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refactor: Rename normalization flags to normalized #2862

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refactor: Rename normalization flags to normalized #2862

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49 changes: 35 additions & 14 deletions R/centrality.R
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Original file line number Diff line number Diff line change
Expand Up @@ -233,6 +233,8 @@ edge.betweenness <- function(
#' `bonpow()` was renamed to [power_centrality()] to create a more
#' consistent API.
#' @inheritParams power_centrality
#' @param rescale `r lifecycle::badge("deprecated")` Use `normalized` in
#' [power_centrality()] instead.
#' @keywords internal
#' @export
bonpow <- function(
Expand All @@ -251,7 +253,7 @@ bonpow <- function(
nodes = nodes,
loops = loops,
exponent = exponent,
rescale = rescale,
normalized = rescale,
tol = tol,
sparse = sparse
)
Expand Down Expand Up @@ -1719,7 +1721,7 @@ diversity <- function(
#' scores are the same as authority scores.
#'
#' @param graph The input graph.
#' @param scale Logical, whether to scale the result to have a maximum
#' @param normalized Logical, whether to scale the result to have a maximum
#' score of one. If no scaling is used then the result vector has unit length
#' in the Euclidean norm.
#' @param weights Optional positive weight vector for calculating weighted
Expand All @@ -1729,6 +1731,7 @@ diversity <- function(
#' edges are effectively added up.
#' @param options A named list, to override some ARPACK options. See
#' [arpack()] for details. The default `NULL` uses [arpack_defaults()].
#' @param scale `r lifecycle::badge("deprecated")` Use `normalized` instead.
#' @inheritParams rlang::args_dots_empty
#' @return A named list with members:
#' \describe{
Expand Down Expand Up @@ -1766,19 +1769,35 @@ diversity <- function(
hits_scores <- function(
graph,
...,
scale = TRUE,
normalized = TRUE,
weights = NULL,
options = NULL
options = NULL,
scale = deprecated()
) {
rlang::check_dots_empty()

if (lifecycle::is_present(scale)) {
if (!missing(normalized)) {
cli::cli_abort(c(
"Argument {.arg normalized} of {.fn hits_scores} was supplied more than once.",
i = "It was also supplied via its legacy name {.arg scale}."
))
}
lifecycle::deprecate_soft(
"3.0.0",
"hits_scores(scale = )",
"hits_scores(normalized = )"
)
normalized <- scale
}

if (is.null(options)) {
options <- arpack_defaults()
}

hub_and_authority_scores_impl(
graph = graph,
scale = scale,
scale = normalized,
weights = weights,
options = options
)
Expand Down Expand Up @@ -1810,7 +1829,7 @@ authority_score <- function(

scores <- hits_scores(
graph = graph,
scale = scale,
normalized = scale,
weights = weights,
options = options
)
Expand Down Expand Up @@ -1855,7 +1874,7 @@ hub_score <- function(

scores <- hits_scores(
graph = graph,
scale = scale,
normalized = scale,
weights = weights,
options = options
)
Expand Down Expand Up @@ -2266,7 +2285,7 @@ bonpow.sparse <- function(
#' loops. `loops` is `FALSE` by default.
#' @param exponent exponent (decay rate) for the Bonacich power centrality
#' score; can be negative
#' @param rescale if true, centrality scores are rescaled such that they sum to
#' @param normalized if true, centrality scores are rescaled such that they sum to
#' 1.
#' @param tol tolerance for near-singularities during matrix inversion (see
#' [solve()])
Expand Down Expand Up @@ -2325,14 +2344,16 @@ power_centrality <- function(
...,
loops = FALSE,
exponent = 1,
rescale = FALSE,
normalized = FALSE,
tol = 1e-7,
sparse = TRUE,
weights = NULL
) {
# BEGIN GENERATED ARG_HANDLE: power_centrality, do not edit, see tools/generate-migrations.R
# fmt: skip
if (...length() > 0L) {
.arg_forbidden <- base::intersect(base::names(base::sys.call()), base::c("n", "no"))
if (base::length(.arg_forbidden) > 0L) cli::cli_abort(base::c("Argument {.arg {(.arg_forbidden)}} matches multiple formal arguments of {.fn power_centrality}.", i = "Spell out the full argument name."))
# Pre-3.0.0 signature: power_centrality(graph, nodes, loops, exponent, rescale, tol, sparse, weights)
.old_signature <- function(loops, exponent, rescale, tol, sparse, weights, ...) {
if (...length() > 0L) {
Expand All @@ -2344,7 +2365,7 @@ power_centrality <- function(
base::c(
if (!base::missing(loops)) base::list(loops = loops),
if (!base::missing(exponent)) base::list(exponent = exponent),
if (!base::missing(rescale)) base::list(rescale = rescale),
if (!base::missing(rescale)) base::list(normalized = rescale),
if (!base::missing(tol)) base::list(tol = tol),
if (!base::missing(sparse)) base::list(sparse = sparse),
if (!base::missing(weights)) base::list(weights = weights)
Expand All @@ -2356,7 +2377,7 @@ power_centrality <- function(
.arg_conflict <- base::intersect(.arg_names, base::c(
if (!base::missing(loops)) "loops",
if (!base::missing(exponent)) "exponent",
if (!base::missing(rescale)) "rescale",
if (!base::missing(normalized)) "normalized",
if (!base::missing(tol)) "tol",
if (!base::missing(sparse)) "sparse",
if (!base::missing(weights)) "weights"
Expand All @@ -2367,7 +2388,7 @@ power_centrality <- function(
"3.0.0",
what = base::I("Calling `power_centrality()` with positional or abbreviated arguments"),
details = base::c(
i = base::paste0("Detected call: power_centrality(", base::paste(base::c("graph", "nodes", .arg_names), collapse = ", "), ")"),
i = base::paste0("Detected call: power_centrality(", base::paste(base::c("graph", "nodes", base::c(loops = "loops", exponent = "exponent", normalized = "rescale", tol = "tol", sparse = "sparse", weights = "weights")[.arg_names]), collapse = ", "), ")"),
i = base::paste0("Use instead: power_centrality(", base::paste(base::c("graph", "nodes", base::paste0(.arg_names, " = ")), collapse = ", "), ")")
)
)
Expand All @@ -2386,7 +2407,7 @@ power_centrality <- function(
nodes,
loops,
exponent,
rescale,
normalized,
tol,
weights = weights
)
Expand All @@ -2396,7 +2417,7 @@ power_centrality <- function(
nodes,
loops,
exponent,
rescale,
normalized,
tol,
weights = weights
)
Expand Down
20 changes: 12 additions & 8 deletions R/tkplot.R
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Expand Up @@ -71,12 +71,14 @@ tkplot.off <- function() {
#' `tkplot.getcoords()` was renamed to [tk_coords()] to create a more
#' consistent API.
#' @inheritParams tk_coords
#' @param norm `r lifecycle::badge("deprecated")` Use `normalized` in
#' [tk_coords()] instead.
#' @keywords internal
#' @export
tkplot.getcoords <- function(tkp.id, norm = FALSE) {
# nocov start
lifecycle::deprecate_warn("2.0.0", "tkplot.getcoords()", "tk_coords()")
tk_coords(tkp.id = tkp.id, norm = norm)
tk_coords(tkp.id = tkp.id, normalized = norm)
} # nocov end

#' Interactive plotting of graphs
Expand Down Expand Up @@ -271,7 +273,7 @@ assign(".next", 1, .tkplot.env)
#' @param width The width of the rectangle for generating new coordinates.
#' @param height The height of the rectangle for generating new coordinates.
#' @param newlayout The new layout, see the `layout` parameter of tkplot.
#' @param norm Logical, should we norm the coordinates.
#' @param normalized Logical, should we norm the coordinates.
#' @param coords Two-column numeric matrix, the new coordinates of the
#' vertices, in absolute coordinates.
#' @param degree The degree to rotate the plot.
Expand Down Expand Up @@ -734,11 +736,13 @@ tk_postscript <- function(tkp.id) {
tk_coords <- function(
tkp.id,
...,
norm = FALSE
normalized = FALSE
) {
# BEGIN GENERATED ARG_HANDLE: tk_coords, do not edit, see tools/generate-migrations.R
# fmt: skip
if (...length() > 0L) {
.arg_ambiguous <- base::intersect(base::names(base::substitute(...())), base::c("n", "no", "nor"))
if (base::length(.arg_ambiguous) > 0L) cli::cli_abort("Argument {.arg {(.arg_ambiguous[[1L]])}} matches multiple arguments of {.fn tk_coords}.")
# Pre-3.0.0 signature: tk_coords(tkp.id, norm)
.old_signature <- function(norm, ...) {
if (...length() > 0L) {
Expand All @@ -748,22 +752,22 @@ tk_coords <- function(
cli::cli_abort(base::c("Unexpected argument passed to {.fn tk_coords}: {.arg {(.arg_extra)}}.", i = "Arguments after {.arg ...} must be spelled out in full."), call = base::parent.frame())
}
base::c(
if (!base::missing(norm)) base::list(norm = norm)
if (!base::missing(norm)) base::list(normalized = norm)
)
}
.arg_handle <- .old_signature(...)
if (base::length(.arg_handle) > 0L) {
.arg_names <- base::names(.arg_handle)
.arg_conflict <- base::intersect(.arg_names, base::c(
if (!base::missing(norm)) "norm"
if (!base::missing(normalized)) "normalized"
))
if (base::length(.arg_conflict) > 0L) cli::cli_abort(base::c("Argument {.arg {(.arg_conflict)}} of {.fn tk_coords} was supplied more than once.", i = "Pass it exactly once, by its new name {.arg {(.arg_conflict)}}."))
base::list2env(.arg_handle, base::environment())
lifecycle::deprecate_soft(
"3.0.0",
what = base::I("Calling `tk_coords()` with positional or abbreviated arguments"),
details = base::c(
i = base::paste0("Detected call: tk_coords(", base::paste(base::c("tkp.id", .arg_names), collapse = ", "), ")"),
i = base::paste0("Detected call: tk_coords(", base::paste(base::c("tkp.id", base::c(normalized = "norm")[.arg_names]), collapse = ", "), ")"),
i = base::paste0("Use instead: tk_coords(", base::paste(base::c("tkp.id", base::paste0(.arg_names, " = ")), collapse = ", "), ")")
)
)
Expand All @@ -774,7 +778,7 @@ tk_coords <- function(
# nocov start
coords <- .tkplot.get(tkp.id, "coords")
coords[, 2] <- max(coords[, 2]) - coords[, 2]
if (norm) {
if (normalized) {
# Shift
coords[, 1] <- coords[, 1] - min(coords[, 1])
coords[, 2] <- coords[, 2] - min(coords[, 2])
Expand Down Expand Up @@ -1845,7 +1849,7 @@ tk_canvas <- function(tkp.id) {
layout$params[[i]]$type == "initial" &&
params[[i]]
) {
realparams[[i]] <- tk_coords(tkp.id, norm = TRUE)
realparams[[i]] <- tk_coords(tkp.id, normalized = TRUE)
}
}
if (as.logical(tcltk::tclvalue(save.default))) {
Expand Down
4 changes: 2 additions & 2 deletions man/bonpow.Rd
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13 changes: 11 additions & 2 deletions man/hits_scores.Rd
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4 changes: 2 additions & 2 deletions man/power_centrality.Rd
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4 changes: 2 additions & 2 deletions man/tkplot.Rd
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3 changes: 2 additions & 1 deletion man/tkplot.getcoords.Rd
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18 changes: 18 additions & 0 deletions tests/testthat/_snaps/centrality.md
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Expand Up @@ -24,6 +24,24 @@
i Please use `arpack_defaults()` instead.
i So the function arpack_defaults(), not an object called arpack_defaults.

# hits_scores(scale = ) is deprecated but still works

Code
res_legacy <- hits_scores(g, scale = FALSE)
Condition
Warning:
The `scale` argument of `hits_scores()` is deprecated as of igraph 3.0.0.
i Please use the `normalized` argument instead.

---

Code
hits_scores(g, normalized = FALSE, scale = FALSE)
Condition
Error in `hits_scores()`:
! Argument `normalized` of `hits_scores()` was supplied more than once.
i It was also supplied via its legacy name `scale`.

# eigen_centrality() deprecated scale argument

Code
Expand Down
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