From a84eb35f0803af6b0296a244804d182455f1e26e Mon Sep 17 00:00:00 2001 From: Aleksander Chlebowski Date: Mon, 23 Oct 2023 14:43:23 +0200 Subject: [PATCH 1/5] improve note in teal_slice --- R/teal_slice.R | 4 +--- man/teal_slice.Rd | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/R/teal_slice.R b/R/teal_slice.R index 053ac1b9d..76b587354 100644 --- a/R/teal_slice.R +++ b/R/teal_slice.R @@ -78,9 +78,7 @@ #' @return A `teal.slice` object. Depending on whether `varname` or `expr` was specified, the resulting #' `teal_slice` also receives class `teal_slice_var` or `teal_slice_expr`, respectively. #' -#' @note When `teal_slice` is printed and contains a `POSIX*t` class in `selected` or `choices` fields, then those -#' fields are converted to `UTC` timezone, for enhanced and unified storage and restoring with `teal::slices_store()` -#' and `teal::slices_restore()`. +#' @note Date time objects of `POSIX*t` classes are printed as strings after converting to UTC timezone. #' #' @examples #' x1 <- teal_slice( diff --git a/man/teal_slice.Rd b/man/teal_slice.Rd index 5de699169..130131f0a 100644 --- a/man/teal_slice.Rd +++ b/man/teal_slice.Rd @@ -122,9 +122,7 @@ Note that a \code{FilterStateExpr} is always considered to have \code{fixed = TR A \code{FilterState} instantiated with \code{anchored = TRUE} cannot be removed. } \note{ -When \code{teal_slice} is printed and contains a \code{POSIX*t} class in \code{selected} or \code{choices} fields, then those -fields are converted to \code{UTC} timezone, for enhanced and unified storage and restoring with \code{teal::slices_store()} -and \code{teal::slices_restore()}. +Date time objects of \code{POSIX*t} classes are printed as strings after converting to UTC timezone. } \section{Filters in \code{SumarizedExperiment} and \code{MultiAssayExperiment} objects}{ From 040fab7211a00465536345954ecf265347596c69 Mon Sep 17 00:00:00 2001 From: Aleksander Chlebowski Date: Mon, 23 Oct 2023 14:44:04 +0200 Subject: [PATCH 2/5] improve note in teal_slices --- R/teal_slices.R | 6 +++--- man/teal_slices.Rd | 5 ++--- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/R/teal_slices.R b/R/teal_slices.R index cfad12948..cd4cbf4b3 100644 --- a/R/teal_slices.R +++ b/R/teal_slices.R @@ -30,9 +30,9 @@ #' @param i (`character` or `numeric` or `logical`) indicating which elements to extract #' @param recursive (`logical(1)`) flag specifying whether to also convert to list the elements of this `teal_slices` #' -#' @note When `teal_slices` are printed and any of `teal_slice` elements contain a `POSIX*t` class in `selected` or -#' `choices` fields, then those fields are converted to `UTC` timezone, for enhanced and unified storage and restoring -#' with `teal::slices_store()` and `teal::slices_restore()`. +#' @note +#' The `teal` package contains robust utilities for saving and loading `teal_slices` in `JSON` format. +#' See [`teal::slices_store`] and [`teal::slices_restore`]. #' #' @return #' `teal_slices`, which is an unnamed list of `teal_slice` objects. diff --git a/man/teal_slices.Rd b/man/teal_slices.Rd index 9658283b1..7fb083fc4 100644 --- a/man/teal_slices.Rd +++ b/man/teal_slices.Rd @@ -84,9 +84,8 @@ Since these could be mutually exclusive, it is impossible to set both allowed an variables for one data set in one \code{teal_slices}. } \note{ -When \code{teal_slices} are printed and any of \code{teal_slice} elements contain a \code{POSIX*t} class in \code{selected} or -\code{choices} fields, then those fields are converted to \code{UTC} timezone, for enhanced and unified storage and restoring -with \code{teal::slices_store()} and \code{teal::slices_restore()}. +The \code{teal} package contains robust utilities for saving and loading \code{teal_slices} in \code{JSON} format. +See \code{\link[teal:slices_store]{teal::slices_store}} and \code{\link[teal:slices_restore]{teal::slices_restore}}. } \examples{ filter_1 <- teal_slice( From 42c69e3e2f2b596ad3771ba8698f26546c7d0913 Mon Sep 17 00:00:00 2001 From: Aleksander Chlebowski Date: Mon, 23 Oct 2023 14:45:26 +0200 Subject: [PATCH 3/5] separate documentation for list_to_teal_slices --- R/teal_slices.R | 7 ++++++- man/list_to_teal_slices.Rd | 15 +++++++++++++++ man/teal_slices.Rd | 3 --- 3 files changed, 21 insertions(+), 4 deletions(-) create mode 100644 man/list_to_teal_slices.Rd diff --git a/R/teal_slices.R b/R/teal_slices.R index cd4cbf4b3..d5800779c 100644 --- a/R/teal_slices.R +++ b/R/teal_slices.R @@ -255,7 +255,12 @@ setdiff_teal_slices <- function(x, y) { } -#' @rdname teal_slices +#' Convert nested list to `teal_slices`. +#' +#' Helper function for converting old style filter specification (nested list) to the new one (`teal_slices`). +#' +#' This function is used internally during deprecation of the old filter panel. +#' #' @export #' @keywords internal #' diff --git a/man/list_to_teal_slices.Rd b/man/list_to_teal_slices.Rd new file mode 100644 index 000000000..a9cc4b7ba --- /dev/null +++ b/man/list_to_teal_slices.Rd @@ -0,0 +1,15 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/teal_slices.R +\name{list_to_teal_slices} +\alias{list_to_teal_slices} +\title{Convert nested list to \code{teal_slices}.} +\usage{ +list_to_teal_slices(x) +} +\description{ +Helper function for converting old style filter specification (nested list) to the new one (\code{teal_slices}). +} +\details{ +This function is used internally during deprecation of the old filter panel. +} +\keyword{internal} diff --git a/man/teal_slices.Rd b/man/teal_slices.Rd index 7fb083fc4..2154439cb 100644 --- a/man/teal_slices.Rd +++ b/man/teal_slices.Rd @@ -9,7 +9,6 @@ \alias{c.teal_slices} \alias{format.teal_slices} \alias{print.teal_slices} -\alias{list_to_teal_slices} \title{Complete filter specification.} \usage{ teal_slices( @@ -33,8 +32,6 @@ as.teal_slices(x) \method{format}{teal_slices}(x, show_all = FALSE, trim_lines = TRUE, ...) \method{print}{teal_slices}(x, ...) - -list_to_teal_slices(x) } \arguments{ \item{...}{any number of \code{teal_slice} objects. For \code{print} and \code{format}, From e817ec14b44d9777de86039b09ed7fdfeab3e295 Mon Sep 17 00:00:00 2001 From: Aleksander Chlebowski Date: Mon, 23 Oct 2023 14:45:49 +0200 Subject: [PATCH 4/5] fix documentation for coalesce_r --- R/teal_slices.R | 2 +- man/coalesce_r.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/teal_slices.R b/R/teal_slices.R index d5800779c..830219d6e 100644 --- a/R/teal_slices.R +++ b/R/teal_slices.R @@ -348,7 +348,7 @@ list_to_teal_slices <- function(x) { # nolint #' #' This function is used internally in `c.teal_slices` to manage `teal_slices` attributes. #' -#' @param `list`, either of atomic vectors or of `named list`s +#' @param x `list`, either of atomic vectors or of `named list`s #' @return #' Either an atomic vector of length 1 or a (potentially nested) list. #' diff --git a/man/coalesce_r.Rd b/man/coalesce_r.Rd index 20ce2d720..ecf8dfa09 100644 --- a/man/coalesce_r.Rd +++ b/man/coalesce_r.Rd @@ -7,7 +7,7 @@ coalesce_r(x) } \arguments{ -\item{`list`, }{either of atomic vectors or of \verb{named list}s} +\item{x}{\code{list}, either of atomic vectors or of \verb{named list}s} } \value{ Either an atomic vector of length 1 or a (potentially nested) list. From 9bfff406bd95338cb1e83253e2a6c4a78d37795c Mon Sep 17 00:00:00 2001 From: Aleksander Chlebowski Date: Mon, 23 Oct 2023 14:46:03 +0200 Subject: [PATCH 5/5] sort WORDLIST --- inst/WORDLIST | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/inst/WORDLIST b/inst/WORDLIST index 3cb668a0d..0a154e285 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,11 +1,11 @@ +cloneable Forkers +funder Hoffmann MultiAssayExperiment -UI -cloneable -funder programmatically repo reproducibility subclasses subtype +UI