epiverse-trace · GeraldineGomez · Jul 5, 2023 · Jun 29, 2023 · Jul 4, 2023 · Jul 4, 2023
diff --git a/.gitignore b/.gitignore
@@ -50,3 +50,5 @@ rsconnect/
 
 # macOS hidden files
 .DS_Store
+inst/doc
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,9 +21,12 @@ Imports:
     survival,
     stats
 Suggests: 
+    knitr,
+    rmarkdown,
     spelling,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Config/Needs/website:
     epiverse-trace/epiversetheme
 Language: en-US
+VignetteBuilder: knitr
diff --git a/R/all_data_prep.R b/R/all_data_prep.R
@@ -18,11 +18,15 @@
 #' @return age_group
 #' @examples
 #' \dontrun{
-#' cohortdata <- data.frame()
-#' cohortdata$age.group <- get_age_group(cohortdata, "age", 80, 9)
+#' cohortdata <- data(cohortdata)
+#' cohortdata$age.group <- get_age_group(
+#' data = cohortdata,
+#' col_age = "age",
+#' max_val = 80,
+#' step = 9)
 #' }
 #' @export
-get_age_group <- function(data, col_age, max_val, step, min_val = 0) {
+get_age_group <- function(data, col_age, max_val, min_val = 0, step) {
   n_steps <- as.integer((max_val - min_val) / step) + 1
   limits_low <- c(as.integer(seq(min_val,
                                  max_val,

diff --git a/R/coh_data_wrangling.R b/R/coh_data_wrangling.R
@@ -28,10 +28,10 @@
 #' @examples
 #' \dontrun{
 #' data("cohortdata")
-#' cohortdata$vaccine.status <- set_status(cohortdata,
-#'                                          c("vaccine_date_1",
-#'                                            "vaccine_date_2"),
-#'                                          status = c("v", "u"))
+#' cohortdata$vaccine_status <- set_status(
+#' data = cohortdata,
+#' col_names = c("vaccine_date_1", "vaccine_date_2"),
+#' status = c("v", "u"))
 #' }
 #' @export
 set_status <- function(data,
@@ -99,10 +99,13 @@ set_status <- function(data,
 #' @examples
 #' \dontrun{
 #' data("cohortdata")
-#' cohortdata$immunization.death <- get_immunization_date(cohortdata,
-#' "death_date", 1, 1,
-#' c("vaccine_date_1", "vaccine_date_2"),
-#' "2021-12-31",
+#' cohortdata$immunization_death <- get_immunization_date(
+#' data = cohortdata,
+#' outcome_date_col = "death_date",
+#' outcome_delay = 0,
+#' immunization_delay = 14,
+#' vacc_date_col = c("vaccine_date_1", "vaccine_date_2"),
+#' end_cohort = "2021-12-31",
 #' take_first = FALSE)
 #' }
 #' @export
@@ -176,23 +179,27 @@ get_immunization_date <- function(data,
 #' @param start_from_immunization TRUE: starts counting time-to-event from
 #' immunization date if available
 #' FALSE: starts counting time-to-event from the start date of the cohort study
-#' @param immunization_date_col name of the column that contains the 
+#' @param immunization_date_col name of the column that contains the
 #' immunization date. Required if start_from_immunization = TRUE
 #' @return time-to-event
 #' @examples
 #' \dontrun{
 #' data("cohortdata")
-#' cohortdata$immunization_death <-
-#'   get_immunization_date(cohortdata,
-#'                        "death_date",
-#'                        1,
-#'                        1,
-#'                        c("vaccine_date_1", "vaccine_date_2"),
-#'                        "2021-12-31",
-#'                        take_first = FALSE)
-#' cohortdata$time_to_death <- get_time_to_event(cohortdata, "death_date",
-#'                                             "2021-01-01", "2021-12-31",
-#'                                             TRUE, "immunization_death")
+#' cohortdata$immunization_death <- get_immunization_date(
+#' data = cohortdata,
+#' outcome_date_col = "death_date",
+#' outcome_delay = 0,
+#' immunization_delay = 14,
+#' vacc_date_col = c("vaccine_date_1", "vaccine_date_2"),
+#' end_cohort = "2021-12-31",
+#' take_first = FALSE)
+#' cohortdata$time_to_death <- get_time_to_event(
+#' data = cohortdata,
+#' outcome_date_col = "death_date",
+#' start_cohort = "2021-01-01",
+#' end_cohort = "2021-12-31",
+#' start_from_immunization = TRUE,
+#' immunization_date_col = "immunization_death")
 #' }
 #' @export
 get_time_to_event <- function(data, outcome_date_col,
@@ -254,19 +261,19 @@ get_time_to_event <- function(data, outcome_date_col,
 #' @examples
 #' \dontrun{
 #' data("cohortdata")
-#' cohortdata$immunization.death
-#'     <- get_immunization_date(cohortdata,
-#'                              "death_date",
-#'                              1,
-#'                              1,
-#'                              c("vaccine_date_1", "vaccine_date_2"),
-#'                              "2021-12-31",
-#'                              take_first = FALSE)
-#' cohortdata$immunization_dose <-
-#'       get_immunization_dose(cohortdata,
-#'                             "immunization_death",
-#'                             c("vaccine_date_1", "vaccine_date_2"),
-#'                             immunization_delay = 14)
+#' cohortdata$immunization_death <- get_immunization_date(
+#' data = cohortdata,
+#' outcome_date_col = "death_date",
+#' outcome_delay = 0,
+#' immunization_delay = 14,
+#' vacc_date_col = c("vaccine_date_1", "vaccine_date_2"),
+#' end_cohort = "2021-12-31",
+#' take_first = FALSE)
+#' cohortdata$immunization_dose <- get_immunization_dose(
+#' data = cohortdata,
+#' immunization_date_col = "immunization_death",
+#' vacc_date_col = c("vaccine_date_1", "vaccine_date_2"),
+#' immunization_delay = 14)
 #' }
 #' @export
 get_immunization_dose <- function(data,
@@ -319,20 +326,20 @@ get_immunization_dose <- function(data,
 #' @examples
 #' \dontrun{
 #' data("cohortdata")
-#' cohortdata$immunization_death
-#'   <- get_immunization_date(cohortdata,
-#'                            "death_date",
-#'                            1,
-#'                            1,
-#'                            c("vaccine_date_1","vaccine_date_2"),
-#'                            "2021-12-31",
-#'                            take_first = FALSE)
-#' cohortdata$immunization.vaccine
-#'   <- get_immunization_vaccine(cohortdata,
-#'                               "immunization_death",
-#'                               c("vaccine_date_1", "vaccine_date_2"),
-#'                               c("vaccine_1", "vaccine_2"),
-#'                               immunization_delay = 14)
+#' cohortdata$immunization_death <- get_immunization_date(
+#' data = cohortdata,
+#' outcome_date_col = "death_date",
+#' outcome_delay = 0,
+#' immunization_delay = 14,
+#' vacc_date_col = c("vaccine_date_1", "vaccine_date_2"),
+#' end_cohort = "2021-12-31",
+#' take_first = FALSE)
+#' cohortdata$immunization_vaccine <- get_immunization_vaccine(
+#' data = cohortdata,
+#' immunization_date_col = "immunization_death",
+#' vacc_date_col = c("vaccine_date_1", "vaccine_date_2"),
+#' vacc_name_col = c("vaccine_1", "vaccine_2"),
+#' immunization_delay = 14)
 #' }
 #' @export
 get_immunization_vaccine <- function(data,
@@ -391,4 +398,4 @@ get_immunization_vaccine <- function(data,
   data <- merge(x = data, y = long1, by = "id", all.x = TRUE)
   data <- data[order(data$id), ]
   return(data$vaccine)
-}
+}
diff --git a/R/coh_effectiveness.R b/R/coh_effectiveness.R
@@ -61,12 +61,12 @@ coh_eff_noconf <- function(data,
     ph <- "accept"
   }
   df_summ <- data.frame(HR = hr,
-                        HR.low = ci025,
-                        HR.high = ci975,
-                        V.eff = 1 - hr,
-                        V.eff.low = 1 - ci975,
-                        V.eff.high = 1 - ci025,
+                        HR_low = ci025,
+                        HR_high = ci975,
+                        V_eff = 1 - hr,
+                        V_eff_low = 1 - ci975,
+                        V_eff_high = 1 - ci025,
                         PH = ph,
-                        p.value = p_value)
+                        p_value = p_value)
   return(df_summ)
-}
+}
diff --git a/R/coh_performance.R b/R/coh_performance.R
@@ -49,4 +49,4 @@ coh_test_noconf <- function(data, outcome_status_col,
                         ~ data[[status_vacc_col]])
   test <- survival::cox.zph(cx)
   return(test)
-}
+}
diff --git a/R/cohortdata.R b/R/cohortdata.R
@@ -12,4 +12,4 @@
 #'
 #' @examples
 #' cohortdata
-"cohortdata"
+"cohortdata"
diff --git a/R/screeningdata.R b/R/screeningdata.R
@@ -0,0 +1,15 @@
+#' Screening method data on vaccineff
+#'
+#' Data from
+#'
+#' @docType data
+#'
+#' @usage screeningdata
+#'
+#' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
+#'
+#' @keywords datasets
+#'
+#' @examples
+#' screeningdata
+"screeningdata"
diff --git a/R/testnegdata.R b/R/testnegdata.R
@@ -0,0 +1,15 @@
+#' Test-negative data on vaccineff
+#'
+#' Data from
+#'
+#' @docType data
+#'
+#' @usage testnegdata
+#'
+#' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
+#'
+#' @keywords datasets
+#'
+#' @examples
+#' testnegdata
+"testnegdata"
diff --git a/README.Rmd b/README.Rmd
@@ -22,7 +22,7 @@ knitr::opts_chunk$set(
 MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
 [![Codecov test
 coverage](https://codecov.io/gh/%7B%7B%20gh_repo%20%7D%7D/branch/main/graph/badge.svg)](https://app.codecov.io/gh/%7B%7B%20gh_repo%20%7D%7D?branch=main)
-[![lifecycle-concept](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-concept.svg)](https://www.reconverse.org/lifecycle.html#concept)
+[![lifecycle-experimental](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-experimental.svg)](https://www.reconverse.org/lifecycle.html#concept)
 
 <!-- badges: end -->
 
@@ -43,8 +43,8 @@ You can install the development version of **vaccineff** from
 [GitHub](https://github.com/) with:
 
 ``` r
-if(!require("remotes")) install.packages("remotes")
-remotes::install_github("TRACE-LAC/vaccineff")
+install.packages("remotes")
+remotes::install_github("epiverse-trace/vaccineff")
 ```
 
 ## Quick start
@@ -63,7 +63,6 @@ data("cohortdata")
 head(cohortdata, 5)
 ```
 
-
 ### Contributions
 
 Contributors to the project include:
@@ -76,3 +75,24 @@ Contributors to the project include:
 -   [Santiago Loaiza](https://github.com/santilo9513) (author)
 
 -   [Geraldine Gómez](https://github.com/GeraldineGomez) (contributor)
+
+-   [Jaime A. Pavlich-Mariscal](https://github.com/jpavlich) (contributor)
+
+## Package vignettes
+
+More details on how to use `vaccineff` can be found in the online documentation as package vignettes, under Get Started with vaccineff, Vaccine Effectiveness Models in vaccineff and Vaccine effectiveness Use Cases for vaccineff
+
+## Help
+
+To report a bug please open an [issue](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
+
+## Contribute 
+
+Contributions to `vaccineff` are welcomed. Please follow the [package contributing guide](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
+
+## Code of Conduct
+
+Please note that the `vaccineff` project is released with a [Contributor
+Code of
+Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
+By contributing to this project, you agree to abide by its terms.
diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
 [![Codecov test
 coverage](https://codecov.io/gh/%7B%7B%20gh_repo%20%7D%7D/branch/main/graph/badge.svg)](https://app.codecov.io/gh/%7B%7B%20gh_repo%20%7D%7D?branch=main)
-[![lifecycle-concept](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-concept.svg)](https://www.reconverse.org/lifecycle.html#concept)
+[![lifecycle-experimental](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-experimental.svg)](https://www.reconverse.org/lifecycle.html#concept)
 
 <!-- badges: end -->
 
@@ -28,8 +28,8 @@ You can install the development version of **vaccineff** from
 [GitHub](https://github.com/) with:
 
 ``` r
-if(!require("remotes")) install.packages("remotes")
-remotes::install_github("TRACE-LAC/vaccineff")
+install.packages("remotes")
+remotes::install_github("epiverse-trace/vaccineff")
 ```
 
 ## Quick start
@@ -62,3 +62,30 @@ Contributors to the project include:
 - [Santiago Loaiza](https://github.com/santilo9513) (author)
 
 - [Geraldine Gómez](https://github.com/GeraldineGomez) (contributor)
+
+- [Jaime A. Pavlich-Mariscal](https://github.com/jpavlich) (contributor)
+
+## Package vignettes
+
+More details on how to use `vaccineff` can be found in the online
+documentation as package vignettes, under Get Started with vaccineff,
+Vaccine Effectiveness Models in vaccineff and Vaccine effectiveness Use
+Cases for vaccineff
+
+## Help
+
+To report a bug please open an
+[issue](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
+
+## Contribute
+
+Contributions to `vaccineff` are welcomed. Please follow the [package
+contributing
+guide](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
+
+## Code of Conduct
+
+Please note that the `vaccineff` project is released with a [Contributor
+Code of
+Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
+By contributing to this project, you agree to abide by its terms.
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,3 +1,4 @@
 url: ~
 template:
-  package: epiversetheme
+  bootstrap: 5
+
diff --git a/data/screeningdata.RData b/data/screeningdata.RData
diff --git a/data/testnegdata.RData b/data/testnegdata.RData
diff --git a/inst/extdata/screeningdata.RData b/inst/extdata/screeningdata.RData
diff --git a/inst/extdata/screeningdata.rds b/inst/extdata/screeningdata.rds
diff --git a/inst/extdata/testnegdata.RData b/inst/extdata/testnegdata.RData
diff --git a/inst/extdata/testnegdata.rds b/inst/extdata/testnegdata.rds
diff --git a/man/get_age_group.Rd b/man/get_age_group.Rd