diff --git a/DESCRIPTION b/DESCRIPTION index 8edd6a5..3e61a9b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: beeca Title: Binary Endpoint Estimation with Covariate Adjustment -Version: 0.1.2 +Version: 0.1.3 Authors@R: c(person(given = "Alex", family = "Przybylski", @@ -24,11 +24,11 @@ Authors@R: email = "dominic.magirr@novartis.com", role = c("aut") )) -Description: A lightweight package to perform estimation of marginal treatment - effects for binary outcomes when using logistic regression working models with - covariate adjustment (see discussions in Magirr et al (2024) ). Implements the variance estimators of - Ge et al (2011) and - Ye et al (2023) . +Description: Performs estimation of marginal treatment effects for binary + outcomes when using logistic regression working models with covariate + adjustment (see discussions in Magirr et al (2024) ). + Implements the variance estimators of Ge et al (2011) + and Ye et al (2023) . Maintainer: Alex Przybylski License: LGPL (>= 3) Encoding: UTF-8 diff --git a/NAMESPACE b/NAMESPACE index 41614af..0d6a44d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -7,6 +7,7 @@ export(average_predictions) export(estimate_varcov) export(get_marginal_effect) export(predict_counterfactuals) +export(sanitize_model) importFrom(dplyr,as_tibble) importFrom(lifecycle,deprecated) importFrom(stats,cov) diff --git a/NEWS.md b/NEWS.md index bee6334..695bee7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# beeca 0.1.2 +# beeca 0.1.3 - Preparation for CRAN submission diff --git a/R/sanitize.R b/R/sanitize.R index 9ff654d..018e853 100644 --- a/R/sanitize.R +++ b/R/sanitize.R @@ -15,6 +15,7 @@ #' @param ... arguments passed to or from other methods. #' @return if model is non-compliant will throw warnings or errors. #' @keywords internal +#' @export sanitize_model <- function(model, ...) { UseMethod("sanitize_model") } @@ -27,10 +28,11 @@ sanitize_model <- function(model, ...) { #' @importFrom stats model.frame model.matrix terms #' @keywords internal #' @export -#' @examples \dontrun{ +#' @examples +#' trial01$trtp <- factor(trial01$trtp) #' fit1 <- glm(aval ~ trtp + bl_cov, family = "binomial", data = trial01) -#' sanitize_model(fit1, "trtp") -#' } +#' fit1 <- sanitize_model(fit1, "trtp") +#' sanitize_model.glm <- function(model, trt, ...) { # sanitize variable sanitize_variable(model, trt) diff --git a/cran-comments.md b/cran-comments.md index 936fa8f..e670830 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -2,15 +2,15 @@ This is a resubmission. In this version I have: -* Corrected URLs, DOIs, ORCID identifiers +* Updated the description to avoid starting with "A lightweight package..." -* Registered S3 methods +* Removed unnecessary \dontrun{} wrapper for an example ## R CMD check results 0 errors | 0 warnings | 1 note -I am aware of one possible note: The suggested package 'margins' was very recently reinstated to CRAN and binaries may not be available for certain platforms / R versions. At time of submission it is not available for Windows r-devel. +I am aware of one possible note: The suggested package 'margins' was very recently reinstated to CRAN and binaries may not be available for certain platforms / R versions. ``` * checking package dependencies ... NOTE diff --git a/man/beeca-package.Rd b/man/beeca-package.Rd index b17e96f..a137665 100644 --- a/man/beeca-package.Rd +++ b/man/beeca-package.Rd @@ -6,7 +6,7 @@ \alias{beeca-package} \title{beeca: Binary Endpoint Estimation with Covariate Adjustment} \description{ -A lightweight package to perform estimation of marginal treatment effects for binary outcomes when using logistic regression working models with covariate adjustment (see discussions in Magirr et al (2024) \url{https://osf.io/9mp58/}). Implements the variance estimators of Ge et al (2011) \doi{10.1177/009286151104500409} and Ye et al (2023) \doi{10.1080/24754269.2023.2205802}. +Performs estimation of marginal treatment effects for binary outcomes when using logistic regression working models with covariate adjustment (see discussions in Magirr et al (2024) \url{https://osf.io/9mp58/}). Implements the variance estimators of Ge et al (2011) \doi{10.1177/009286151104500409} and Ye et al (2023) \doi{10.1080/24754269.2023.2205802}. } \seealso{ Useful links: diff --git a/man/sanitize_model.glm.Rd b/man/sanitize_model.glm.Rd index 9494433..d342b18 100644 --- a/man/sanitize_model.glm.Rd +++ b/man/sanitize_model.glm.Rd @@ -20,9 +20,9 @@ if model is non-compliant will throw warnings or errors. (internal) Sanitize a glm model } \examples{ -\dontrun{ +trial01$trtp <- factor(trial01$trtp) fit1 <- glm(aval ~ trtp + bl_cov, family = "binomial", data = trial01) -sanitize_model(fit1, "trtp") -} +fit1 <- sanitize_model(fit1, "trtp") + } \keyword{internal}