From 6a664c6dce328d829b91b5018899c39de73df894 Mon Sep 17 00:00:00 2001 From: Hanne Oberman Date: Thu, 23 Nov 2023 10:23:12 +0000 Subject: [PATCH 1/3] Remove double comment sign --- R/ampute.continuous.R | 2 +- R/futuremice.R | 2 +- R/mice-package.R | 3 +-- R/mice.R | 2 +- R/mira.R | 2 +- R/parlmice.R | 2 +- 6 files changed, 6 insertions(+), 7 deletions(-) diff --git a/R/ampute.continuous.R b/R/ampute.continuous.R index 5ae5b7cad..130af4b7a 100644 --- a/R/ampute.continuous.R +++ b/R/ampute.continuous.R @@ -24,7 +24,7 @@ #' @author Rianne Schouten [aut, cre], Gerko Vink [aut], Peter Lugtig [ctb], 2016 #' @seealso \code{\link{ampute}}, \code{\link{ampute.default.type}} #' @references -#' #'Van Buuren, S. (2018). +#' Van Buuren, S. (2018). #' \href{https://stefvanbuuren.name/fimd/sec-linearnormal.html#sec:generateuni}{\emph{Flexible Imputation of Missing Data. Second Edition.}} #' Chapman & Hall/CRC. Boca Raton, FL. #' @keywords internal diff --git a/R/futuremice.R b/R/futuremice.R index 677a7ce2c..4142e8935 100644 --- a/R/futuremice.R +++ b/R/futuremice.R @@ -61,7 +61,7 @@ #' Volker, T.B. and Vink, G. (2022). futuremice: The future starts today. #' \url{https://www.gerkovink.com/miceVignettes/futuremice/Vignette_futuremice.html} #' -#' #'Van Buuren, S. (2018). +#' Van Buuren, S. (2018). #' \href{https://stefvanbuuren.name/fimd/parallel-computation.html}{\emph{Flexible Imputation of Missing Data. Second Edition.}} #' Chapman & Hall/CRC. Boca Raton, FL. #' diff --git a/R/mice-package.R b/R/mice-package.R index 925085be5..42f97159b 100644 --- a/R/mice-package.R +++ b/R/mice-package.R @@ -47,8 +47,7 @@ #' \item \href{https://www.gerkovink.com/miceVignettes/Multi_level/Multi_level_data.html}{Imputing multilevel data} #' \item \href{https://www.gerkovink.com/miceVignettes/Sensitivity_analysis/Sensitivity_analysis.html}{Sensitivity analysis with \pkg{mice}} #' } -#' -#' #'Van Buuren, S. (2018). +#' Van Buuren, S. (2018). #' Boca Raton, FL.: Chapman & Hall/CRC Press. #' The book diff --git a/R/mice.R b/R/mice.R index c89c74616..8bc2d0f02 100644 --- a/R/mice.R +++ b/R/mice.R @@ -110,7 +110,7 @@ #' visited. In that way, deterministic relation between columns will always be #' synchronized. #' -#' #'A new argument \code{ls.meth} can be parsed to the lower level +#' A new argument \code{ls.meth} can be parsed to the lower level #' \code{.norm.draw} to specify the method for generating the least squares #' estimates and any subsequently derived estimates. Argument \code{ls.meth} #' takes one of three inputs: \code{"qr"} for QR-decomposition, \code{"svd"} for diff --git a/R/mira.R b/R/mira.R index 18d826fe5..a8ab50a22 100644 --- a/R/mira.R +++ b/R/mira.R @@ -32,7 +32,7 @@ #' methods and add these to \code{broom} according to the specifications #' given in \url{https://broom.tidymodels.org}. #' -#' #'The \code{mira} class of objects has methods for the +#' The \code{mira} class of objects has methods for the #' following generic functions: \code{print}, \code{summary}. #' #' Many of the functions of the \code{mice} package do not use the diff --git a/R/parlmice.R b/R/parlmice.R index b78748991..e02464fff 100644 --- a/R/parlmice.R +++ b/R/parlmice.R @@ -50,7 +50,7 @@ #' Schouten, R. and Vink, G. (2017). parlmice: faster, paraleller, micer. #' \url{https://www.gerkovink.com/parlMICE/Vignette_parlMICE.html} #' -#' #'Van Buuren, S. (2018). +#' Van Buuren, S. (2018). #' \href{https://stefvanbuuren.name/fimd/parallel-computation.html}{\emph{Flexible Imputation of Missing Data. Second Edition.}} #' Chapman & Hall/CRC. Boca Raton, FL. #' From 3a0651df53c59bcddca06568479105812190650c Mon Sep 17 00:00:00 2001 From: hanneoberman Date: Thu, 23 Nov 2023 12:01:00 +0100 Subject: [PATCH 2/3] Update corresponding `.Rd` files --- man/ampute.continuous.Rd | 2 +- man/futuremice.Rd | 2 +- man/mice.Rd | 5 ++--- man/mira-class.Rd | 2 +- man/parlmice.Rd | 2 +- 5 files changed, 6 insertions(+), 7 deletions(-) diff --git a/man/ampute.continuous.Rd b/man/ampute.continuous.Rd index 3f0c72e9c..590d15828 100644 --- a/man/ampute.continuous.Rd +++ b/man/ampute.continuous.Rd @@ -36,7 +36,7 @@ weighted sum scores, calculated earlier in the multivariate amputation function \code{\link{ampute}}. } \references{ -#'Van Buuren, S. (2018). +Van Buuren, S. (2018). \href{https://stefvanbuuren.name/fimd/sec-linearnormal.html#sec:generateuni}{\emph{Flexible Imputation of Missing Data. Second Edition.}} Chapman & Hall/CRC. Boca Raton, FL. } diff --git a/man/futuremice.Rd b/man/futuremice.Rd index 238f9f8a9..021a4ae99 100644 --- a/man/futuremice.Rd +++ b/man/futuremice.Rd @@ -99,7 +99,7 @@ pool(fit) Volker, T.B. and Vink, G. (2022). futuremice: The future starts today. \url{https://www.gerkovink.com/miceVignettes/futuremice/Vignette_futuremice.html} -#'Van Buuren, S. (2018). +Van Buuren, S. (2018). \href{https://stefvanbuuren.name/fimd/parallel-computation.html}{\emph{Flexible Imputation of Missing Data. Second Edition.}} Chapman & Hall/CRC. Boca Raton, FL. } diff --git a/man/mice.Rd b/man/mice.Rd index 38a9dfbc7..9527966a5 100644 --- a/man/mice.Rd +++ b/man/mice.Rd @@ -287,7 +287,7 @@ to specify \code{visitSequence} such that the column that is imputed by the visited. In that way, deterministic relation between columns will always be synchronized. -#'A new argument \code{ls.meth} can be parsed to the lower level +A new argument \code{ls.meth} can be parsed to the lower level \code{.norm.draw} to specify the method for generating the least squares estimates and any subsequently derived estimates. Argument \code{ls.meth} takes one of three inputs: \code{"qr"} for QR-decomposition, \code{"svd"} for @@ -335,8 +335,7 @@ We suggest going through these vignettes in the following order \item \href{https://www.gerkovink.com/miceVignettes/Multi_level/Multi_level_data.html}{Imputing multilevel data} \item \href{https://www.gerkovink.com/miceVignettes/Sensitivity_analysis/Sensitivity_analysis.html}{Sensitivity analysis with \pkg{mice}} } - -#'Van Buuren, S. (2018). +Van Buuren, S. (2018). Boca Raton, FL.: Chapman & Hall/CRC Press. The book \href{https://stefvanbuuren.name/fimd/}{\emph{Flexible Imputation of Missing Data. Second Edition.}} diff --git a/man/mira-class.Rd b/man/mira-class.Rd index ced37437f..2549106fb 100644 --- a/man/mira-class.Rd +++ b/man/mira-class.Rd @@ -25,7 +25,7 @@ way to solve this problem is to write your own \code{glance()} and \code{tidy()} methods and add these to \code{broom} according to the specifications given in \url{https://broom.tidymodels.org}. -#'The \code{mira} class of objects has methods for the +The \code{mira} class of objects has methods for the following generic functions: \code{print}, \code{summary}. Many of the functions of the \code{mice} package do not use the diff --git a/man/parlmice.Rd b/man/parlmice.Rd index c3ca0f503..84dd6c00e 100644 --- a/man/parlmice.Rd +++ b/man/parlmice.Rd @@ -84,7 +84,7 @@ pool(fit) Schouten, R. and Vink, G. (2017). parlmice: faster, paraleller, micer. \url{https://www.gerkovink.com/parlMICE/Vignette_parlMICE.html} -#'Van Buuren, S. (2018). +Van Buuren, S. (2018). \href{https://stefvanbuuren.name/fimd/parallel-computation.html}{\emph{Flexible Imputation of Missing Data. Second Edition.}} Chapman & Hall/CRC. Boca Raton, FL. } From 47451a2f1f0d3875700b6289624249a1670fb276 Mon Sep 17 00:00:00 2001 From: Hanne Oberman Date: Thu, 23 Nov 2023 13:17:18 +0100 Subject: [PATCH 3/3] `Matrix` dependency in CM check See https://github.com/r-lib/actions/issues/780 --- .github/workflows/R-CMD-check.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a3ac61827..50c48b234 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -41,7 +41,8 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck + extra-packages: any::rcmdcheck, Matrix + pak-version: devel needs: check - uses: r-lib/actions/check-r-package@v2