From 7c067063f25e4b17d96f260d8ba7d086d82fd29d Mon Sep 17 00:00:00 2001 From: nfrerebeau Date: Wed, 20 Nov 2024 15:39:15 +0100 Subject: [PATCH] Rename some methods for consistency --- NAMESPACE | 9 ++++++--- R/AllGenerics.R | 18 +++++++++--------- R/arkhe-deprecated.R | 25 +++++++++++++++++++++++-- R/compact.R | 4 ++-- R/discard.R | 4 ++-- R/keep.R | 4 ++-- inst/tinytest/test_compact.R | 10 +++++----- inst/tinytest/test_discard.R | 8 ++++---- inst/tinytest/test_keep.R | 10 +++++----- man/arkhe-deprecated.Rd | 11 ++++++++++- man/compact.Rd | 10 +++++----- man/discard.Rd | 10 +++++----- man/keep.Rd | 10 +++++----- 13 files changed, 83 insertions(+), 50 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 4b405f7..907f3f6 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -34,6 +34,8 @@ export(assert_type) export(assert_unique) export(assert_whole) export(check_class) +export(compact_cols) +export(discard_cols) export(has_colnames) export(has_duplicates) export(has_infinite) @@ -75,6 +77,7 @@ export(is_vector) export(is_warning) export(is_whole) export(is_zero) +export(keep_cols) export(label_percent) export(needs) export(scale_midpoint) @@ -87,7 +90,7 @@ exportMethods(assign_rownames) exportMethods(bootstrap) exportMethods(clean_whitespace) exportMethods(compact) -exportMethods(compact_cols) +exportMethods(compact_columns) exportMethods(compact_rows) exportMethods(confidence_binomial) exportMethods(confidence_mean) @@ -96,7 +99,7 @@ exportMethods(count) exportMethods(describe) exportMethods(detect) exportMethods(discard) -exportMethods(discard_cols) +exportMethods(discard_columns) exportMethods(discard_rows) exportMethods(get_columns) exportMethods(get_rows) @@ -104,7 +107,7 @@ exportMethods(interval_credible) exportMethods(interval_hdr) exportMethods(jackknife) exportMethods(keep) -exportMethods(keep_cols) +exportMethods(keep_columns) exportMethods(keep_rows) exportMethods(math_gcd) exportMethods(math_lcm) diff --git a/R/AllGenerics.R b/R/AllGenerics.R index 18329bd..4c482cc 100644 --- a/R/AllGenerics.R +++ b/R/AllGenerics.R @@ -64,10 +64,10 @@ setGeneric( ) #' @rdname keep -#' @aliases keep_cols-method +#' @aliases keep_columns-method setGeneric( - name = "keep_cols", - def = function(x, ...) standardGeneric("keep_cols") + name = "keep_columns", + def = function(x, ...) standardGeneric("keep_columns") ) #' @rdname keep @@ -95,10 +95,10 @@ setGeneric( ) #' @rdname discard -#' @aliases discard_cols-method +#' @aliases discard_columns-method setGeneric( - name = "discard_cols", - def = function(x, ...) standardGeneric("discard_cols") + name = "discard_columns", + def = function(x, ...) standardGeneric("discard_columns") ) #' @rdname discard @@ -130,10 +130,10 @@ setGeneric( ) #' @rdname compact -#' @aliases compact_cols-method +#' @aliases compact_columns-method setGeneric( - name = "compact_cols", - def = function(x, ...) standardGeneric("compact_cols") + name = "compact_columns", + def = function(x, ...) standardGeneric("compact_columns") ) #' @rdname compact diff --git a/R/arkhe-deprecated.R b/R/arkhe-deprecated.R index e17a6eb..3840069 100644 --- a/R/arkhe-deprecated.R +++ b/R/arkhe-deprecated.R @@ -11,7 +11,28 @@ NULL #' @export #' @rdname arkhe-deprecated -assert_dimensions <- function(x, expected) { +assert_dimensions <- function(...) { # .Deprecated("assert_dim()", old = "assert_dimensions()") - assert_dim(x, expected) + assert_dim(...) +} + +#' @export +#' @rdname arkhe-deprecated +compact_cols <- function(...) { + # .Deprecated("compact_columns()", old = "compact_cols()") + compact_columns(...) +} + +#' @export +#' @rdname arkhe-deprecated +discard_cols <- function(...) { + # .Deprecated("discard_columns()", old = "discard_cols()") + discard_columns(...) +} + +#' @export +#' @rdname arkhe-deprecated +keep_cols <- function(...) { + # .Deprecated("keep_columns()", old = "keep_cols()") + keep_columns(...) } diff --git a/R/compact.R b/R/compact.R index 8a685cf..a34ea19 100644 --- a/R/compact.R +++ b/R/compact.R @@ -24,9 +24,9 @@ setMethod( #' @export #' @rdname compact -#' @aliases compact_cols,ANY-method +#' @aliases compact_columns,ANY-method setMethod( - f = "compact_cols", + f = "compact_columns", signature = c(x = "ANY"), definition = function(x, na.rm = FALSE, verbose = getOption("arkhe.verbose")) { compact(x, margin = 2, na.rm = na.rm, verbose = verbose) diff --git a/R/discard.R b/R/discard.R index eb90edb..526a05d 100644 --- a/R/discard.R +++ b/R/discard.R @@ -36,9 +36,9 @@ setMethod( #' @export #' @rdname discard -#' @aliases discard_cols,ANY-method +#' @aliases discard_columns,ANY-method setMethod( - f = "discard_cols", + f = "discard_columns", signature = c(x = "ANY"), definition = function(x, f, negate = FALSE, all = FALSE, na.rm = FALSE, verbose = getOption("arkhe.verbose"), ...) { diff --git a/R/keep.R b/R/keep.R index ddc3cf1..ff154a8 100644 --- a/R/keep.R +++ b/R/keep.R @@ -36,9 +36,9 @@ setMethod( #' @export #' @rdname keep -#' @aliases keep_cols,ANY-method +#' @aliases keep_columns,ANY-method setMethod( - f = "keep_cols", + f = "keep_columns", signature = c(x = "ANY"), definition = function(x, f, negate = FALSE, all = FALSE, na.rm = FALSE, verbose = getOption("arkhe.verbose"), ...) { diff --git a/inst/tinytest/test_compact.R b/inst/tinytest/test_compact.R index 8090460..5a36c74 100644 --- a/inst/tinytest/test_compact.R +++ b/inst/tinytest/test_compact.R @@ -16,7 +16,7 @@ expect_equal(nrow(clean_row), 4) expect_equal(ncol(clean_row), ncol(mtx0)) ## Remove columns -clean_col <- compact_cols(mtx0) +clean_col <- compact_columns(mtx0) expect_equal(ncol(clean_col), 2) expect_equal(nrow(clean_col), nrow(mtx0)) @@ -38,7 +38,7 @@ expect_equal(nrow(clean_row), 4) expect_equal(ncol(clean_row), ncol(charBlank)) ## Remove columns -clean_col <- compact_cols(charBlank) +clean_col <- compact_columns(charBlank) expect_equal(ncol(clean_col), 2) expect_equal(nrow(clean_col), nrow(charBlank)) @@ -51,7 +51,7 @@ bin <- matrix(c(FALSE, TRUE, TRUE, TRUE, FALSE, ## Nothing to remove clean <- compact_rows(bin) expect_equal(nrow(clean), 4) -clean <- compact_cols(bin) +clean <- compact_columns(bin) expect_equal(ncol(clean), 2) binNA <- bin @@ -66,8 +66,8 @@ expect_equal(nrow(clean_row), 4) expect_equal(ncol(clean_row), ncol(binNA)) ## Remove columns -clean_col <- compact_cols(binNA) # Nothing to remove +clean_col <- compact_columns(binNA) # Nothing to remove expect_equal(dim(clean_col), dim(binNA)) -clean_col <- compact_cols(binNA, na.rm = TRUE) +clean_col <- compact_columns(binNA, na.rm = TRUE) expect_equal(ncol(clean_col), 2) expect_equal(nrow(clean_col), nrow(binNA)) diff --git a/inst/tinytest/test_discard.R b/inst/tinytest/test_discard.R index 292c18c..4e56619 100644 --- a/inst/tinytest/test_discard.R +++ b/inst/tinytest/test_discard.R @@ -9,9 +9,9 @@ expect_message(discard_rows(mtx, f = is_zero, verbose = TRUE)) mtx[1, ] <- 0 # Add zeros ## Nothing to remove -clean <- discard_cols(mtx, f = is_zero, all = TRUE) +clean <- discard_columns(mtx, f = is_zero, all = TRUE) expect_equal(dim(clean), dim(mtx)) -expect_message(discard_cols(mtx, f = is_zero, all = TRUE, verbose = TRUE)) +expect_message(discard_columns(mtx, f = is_zero, all = TRUE, verbose = TRUE)) mtx[, 1] <- 0 # Add zeros @@ -22,7 +22,7 @@ expect_equal(ncol(clean_row), ncol(mtx)) expect_message(discard_rows(mtx, f = is_zero, all = TRUE, verbose = TRUE)) ## Remove columns -clean_col <- discard_cols(mtx, f = is_zero, all = TRUE) +clean_col <- discard_columns(mtx, f = is_zero, all = TRUE) expect_equal(ncol(clean_col), ncol(mtx) - 1L) expect_equal(nrow(clean_col), nrow(mtx)) -expect_message(discard_cols(mtx, f = is_zero, all = TRUE, verbose = TRUE)) +expect_message(discard_columns(mtx, f = is_zero, all = TRUE, verbose = TRUE)) diff --git a/inst/tinytest/test_keep.R b/inst/tinytest/test_keep.R index bf23a6b..56fdedf 100644 --- a/inst/tinytest/test_keep.R +++ b/inst/tinytest/test_keep.R @@ -8,7 +8,7 @@ expect_equal(dim(clean), c(0, 3)) mtx[1, ] <- 0 # Add zeros # Nothing to keep -clean <- keep_cols(mtx, f = is_zero, all = TRUE) +clean <- keep_columns(mtx, f = is_zero, all = TRUE) expect_equal(dim(clean), c(5, 0)) mtx[, 1] <- 0 # Add zeros @@ -18,9 +18,9 @@ clean_row <- keep_rows(mtx, f = is_zero, all = FALSE) expect_equal(clean_row, mtx) expect_message(keep_rows(mtx, f = is_zero, verbose = TRUE)) -clean_col <- keep_cols(mtx, f = is_zero, all = FALSE) +clean_col <- keep_columns(mtx, f = is_zero, all = FALSE) expect_equal(clean_col, mtx) -expect_message(keep_cols(mtx, f = is_zero, verbose = TRUE)) +expect_message(keep_columns(mtx, f = is_zero, verbose = TRUE)) # Remove rows clean_row <- keep_rows(mtx, f = is_zero, all = TRUE) @@ -28,6 +28,6 @@ expect_equal(dim(clean_row), c(1, 3)) expect_message(keep_rows(mtx, f = is_zero, all = TRUE, verbose = TRUE)) # Remove columns -clean_col <- keep_cols(mtx, f = is_zero, all = TRUE) +clean_col <- keep_columns(mtx, f = is_zero, all = TRUE) expect_equal(dim(clean_col), c(5, 1)) -expect_message(keep_cols(mtx, f = is_zero, all = TRUE, verbose = TRUE)) +expect_message(keep_columns(mtx, f = is_zero, all = TRUE, verbose = TRUE)) diff --git a/man/arkhe-deprecated.Rd b/man/arkhe-deprecated.Rd index e0ef7f9..8018820 100644 --- a/man/arkhe-deprecated.Rd +++ b/man/arkhe-deprecated.Rd @@ -3,9 +3,18 @@ \name{arkhe-deprecated} \alias{arkhe-deprecated} \alias{assert_dimensions} +\alias{compact_cols} +\alias{discard_cols} +\alias{keep_cols} \title{Deprecated Functions in arkhe} \usage{ -assert_dimensions(x, expected) +assert_dimensions(...) + +compact_cols(...) + +discard_cols(...) + +keep_cols(...) } \description{ These functions still work but will be removed (defunct) in the next version. diff --git a/man/compact.Rd b/man/compact.Rd index 81162c4..5721af8 100644 --- a/man/compact.Rd +++ b/man/compact.Rd @@ -4,24 +4,24 @@ \name{compact} \alias{compact} \alias{compact-method} -\alias{compact_cols} -\alias{compact_cols-method} +\alias{compact_columns} +\alias{compact_columns-method} \alias{compact_rows} \alias{compact_rows-method} \alias{compact,ANY-method} -\alias{compact_cols,ANY-method} +\alias{compact_columns,ANY-method} \alias{compact_rows,ANY-method} \title{Remove Empty Rows/Columns} \usage{ compact(x, ...) -compact_cols(x, ...) +compact_columns(x, ...) compact_rows(x, ...) \S4method{compact}{ANY}(x, margin = 1, na.rm = FALSE, verbose = getOption("arkhe.verbose")) -\S4method{compact_cols}{ANY}(x, na.rm = FALSE, verbose = getOption("arkhe.verbose")) +\S4method{compact_columns}{ANY}(x, na.rm = FALSE, verbose = getOption("arkhe.verbose")) \S4method{compact_rows}{ANY}(x, na.rm = FALSE, verbose = getOption("arkhe.verbose")) } diff --git a/man/discard.Rd b/man/discard.Rd index 8d58e82..3b2e934 100644 --- a/man/discard.Rd +++ b/man/discard.Rd @@ -4,18 +4,18 @@ \name{discard} \alias{discard} \alias{discard-method} -\alias{discard_cols} -\alias{discard_cols-method} +\alias{discard_columns} +\alias{discard_columns-method} \alias{discard_rows} \alias{discard_rows-method} \alias{discard,ANY-method} \alias{discard_rows,ANY-method} -\alias{discard_cols,ANY-method} +\alias{discard_columns,ANY-method} \title{Remove Rows/Columns Using a Predicate} \usage{ discard(x, ...) -discard_cols(x, ...) +discard_columns(x, ...) discard_rows(x, ...) @@ -40,7 +40,7 @@ discard_rows(x, ...) ... ) -\S4method{discard_cols}{ANY}( +\S4method{discard_columns}{ANY}( x, f, negate = FALSE, diff --git a/man/keep.Rd b/man/keep.Rd index d06d80f..6923852 100644 --- a/man/keep.Rd +++ b/man/keep.Rd @@ -4,18 +4,18 @@ \name{keep} \alias{keep} \alias{keep-method} -\alias{keep_cols} -\alias{keep_cols-method} +\alias{keep_columns} +\alias{keep_columns-method} \alias{keep_rows} \alias{keep_rows-method} \alias{keep,ANY-method} \alias{keep_rows,ANY-method} -\alias{keep_cols,ANY-method} +\alias{keep_columns,ANY-method} \title{Keep Rows/Columns Using a Predicate} \usage{ keep(x, ...) -keep_cols(x, ...) +keep_columns(x, ...) keep_rows(x, ...) @@ -40,7 +40,7 @@ keep_rows(x, ...) ... ) -\S4method{keep_cols}{ANY}( +\S4method{keep_columns}{ANY}( x, f, negate = FALSE,