reformatting code to select needed df for analysis
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a6cbaab40a
commit
b72c4df796
7 changed files with 243 additions and 102 deletions
61
read_data.R
61
read_data.R
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@ -30,11 +30,11 @@ meta_data_cols = c("mosaic", "gender", "age"
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, "adult"
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, "flustat", "type"
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, "obesity"
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, "obese2"
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, "height", "height_unit"
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, "weight", "weight_unit"
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, "ia_height_ftin", "ia_height_m", "ia_weight"
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, "visual_est_bmi", "bmi_rating"
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#, "obese2"
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#, "height", "height_unit"
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#, "weight", "weight_unit"
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#, "ia_height_ftin", "ia_height_m", "ia_weight"
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#, "visual_est_bmi", "bmi_rating"
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)
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# check if these columns to select are present in the data
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@ -55,9 +55,9 @@ if (table(adult_df$adult == 1)[[1]] == nrow(adult_df) ){
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cat ("\nFAIL: adult df number mismatch!")
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}
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#==============
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#=================================
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# FLU positive: adult patients
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#==============
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#=================================
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# extract the flu positive population
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fp_adults = adult_df[adult_df$flustat == 1,]
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@ -67,6 +67,53 @@ if (table(fp_adults$flustat == 1)[[1]] == nrow(fp_adults) ){
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cat ("\nFAIL: adult df number mismatch!")
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}
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#=============================================
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# FLU positive adult patients: without asthma
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#=============================================
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#-----------------------------------
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# asthma and copd status correction
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# for conflicting field!
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#------------------------------------
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# Reassign the copd and asthma status and do some checks
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table(fp_adults$ia_exac_copd); sum(is.na(fp_adults$ia_exac_copd))
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fp_adults$ia_exac_copd[fp_adults$ia_exac_copd< 1]<- 0
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fp_adults$ia_exac_copd[is.na(fp_adults$ia_exac_copd)] <- 0
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table(fp_adults$ia_exac_copd); sum(is.na(fp_adults$ia_exac_copd))
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# check copd and asthma status
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table(fp_adults$ia_exac_copd, fp_adults$asthma)
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check_copd_and_asthma_1<- subset(fp_adults, ia_exac_copd ==1 & asthma == 1) # check this is 3
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# reassign these 3 so these are treated as non-asthmatics as copd with asthma is NOT TRUE asthma
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fp_adults$asthma[fp_adults$ia_exac_copd == 1 & fp_adults$asthma == 1]= 0
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table(fp_adults$ia_exac_copd, fp_adults$asthma)
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foo<- subset(fp_adults, asthma==1 & ia_exac_copd ==1) # check that its 0
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rm(check_copd_and_asthma_1, foo)
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if ( table(fp_adults$ia_exac_copd, fp_adults$asthma) [[2,2]] == 0 ){
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cat("\nPASS: asthma and copd do not conflict")
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} else{
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cat ("\nFAIL: asthma and copd conflict not resolved!")
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quit()
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}
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cat("\nExtracting flu positive without asthma")
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table(fp_adults$asthma)
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cat("\nNo. of asthmatics:", table(fp_adults$asthma)[[2]]
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, "\nNo. of non-asthmatics:", table(fp_adults$asthma)[[1]])
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str(fp_adults$asthma)
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table(fp_adults$obesity)
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table(fp_adults$obesity, fp_adults$asthma)
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fp_adults_na = fp_adults[fp_adults$asthma == 0,]
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table(fp_adults_na$obesity)
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table(fp_adults_na$obesity, fp_adults_na$asthma)
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#============
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# hc
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#============
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