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throat_ab.R
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throat_ab.R
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library("tidyverse")
library('dplyr')#conflict with plyr; load after plyr
library('lubridate')
rm(list=ls())
setwd(here::here("output", "measures"))
DF=read_rds('ab_type_2019.rds')
#dat=rbindlist(DF)
dat=bind_rows(DF)
rm(DF)
# recode
dat$infection=recode(dat$infection,
asthma ="Asthma",
cold="Cold",
cough="Cough",
copd="COPD",
pneumonia="Pneumonia",
renal="Renal",
sepsis="Sepsis",
throat="Sore throat",
uti = "UTI",
lrti = "LRTI",
urti = "URTI",
sinusits = "Sinusitis",
otmedia = "Otitis media",
ot_externa = "Otitis externa")
dat$infection=ifelse(dat$infection=="","uncoded",dat$infection)
##Sore throat
df1 <- dat %>% filter(infection=='Sore throat')
rm(dat)
DF=read_rds('ab_type_2020.rds')
#dat=rbindlist(DF)
dat=bind_rows(DF)
rm(DF)
# recode
dat$infection=recode(dat$infection,
asthma ="Asthma",
cold="Cold",
cough="Cough",
copd="COPD",
pneumonia="Pneumonia",
renal="Renal",
sepsis="Sepsis",
throat="Sore throat",
uti = "UTI",
lrti = "LRTI",
urti = "URTI",
sinusits = "Sinusitis",
otmedia = "Otitis media",
ot_externa = "Otitis externa")
dat$infection=ifelse(dat$infection=="","uncoded",dat$infection)
##Sore throat
df2 <- dat %>% filter(infection=='Sore throat')
rm(dat)
DF=read_rds('ab_type_2021.rds')
#dat=rbindlist(DF)
dat=bind_rows(DF)
rm(DF)
# recode
dat$infection=recode(dat$infection,
asthma ="Asthma",
cold="Cold",
cough="Cough",
copd="COPD",
pneumonia="Pneumonia",
renal="Renal",
sepsis="Sepsis",
throat="Sore throat",
uti = "UTI",
lrti = "LRTI",
urti = "URTI",
sinusits = "Sinusitis",
otmedia = "Otitis media",
ot_externa = "Otitis externa")
dat$infection=ifelse(dat$infection=="","uncoded",dat$infection)
##Sore throat
df3 <- dat %>% filter(infection=='Sore throat')
rm(dat)
dat=read_rds('ab_type_2022.rds')
# recode
dat$infection=recode(dat$infection,
asthma ="Asthma",
cold="Cold",
cough="Cough",
copd="COPD",
pneumonia="Pneumonia",
renal="Renal",
sepsis="Sepsis",
throat="Sore throat",
uti = "UTI",
lrti = "LRTI",
urti = "URTI",
sinusits = "Sinusitis",
otmedia = "Otitis media",
ot_externa = "Otitis externa")
dat$infection=ifelse(dat$infection=="","uncoded",dat$infection)
##Sore throat
df4 <- dat %>% filter(infection=='Sore throat')
rm(dat)
df <- rbind(df1,df2,df3,df4)
rm(df1,df2,df3,df4)
df_throat <- df %>%
count(type, name="n") %>%
mutate(freq_rel=n / sum(n))
# df_throat$deviation <- 'NA'
# df_throat$deviation <- ifelse(df_throat$type != '', 1 , df$deviation)
# df_throat$deviation <- ifelse(df_throat$type == 'Phenoxymethylpenicillin', 0 , df$deviation)
# df_throat$deviation <- ifelse(df_throat$type == 'Clarithromycin', 0 , df$deviation)
# df_throat$deviation <- ifelse(df_throat$type == 'Erythromycin', 0 , df$deviation)
write_csv(df_throat, here::here("output", "ab_throat.csv"))