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add as_p
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@strengejacke
strengejacke committed Aug 31, 2024
1 parent b2ef7f6 commit bcb3416
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3 changes: 3 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,9 @@

- Results from `p_direction()` can directly be used in `pd_to_p()`.

- `p_direction()` gets an `as_p` argument, to directly convert pd-values into
frequentist p-values.

## Bug fixes

* Fixed warning in CRAN check results.
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66 changes: 47 additions & 19 deletions R/p_direction.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@
#' such as `"kernel"`, `"logspline"` or `"KernSmooth"`. See details.
#' @param null The value considered as a "null" effect. Traditionally 0, but
#' could also be 1 in the case of ratios of change (OR, IRR, ...).
#' @param as_p If `TRUE`, the p-direction (pd) values are converted to a
#' frequentist p-value using [`pd_to_p()`].
#' @inheritParams hdi
#'
#' @details
Expand Down Expand Up @@ -165,24 +167,24 @@ p_direction.default <- function(x, ...) {

#' @rdname p_direction
#' @export
p_direction.numeric <- function(x, method = "direct", null = 0, ...) {
p_direction.numeric <- function(x, method = "direct", null = 0, as_p = FALSE, ...) {
obj_name <- insight::safe_deparse_symbol(substitute(x))
out <- p_direction(data.frame(Posterior = x), method = method, null = null, ...)
out <- p_direction(data.frame(Posterior = x), method = method, null = null, as_p = as_p, ...)
attr(out, "object_name") <- obj_name
out
}


#' @rdname p_direction
#' @export
p_direction.data.frame <- function(x, method = "direct", null = 0, ...) {
p_direction.data.frame <- function(x, method = "direct", null = 0, as_p = FALSE, ...) {
obj_name <- insight::safe_deparse_symbol(substitute(x))
x <- .select_nums(x)

if (ncol(x) == 1) {
pd <- .p_direction(x[[1]], method = method, null = null, ...)
pd <- .p_direction(x[[1]], method = method, null = null, as_p = as_p, ...)
} else {
pd <- sapply(x, .p_direction, method = method, null = null, simplify = TRUE, ...)
pd <- sapply(x, .p_direction, method = method, null = null, as_p = as_p, simplify = TRUE, ...)
}

out <- data.frame(
Expand All @@ -192,6 +194,11 @@ p_direction.data.frame <- function(x, method = "direct", null = 0, ...) {
stringsAsFactors = FALSE
)

# rename column
if (as_p) {
colnames(out)[2] <- "p"
}

attr(out, "object_name") <- obj_name
class(out) <- unique(c("p_direction", "see_p_direction", class(out)))

Expand All @@ -200,8 +207,8 @@ p_direction.data.frame <- function(x, method = "direct", null = 0, ...) {


#' @export
p_direction.draws <- function(x, method = "direct", null = 0, ...) {
p_direction(.posterior_draws_to_df(x), method = method, null = null, ...)
p_direction.draws <- function(x, method = "direct", null = 0, as_p = FALSE, ...) {
p_direction(.posterior_draws_to_df(x), method = method, null = null, as_p = as_p, ...)
}

#' @export
Expand All @@ -210,11 +217,12 @@ p_direction.rvar <- p_direction.draws

#' @rdname p_direction
#' @export
p_direction.MCMCglmm <- function(x, method = "direct", null = 0, ...) {
p_direction.MCMCglmm <- function(x, method = "direct", null = 0, as_p = FALSE, ...) {
nF <- x$Fixed$nfl
out <- p_direction(as.data.frame(x$Sol[, 1:nF, drop = FALSE]),
method = method,
null = null,
as_p = as_p,
...
)
attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
Expand All @@ -223,20 +231,20 @@ p_direction.MCMCglmm <- function(x, method = "direct", null = 0, ...) {


#' @export
p_direction.mcmc <- function(x, method = "direct", null = 0, ...) {
p_direction(as.data.frame(x), method = method, null = null, ...)
p_direction.mcmc <- function(x, method = "direct", null = 0, as_p = FALSE, ...) {
p_direction(as.data.frame(x), method = method, null = null, as_p = as_p, ...)
}


#' @export
p_direction.BGGM <- function(x, method = "direct", null = 0, ...) {
p_direction(as.data.frame(x), method = method, null = null, ...)
p_direction.BGGM <- function(x, method = "direct", null = 0, as_p = FALSE, ...) {
p_direction(as.data.frame(x), method = method, null = null, as_p = as_p, ...)
}


#' @export
p_direction.bcplm <- function(x, method = "direct", null = 0, ...) {
p_direction(insight::get_parameters(x), method = method, null = null, ...)
p_direction.bcplm <- function(x, method = "direct", null = 0, as_p = FALSE, ...) {
p_direction(insight::get_parameters(x), method = method, null = null, as_p = as_p, ...)
}

#' @export
Expand All @@ -253,13 +261,15 @@ p_direction.bayesQR <- p_direction.bcplm
p_direction.bamlss <- function(x,
method = "direct",
null = 0,
as_p = FALSE,
component = c("all", "conditional", "location"),
...) {
component <- match.arg(component)
out <- p_direction(
insight::get_parameters(x, component = component),
method = method,
null = null,
as_p = as_p,
...
)
out <- .add_clean_parameters_attribute(out, x)
Expand All @@ -269,10 +279,10 @@ p_direction.bamlss <- function(x,

#' @rdname p_direction
#' @export
p_direction.emmGrid <- function(x, method = "direct", null = 0, ...) {
p_direction.emmGrid <- function(x, method = "direct", null = 0, as_p = FALSE, ...) {
xdf <- insight::get_parameters(x)

out <- p_direction(xdf, method = method, null = null, ...)
out <- p_direction(xdf, method = method, null = null, as_p = as_p, ...)
attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
out
}
Expand All @@ -289,6 +299,7 @@ p_direction.emm_list <- p_direction.emmGrid
parameters,
method = "direct",
null = 0,
as_p = FALSE,
...) {
p_direction(
insight::get_parameters(
Expand All @@ -299,6 +310,7 @@ p_direction.emm_list <- p_direction.emmGrid
),
method = method,
null = null,
as_p = as_p,
...
)
}
Expand All @@ -310,6 +322,7 @@ p_direction.sim.merMod <- function(x,
parameters = NULL,
method = "direct",
null = 0,
as_p = FALSE,
...) {
effects <- match.arg(effects)

Expand All @@ -320,6 +333,7 @@ p_direction.sim.merMod <- function(x,
parameters = parameters,
method = method,
null = null,
as_p = as_p,
...
)
attr(out, "data") <- insight::get_parameters(x, effects = effects, parameters = parameters)
Expand All @@ -332,6 +346,7 @@ p_direction.sim <- function(x,
parameters = NULL,
method = "direct",
null = 0,
as_p = FALSE,
...) {
out <- .p_direction_models(
x = x,
Expand All @@ -340,6 +355,7 @@ p_direction.sim <- function(x,
parameters = parameters,
method = method,
null = null,
as_p = as_p,
...
)
attr(out, "data") <- insight::get_parameters(x, parameters = parameters)
Expand All @@ -356,6 +372,7 @@ p_direction.stanreg <- function(x,
parameters = NULL,
method = "direct",
null = 0,
as_p = FALSE,
...) {
effects <- match.arg(effects)
component <- match.arg(component)
Expand All @@ -371,6 +388,7 @@ p_direction.stanreg <- function(x,
),
method = method,
null = null,
as_p = as_p,
...
),
cleaned_parameters,
Expand Down Expand Up @@ -398,6 +416,7 @@ p_direction.brmsfit <- function(x,
parameters = NULL,
method = "direct",
null = 0,
as_p = FALSE,
...) {
effects <- match.arg(effects)
component <- match.arg(component)
Expand All @@ -413,6 +432,7 @@ p_direction.brmsfit <- function(x,
),
method = method,
null = null,
as_p = as_p,
...
),
cleaned_parameters
Expand All @@ -427,8 +447,8 @@ p_direction.brmsfit <- function(x,

#' @rdname p_direction
#' @export
p_direction.BFBayesFactor <- function(x, method = "direct", null = 0, ...) {
out <- p_direction(insight::get_parameters(x), method = method, null = null, ...)
p_direction.BFBayesFactor <- function(x, method = "direct", null = 0, as_p = FALSE, ...) {
out <- p_direction(insight::get_parameters(x), method = method, null = null, as_p = as_p, ...)
attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
out
}
Expand All @@ -438,6 +458,7 @@ p_direction.BFBayesFactor <- function(x, method = "direct", null = 0, ...) {
p_direction.get_predicted <- function(x,
method = "direct",
null = 0,
as_p = FALSE,
use_iterations = FALSE,
verbose = TRUE,
...) {
Expand All @@ -447,6 +468,7 @@ p_direction.get_predicted <- function(x,
as.data.frame(t(attributes(x)$iterations)),
method = method,
null = null,
as_p = as_p,
verbose = verbose,
...
)
Expand All @@ -458,6 +480,7 @@ p_direction.get_predicted <- function(x,
out <- p_direction(as.numeric(x),
method = method,
null = null,
as_p = as_p,
verbose = verbose,
...
)
Expand Down Expand Up @@ -490,7 +513,7 @@ p_direction.parameters_model <- function(x, ...) {


#' @keywords internal
.p_direction <- function(x, method = "direct", null = 0, ...) {
.p_direction <- function(x, method = "direct", null = 0, as_p = FALSE, ...) {
if (method == "direct") {
pdir <- max(
length(x[x > null]), # pd positive
Expand All @@ -510,6 +533,11 @@ p_direction.parameters_model <- function(x, ...) {
}
}

# convert to frequentist p?
if (as_p) {
pdir <- pd_to_p(pdir)
}

pdir
}

Expand Down
16 changes: 11 additions & 5 deletions man/p_direction.Rd
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