From 20bf94f7b8004793a4f401c3703e1baf366b025a Mon Sep 17 00:00:00 2001 From: Nicholas Clark Date: Thu, 9 Nov 2023 08:00:35 +1000 Subject: [PATCH] few roxygen edits --- R/plot_mvgam_factors.R | 2 +- R/plot_mvgam_fc.R | 2 +- R/plot_mvgam_pterms.R | 1 + R/plot_mvgam_randomeffects.R | 1 + R/plot_mvgam_resids.R | 2 +- R/plot_mvgam_smooth.R | 1 + R/plot_mvgam_trend.R | 2 +- R/plot_mvgam_uncertainty.R | 2 +- man/mcmc_plot.mvgam.Rd | 2 +- man/plot_mvgam_factors.Rd | 2 ++ man/plot_mvgam_forecasts.Rd | 2 ++ man/plot_mvgam_pterms.Rd | 2 ++ man/plot_mvgam_randomeffects.Rd | 2 ++ man/plot_mvgam_resids.Rd | 2 ++ man/plot_mvgam_smooth.Rd | 2 ++ man/plot_mvgam_trend.Rd | 2 ++ man/plot_mvgam_uncertainty.Rd | 2 ++ src/mvgam.dll | Bin 1064960 -> 1064960 bytes 18 files changed, 25 insertions(+), 6 deletions(-) diff --git a/R/plot_mvgam_factors.R b/R/plot_mvgam_factors.R index be035c72..a4628af9 100644 --- a/R/plot_mvgam_factors.R +++ b/R/plot_mvgam_factors.R @@ -3,7 +3,7 @@ #'This function takes a fitted \code{mvgam} object and returns plots and summary statistics for #'the latent dynamic factors #' -#'@inheritParams plot.mvgam +#'@param object \code{list} object returned from \code{mvgam}. See [mvgam()] #'@param plot \code{logical} specifying whether factors should be plotted #'@author Nicholas J Clark #'@details If the model in \code{object} was estimated using dynamic factors, it is possible that not all factors diff --git a/R/plot_mvgam_fc.R b/R/plot_mvgam_fc.R index 45729449..15317bc9 100644 --- a/R/plot_mvgam_fc.R +++ b/R/plot_mvgam_fc.R @@ -1,6 +1,6 @@ #'Plot mvgam posterior predictions for a specified series #'@importFrom stats formula terms -#'@inheritParams plot.mvgam +#'@param object \code{list} object returned from \code{mvgam}. See [mvgam()] #'@param series \code{integer} specifying which series in the set is to be plotted #'@param newdata Optional \code{dataframe} or \code{list} of test data containing at least 'series' and 'time' #'in addition to any other variables included in the linear predictor of the original \code{formula}. If included, the diff --git a/R/plot_mvgam_pterms.R b/R/plot_mvgam_pterms.R index 6feebec6..5ebaa0e0 100644 --- a/R/plot_mvgam_pterms.R +++ b/R/plot_mvgam_pterms.R @@ -5,6 +5,7 @@ #'@importFrom graphics layout title rug bxp #'@importFrom stats coef predict #'@inheritParams plot.mvgam +#'@param object \code{list} object returned from \code{mvgam}. See [mvgam()] #'@details Posterior empirical quantiles of each parametric term's partial effect estimates #'(on the link scale) are calculated and visualised as ribbon plots. These effects can #'be interpreted as the partial effect that a parametric term contributes when all other diff --git a/R/plot_mvgam_randomeffects.R b/R/plot_mvgam_randomeffects.R index 3f05d65f..01f9ac4b 100644 --- a/R/plot_mvgam_randomeffects.R +++ b/R/plot_mvgam_randomeffects.R @@ -4,6 +4,7 @@ #' #'@importFrom graphics layout title #'@inheritParams plot.mvgam +#'@param object \code{list} object returned from \code{mvgam}. See [mvgam()] #'@details Posterior empirical quantiles of random effect coefficient estimates #'(on the link scale) are calculated and visualised as ribbon plots. #'Labels for coefficients are taken from the levels of the original factor variable diff --git a/R/plot_mvgam_resids.R b/R/plot_mvgam_resids.R index 0318da36..fa60a65d 100644 --- a/R/plot_mvgam_resids.R +++ b/R/plot_mvgam_resids.R @@ -5,7 +5,7 @@ #'@importFrom graphics layout title #'@importFrom stats complete.cases qqnorm qqline acf pacf na.pass #'@importFrom mgcv bam -#'@inheritParams plot.mvgam +#'@param object \code{list} object returned from \code{mvgam}. See [mvgam()] #'@param series \code{integer} specifying which series in the set is to be plotted #'@param newdata Optional \code{dataframe} or \code{list} of test data containing at least 'series', 'y', and 'time' #'in addition to any other variables included in the linear predictor of \code{formula}. If included, the diff --git a/R/plot_mvgam_smooth.R b/R/plot_mvgam_smooth.R index 2ce98030..23274c9c 100644 --- a/R/plot_mvgam_smooth.R +++ b/R/plot_mvgam_smooth.R @@ -5,6 +5,7 @@ #'@importFrom grDevices hcl.colors #'@importFrom stats quantile predict #'@inheritParams plot.mvgam +#'@param object \code{list} object returned from \code{mvgam}. See [mvgam()] #'@param series \code{integer} specifying which series in the set is to be plotted #'@param smooth either a \code{character} or \code{integer} specifying which smooth term to be plotted #'@param residuals \code{logical}. If \code{TRUE} then posterior quantiles of partial residuals are added diff --git a/R/plot_mvgam_trend.R b/R/plot_mvgam_trend.R index 5fadbb6b..6bbfade9 100644 --- a/R/plot_mvgam_trend.R +++ b/R/plot_mvgam_trend.R @@ -1,7 +1,7 @@ #'Plot mvgam latent trend for a specified series #'@importFrom graphics par lines polygon box abline #'@importFrom stats sd quantile -#'@inheritParams plot.mvgam +#'@param object \code{list} object returned from \code{mvgam}. See [mvgam()] #'@param series \code{integer} specifying which series in the set is to be plotted #'@param newdata Optional \code{dataframe} or \code{list} of test data containing at least 'series' and 'time' #'in addition to any other variables included in the linear predictor of the original \code{formula}. diff --git a/R/plot_mvgam_uncertainty.R b/R/plot_mvgam_uncertainty.R index 2a095449..ce8f4ade 100644 --- a/R/plot_mvgam_uncertainty.R +++ b/R/plot_mvgam_uncertainty.R @@ -1,7 +1,7 @@ #'Plot mvgam forecast uncertainty contributions for a specified series #'@importFrom graphics legend #'@importFrom stats predict -#'@inheritParams plot.mvgam +#'@param object \code{list} object returned from \code{mvgam}. See [mvgam()] #'@param series \code{integer} specifying which series in the set is to be plotted #'@param newdata A \code{dataframe} or \code{list} containing at least 'series' and 'time' for the forecast horizon, in #'addition to any other variables included in the linear predictor of \code{formula} diff --git a/man/mcmc_plot.mvgam.Rd b/man/mcmc_plot.mvgam.Rd index 7e178f76..37494321 100644 --- a/man/mcmc_plot.mvgam.Rd +++ b/man/mcmc_plot.mvgam.Rd @@ -22,7 +22,7 @@ Supported types are (as names) \code{hist}, \code{dens}, \code{violin}, \code{intervals}, \code{areas}, \code{areas_ridges}, \code{combo}, \code{acf}, \code{acf_bar}, \code{trace}, \code{trace_highlight}, -\code{scatter}, \code{violin}, +\code{scatter}, \code{hex}, \code{pairs}, \code{violin}, \code{rhat}, \code{rhat_hist}, \code{neff}, \code{neff_hist} and \code{nuts_energy}. For an overview on the various plot types see diff --git a/man/plot_mvgam_factors.Rd b/man/plot_mvgam_factors.Rd index d9f81f1e..c4d7e3d2 100644 --- a/man/plot_mvgam_factors.Rd +++ b/man/plot_mvgam_factors.Rd @@ -7,6 +7,8 @@ plot_mvgam_factors(object, plot = TRUE) } \arguments{ +\item{object}{\code{list} object returned from \code{mvgam}. See \code{\link[=mvgam]{mvgam()}}} + \item{plot}{\code{logical} specifying whether factors should be plotted} } \value{ diff --git a/man/plot_mvgam_forecasts.Rd b/man/plot_mvgam_forecasts.Rd index 81bfe154..e31a4bfc 100644 --- a/man/plot_mvgam_forecasts.Rd +++ b/man/plot_mvgam_forecasts.Rd @@ -37,6 +37,8 @@ plot_mvgam_fc( ) } \arguments{ +\item{object}{\code{list} object returned from \code{mvgam}. See \code{\link[=mvgam]{mvgam()}}} + \item{series}{\code{integer} specifying which series in the set is to be plotted} \item{newdata}{Optional \code{dataframe} or \code{list} of test data containing at least 'series' and 'time' diff --git a/man/plot_mvgam_pterms.Rd b/man/plot_mvgam_pterms.Rd index 1799f82d..11065434 100644 --- a/man/plot_mvgam_pterms.Rd +++ b/man/plot_mvgam_pterms.Rd @@ -7,6 +7,8 @@ plot_mvgam_pterms(object, trend_effects = FALSE) } \arguments{ +\item{object}{\code{list} object returned from \code{mvgam}. See \code{\link[=mvgam]{mvgam()}}} + \item{trend_effects}{logical. If \code{TRUE} and a \code{trend_formula} was used in model fitting, terms from the trend (i.e. process) model will be plotted} } diff --git a/man/plot_mvgam_randomeffects.Rd b/man/plot_mvgam_randomeffects.Rd index 9210005f..f1bca3ee 100644 --- a/man/plot_mvgam_randomeffects.Rd +++ b/man/plot_mvgam_randomeffects.Rd @@ -7,6 +7,8 @@ plot_mvgam_randomeffects(object, trend_effects = FALSE) } \arguments{ +\item{object}{\code{list} object returned from \code{mvgam}. See \code{\link[=mvgam]{mvgam()}}} + \item{trend_effects}{logical. If \code{TRUE} and a \code{trend_formula} was used in model fitting, terms from the trend (i.e. process) model will be plotted} } diff --git a/man/plot_mvgam_resids.Rd b/man/plot_mvgam_resids.Rd index 22503ad3..63719dfc 100644 --- a/man/plot_mvgam_resids.Rd +++ b/man/plot_mvgam_resids.Rd @@ -7,6 +7,8 @@ plot_mvgam_resids(object, series = 1, newdata, data_test) } \arguments{ +\item{object}{\code{list} object returned from \code{mvgam}. See \code{\link[=mvgam]{mvgam()}}} + \item{series}{\code{integer} specifying which series in the set is to be plotted} \item{newdata}{Optional \code{dataframe} or \code{list} of test data containing at least 'series', 'y', and 'time' diff --git a/man/plot_mvgam_smooth.Rd b/man/plot_mvgam_smooth.Rd index 6bf28bf6..d42412a4 100644 --- a/man/plot_mvgam_smooth.Rd +++ b/man/plot_mvgam_smooth.Rd @@ -18,6 +18,8 @@ plot_mvgam_smooth( ) } \arguments{ +\item{object}{\code{list} object returned from \code{mvgam}. See \code{\link[=mvgam]{mvgam()}}} + \item{trend_effects}{logical. If \code{TRUE} and a \code{trend_formula} was used in model fitting, terms from the trend (i.e. process) model will be plotted} diff --git a/man/plot_mvgam_trend.Rd b/man/plot_mvgam_trend.Rd index 900b09ce..3fd99417 100644 --- a/man/plot_mvgam_trend.Rd +++ b/man/plot_mvgam_trend.Rd @@ -20,6 +20,8 @@ plot_mvgam_trend( ) } \arguments{ +\item{object}{\code{list} object returned from \code{mvgam}. See \code{\link[=mvgam]{mvgam()}}} + \item{series}{\code{integer} specifying which series in the set is to be plotted} \item{newdata}{Optional \code{dataframe} or \code{list} of test data containing at least 'series' and 'time' diff --git a/man/plot_mvgam_uncertainty.Rd b/man/plot_mvgam_uncertainty.Rd index 8e217ee7..905a68df 100644 --- a/man/plot_mvgam_uncertainty.Rd +++ b/man/plot_mvgam_uncertainty.Rd @@ -14,6 +14,8 @@ plot_mvgam_uncertainty( ) } \arguments{ +\item{object}{\code{list} object returned from \code{mvgam}. See \code{\link[=mvgam]{mvgam()}}} + \item{series}{\code{integer} specifying which series in the set is to be plotted} \item{newdata}{A \code{dataframe} or \code{list} containing at least 'series' and 'time' for the forecast horizon, in diff --git a/src/mvgam.dll b/src/mvgam.dll index ab047ba9f0cce1a8c53283e6d7dbc94693dd2309..8f336fdada146f49df2c4334257bf5010b9d841d 100644 GIT binary patch delta 77 zcmWm5I}Ly^07cQz^8eKbF1mvNj4+qsB_u3G48hCY!2=uN>?Z^tf{&YB%y{gRF>ysC f!U!u;k%?Rsq7;>=MI&0#iT=b5_g}B#aqs*A4RayR delta 77 zcmZo@aBOIBoY29%(%gGuw=YxLuf|)gw-{S*F}2=eZoS3QdW*I77F+8r_SRb*t+zN^ hZ*jHW;%>dg(|U`y^%mdOTl`v2L0Y%7KjZ%y2>@KQBWeHu