Address CRAN comments

Author: NightlordTW

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SimTOST
 Title: Sample Size Estimation for Bio-Equivalence Trials Through Simulation
-Version: 1.0.0
+Version: 1.0.1
 Authors@R: c(
     person(given = "Thomas", 
            family = "Debray", 
@@ -29,7 +29,17 @@ Authors@R: c(
            role = c("ctb")),
     person("Biogen Inc", role = c("cph", "fnd"))
     )
-Description: Conducts sample size estimation for bio-equivalence trials using the Two One-Sided Tests procedure. A simulation-based approach enables flexible hypothesis testing, supports multiple treatments, and accommodates correlated endpoints.
+Description: 
+    Sample size estimation for bio-equivalence trials is supported through a simulation-based approach 
+    that extends the Two One-Sided Tests (TOST) procedure. The methodology provides flexibility in 
+    hypothesis testing, accommodates multiple treatment comparisons, and accounts for correlated endpoints. 
+    Users can model complex trial scenarios, including parallel and crossover designs, intra-subject variability, 
+    and different equivalence margins. Monte Carlo simulations enable accurate estimation of power and type I error 
+    rates, ensuring well-calibrated study designs. The statistical framework builds on established methods for 
+    equivalence testing and multiple hypothesis testing in bio-equivalence studies, as described in Schuirmann (1987) 
+    <doi:10.1007/BF01068419>, Mielke et al. (2018) <doi:10.1080/19466315.2017.1371071>, Shieh (2022) 
+    <doi:10.1371/journal.pone.0269128>, and Sozu et al. (2015) <doi:10.1007/978-3-319-22005-5>. 
+    Comprehensive documentation and vignettes guide users through implementation and interpretation of results.
 License: Apache License (== 2.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,4 +1,8 @@
+# SimTOST 1.0.1
+- Fixed CRAN review issues: expanded description, added references, documented function outputs.
+
 # SimTOST 1.0.0
+* Initial CRAN submission.
 
 # SimTOST 0.6.0
 
@@ -12,4 +16,4 @@
 
 # SimTOST 0.1.0
 
-* Initial CRAN submission.
+

R/SampleSize.R

@@ -54,9 +54,21 @@
 #' }
 #'
 #' @references
-#' Mielke, J., Jones, B., Jilma, B., & König, F. (2018). Sample size for multiple hypothesis testing in biosimilar development. \emph{Statistics in Biopharmaceutical Research, 10}(1), 39-49.
+#' Schuirmann, D. J. (1987). A comparison of the Two One-Sided Tests procedure and the
+#' Power approach for assessing the equivalence of average bioavailability.
+#' \emph{Journal of Pharmacokinetics and Biopharmaceutics, 15}(6), 657-680.
+#' <doi:10.1007/BF01068419>
 #'
-#' Berger, R. L., & Hsu, J. C. (1996). Bioequivalence trials, intersection-union tests, and equivalence confidence sets. \emph{Statistical Science}, 283-302.
+#' Mielke, J., Jones, B., Jilma, B., & König, F. (2018). Sample size for multiple hypothesis
+#' testing in biosimilar development. \emph{Statistics in Biopharmaceutical Research, 10}(1), 39-49.
+#' <doi:10.1080/19466315.2017.1371071>
+#'
+#' Berger, R. L., & Hsu, J. C. (1996). Bioequivalence trials, intersection-union tests, and
+#' equivalence confidence sets. \emph{Statistical Science}, 283-302.
+#'
+#' Sozu, T., Sugimoto, T., Hamasaki, T., & Evans, S. R. (2015). "Sample Size Determination in
+#' Clinical Trials with Multiple Endpoints." \emph{SpringerBriefs in Statistics}.
+#' <doi:10.1007/978-3-319-22005-5>
 #'
 #' @author Johanna Muñoz \email{johanna.munoz@fromdatatowisdom.com}
 #'

R/helper.r

@@ -1,12 +1,26 @@
-#' Display the summary results of the sample size estimation
+#' Print Summary of Sample Size Estimation
+#'
+#' @description
+#' Prints the summary results of the sample size estimation for bioequivalence trials,
+#' including achieved power, total sample size, and power confidence intervals.
+#' The function also details the study design, primary endpoint comparisons,
+#' and applied multiplicity corrections.
+#'
 #' @details
-#' This function displays the summary results of the sample size estimation.
+#' This function displays key metrics from a sample size estimation analysis.
+#' It provides an overview of the study design, treatment comparisons,
+#' tested endpoints, significance level adjustments, and estimated sample size.
+#' For studies with multiple primary endpoints, it describes the multiplicity correction applied.
 #'
+#' @param x An object of class `"simss"`, typically generated by a sample size estimation function.
+#' @param ... Optional arguments to be passed from or to other methods.
+#'
+#' @return No return value, called for side effects. The function prints the summary results
+#' of the sample size estimation to the console in a structured format.
 #'
-#' @param x An object of class "simss"
-#' @param ...  Optional arguments to be passed from or to other methods.
 #' @author
 #' Thomas Debray \email{tdebray@fromdatatowisdom.com}
+#'
 #' @method print simss
 #' @export
 print.simss <- function(x, ...) {

README.Rmd

@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/smartdata-analysis-and-statistics/SimTOST/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/smartdata-analysis-and-statistics/SimTOST/actions/workflows/R-CMD-check.yml)
 [![CRAN status](https://www.r-pkg.org/badges/version/SimTOST)](https://CRAN.R-project.org/package=SimTOST)
-[![Codecov test coverage](https://codecov.io/gh/smartdata-analysis-and-statistics/SimTOST/branch/main/graph/badge.svg)](https://app.codecov.io/gh/smartdata-analysis-and-statistics/SimTOST?branch=main)
+[![metacran downloads](https://cranlogs.r-pkg.org/badges/last-month/SimTOST)](https://cran.r-project.org/package=SimTOST)
 <!-- badges: end -->
 
 `SimTOST` is an R package specifically designed for bioequivalence studies, providing simulation-based sample size estimation for the Two One-Sided Tests (TOST) procedure. It offers flexible options to handle complex study designs, including trials with multiple correlated primary endpoints, multiple hypotheses, and treatment arms. By incorporating correlations between endpoints, `SimTOST` ensures accurate and robust planning of bioequivalence trials, making it a powerful tool for studies with intricate requirements.

README.md

@@ -8,8 +8,8 @@
 [![R-CMD-check](https://github.com/smartdata-analysis-and-statistics/SimTOST/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/smartdata-analysis-and-statistics/SimTOST/actions/workflows/R-CMD-check.yml)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/SimTOST)](https://CRAN.R-project.org/package=SimTOST)
-[![Codecov test
-coverage](https://codecov.io/gh/smartdata-analysis-and-statistics/SimTOST/branch/main/graph/badge.svg)](https://app.codecov.io/gh/smartdata-analysis-and-statistics/SimTOST?branch=main)
+[![metacran
+downloads](https://cranlogs.r-pkg.org/badges/last-month/SimTOST)](https://cran.r-project.org/package=SimTOST)
 <!-- badges: end -->
 
 `SimTOST` is an R package specifically designed for bioequivalence