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b/NHANES_R/03_imputation.R index 0528a39..fc3427e 100644 --- a/NHANES_R/03_imputation.R +++ b/NHANES_R/03_imputation.R @@ -1,17 +1,30 @@ # Set working directory -setwd("~/GitHub/NHANES_T2D/Data") +setwd("~/Documents/GitHub/NHANES_T2D/Data") # I need to use the Documents directory in MAC-OS # load necessary libraries library(mice) +library(tidyverse) + # load complete merged data to obtain survey number levels # nothing to do with this data, we only need the factor levels for the loop cleaned_full_df <- readRDS("cleaned_full_df.rds") + +# Correctly fill the missing values of now_BP_meds variable + +cleaned_full_df <- cleaned_full_df |> mutate(now_BP_meds = + if_else(hypertension_ever == 'no hypertension' & is.na(now_BP_meds), + 'no BP meds', as.character(now_BP_meds))) + +# Recode the now_BP_meds variable as factor + +cleaned_full_df$now_BP_meds <- as.factor(cleaned_full_df$now_BP_meds) + cleaned_full_df_used <- cleaned_full_df[cleaned_full_df$survey_nr %in% c("1999-2000","2001-2002","2003_2004","2005_2006","2007_2008","2009_2010"),] # calculate average missingness in data (sum(is.na(cleaned_full_df))/prod(dim(cleaned_full_df)))*100 -# it is 13.9%, which we round up to 15% - so we will make 15 imputed copies +# it is 11.9%, which we round up to 15% - so we will make 15 imputed copies # load data per survey (loop) for (i in levels(cleaned_full_df$survey_nr)) { @@ -28,7 +41,10 @@ SDMVSTRA <- full_df$SDMVSTRA full_df$SDMVSTRA <- NULL # imputation: 5 copies, 5 iterations, random forest algorithm -imputation_object <- mice(full_df, method = "rf", m = 15, maxit = 5, seed = 64370) + +# After changes in the mice +# We specify in mice that rfPackage = 'randomForest', otherwise we receive error of incorrect dimensions +imputation_object <- mice(full_df, rfPackage = 'randomForest', m = 15, maxit = 5, seed = 64370) # investigate convergence visually # imputation_object$method #those variables with no missing have "" as method - they are still used for imputation