vignette update)

.Rhistory

@@ -297,3 +297,193 @@ 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()

.Rproj.user/EC080363/rmd-outputs

@@ -1,5 +1,9 @@
-C:/Users/david/AppData/Local/Temp/RtmpohDzTZ/preview-471c12a9367.dir/count_based_models.html
-C:/Users/david/AppData/Local/Temp/RtmpohDzTZ/preview-471c371a2884.dir/marginal_models.html
-C:/Users/david/AppData/Local/Temp/RtmpohDzTZ/preview-471c7d1c4e9c.dir/event_specific_estimates.html
-C:/Users/david/AppData/Local/Temp/RtmpohDzTZ/preview-471c27c6406d.dir/simulated_data.html
+C:/Users/david/AppData/Local/Temp/Rtmpqo9Cld/preview-46182e5b13b8.dir/revents.html
+C:/Users/david/AppData/Local/Temp/Rtmpqo9Cld/preview-46185e227c7e.dir/database_layout.html
+C:/Users/david/AppData/Local/Temp/Rtmpqo9Cld/preview-406846c43cc0.html
+C:/Users/david/AppData/Local/Temp/Rtmpqo9Cld/preview-461817351a80.dir/revents.html
+C:/Users/david/AppData/Local/Temp/Rtmpqo9Cld/preview-46183c38ffe.dir/simulated_data.html
+
+
+
 

.Rproj.user/EC080363/sources/prop/E8B9DAAB

@@ -1,6 +1,6 @@
 {
     "source_window_id": "",
     "Source": "Source",
-    "cursorPosition": "16,20",
-    "scrollLine": "0"
+    "cursorPosition": "11,20",
+    "scrollLine": "4"
 }

.Rproj.user/shared/notebooks/paths

@@ -4,7 +4,6 @@ C:/Users/david/revents/NAMESPACE="F578CE44"
 C:/Users/david/revents/R/data_layout.R="CC5DC09A"
 C:/Users/david/revents/R/df_revents.R="11165C0E"
 C:/Users/david/revents/README.Rmd="8A2B2F00"
-C:/Users/david/revents/_pkgdown.yml="DD6EAD8E"
 C:/Users/david/revents/data-raw/data_layout_1.R="2B6C7008"
 C:/Users/david/revents/data-raw/data_layout_2.R="8D82ED10"
 C:/Users/david/revents/data-raw/data_layout_3.R="7CDD99B3"

R/data_layout.R

@@ -1,22 +1,52 @@
 #' Datos layout_1 for conditional and marginal rates models
 #'
-#'
+#'   \item{ID}{participant ID}
+#'   \item{PARAMCD}{parameter}
+#'   \item{TSTART}{time study start}
+#'   \item{TSTOP}{time stop observation}
+#'   \item{TGAP}{time gap between events}
+#'   \item{STATUS}{status of the event}
+#'   \item{SEVENT}{sequence number of event per id}
+#'   \item{AGE}{age of the participant}
+#'   \item{SEX}{Sex of the participant}
+#'   \item{DISEASE_COURSE}{type of disease course}
+#'   \item{RACE}{race of the participant}
+#'   \item{TIME_SINCE_DIAGNOSIS}{time since diagnosis}#'
 #'
 #' @format Un data frame con 6347 rows y 13 columns.
 #' @source data simulated from MSOAC parameters
 "data_layout_1"
 
 #' Data layout_2 for marginal hazard models
 #'
-#'
+#'   \item{ID}{participant ID}
+#'   \item{PARAMCD}{parameter}
+#'   \item{TSTART}{time study start}
+#'   \item{TSTOP}{time stop observation}
+#'   \item{TGAP}{time gap between events}
+#'   \item{STATUS}{status of the event}
+#'   \item{SEVENT}{sequence number of event per id}
+#'   \item{AGE}{age of the participant}
+#'   \item{SEX}{Sex of the participant}
+#'   \item{DISEASE_COURSE}{type of disease course}
+#'   \item{RACE}{race of the participant}
+#'   \item{TIME_SINCE_DIAGNOSIS}{time since diagnosis}
 #'
 #' @format a data frame with con 15765 rows y 12 columns.
 #' @source data simulated from MSOAC parameters
 "data_layout_2"
 
 #' Data layout_3 for count-based models
 #'
-#'
+#'   \item{ID}{participant ID}
+#'   \item{PARAMCD}{parameter}
+#'   \item{COUNT}{number of confirmed events}
+#'   \item{SEVENT}{sequence number of event per id}
+#'   \item{AGE}{age of the participant}
+#'   \item{SEX}{Sex of the participant}
+#'   \item{DISEASE_COURSE}{type of disease course}
+#'   \item{RACE}{race of the participant}
+#'   \item{TIME_SINCE_DIAGNOSIS}{time since diagnosis}
 #'
 #' @format Un data frame con 1313 rows y 9 columns.
 #' @source data simulated from MSOAC parameters