epiverse-trace · davidsantiagoquevedo · Oct 30, 2024 · Oct 1, 2024 · Oct 1, 2024 · Oct 1, 2024
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,55 +2,55 @@ Package: vaccineff
 Title: Estimate Vaccine Effectiveness Based on Different Study Designs
 Version: 0.0.4
 Authors@R: c(
-    person(given = "David Santiago", family = "Quevedo", email = "[email protected]", role = c("aut"),
-        comment = c(ORCID = "0000-0003-1583-4262")),
-    person(given = "Zulma M.", family = "Cucunubá", email = "[email protected]", role = c("aut", "cre"),
-        comment = c(ORCID = "0000-0002-8165-3198")),
-    person("International Development Research Center (IDRC)", role = c("fnd")),
-    person(given = "Geraldine", family = "Gómez Millán", email = "[email protected]", role = c("ctb"),
-        comment = c(ORCID = "0009-0007-8701-0568")),
-    person(given = "Pratik", family = "Gupte", email = "[email protected]", role = c("ctb"), 
-        comment = c(ORCID = "0000-0001-5294-7819")),
-    person(given = "Érika J", family = "Cantor", email = "[email protected]", role = c("ctb"), 
-        comment = c(ORCID = "0000-0003-3320-6032")),
-    person(given = "Santiago", family = "Loaiza", email = "[email protected]", role = c("ctb"),
-        comment = c(ORCID = "0000-0002-2092-3262")),
-    person(given = "Jaime", family = "Pavlich-Mariscal", email = "[email protected]", role = c("ctb"),
+    person("David Santiago", "Quevedo", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0003-1583-4262")),
+    person("Zulma M.", "Cucunubá", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-8165-3198")),
+    person("International Development Research Center (IDRC)", role = "fnd"),
+    person("Geraldine", "Gómez Millán", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0009-0007-8701-0568")),
+    person("Pratik", "Gupte", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0001-5294-7819")),
+    person("Érika J", "Cantor", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0003-3320-6032")),
+    person("Santiago", "Loaiza", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-2092-3262")),
+    person("Jaime", "Pavlich-Mariscal", , "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0002-3892-6680")),
-    person(given = "Hugo", family = "Gruson", email = "[email protected]", role = c("ctb"),
+    person("Hugo", "Gruson", , "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0002-4094-1476")),
-    person(given = "Chris", family = "Hartgerink", email = "[email protected]", role = "ctb",
+    person("Chris", "Hartgerink", , "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0003-1050-6809")),
-    person(given = "Felipe Segundo", family = "Abril", email = "[email protected]", role = "ctb",
+    person("Felipe Segundo", "Abril", , "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0002-2512-4929"))
   )
 Description: Tools for estimating vaccine effectiveness and vaccine related metrics.
 URL: https://github.com/epiverse-trace/vaccineff, https://epiverse-trace.github.io/vaccineff/
 BugReports: https://github.com/epiverse-trace/vaccineff/issues
 License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
 Depends: 
     R (>= 3.5.0)
 Imports: 
-    survival,
-    stats,
     checkmate,
     ggplot2,
-    scales,
-    rlang,
+    linelist,
     MatchIt,
-    linelist
+    rlang,
+    scales,
+    stats,
+    survival
 Suggests: 
     knitr,
+    qtl,
     rmarkdown,
     spelling,
-    testthat (>= 3.0.0),
-    qtl
+    testthat (>= 3.0.0)
+VignetteBuilder: 
+    knitr
+Config/Needs/website:epiverse-trace/epiversetheme
 Config/testthat/edition: 3
-Config/Needs/website:
-    epiverse-trace/epiversetheme
+Encoding: UTF-8
 Language: en-US
-VignetteBuilder: knitr
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2023
+YEAR: 2024
 COPYRIGHT HOLDER: vaccineff authors
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2023 vaccineff authors
+Copyright (c) 2024 vaccineff authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/R/coh_data_wrangling.R b/R/coh_data_wrangling.R
@@ -9,7 +9,7 @@
 #' the other hand, if the logical operator is `|`, it is enough to find one
 #' column with information indicating success. It is recommended to use this
 #' method when working with several outcomes or several vaccine doses. By
-#' default, it returns a binary column where 0 means no outcome or no vaccine
+#' default, it returns a binary column where `0` means no outcome or no vaccine
 #' and `1` means the opposite. However, it can also receive custom
 #' options, e.g., `c("v", "u")` for vaccinated and unvaccinated.
 #'
@@ -297,7 +297,7 @@ adjust_time_to_event <- function(data_set) {
 
   msg <- paste0("\nThe start date of the cohort was defined as",
     " the mininimum immunization date. \n",
-    n0 - nf, " registers were removed with outocomes before the start date.\n"
+    n0 - nf, " registers were removed with outcomes before the start date.\n"
   )
   warning(msg)
 

diff --git a/R/coh_immunization.R b/R/coh_immunization.R
@@ -11,7 +11,7 @@
 #'
 #' The function also works with vaccination information spread across several
 #' columns. If this is the case, the parameter `vacc_date_col` must be passed
-#' as a vector with the names of all the columns to use (see example).
+#' as a vector with the names of all the columns to use.
 #' The function uses by default the latest date found. However, it can also
 #' select the first date by setting `take_first = TRUE`.
 #'
@@ -24,7 +24,7 @@
 #' vaccine selected as immunizing. This information must be passed in the
 #' parameter `vacc_name_col`, as a vector in the same order as `vacc_date_col`.
 #'
-#' @param data_set `data.frame` with cohort information (see example).
+#' @param data_set `data.frame` with cohort information.
 #' @param outcome_date_col Name of the column that contains the outcome dates.
 #' @param censoring_date_col Name of the column that contains the censoring
 #' date. NULL by default.

diff --git a/R/coh_match.R b/R/coh_match.R
@@ -23,7 +23,7 @@
 #' before their outcomes. Rolling calendar matching method will be included in
 #' future releases.
 #'
-#' @param data_set `data.frame` with cohort information (see example).
+#' @param data_set `data.frame` with cohort information.
 #' @param outcome_date_col Name of the column that contains the outcome dates.
 #' @param censoring_date_col Name of the column that contains the censoring
 #' date. `NULL` by default.

diff --git a/R/make_vaccineff_data.R b/R/make_vaccineff_data.R
@@ -4,7 +4,7 @@
 #' `vaccineff_data` that contains all the relevant information for the study.
 #' to estimate the effectiveness.
 #'
-#' @param data_set `data.frame` with cohort information (see example).
+#' @param data_set `data.frame` with cohort information.
 #' @param outcome_date_col Name of the column that contains the outcome dates.
 #' @param censoring_date_col Name of the column that contains the censoring
 #' date. NULL by default.
@@ -101,19 +101,16 @@ make_vaccineff_data <- function(data_set,
         end_cohort = end_cohort,
         take_first = take_first
       )
-    )
-  )
-
-  # Define linelist object
-  cohort_data <- linelist::set_tags(
-    x = cohort_data,
+    ),
+    # here come the ... params
     outcome_date_col = outcome_date_col,
     censoring_date_col = censoring_date_col,
     vacc_date_col = vacc_date_col,
     vacc_name_col = vacc_name_col,
     immunization_date_col = "immunization_date",
     vacc_status_col = "vaccine_status",
     allow_extra = TRUE
+
   )
 
   # Define start date of the cohort

diff --git a/R/utils_coverage.R b/R/utils_coverage.R
@@ -6,7 +6,7 @@
 #' records for some dates, the function assigns 0 instead of NA to calculate
 #' the cumulative coverage.
 #'
-#' @param data_set `data.frame` with cohort information (see example).
+#' @param data_set `data.frame` with cohort information.
 #' @param vacc_date_col Name of the column(s) that contain the vaccine date to
 #' calculate the coverage.
 #' @param unit Aggregation unit, must be either "year", "month", or "day".
@@ -43,7 +43,7 @@ coh_coverage <- function(data_set,
   )
 
   # Create continuous date column
-  # For fixed intervals, use date_intervales
+  # For fixed intervals, use date_intervals
   # In other case use min and max of data_set
   if (is.null(date_interval)) {
     start <- min(data_set[[vacc_date_col]], na.rm = TRUE)

diff --git a/man/adjust_time_to_event.Rd b/man/adjust_time_to_event.Rd
diff --git a/man/check_vaccineff_inputs.Rd b/man/check_vaccineff_inputs.Rd
diff --git a/man/coh_coverage.Rd b/man/coh_coverage.Rd
diff --git a/man/get_immunization_date.Rd b/man/get_immunization_date.Rd
diff --git a/man/get_immunization_dose.Rd b/man/get_immunization_dose.Rd
diff --git a/man/get_immunization_vaccine.Rd b/man/get_immunization_vaccine.Rd
diff --git a/man/get_time_to_event.Rd b/man/get_time_to_event.Rd
diff --git a/man/make_immunization.Rd b/man/make_immunization.Rd
diff --git a/man/make_vaccineff_data.Rd b/man/make_vaccineff_data.Rd
diff --git a/man/match_cohort.Rd b/man/match_cohort.Rd
diff --git a/man/match_cohort_.Rd b/man/match_cohort_.Rd
diff --git a/man/match_pair_info.Rd b/man/match_pair_info.Rd
diff --git a/man/set_event_status.Rd b/man/set_event_status.Rd
diff --git a/man/set_status.Rd b/man/set_status.Rd
diff --git a/man/static_match.Rd b/man/static_match.Rd
diff --git a/man/truncate_time_to_event.Rd b/man/truncate_time_to_event.Rd
diff --git a/vignettes/vaccineff.Rmd b/vignettes/vaccineff.Rmd
@@ -79,7 +79,6 @@ The current release of the package bases the estimation of $VE$ in the cohort de
 The integrated dataset `cohortdata` serves as a minimal example of the package's input. The data is accessed using `data("cohortdata")`.
 
 `vaccineff` has three main functions:
-
 1. `make_vaccineff_data`: This function returns an S3 object of the class `vaccineff_data` with the relevant information for the study. This function also allows to create a matched cohort to control for confounding variables by setting `match = TRUE` and passing the corresponding `exact` and `nearest` arguments.
 `make_vaccineff_data`  supports the method `summary()` to check the characteristics of the cohort, the matching balance and the sizes of matched, excluded, and removed populations.