update calls to epikit

NAMESPACE

@@ -25,6 +25,7 @@ importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_all)
 importFrom(dplyr,ungroup)
+importFrom(epikit,merge_ci_df)
 importFrom(rlang,"!!")
 importFrom(rlang,".data")
 importFrom(rlang,":=")

R/cfr.R

@@ -27,13 +27,15 @@
 #'   the total value across all groups.
 #'
 #' @param digits if `mergeCI = TRUE`, this determines how many digits are printed
-#' 
+#'
 #' @return a data frame with five columns that represent the numerator,
 #'   denominator, rate, lower bound, and upper bound.
 #'
 #'  - `attack_rate()`: cases, population, ar, lower, upper
 #'  - `case_fatality_rate()`: deaths, population, cfr, lower, upper
-#'  
+#'
+#' @importFrom epikit merge_ci_df
+#'
 #' @export
 #'
 #' @rdname attack_rate
@@ -43,13 +45,13 @@
 #' print(ar <- attack_rate(10, 50), digits = 4) # 20% attack rate
 #'
 #' # print them inline using `fmt_ci_df()`
-#' fmt_ci_df(ar)
+#' epikit::fmt_ci_df(ar)
 #'
 #' # Alternatively, if you want one column for the CI, use `mergeCI = TRUE`
 #' attack_rate(10, 50, mergeCI = TRUE, digits = 2) # 20% attack rate
 #'
 #' print(cfr <- case_fatality_rate(1, 100), digits = 2) # CFR of 1%
-#' fmt_ci_df(cfr)
+#' epikit::fmt_ci_df(cfr)
 #'
 #' # using a data frame
 #' if (require("outbreaks")) {
@@ -68,7 +70,7 @@ attack_rate <- function(cases, population, conf_level = 0.95,
   res <- proportion(cases, population, multiplier = multiplier, conf_level = conf_level)
   colnames(res) <- c("cases", "population", "ar", "lower", "upper")
   if (mergeCI == TRUE) {
-    res <- merge_ci_df(res, digits = digits)
+    res <- epikit::merge_ci_df(res, digits = digits)
   }
   res
 }
@@ -80,7 +82,7 @@ case_fatality_rate <- function(deaths, population, conf_level = 0.95,
   res <- proportion(deaths, population, multiplier = multiplier, conf_level = conf_level)
   colnames(res) <- c("deaths", "population", "cfr", "lower", "upper")
   if (mergeCI == TRUE) {
-    res <- merge_ci_df(res, digits = digits)
+    res <- epikit::merge_ci_df(res, digits = digits)
   }
   res
 }
@@ -106,11 +108,11 @@ case_fatality_rate_df <- function(x, deaths, group = NULL, conf_level = 0.95,
   # This creates a list column for the case fatality rate based on the
   # calculated deaths and population before... so this means that
   # THE ORDER OF THE STATEMENTS MATTER
-  # 
+  #
   # Wed Feb 19 09:25:26 2020 ---------------------------------------------
-  # This was modified to count the population for the non-missing cases, 
-  # assuming the deaths columns would either be TRUE, FALSE, or NA for 
-  # a death, recovery, or undetermined. 
+  # This was modified to count the population for the non-missing cases,
+  # assuming the deaths columns would either be TRUE, FALSE, or NA for
+  # a death, recovery, or undetermined.
   res <- dplyr::summarise(
     x,
     !!quote(deaths) := sum(!!qdeath, na.rm = TRUE),
@@ -142,7 +144,7 @@ case_fatality_rate_df <- function(x, deaths, group = NULL, conf_level = 0.95,
       !!qgroup := factor("Total"),
       deaths = tot$deaths,
       population = tot$population,
-      cfr = tot$cfr, 
+      cfr = tot$cfr,
       .name_repair = "minimal"
     )
     # merge CI gives different numbers of columns, this accounts for that.
@@ -166,7 +168,7 @@ mortality_rate <- function(deaths, population, conf_level = 0.95,
   est_label <- paste0("mortality per ", scales::number(multiplier))
   colnames(res) <- c("deaths", "population", est_label, "lower", "upper")
   if (mergeCI == TRUE) {
-    res <- merge_ci_df(res, digits = digits)
+    res <- epikit::merge_ci_df(res, digits = digits)
   }
   res
 }

R/gt_wrappers.R

@@ -1,7 +1,7 @@
-# gtsummary and epikit wrapper functions
+# gtsummary wrapper functions
 
 
-#' An attack rate wrapper function (using gtsummary and epikit packages)that takes
+#' An attack rate wrapper function (using the gtsummary package)that takes
 #' a gtsummary object and returns a gtsummary object with attack rate (per given
 #'  multiple) with 95% confidence interval
 #'
@@ -16,7 +16,7 @@
 #' function (e.g. illness).
 #'
 #'#'@param population the number of individuals in the population, passed to
-#'`epikit::mortality_rate`
+#'`epitabulate::mortality_rate`
 #'
 #' @param ... additional params that may be passed from gtsummary functions.
 #'
@@ -91,7 +91,7 @@ add_mr <- function(gts_object,
   return(gts_object)
 }
 
-#' An attack rate wrapper function (using gtsummary and epikit packages)that takes
+#' An attack rate wrapper function (using the gtsummary package)that takes
 #' a gtsummary object and returns a gtsummary object withattack rate (per given
 #'  multiple) with 95% confidence interval
 #'
@@ -104,12 +104,12 @@ add_mr <- function(gts_object,
 #' function (e.g. illness).
 #'
 #'#'@param population the number of individuals in the population, passed to
-#'`epikit::attack_rate`
+#'`epitabulate::attack_rate`
 #'
 #'@param multiplier The base by which to multiply the output:
 # '1: multiplier = 1: ratio between 0 and 1;
 # '2: multiplier = 100:proportion;
-# '3: multiplier = 10^4: x per 10,000 people; passed to `epikit::attack_rate`
+# '3: multiplier = 10^4: x per 10,000 people; passed to `epitabulate::attack_rate`
 #'
 #' @param ... additional params that may be passed from gtsummary functions.
 #'
@@ -185,7 +185,7 @@ add_ar <- function(gts_object,
 
 
 
-#' An case fatality rate wrapper function (using gtsummary and epikit packages)
+#' An case fatality rate wrapper function (using the gtsummary package)
 #' that takes a gtsummary object and returns a gtsummary object with number
 #' of deaths, case fatality rate, and 95% confidence interval.
 #'
@@ -198,7 +198,7 @@ add_ar <- function(gts_object,
 #'   (e.g. illness).
 #'
 #' @param deaths_var the name of a logical column in the data that indicates that the case died,
-#' is passed as the first argument to `epikit::case_fatality_rate_df`
+#' is passed as the first argument to `epitabulate::case_fatality_rate_df`
 #'
 #' @param ... additional params that may be passed from gtsummary functions.
 #'
@@ -463,7 +463,7 @@ add_crosstabs <- function(
 #' function (e.g. illness).
 #'
 #'#'@param population the number of individuals in the population, passed to
-#'`epikit::mortality_rate`
+#'`epitabulate::mortality_rate`
 #'
 #' @param ... additional params that may be passed from gtsummary functions.
 #'

R/gt_wrappers_internal.R

@@ -2,7 +2,7 @@
 
 #' A case fatality rate wrapper function to be passed to the gtsummary::add_stat
 #' function, which returns a data frame with a single row to be used with
-#' dichotomous data or overall data.Calls epikit::case_fatality_rate_df.
+#' dichotomous data or overall data.Calls epitabulate::case_fatality_rate_df.
 #'
 #' @param data A data frame, passed by the gtsummary::add_stat function.
 #'
@@ -13,7 +13,7 @@
 #'   (eov.g. illness).
 #'
 #' @param deaths_var the name of a logical column in the data that indicates that the case died,
-#' is passed as the first argument to `epikit::case_fatality_rate_df`
+#' is passed as the first argument to `epitabulate::case_fatality_rate_df`
 #'
 #' @param ... additional params that may be passed from gtsummary functions.
 #'
@@ -22,6 +22,9 @@
 #'
 #' @rdname gtsummary_wrappers
 #' @import dplyr
+#' @importFrom epikit merge_ci_df
+#'
+#'
 #'
 add_gt_cfr_stat_label  <- function(data, variable, by, deaths_var, ...) {
 
@@ -32,7 +35,7 @@ add_gt_cfr_stat_label  <- function(data, variable, by, deaths_var, ...) {
   }
 
   stat_new <- data %>%
-    epikit::case_fatality_rate_df(
+    epitabulate::case_fatality_rate_df(
       deaths = data[[deaths_var]],
       mergeCI = TRUE) %>%
     dplyr::mutate(deaths = formatC(deaths, digits = 0, format = "f")) %>%
@@ -47,7 +50,7 @@ add_gt_cfr_stat_label  <- function(data, variable, by, deaths_var, ...) {
 
 #' A case fatality rate wrapper function to be passed to the gtsummary::add_stat function,
 #' which returns a data frame with multiple rows to be used when location is set
-#' to "level" for multi-level categorical data. Calls epikit::case_fatality_rate_df.
+#' to "level" for multi-level categorical data. Calls epitabulate::case_fatality_rate_df.
 #'
 #' @param data A data frame, passed by the gtsummary::add_stat function.
 #'
@@ -81,14 +84,14 @@ add_gt_cfr_stat_level <- function(data, variable, by, deaths_var, ...) {
       dplyr::filter(variable %in% variable & !is.na(stat_0))
     var_levels <- unique(var_dt$label)
 
-    # create rlang::enquo objects to use in epikit::case_fatality_rate_df
+    # create rlang::enquo objects to use in epitabulate::case_fatality_rate_df
     deaths_sym <- as.symbol(deaths_var)
     qdeaths <- rlang::enquo(deaths_sym)
     var_sym <- as.symbol(variable)
     qvariable <- rlang::enquo(var_sym)
 
     stat_new <- data %>%
-      epikit::case_fatality_rate_df(deaths = !!qdeaths, group =  !!qvariable , mergeCI = TRUE) %>%
+      epitabulate::case_fatality_rate_df(deaths = !!qdeaths, group =  !!qvariable , mergeCI = TRUE) %>%
       dplyr::filter(!!qvariable %in% var_levels) %>%
       dplyr::mutate(deaths = formatC(deaths, digits = 0, format = "f")) %>%
       dplyr::mutate(cfr =  formatC(cfr, digits = 2, format = "f")) %>%
@@ -102,7 +105,7 @@ add_gt_cfr_stat_level <- function(data, variable, by, deaths_var, ...) {
 
 #' An attack rate wrapper function to be passed to the gtsummary::add_stat
 #' function, which returns a data frame with a single row to be used with
-#' dichotomous data or overall data. Calls epikit::attack_rate.
+#' dichotomous data or overall data. Calls epitabulate::attack_rate.
 #'
 #' @param data A data frame, passed by the gtsummary::add_stat function.
 #'
@@ -115,7 +118,7 @@ add_gt_cfr_stat_level <- function(data, variable, by, deaths_var, ...) {
 #'@param multiplier The base by which to multiply the output:
 # '1: multiplier = 1: ratio between 0 and 1;
 # '2: multiplier = 100:proportion;
-# '3: multiplier = 10^4: x per 10,000 people; passed to `epikit::attack_rate`
+# '3: multiplier = 10^4: x per 10,000 people; passed to `epitabulate::attack_rate`
 #'
 #'@param drop_total whether or not to include the population column; default TRUE
 #'
@@ -152,7 +155,7 @@ add_gt_attack_rate_stat_label <-
 
   ar_label <- paste0("AR (per ", format(multiplier, big.mark=","), ")")
   cols_rename <- setNames("ar", ar_label)
-  ar <- epikit::attack_rate(cases = cases,
+  ar <- epitabulate::attack_rate(cases = cases,
                             population = population,
                             multiplier = multiplier) %>%
     epikit::merge_ci_df(e = 3) %>%
@@ -180,7 +183,7 @@ add_gt_attack_rate_stat_label <-
 
 #' An attack rate wrapper function to be passed to the gtsummary::add_stat function,
 #' which returns a data frame with multiple rows to be used when location is set
-#' to "level" for multi-level categorical data. Calls epikit::attack_rate.
+#' to "level" for multi-level categorical data. Calls epitabulate::attack_rate.
 #'
 #' @param data A data frame, passed by the gtsummary::add_stat function.
 #'
@@ -193,7 +196,7 @@ add_gt_attack_rate_stat_label <-
 #'@param multiplier The base by which to multiply the output:
 # '1: multiplier = 1: ratio between 0 and 1;
 # '2: multiplier = 100:proportion;
-# '3: multiplier = 10^4: x per 10,000 people; passed to `epikit::attack_rate`
+# '3: multiplier = 10^4: x per 10,000 people; passed to `epitabulate::attack_rate`
 #'
 #' @param ... additional params that may be passed from gtsummary functions.
 #'
@@ -245,7 +248,7 @@ add_gt_attack_rate_level <-
 
   ar_label <- paste0("AR (per ", format(multiplier, big.mark=","), ")")
   cols_rename <- setNames("ar", ar_label)
-  ar <- epikit::attack_rate(cases = counts$case_n,
+  ar <- epitabulate::attack_rate(cases = counts$case_n,
                             population = population,
                             multiplier = multiplier) %>%
     epikit::merge_ci_df(e = 3) %>% # merge the lower and upper CI into one column
@@ -295,7 +298,7 @@ add_gt_mortality_rate_stat_label <-
     deaths <- sum(data[[deaths_var]])
     mr_label <- paste0("MR (per ", format(multiplier, big.mark=","), ")")
     cols_rename <- setNames("mortality per 10 000", mr_label)
-    mr <- epikit::mortality_rate(deaths = deaths,
+    mr <- epitabulate::mortality_rate(deaths = deaths,
                                  population = population,
                                  multiplier = multiplier) %>%
       epikit::merge_ci_df(e = 3) %>%
@@ -325,7 +328,7 @@ add_gt_mortality_rate_stat_label <-
 
 #' A mortality rate wrapper function to be passed to the gtsummary::add_stat function,
 #' which returns a data frame with multiple rows to be used when location is set
-#' to "level" for multi-level categorical data. Calls epikit::attack_rate.
+#' to "level" for multi-level categorical data. Calls epitabulate::attack_rate.
 #'
 #' @param data A data frame, passed by the gtsummary::add_stat function.
 #'
@@ -338,7 +341,7 @@ add_gt_mortality_rate_stat_label <-
 #'@param multiplier The base by which to multiply the output:
 # '1: multiplier = 1: ratio between 0 and 1;
 # '2: multiplier = 100:proportion;
-# '3: multiplier = 10^4: x per 10,000 people; passed to `epikit::attack_rate`
+# '3: multiplier = 10^4: x per 10,000 people; passed to `epitabulate::attack_rate`
 #'
 #' @param ... additional params that may be passed from gtsummary functions.
 #'
@@ -397,7 +400,7 @@ add_gt_mortality_rate_level <- function(data,
 
   mr_label <- paste0("MR (per ", format(multiplier, big.mark=","), ")")
   cols_rename <- setNames("mortality per 10 000", mr_label)
-  mr <- epikit::mortality_rate(deaths = counts$deaths_n,
+  mr <- epitabulate::mortality_rate(deaths = counts$deaths_n,
                                population = population,
                                multiplier = multiplier) %>%
     epikit::merge_ci_df(e = 3) %>% # merge the lower and upper CI into one column