.Rhistory

library(reda)
install.packages("reda")
library(reda)
install.packages("frailtyEM")
library(frailtyEM)
install.packages("reReg")
library(reReg)
library(revents)
pkgdown::build_site()
pkgdown::build_site()
pkgdown::build_articles()
pkgdown::build_articles()
pkgdown::build_articles()
pkgdown::build_site()
usethis::use_git()
pkgdown::build_articles()
pkgdown::build_site()
usethis::use_pkgdown_github_pages()
pkgdown::build_site()
devtools::document()
deploy_to_branch()
library(revents)
library(utils)
# Load data layout corresponding to the third layout
file_path_data_csv <- "revents/inst/data_layout_1.csv"
data_layout_1 <- read.csv(file_path_data_csv)
library(here)
knitr::opts_chunk$set(warning = FALSE, message = FALSE)
suppressWarnings({
suppressMessages({
library(survival)
library(broom)
library(dplyr)
library(utils)
library(frailtyEM)
library(here)
})
})
# Load data layout corresponding to the third layout
file_path_data_csv <- here("data", "data_layout_1.csv")
data_layout_1 <- read.csv(file_path_data_csv)
# Load data layout corresponding to the third layout
file_path_data_csv <- here("data", "data_layout_1.csv")
data_layout_1 <- read.csv(file_path_data_csv)
# Load data layout corresponding to the third layout
file_path_data_csv <- here("inst", "data_layout_1.csv")
data_layout_1 <- read.csv(file_path_data_csv)
# Load data layout corresponding to the third layout
library(here)
file_path_data_csv <- here("inst", "data_layout_1.csv")
data_layout_1 <- read.csv(file_path_data_csv)
pkgdown::build_articles()
usethis::use_data_raw("data_layout_1")
usethis::use_data_raw("data_layout_2")
usethis::use_data_raw("data_layout_3")
data_layout_1 <- readr::read_csv("data-raw/data_layout_1.csv")
data_layout_2 <- readr::read_csv("data-raw/data_layout_2.csv")
data_layout_3 <- readr::read_csv("data-raw/data_layout_3.csv")
usethis::use_data(data_layout_1, overwrite = TRUE)
usethis::use_data(data_layout_3, overwrite = TRUE)
usethis::use_data(data_layout_2, overwrite = TRUE)
usethis::use_r("data_layout_1")
usethis::use_r("data_layout_2")
usethis::use_r("data_layout_3")
# Load data layout corresponding to the third layout
data("data_layout_1", package = "revents")
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
knitr::opts_chunk$set(warning = FALSE, message = FALSE)
suppressWarnings({
suppressMessages({
library(survival)
library(broom)
library(dplyr)
library(frailtyEM)
})
})
# Load data layout corresponding to the third layout
data("data_layout_1", package = "revents")
# Load data layout corresponding to the third layout
data("data_layout_1", package = "revents")
devtools::document()
# Load data layout corresponding to the third layout
data("data_layout_1", package = "revents")
devtools::load_all(".")
data("data_layout_1", package = "revents")
?revents::data_layout_1
View(data_layout_1)
knitr::opts_chunk$set(warning = FALSE, message = FALSE)
suppressWarnings({
suppressMessages({
library(survival)
library(broom)
library(dplyr)
library(frailtyEM)
})
})
# Load data layout corresponding to the third layout
data_layout_1 <- data("data_layout_1", package = "revents")
# Load data layout corresponding to the third layout
data("data_layout_1", package = "revents")
data_layout_1 <- revents::data_layout_1
devtools::document()
# Load data layout corresponding to the third layout
data("data_layout_1", package = "revents")
data_layout_1 <- revents::data_layout_1
# set scientific notation to FALSE
options(scipen = 999)
cox.relapses <- coxph(Surv(TSTART, TSTOP, STATUS) ~ DISEASE_COURSE + AGE + SEX
+ RACE + TIME_SINCE_DIAGNOSIS, ties = "breslow",
data = subset(data_layout_1, SEVENT == 1))
cox.relapses
# Load data layout corresponding to the third layout
data("data_layout_1", package = "revents")
data_layout_1 <- revents::data_layout_1
# set scientific notation to FALSE
options(scipen = 999)
cox.relapses <- coxph(Surv(TSTART, TSTOP, STATUS) ~ DISEASE_COURSE + AGE + SEX
+ RACE + TIME_SINCE_DIAGNOSIS, ties = "breslow",
data = subset(data_layout_1, SEVENT == 1))
cox.relapses
View(data_layout_1)
coldesc <- rep("", ncol(data_layout_1))
names(coldesc) <- names(data_layout_1)
dput(coldesc)
devtools::document()
?revents::data_layout_1
library(roxygen2)
devtools::document()
install.packages("roxygen2")
devtools::document()
library(roxygen2)
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
source("data-raw/create_data.R")
devtools::document()
## code to prepare `data_layout_1` dataset goes here
usethis::use_data(data_layout_1, overwrite = TRUE)
data_layout_1 <- readr::read_csv("data-raw/data_layout_1.csv")
usethis::use_data(data_layout_1, overwrite = TRUE)
vars <- c(
ID = "participant ID",
PARAMCD = "parameter",
TSTART = "time study start",
TSTOP = "time stop observation",
TGAP = "time gap between events",
STATUS = "status of the event",
SEVENT = "sequence number of event per id",
AGE = "age of the participant",
SEX = "Sex of the participant",
DISEASE_COURSE = "type of disease course",
RACE = "race of the participant",
TIME_SINCE_DIAGNOSIS = "time since diagnosis"
)
glue::glue("#'   \\item{[colname]}{[coldesc]}",
colname = names(vars),
coldesc = vars,
.open = "[",
.close = "]")
## code to prepare `data_layout_2` dataset goes here
usethis::use_data(data_layout_2, overwrite = TRUE)
data_layout_2 <- readr::read_csv("data-raw/data_layout_2.csv")
usethis::use_data(data_layout_2, overwrite = TRUE)
vars <- c(
ID = "participant ID",
PARAMCD = "parameter",
TSTART = "time study start",
TSTOP = "time stop observation",
TGAP = "time gap between events",
STATUS = "status of the event",
SEVENT = "sequence number of event per id",
AGE = "age of the participant",
SEX = "Sex of the participant",
DISEASE_COURSE = "type of disease course",
RACE = "race of the participant",
TIME_SINCE_DIAGNOSIS = "time since diagnosis"
)
glue::glue("#'   \\item{[colname]}{[coldesc]}",
colname = names(vars),
coldesc = vars,
.open = "[",
.close = "]")
## code to prepare `data_layout_3` dataset goes here
usethis::use_data(data_layout_3, overwrite = TRUE)
data_layout_3 <- readr::read_csv("data-raw/data_layout_3.csv")
usethis::use_data(data_layout_3, overwrite = TRUE)
vars <- c(
ID = "participant ID",
PARAMCD = "parameter",
TSTART = "time study start",
TSTOP = "time stop observation",
TGAP = "time gap between events",
STATUS = "status of the event",
SEVENT = "sequence number of event per id",
AGE = "age of the participant",
SEX = "Sex of the participant",
DISEASE_COURSE = "type of disease course",
RACE = "race of the participant",
TIME_SINCE_DIAGNOSIS = "time since diagnosis"
)
glue::glue("#'   \\item{[colname]}{[coldesc]}",
colname = names(vars),
coldesc = vars,
.open = "[",
.close = "]")
devtools::document()
# Load data layout corresponding to the third layout
data("data_layout_1", package = "revents")
data_layout_1 <- revents::data_layout_1
devtools::load_all(".")
devtools::load_all(".")
usethis::use_data(data_layout_1, overwrite = TRUE)
usethis::use_data(data_layout_1, overwrite = TRUE)
source("data-raw/create_data.R")
source("data-raw/create_data.R")
source("data-raw/create_data.R")
library(revents)
devtools::document()
devtools::document()
devtools::document()
# Cargar librerías necesarias
library(here)
# Definir rutas a los archivos CSV
file_path_data_csv_1 <- here::here("data-raw", "data_layout_1.csv")
file_path_data_csv_2 <- here::here("data-raw", "data_layout_2.csv")
file_path_data_csv_3 <- here::here("data-raw", "data_layout_3.csv")
# Leer los archivos CSV
data_layout_1 <- read.csv(file_path_data_csv_1)
data_layout_2 <- read.csv(file_path_data_csv_2)
data_layout_3 <- read.csv(file_path_data_csv_3)
# Guardar los objetos en archivos .rda en el directorio `data`
save(data_layout_1, file = here::here("data", "data_layout_1.rda"))
source("data-raw/create_data.R")
# Cargar librerías necesarias
library(here)
# Definir rutas a los archivos CSV
file_path_data_csv_1 <- here::here("data-raw", "data_layout_1.csv")
file_path_data_csv_2 <- here::here("data-raw", "data_layout_2.csv")
file_path_data_csv_3 <- here::here("data-raw", "data_layout_3.csv")
# Leer los archivos CSV
data_layout_1 <- read.csv(file_path_data_csv_1)
data_layout_2 <- read.csv(file_path_data_csv_2)
data_layout_3 <- read.csv(file_path_data_csv_3)
# Guardar los objetos en archivos .rda en el directorio `data`
save(data_layout_1, file = here::here("data", "data_layout_1.rda"))
save(data_layout_2, file = here::here("data", "data_layout_2.rda"))
save(data_layout_3, file = here::here("data", "data_layout_3.rda"))
source("data-raw/create_data.R")
devtools::document()
devtools::document()
devtools::load_all(".")
?revents::data_layout_1
data("data_layout_1",package = "revents")
usethis::use_data(data_layout_1)
devtools::check_man()
data_layout_1 <- readr::read_csv("data/data_layout_1.csv")
usethis::use_data(data_layout_1, overwrite = TRUE)
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glue::glue("#'   \\item{[colname]}{[coldesc]}",
colname = names(vars),
coldesc = vars,
.open = "[",
.close = "]")
vars <- c(
ID = "participant ID",
PARAMCD = "parameter",
TSTART = "time study start",
TSTOP = "time stop observation",
TGAP = "time gap between events",
STATUS = "status of the event",
SEVENT = "sequence number of event per id",
AGE = "age of the participant",
SEX = "Sex of the participant",
DISEASE_COURSE = "type of disease course",
RACE = "race of the participant",
TIME_SINCE_DIAGNOSIS = "time since diagnosis"
)
glue::glue("#'   \\item{[colname]}{[coldesc]}",
colname = names(vars),
coldesc = vars,
.open = "[",
.close = "]")
devtools::check_man()
devtools::document()
data_layout_2 <- readr::read_csv("data-raw/data_layout_2.csv")
usethis::use_data(data_layout_2, overwrite = TRUE)
data_layout_1 <- readr::read_csv("data-raw/data_layout_1.csv")
usethis::use_data(data_layout_1, overwrite = TRUE)
data_layout_3 <- readr::read_csv("data-raw/data_layout_3.csv")
usethis::use_data(data_layout_3, overwrite = TRUE)
devtools::document()
devtools::document()
devtools::document()
devtools::document()
library(revents)
head(revents::data_layout_1)
# Load data layout corresponding to the third layout
data("data_layout_1", package = "revents")
data_layout_1 <- revents::data_layout_1
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
knitr::opts_chunk$set(warning = FALSE, message = FALSE)
suppressWarnings({
suppressMessages({
library(revents)
library(survival)
library(broom)
library(dplyr)
library(frailtyEM)
})
})
# Load data layout corresponding to the third layout
data("data_layout_1", package = "revents")
data_layout_1 <- revents::data_layout_1
# set scientific notation to FALSE
options(scipen = 999)
cox.relapses <- coxph(Surv(TSTART, TSTOP, STATUS) ~ DISEASE_COURSE + AGE + SEX
+ RACE + TIME_SINCE_DIAGNOSIS, ties = "breslow",
data = subset(data_layout_1, SEVENT == 1))
cox.relapses
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(dplyr)
library(purrr)
library(tibble)
library(reda)
library(tidyr)
library(gtsummary)
library(writexl)
library(kableExtra)
# Set seed for reproducibility
set.seed(123)
# Define a function to simulate recurrent event data using reda
simulate_recurrent_event_data <- function(n, max_event, mean_follow_up_time, max_follow_up_time, mstype, outcome) {
simulate_individual_data <- function(id) {
# Generate baseline hazard times (exponential distribution)
basehaz <- rexp(n = pmax(pmin(round(rnorm(1, max_event/2, max_event/4)), max_event), 1),
rate = 1 / mean_follow_up_time)
basehaz <- basehaz[basehaz < max_follow_up_time]
basehaz <- c(basehaz,max_follow_up_time)
# Create a tibble for the individual's data
tibble(
id = id,
status = c(rep(1, length(basehaz) - 1), 0),
time = basehaz,
mstype = mstype,
outcome = outcome
)
}
# Use purrr::map_dfr to apply the helper function to each individual and combine the results
sim_data_all <- map_dfr(1:n, simulate_individual_data) %>%
arrange(id, time)
# Return the simulated data
return(sim_data_all)
}
# Generate the datasets for relapses in RRMS and SPMS patients
# this parameters have been changed in order to find differences between groups
# just for illustrative purposes
rrms_relapse_data<-simulate_recurrent_event_data(n = 791,
max_event = 10,
mean_follow_up_time = 8,
max_follow_up_time = 10,
mstype = "RRMS",
outcome = "RELAPSE")
spms_relapse_data<-simulate_recurrent_event_data(n = 522,
max_event = 4,
mean_follow_up_time = 5,
max_follow_up_time = 10,
mstype = "SPMS",
outcome = "RELAPSE")
spms_relapse_data$id <- spms_relapse_data$id + 791
# Bind datasets
df <- bind_rows(rrms_relapse_data,
spms_relapse_data)
#Add baaseline characteristics
# Function to generate data for RRMS
generate_rrms_data <- function(n) {
tibble(
id = 1:n,
Age = rnorm(n, mean = 36.5, sd = 9.1),
Sex = factor(rbinom(n, 1, prob = 0.70), labels = c("Male", "Female")),
Race = factor(rbinom(n, 1, prob = 0.88), labels = c("No white", "White")),
Time_since_diagnosis = rlnorm(n, meanlog = log(2), sdlog = log(5/2)),
EDSS_overall = rlnorm(n, meanlog = log(2), sdlog = log(3.5/1.5))
)
}
# Function to generate data for SPMS
generate_spms_data <- function(n) {
tibble(
id = 1:n,
Age = rnorm(n, mean = 49.4, sd = 8.1),
Sex = factor(rbinom(n, 1, prob = 0.63), labels = c("Male", "Female")),
Race = factor(rbinom(n, 1, prob = 0.96), labels = c("No white", "White")),
Time_since_diagnosis = rlnorm(n, meanlog = log(14.5), sdlog = log(22/7.8)), # approximate log-normal
EDSS_overall = rlnorm(n, meanlog = log(6), sdlog = log(6.5/4.5)) # approximate log-normal
)
}
# Generate the datasets
rrms_data <- generate_rrms_data(791)
spms_data <- generate_spms_data(522)
spms_data$id <- spms_data$id + 791
#Merge with the previous part
df_revents <- inner_join(bind_rows(rrms_data, spms_data),df, by="id")
kbl(df_revents[1:10,]) %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed"))
# Save data as CSV
file_path_data_csv <- "C:/Users/david/revents/inst/simulated_data.csv"
write.csv(as.data.frame(df_revents), file_path_data_csv)
usethis::use_data(simulated_data, overwrite = TRUE)
df_revents <- readr::read_csv("data-raw/simulated_data.csv")
usethis::use_data(data_layout_3, overwrite = TRUE)
usethis
usethis::use_r("simulated_data")
devtools::document()
library(revents)
devtools::document()
library(revents)
library(revents)
devtools::document()
devtools::load_all(".")
df_revents <- readr::read_csv("data-raw/simulated_data.csv")
usethis::use_data(data_layout_3, overwrite = TRUE)
usethis::use_data(simulated_data, overwrite = TRUE)
# Cargar librerías necesarias
library(here)
file_path_data_csv_simulated <- here::here("data-raw", "simulated_data.csv")
df_revents <- read.csv(file_path_data_csv_1)
file_path_data_csv_simulated <- here::here("data-raw", "simulated_data.csv")
df_revents <- read.csv(file_path_data_csv_simulated)
save(df_revents, file = here::here("data", "simulated_data.rda"))
devtools::document()
devtools::document()
head(revents::df_revents)
df_revents <- readr::read_csv("data-raw/df_revents.csv")
usethis::use_data(simulated_data, overwrite = TRUE)
usethis::use_data(df_revents, overwrite = TRUE)
df_revents <- readr::read_csv("data-raw/df_revents.csv")
usethis::use_data(df_revents, overwrite = TRUE)
devtools::document()
devtools::load_all(".")
head(revents::df_revents)
library(revents)
# Load the simulated data
data("df_revents", package = "revents")
df_revents <- revents::df_revents
# Load the simulated data
data("df_revents", package = "revents")
df_revents <- revents::df_revents
df_revents <- revents::df_revents
pkgdown::build_articles()
pkgdown::build_site()
pkgdown::build_articles()
pkgdown::build_articles()
usethis::use_pkgdown_github_pages()
devtools::document()
# Find the maximum SEVENT value in your data
max_SEVENT <- max(data_layout_1$SEVENT)
# Create a data frame with all combinations of USUBJID and SEVENT
combinations <- expand.grid(ID = unique(data_layout_1$ID), SEVENT = 1:max_SEVENT)
# Merge the original data frame with all combinations of USUBJID and SEVENT
data_layout_2 <-
merge(combinations, data_layout_1,
by = c("ID", "SEVENT"),
all.x = TRUE
) %>%
arrange(ID, SEVENT) %>%
# select only necessary variables (TGAP are not necessary in this layout)
dplyr::select(-TGAP) %>%
# fill in missing values by repeating the value of the last cell
fill(PARAMCD, TSTART, TSTOP, STATUS, SEVENT, DISEASE_COURSE, SEX, AGE, RACE,
TIME_SINCE_DIAGNOSIS
)
kbl(data_layout_2[1:20,]) %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed"))
kbl(data_layout_2[1:20,]) %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed"))
pkgdown::build_articles()
usethis::use_pkgdown_github_pages()
devtools::document()
vars <- c(
ID = "participant ID",
PARAMCD = "parameter",
TSTART = "time study start",
TSTOP = "time stop observation",
TGAP = "time gap between events",
STATUS = "status of the event",
SEVENT = "sequence number of event per id",
AGE = "age of the participant",
SEX = "Sex of the participant",
DISEASE_COURSE = "type of disease course",
RACE = "race of the participant",
TIME_SINCE_DIAGNOSIS = "time since diagnosis"
)
glue::glue("#'   \\item{[colname]}{[coldesc]}",
colname = names(vars),
coldesc = vars,
.open = "[",
.close = "]")
head(revents::data_layout_2)
head(revents::data_layout_3)