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Descriptive_trends.R
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Descriptive_trends.R
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### INFO
# project: Project #: Prostate cancer prevalence
# author: Agz Leman
# October 2023
# Plots monthly rates
###
## library
library(tidyverse)
library(here)
library(MASS)
library(plyr)
## Redactor code (W.Hulme)
redactor <- function(n, threshold=7,e_overwrite=NA_integer_){
# given a vector of frequencies, this returns a boolean vector that is TRUE if
# a) the frequency is <= the redaction threshold and
# b) if the sum of redacted frequencies in a) is still <= the threshold, then the
# next largest frequency is also redacted
n <- as.integer(n)
leq_threshold <- dplyr::between(n, 1, threshold)
n_sum <- sum(n)
# redact if n is less than or equal to redaction threshold
redact <- leq_threshold
# also redact next smallest n if sum of redacted n is still less than or equal to threshold
if((sum(n*leq_threshold) <= threshold) & any(leq_threshold)){
redact[which.min(dplyr::if_else(leq_threshold, n_sum+1L, n))] = TRUE
}
n_redacted <- if_else(redact, e_overwrite, n)
}
start <- "2020-03-01"
for (i in c("measure_incidence_rate.csv",
"measure_prevalence_rate.csv","measure_mortality_rate.csv")){
Rates <- read_csv(here::here("output", "measures", i))
Rates_rounded <- as.data.frame(Rates)
###
# Redact and round counts
###
Rates_rounded[,1] <- redactor(Rates_rounded[,1])
#round to the nearest 5
for (j in 1:2){
Rates_rounded[,j] <- plyr::round_any(Rates_rounded[,j], 5, f = round)}
# calculate the rates
Rates_rounded$value <- round(Rates_rounded[,1]/Rates_rounded$population,1)
# calc rate per 100,000
Rates_rounded$value2 <- round((Rates_rounded[,1]/Rates_rounded$population)*100000,1)
write.table(Rates_rounded, here::here("output", paste0("Rates_rounded_",colnames(Rates_rounded)[1],".csv")),
sep = ",",row.names = FALSE)
###
# Plot
###
p <- ggplot(data = Rates_rounded,aes(date, value2)) +
geom_line()+
geom_point()+
scale_x_date(date_breaks = "2 month",
date_labels = "%Y-%m")+
labs(title = paste0(colnames(Rates_rounded)[1]),
x = "", y = "Rate per 100,000")+
theme_bw()+
theme(axis.text.x = element_text(angle = 45, hjust = 1))
p <- p + geom_vline(xintercept=as.Date(start, format="%Y-%m-%d"), size=0.3, colour="red")
p <- p + geom_text(aes(x=as.Date(start, format="%Y-%m-%d")+5, y=min(value2)+(sd(value2)*2)),
color = "red",label="Start of\nrestrictions", angle = 90, size = 3)
p <- p + labs(caption="OpenSafely-TPP October 2023")
p <- p + theme(plot.caption = element_text(size=8))
p <- p + theme(plot.title = element_text(size = 10))
ggsave(
plot= p, dpi=800,width = 20,height = 10, units = "cm",
filename=paste0(colnames(Rates_rounded)[1],".png"), path=here::here("output"),
)
}
for (i in c("measure_incidencebyAge_rate.csv","measure_incidencebyEthnicity_rate.csv",
"measure_incidencebyIMD_rate.csv","measure_incidencebyRegion_rate.csv",
"measure_prevalencebyAge_rate.csv","measure_prevalencebyEthnicity_rate.csv",
"measure_prevalencebyIMD_rate.csv","measure_prevalencebyRegion_rate.csv")){
Rates <- read_csv(here::here("output", "measures", i))
Rates_rounded <- as.data.frame(Rates)
###
# Redact and round counts
###
Rates_rounded[which(is.na(Rates_rounded[,2])),2] <- 1
Rates_rounded[,2] <- redactor(Rates_rounded[,2])
#round to the nearest 5
for (j in 2:3){
Rates_rounded[,j] <- plyr::round_any(Rates_rounded[,j], 5, f = round)}
Rates_rounded$value <- round(Rates_rounded[,2]/Rates_rounded$population,1)
# calc rate per 100,000
Rates_rounded$value2 <- round((Rates_rounded[,2]/Rates_rounded$population)*100000,1)
write.table(Rates_rounded, here::here("output", paste0("Rates_rounded_",colnames(Rates_rounded)[2],"_by_",colnames(Rates_rounded)[1],".csv")),
sep = ",",row.names = FALSE)
p <- ggplot(data = Rates_rounded,aes(date, value2, color = Rates_rounded[,1], lty = Rates_rounded[,1])) +
geom_line()+
scale_x_date(date_breaks = "2 month",
date_labels = "%Y-%m")+
labs(title = paste0(substr(i, 9, 17),"_by_",colnames(Rates_rounded)[1]),
x = "", y = "Rate per 100,000")+
theme_bw()+
theme(axis.text.x = element_text(angle = 45, hjust = 1), legend.position="bottom")
p <- p + geom_vline(xintercept=as.Date(start, format="%Y-%m-%d"), size=0.3, colour="red")
p <- p + geom_text(aes(x=as.Date(start, format="%Y-%m-%d")+5, y=min(value2)+(sd(value2)*2)),
color = "red",label="Start of\nrestrictions", angle = 90, size = 3)
p <- p + labs(caption="OpenSafely-TPP October 2023")
p <- p + theme(plot.caption = element_text(size=8))
p <- p + theme(plot.title = element_text(size = 10))
ggsave(
plot= p, dpi=800,width = 20,height = 10, units = "cm",
filename=paste0(substr(i, 9, 17),"_by_",colnames(Rates_rounded)[1],".png"), path=here::here("output"),
)
}
###
# Summarise population data from the input.csv
###
n <- 1; #rounding level
#Input <- read_csv(here::here("output", "input.csv"),show_col_types = FALSE)
Input <- read_csv(here::here("output", "input.csv"),col_types = cols(patient_id = col_integer()))
Table1 <- as.data.frame(NA)
xx <- c("preva","ageP","sdP","inci","ageI","sdI",
"inci15","ageI15","sdI15","inci16","ageI16","sdI16",
"inci17","ageI17","sdI17","inci18","ageI18","sdI18",
"inci19","ageI19","sdI19","inci20","ageI20","sdI20",
"inci21","ageI21","sdI21","inci22","ageI22","sdI22",
"inci23","ageI23","sdI23","m1","m2")
Table1[xx] <- NA
Table1[1,"preva"] <- plyr::round_any(length(which(Input$prostate_ca==1)), 5, f = round)
Table1[1,"ageP"] <- round(mean(Input$age_pa_ca),n)
xl <- Input$age_pa_ca; Table1[1,"sdP"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")")
Input2 <- Input[Input$prostate_ca_date>= "2015-01-01",]
Table1[1,"inci"] <- plyr::round_any(length(which(Input2$prostate_ca==1)), 5, f = round)
Table1[1,"ageI"] <- round(mean(Input2$age_pa_ca),n)
xl <- Input2$age_pa_ca; Table1[1,"sdI"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")"); rm(Input2)
Input$ethnicity[which(is.na(Input$ethnicity))] <- "NAs"; Table1[names(table(Input$ethnicity, exclude=NULL))] <- NA
Table1[1,names(table(Input$ethnicity, exclude=NULL))] <- plyr::round_any(as.numeric(table(Input$ethnicity, exclude=NULL)), 5, f = round)
Input$sex[which(is.na(Input$sex))] <- "NAs"; Table1[names(table(Input$sex, exclude=NULL))] <- NA
Table1[1,names(table(Input$sex, exclude=NULL))] <- plyr::round_any(as.numeric(table(Input$sex, exclude=NULL)), 5, f = round)
Input$imd_cat[which(is.na(Input$imd_cat))] <- "NAs"; Table1[names(table(Input$imd_cat, exclude=NULL))] <- NA
Table1[1,names(table(Input$imd_cat, exclude=NULL))] <- plyr::round_any(as.numeric(table(Input$imd_cat, exclude=NULL)), 5, f = round)
Input2 <- Input[Input$prostate_ca_date>= "2015-01-01" & Input$prostate_ca_date<= "2015-12-31",]
Table1[1,"inci15"] <- plyr::round_any(length(which(Input2$prostate_ca==1)), 5, f = round)
Table1[1,"ageI15"] <- round(mean(Input2$age_pa_ca),n)
xl <- Input2$age_pa_ca; Table1[1,"sdI15"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")");
Input3 <- Input[Input$prostate_ca_date>= "2016-01-01" & Input$prostate_ca_date<= "2016-12-31",]
Table1[1,"inci16"] <- plyr::round_any(length(which(Input3$prostate_ca==1)), 5, f = round)
Table1[1,"ageI16"] <- paste0(round(mean(Input3$age_pa_ca),n)," (p=",
round(t.test(Input3$age_pa_ca,Input2$age_pa_ca)$p.value,3),")")
xl <- Input3$age_pa_ca; Table1[1,"sdI16"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")"); rm(Input2)
Input2 <- Input[Input$prostate_ca_date>= "2017-01-01" & Input$prostate_ca_date<= "2017-12-31",]
Table1[1,"inci17"] <- plyr::round_any(length(which(Input2$prostate_ca==1)), 5, f = round)
Table1[1,"ageI17"] <- paste0(round(mean(Input2$age_pa_ca),n)," (p=",
round(t.test(Input3$age_pa_ca,Input2$age_pa_ca)$p.value,3),")")
xl <- Input2$age_pa_ca; Table1[1,"sdI17"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")"); rm(Input3)
Input3 <- Input[Input$prostate_ca_date>= "2018-01-01" & Input$prostate_ca_date<= "2018-12-31",]
Table1[1,"inci18"] <- plyr::round_any(length(which(Input3$prostate_ca==1)), 5, f = round)
Table1[1,"ageI18"] <- paste0(round(mean(Input3$age_pa_ca),n)," (p=",
round(t.test(Input3$age_pa_ca,Input2$age_pa_ca)$p.value,3),")")
xl <- Input3$age_pa_ca; Table1[1,"sdI18"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")"); rm(Input2)
Input2 <- Input[Input$prostate_ca_date>= "2019-01-01" & Input$prostate_ca_date<= "2019-12-31",]
Table1[1,"inci19"] <- plyr::round_any(length(which(Input2$prostate_ca==1)), 5, f = round)
Table1[1,"ageI19"] <- paste0(round(mean(Input2$age_pa_ca),n)," (p=",
round(t.test(Input3$age_pa_ca,Input2$age_pa_ca)$p.value,3),")")
xl <- Input2$age_pa_ca; Table1[1,"sdI19"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")"); rm(Input3)
Input3 <- Input[Input$prostate_ca_date>= "2020-01-01" & Input$prostate_ca_date<= "2020-12-31",]
Table1[1,"inci20"] <- plyr::round_any(length(which(Input3$prostate_ca==1)), 5, f = round)
Table1[1,"ageI20"] <- paste0(round(mean(Input3$age_pa_ca),n)," (p=",
round(t.test(Input3$age_pa_ca,Input2$age_pa_ca)$p.value,3),")")
xl <- Input3$age_pa_ca; Table1[1,"sdI20"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")"); rm(Input2)
Input2 <- Input[Input$prostate_ca_date>= "2021-01-01" & Input$prostate_ca_date<= "2021-12-31",]
Table1[1,"inci21"] <- plyr::round_any(length(which(Input2$prostate_ca==1)), 5, f = round)
Table1[1,"ageI21"] <- paste0(round(mean(Input2$age_pa_ca),n)," (p=",
round(t.test(Input3$age_pa_ca,Input2$age_pa_ca)$p.value,3),")")
xl <- Input2$age_pa_ca; Table1[1,"sdI21"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")"); rm(Input3)
Input3 <- Input[Input$prostate_ca_date>= "2022-01-01" & Input$prostate_ca_date<= "2022-12-31",]
Table1[1,"inci22"] <- plyr::round_any(length(which(Input3$prostate_ca==1)), 5, f = round)
Table1[1,"ageI22"] <- paste0(round(mean(Input3$age_pa_ca),n)," (p=",
round(t.test(Input3$age_pa_ca,Input2$age_pa_ca)$p.value,3),")")
xl <- Input3$age_pa_ca; Table1[1,"sdI22"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")"); rm(Input2)
Input2 <- Input[Input$prostate_ca_date>= "2023-01-01" & Input$prostate_ca_date<= "2023-12-31",]
Table1[1,"inci23"] <- plyr::round_any(length(which(Input2$prostate_ca==1)), 5, f = round)
Table1[1,"ageI23"] <- paste0(round(mean(Input2$age_pa_ca),n)," (p=",
round(t.test(Input3$age_pa_ca,Input2$age_pa_ca)$p.value,3),")")
xl <- Input2$age_pa_ca; Table1[1,"sdI23"] <- paste0(round(sd(xl),n),
" (95CIs: ",round(t.test(xl)$conf.int[1],n)," to ",
round(t.test(xl)$conf.int[2],n),")"); #rm(Input3)
Table1[1,"m1"] <-dim(Input2)[1]
Table1[1,"m2"] <-dim(Input2)[2]
Table1 <- t(Table1)
Table1 <- as.data.frame(Table1)
colnames(Table1) <- "summaryStat"
Table1$var <- row.names(Table1)
Table1 <- Table1[,c(2,1)]
# Table1$summaryStat <- round(Table1$summaryStat,1)
write.table(Table1, here::here("output", "Table1.csv"),sep = ",",row.names = FALSE)