From 00c6f6687e902301fa108f8e9ac360b28da61ccb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul-Christian=20B=C3=BCrkner?= Date: Fri, 5 Aug 2022 13:33:31 +0200 Subject: [PATCH] fix issue #1388 --- DESCRIPTION | 2 +- R/posterior_epred.R | 4 ++-- man/AsymLaplace.Rd | 4 +--- man/BetaBinomial.Rd | 4 +--- man/Dirichlet.Rd | 2 -- man/ExGaussian.Rd | 4 +--- man/Frechet.Rd | 4 +--- man/GenExtremeValue.Rd | 4 +--- man/Hurdle.Rd | 8 ++------ man/InvGaussian.Rd | 4 +--- man/LogisticNormal.Rd | 2 -- man/MultiNormal.Rd | 2 -- man/MultiStudentT.Rd | 2 -- man/Shifted_Lognormal.Rd | 4 +--- man/SkewNormal.Rd | 4 +--- man/VonMises.Rd | 4 +--- man/Wiener.Rd | 4 ---- man/ZeroInflated.Rd | 8 ++------ man/posterior_linpred.brmsfit.Rd | 4 ++-- man/set_prior.Rd | 10 +++++----- 20 files changed, 23 insertions(+), 61 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6bb8b22b4..d1ad0132d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -93,4 +93,4 @@ Additional_repositories: VignetteBuilder: knitr, R.rsp -RoxygenNote: 7.2.0 +RoxygenNote: 7.2.1 diff --git a/R/posterior_epred.R b/R/posterior_epred.R index 97a1b3d84..72538bdbf 100644 --- a/R/posterior_epred.R +++ b/R/posterior_epred.R @@ -278,8 +278,8 @@ fitted.brmsfit <- function(object, newdata = NULL, re_formula = NULL, #' @param object An object of class \code{brmsfit}. #' @param transform Logical; if \code{FALSE} #' (the default), draws of the linear predictor are returned. -#' If \code{TRUE}, draws of transformed linear predictor, -#' that is, after applying the link function are returned. +#' If \code{TRUE}, draws of the transformed linear predictor, +#' that is, after applying the inverse link function are returned. #' @param dpar Name of a predicted distributional parameter #' for which draws are to be returned. By default, draws #' of the main distributional parameter(s) \code{"mu"} are returned. diff --git a/man/AsymLaplace.Rd b/man/AsymLaplace.Rd index 1d443f28d..f5d9b5746 100644 --- a/man/AsymLaplace.Rd +++ b/man/AsymLaplace.Rd @@ -40,13 +40,11 @@ rasym_laplace(n, mu = 0, sigma = 1, quantile = 0.5) \item{quantile}{Asymmetry parameter corresponding to quantiles in quantile regression (hence the name).} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{p}{Vector of probabilities.} \item{n}{Number of draws to sample from the distribution.} diff --git a/man/BetaBinomial.Rd b/man/BetaBinomial.Rd index 2280b8ef4..206a9773b 100644 --- a/man/BetaBinomial.Rd +++ b/man/BetaBinomial.Rd @@ -22,13 +22,11 @@ rbeta_binomial(n, size, mu, phi) \item{phi}{Vector of precisions.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{n}{Number of draws to sample from the distribution.} } \description{ diff --git a/man/Dirichlet.Rd b/man/Dirichlet.Rd index a035cff0e..567613642 100644 --- a/man/Dirichlet.Rd +++ b/man/Dirichlet.Rd @@ -16,8 +16,6 @@ rdirichlet(n, alpha) \item{alpha}{Matrix of positive shape parameters. Each row corresponds to one probability vector.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{n}{Number of draws to sample from the distribution.} } \description{ diff --git a/man/ExGaussian.Rd b/man/ExGaussian.Rd index 82de772af..a17983322 100644 --- a/man/ExGaussian.Rd +++ b/man/ExGaussian.Rd @@ -22,13 +22,11 @@ rexgaussian(n, mu, sigma, beta) \item{beta}{Vector of scales of the exponential component.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{n}{Number of draws to sample from the distribution.} } \description{ diff --git a/man/Frechet.Rd b/man/Frechet.Rd index 98ecb2b32..a23403ab9 100644 --- a/man/Frechet.Rd +++ b/man/Frechet.Rd @@ -25,13 +25,11 @@ rfrechet(n, loc = 0, scale = 1, shape = 1) \item{shape}{Vector of shapes.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{p}{Vector of probabilities.} \item{n}{Number of draws to sample from the distribution.} diff --git a/man/GenExtremeValue.Rd b/man/GenExtremeValue.Rd index 799ce2a38..9f489f5e0 100644 --- a/man/GenExtremeValue.Rd +++ b/man/GenExtremeValue.Rd @@ -29,13 +29,11 @@ rgen_extreme_value(n, mu = 0, sigma = 1, xi = 0) \item{xi}{Vector of shapes.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{n}{Number of draws to sample from the distribution.} } \description{ diff --git a/man/Hurdle.Rd b/man/Hurdle.Rd index c904d7716..fad73f986 100644 --- a/man/Hurdle.Rd +++ b/man/Hurdle.Rd @@ -29,19 +29,15 @@ dhurdle_lognormal(x, mu, sigma, hu, log = FALSE) phurdle_lognormal(q, mu, sigma, hu, lower.tail = TRUE, log.p = FALSE) } \arguments{ -\item{x}{Vector of quantiles.} +\item{x, q}{Vector of quantiles.} \item{hu}{hurdle probability} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} - -\item{q}{Vector of quantiles.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{mu, lambda}{location parameter} \item{shape}{shape parameter} diff --git a/man/InvGaussian.Rd b/man/InvGaussian.Rd index 9fd023048..633fd6e91 100644 --- a/man/InvGaussian.Rd +++ b/man/InvGaussian.Rd @@ -20,13 +20,11 @@ rinv_gaussian(n, mu = 1, shape = 1) \item{shape}{Vector of shapes.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{n}{Number of draws to sample from the distribution.} } \description{ diff --git a/man/LogisticNormal.Rd b/man/LogisticNormal.Rd index 5b9b00547..c82fedba7 100644 --- a/man/LogisticNormal.Rd +++ b/man/LogisticNormal.Rd @@ -21,8 +21,6 @@ each row is taken to be a quantile.} \item{refcat}{A single integer indicating the reference category. Defaults to \code{1}.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{check}{Logical; Indicates whether several input checks should be performed. Defaults to \code{FALSE} to improve efficiency.} diff --git a/man/MultiNormal.Rd b/man/MultiNormal.Rd index a669b1abb..1e8cdd687 100644 --- a/man/MultiNormal.Rd +++ b/man/MultiNormal.Rd @@ -18,8 +18,6 @@ each row is taken to be a quantile.} \item{Sigma}{Covariance matrix.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{check}{Logical; Indicates whether several input checks should be performed. Defaults to \code{FALSE} to improve efficiency.} diff --git a/man/MultiStudentT.Rd b/man/MultiStudentT.Rd index eb76cc23c..df73f8889 100644 --- a/man/MultiStudentT.Rd +++ b/man/MultiStudentT.Rd @@ -20,8 +20,6 @@ each row is taken to be a quantile.} \item{Sigma}{Covariance matrix.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{check}{Logical; Indicates whether several input checks should be performed. Defaults to \code{FALSE} to improve efficiency.} diff --git a/man/Shifted_Lognormal.Rd b/man/Shifted_Lognormal.Rd index ed929966e..21e0be052 100644 --- a/man/Shifted_Lognormal.Rd +++ b/man/Shifted_Lognormal.Rd @@ -39,13 +39,11 @@ rshifted_lnorm(n, meanlog = 0, sdlog = 1, shift = 0) \item{shift}{Vector of shifts.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{p}{Vector of probabilities.} \item{n}{Number of draws to sample from the distribution.} diff --git a/man/SkewNormal.Rd b/man/SkewNormal.Rd index 299be9026..d9578c7e9 100644 --- a/man/SkewNormal.Rd +++ b/man/SkewNormal.Rd @@ -58,13 +58,11 @@ If \code{NULL} (the default), will be computed internally.} \item{omega}{Optional vector of scale values. If \code{NULL} (the default), will be computed internally.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{p}{Vector of probabilities.} \item{tol}{Tolerance of the approximation used in the diff --git a/man/VonMises.Rd b/man/VonMises.Rd index b4cbd7843..b6a29c300 100644 --- a/man/VonMises.Rd +++ b/man/VonMises.Rd @@ -20,13 +20,11 @@ rvon_mises(n, mu, kappa) \item{kappa}{Vector of precision values.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{acc}{Accuracy of numerical approximations.} \item{n}{Number of draws to sample from the distribution.} diff --git a/man/Wiener.Rd b/man/Wiener.Rd index 448f4fb4b..972335107 100644 --- a/man/Wiener.Rd +++ b/man/Wiener.Rd @@ -28,8 +28,6 @@ rwiener( ) } \arguments{ -\item{x}{Vector of quantiles.} - \item{alpha}{Boundary separation parameter.} \item{tau}{Non-decision time parameter.} @@ -43,8 +41,6 @@ If no character vector, it is coerced to logical where \code{TRUE} indicates \code{"upper"} and \code{FALSE} indicates \code{"lower"}.} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{backend}{Name of the package to use as backend for the computations. Either \code{"Rwiener"} (the default) or \code{"rtdists"}. Can be set globally for the current \R session via the diff --git a/man/ZeroInflated.Rd b/man/ZeroInflated.Rd index 6ea1e48b2..0d19122f4 100644 --- a/man/ZeroInflated.Rd +++ b/man/ZeroInflated.Rd @@ -43,19 +43,15 @@ dzero_inflated_beta(x, shape1, shape2, zi, log = FALSE) pzero_inflated_beta(q, shape1, shape2, zi, lower.tail = TRUE, log.p = FALSE) } \arguments{ -\item{x}{Vector of quantiles.} +\item{x, q}{Vector of quantiles.} \item{zi}{zero-inflation probability} -\item{log}{Logical; If \code{TRUE}, values are returned on the log scale.} - -\item{q}{Vector of quantiles.} +\item{log, log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} \item{lower.tail}{Logical; If \code{TRUE} (default), return P(X <= x). Else, return P(X > x) .} -\item{log.p}{Logical; If \code{TRUE}, values are returned on the log scale.} - \item{mu, lambda}{location parameter} \item{shape, shape1, shape2}{shape parameter} diff --git a/man/posterior_linpred.brmsfit.Rd b/man/posterior_linpred.brmsfit.Rd index 7e69d21a8..e4a57a53b 100644 --- a/man/posterior_linpred.brmsfit.Rd +++ b/man/posterior_linpred.brmsfit.Rd @@ -26,8 +26,8 @@ \item{transform}{Logical; if \code{FALSE} (the default), draws of the linear predictor are returned. -If \code{TRUE}, draws of transformed linear predictor, -that is, after applying the link function are returned.} +If \code{TRUE}, draws of the transformed linear predictor, +that is, after applying the inverse link function are returned.} \item{newdata}{An optional data.frame for which to evaluate predictions. If \code{NULL} (default), the original data of the model is used. diff --git a/man/set_prior.Rd b/man/set_prior.Rd index 8b8fe3162..bde9adac0 100644 --- a/man/set_prior.Rd +++ b/man/set_prior.Rd @@ -343,18 +343,18 @@ Define priors for specific parameters or classes of parameters. } \section{Functions}{ \itemize{ -\item \code{prior}: Alias of \code{set_prior} allowing to +\item \code{prior()}: Alias of \code{set_prior} allowing to specify arguments as expressions without quotation marks. -\item \code{prior_}: Alias of \code{set_prior} allowing to specify +\item \code{prior_()}: Alias of \code{set_prior} allowing to specify arguments as as one-sided formulas or wrapped in \code{quote}. -\item \code{prior_string}: Alias of \code{set_prior} allowing to +\item \code{prior_string()}: Alias of \code{set_prior} allowing to specify arguments as strings. -\item \code{empty_prior}: Create an empty \code{brmsprior} object. -}} +\item \code{empty_prior()}: Create an empty \code{brmsprior} object. +}} \examples{ ## use alias functions (prior1 <- prior(cauchy(0, 1), class = sd))