add weighted two arm data (#118)

Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: Isaac Gravestock <83659704+gravesti@users.noreply.github.com>
hta-pharma · Jul 12, 2024 · 24e4a02 · 24e4a02
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Showing 16 changed files with 100 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -40,4 +40,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1.9000
+RoxygenNote: 7.3.2
diff --git a/R/data.R b/R/data.R
@@ -208,6 +208,40 @@
 #' @family anchored datasets
 "centered_ipd_twt"
 
+#' Weighted object for two arm trial data
+#' @format A `maicplus_estimate_weights` object created by [estimate_weights()] containing
+#' \describe{
+#' \item{data}{patient level data with weights}
+#' \item{centered_colnames}{Columns used in MAIC}
+#' \item{nr_missing}{Number of observations with missing data}
+#' \item{ess}{Expected sample size}
+#' \item{opt}{Information from `optim` from weight calculation}
+#' \item{boot}{Parameters and bootstrap sample weights for the 100 samples}
+#' }
+#' @description
+#' The weighted patient data for a two arm trial generated from the centered patient data ([centered_ipd_twt]).
+#' It has weights calculated for 100 bootstrap samples.
+#'
+#' The object is generated using the following code:
+#' ```
+#' estimate_weights(
+#' data = centered_ipd_twt,
+#' centered_colnames = c(
+#' "AGE_CENTERED",
+#' "AGE_MEDIAN_CENTERED",
+#' "AGE_SQUARED_CENTERED",
+#' "SEX_MALE_CENTERED",
+#' "ECOG0_CENTERED",
+#' "SMOKE_CENTERED"
+#' ),
+#' n_boot_iteration = 100
+#' )
+#' ```
+#'
+#' @keywords dataset
+#' @family anchored datasets
+"weighted_twt"
+
 
 if (FALSE) {
  make_roxygen_data <- function(df) {

diff --git a/R/plot_km2.R b/R/plot_km2.R
@@ -198,7 +198,7 @@ basic_kmplot2 <- function(kmlist,
  ylab = endpoint_name,
  legend.title = "Treatment",
  legend = c(0.85, 0.82),
- title = paste0(main_title, "\nEndpoint:", endpoint_name),
+ title = paste0(main_title, "\nEndpoint: ", endpoint_name),
  legend.labs = kmlist_name,
  tables.theme = survminer::theme_cleantable(),
  ggtheme = ggplot2::theme_classic(base_size = 10),

diff --git a/data-raw/dummy_anchored.R b/data-raw/dummy_anchored.R
@@ -73,8 +73,11 @@ agd <- process_agd(agd)
 adsl_twt <- dummize_ipd(adsl_twt, dummize_cols = c("SEX"), dummize_ref_level = c("Female"))
 centered_ipd_twt <- center_ipd(ipd = adsl_twt, agd = agd)
 
+centered_colnames <- paste0(c("AGE", "AGE_MEDIAN", "AGE_SQUARED", "SEX_MALE", "ECOG0", "SMOKE"), "_CENTERED")
+weighted_twt <- estimate_weights(data = centered_ipd_twt, centered_colnames = centered_colnames, n_boot_iteration = 100)
+
 
 ### Output
-usethis::use_data(adsl_twt, adtte_twt, pseudo_ipd_twt, centered_ipd_twt, adrs_twt,
+usethis::use_data(adsl_twt, adtte_twt, pseudo_ipd_twt, centered_ipd_twt, adrs_twt, weighted_twt,
  internal = FALSE, overwrite = TRUE
 )
diff --git a/data/adrs_twt.rda b/data/adrs_twt.rda
diff --git a/data/adsl_twt.rda b/data/adsl_twt.rda
diff --git a/data/adtte_twt.rda b/data/adtte_twt.rda
diff --git a/data/centered_ipd_twt.rda b/data/centered_ipd_twt.rda
diff --git a/data/pseudo_ipd_twt.rda b/data/pseudo_ipd_twt.rda
diff --git a/data/weighted_twt.rda b/data/weighted_twt.rda
diff --git a/man/adsl_twt.Rd b/man/adsl_twt.Rd
diff --git a/man/adtte_twt.Rd b/man/adtte_twt.Rd
diff --git a/man/agd.Rd b/man/agd.Rd
diff --git a/man/centered_ipd_twt.Rd b/man/centered_ipd_twt.Rd
diff --git a/man/pseudo_ipd_twt.Rd b/man/pseudo_ipd_twt.Rd
diff --git a/man/weighted_twt.Rd b/man/weighted_twt.Rd