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renamed file to reflect data_extraction_mediator

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Tanushree Tunstall 2020-11-27 17:47:05 +00:00
parent 52a2453327
commit 3a380a5be1
11 changed files with 95 additions and 1963 deletions
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60
colnames_clinical_meds.R
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@ -6,18 +6,28 @@ getwd()
# TASK: Extract relevant columns from mosaic fp adults data for regression
# clinical and sig meds
########################################################################
########################################################################
clinical_cols_data = c("mosaic"
, "ia_exac_copd"
, "death"
#, "obese2" #inc peaeds, but once you subset data for adults, its the same!
, "obesity"
, "flustat"
# meta data columns
meta_data_cols = c("mosaic"
, "gender"
, "age"
, "adult"
, "flustat"
, "type"
#, "obese2" #inc peaeds, but once you subset data for adults, its the same!
#, "height", "height_unit"
#, "weight", "weight_unit"
#, "ia_height_ftin", "ia_height_m", "ia_weight"
#, "visual_est_bmi", "bmi_rating"
, "obesity")
clinical_cols = c("death"
, "sfluv"
, "h1n1v"
, "age"
, "gender"
, "ia_exac_copd"
, "onset_2_t1"
, "asthma"
, "vl_pfu_ul_npa1"
, "los"
@ -36,13 +46,13 @@ clinical_cols_data = c("mosaic"
, "inresp_sev"
, "steroid")
clinical_cols_added = c("age_bins"
, "o2_sat_bin"
, "onset_initial_bin"
, "steroid_ics"
, "t1_resp_recoded" )
#clinical_cols_added = c("age_bins"
# , "o2_sat_bin"
# , "onset_initial_bin"
# , "steroid_ics"
# , "t1_resp_recoded")
clinical_cols = c(clinical_cols_data, clinical_cols_added)
meta_clinical_cols = c(meta_data_cols, clinical_cols)
sig_npa_cols = c("eotaxin_npa1"
, "eotaxin3_npa1"
@ -83,15 +93,15 @@ sig_npa_cols = c("eotaxin_npa1"
, "tnfr2_npa2"
, "tnfr2_npa3")
cols_to_extract = c(clinical_cols, sig_npa_cols)
#cols_to_extract = c(clinical_cols, sig_npa_cols, clinical_cols_added)
if ( length(cols_to_extract) == length(clinical_cols) + length(sig_npa_cols) ){
cat("PASS: length match"
, "\nTotal no. of cols to extract for regression:", length(cols_to_extract)
, "\nNo. of clinical cols:", length(clinical_cols)
, "\nNo. of sig npa cols: ", length(sig_npa_cols))
}else{
cat("FAIL: length mismatch"
, "\nAborting!")
quit()
}
#if ( length(cols_to_extract) == length(clinical_cols) + length(sig_npa_cols) + length(clinical_cols_added) ){
# cat("PASS: length match"
# , "\nTotal no. of cols to extract for regression:", length(cols_to_extract)
# , "\nNo. of clinical cols:", length(clinical_cols)
# , "\nNo. of sig npa cols: ", length(sig_npa_cols))
#}else{
# cat("FAIL: length mismatch"
# , "\nAborting!")
# quit()
#}