ado $(UTILITIES)/new_deviation.ado $(RESTIMATES)/ssa_means.dta $(RESTIMATES)/ssa_vcmatrix.dta
	cd FEM_Stata/Makedata/HRS && SCENARIO=status_quo TREND=status_quo BIOMARKERS=1 BREP=0 RES=1 FYEAR=$(FYEAR) LYEAR=$(LYEAR) $(STATA) new51_simulate.do

$(DATADIR)/stock_hrs_2010_bio.dta: $(COMMON) $(HRSDIR)/bio_hrs_recoded_impfinal.dta FEM_Stata/Makedata/HRS/save_stock_hrs_2010_faked_bio.do  $(DATADIR)/all2010_pop_adjusted.dta $(DATADIR)/imputed_ssa_ret_2010.dta $(DATADIR)/imputed_ssa_notret_2010.dta $(UTILITIES)/multiply_persons.ado expansion.makefile 
	cd FEM_Stata/Makedata/HRS && EXPAND=$(EXPANSION_FACTOR) $(STATA) save_stock_hrs_2010_faked_bio.do

$(HRSDIR)/hrs113r_transition_bio.dta: $(COMMON) $(DATADIR)/hrs113_transition.dta $(HRSDIR)/bio_hrs_recoded_impfinal.dta FEM_Stata/Makedata/HRS/transition_select_biomarker.do
	cd FEM_Stata/Makedata/HRS && $(STATA) transition_select_biomarker.do
	
## Make biomarker estimation model

estimation_bio: $(ESTIMATES)/biomarkers/estimatesbiomarkers.xls

estimation_bio_cpp: $(COMMON)
	cd FEM_Stata/Estimation && datain=$(ESTIMATES)/biomarkers dataout=$(ROOT)/FEM_CPP_settings/biomarkers/models $(STATA) save_est_cpp.do

	
$(ESTIMATES)/biomarkers/estimatesbiomarkers.xls: $(COMMON) fem_env.do FEM_Stata/Estimation/init_transition.do $(TRANSDATA_BIO) $(UTILITIES)/takestring.ado FEM_Stata/Estimation/hrs_covariate_definitionsbiomarkers.do $(DATADIR)/crossvalidation.dta FEM_Stata/Estimation/define_modelsbiomarkers.do 
	cd FEM_Stata/Estimation && USERVARS=$(USERVARS) DATAIN=$(TRANSDATA_BIO) EXTVAL=0 suffix=biomarkers $(STATA) init_transition.do

## Summary Output Generation script for biomarkers
summary_output_bio: 
	cd FEM_CPP_settings/ && $(STATA) summary_output_gen_bio.do

bio_descriptive:
	cd analysis/ && $(STATA) biomarker_imp_descriptive_0722.do