diff --git a/DESCRIPTION b/DESCRIPTION index 3aa741f..f19647d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: ggfortify Type: Package Title: Data Visualization Tools for Statistical Analysis Results Version: 0.4.6 -Date: 2018-05-26 +Date: 2019-03-12 Authors@R: c( person("Masaaki", "Horikoshi", role = c("aut"), email = "sinhrks@gmail.com"), @@ -67,4 +67,4 @@ Suggests: xts, zoo, lfda -RoxygenNote: 6.0.1 +RoxygenNote: 6.1.0 diff --git a/man/autoplot.acf.Rd b/man/autoplot.acf.Rd index bbee5ba..b0d0326 100644 --- a/man/autoplot.acf.Rd +++ b/man/autoplot.acf.Rd @@ -8,9 +8,10 @@ standard plot output} \method{autoplot}{acf}(object, colour = "#000000", linetype = "solid", conf.int = TRUE, conf.int.colour = "#0000FF", conf.int.linetype = "dashed", conf.int.fill = NULL, - conf.int.alpha = 0.3, conf.int.value = 0.95, conf.int.type = "white", - xlim = c(NA, NA), ylim = c(NA, NA), log = "", main = NULL, - xlab = NULL, ylab = "ACF", asp = NULL, ...) + conf.int.alpha = 0.3, conf.int.value = 0.95, + conf.int.type = "white", xlim = c(NA, NA), ylim = c(NA, NA), + log = "", main = NULL, xlab = NULL, ylab = "ACF", asp = NULL, + ...) } \arguments{ \item{object}{\code{stats::acf} instance} diff --git a/man/autoplot.breakpoints.Rd b/man/autoplot.breakpoints.Rd index cc0877e..7159f45 100644 --- a/man/autoplot.breakpoints.Rd +++ b/man/autoplot.breakpoints.Rd @@ -5,8 +5,8 @@ \alias{autoplot.breakpointsfull} \title{Autoplot \code{strucchange::breakpoints}} \usage{ -\method{autoplot}{breakpoints}(object, data = NULL, cpt.colour = "#FF0000", - cpt.linetype = "dashed", ...) +\method{autoplot}{breakpoints}(object, data = NULL, + cpt.colour = "#FF0000", cpt.linetype = "dashed", ...) } \arguments{ \item{object}{\code{strucchange::breakpoints} or \code{strucchange::breakpointsfull} instance.} diff --git a/man/autoplot.cv.glmnet.Rd b/man/autoplot.cv.glmnet.Rd index e1ef824..82319ab 100644 --- a/man/autoplot.cv.glmnet.Rd +++ b/man/autoplot.cv.glmnet.Rd @@ -7,10 +7,11 @@ \method{autoplot}{cv.glmnet}(object, sign.lambda = 1, label.n = 12, label = TRUE, label.label = "nz", label.colour = NULL, label.alpha = NULL, label.size = NULL, label.angle = NULL, - label.family = NULL, label.fontface = NULL, label.lineheight = NULL, - label.hjust = NULL, label.vjust = NULL, label.repel = FALSE, - xlim = c(NA, NA), ylim = c(NA, NA), log = "", main = NULL, - xlab = NULL, ylab = NULL, asp = NULL, ...) + label.family = NULL, label.fontface = NULL, + label.lineheight = NULL, label.hjust = NULL, label.vjust = NULL, + label.repel = FALSE, xlim = c(NA, NA), ylim = c(NA, NA), + log = "", main = NULL, xlab = NULL, ylab = NULL, asp = NULL, + ...) } \arguments{ \item{object}{\code{glmnet::cv.glmnet} instance} diff --git a/man/autoplot.density.Rd b/man/autoplot.density.Rd index a812280..fbd7465 100644 --- a/man/autoplot.density.Rd +++ b/man/autoplot.density.Rd @@ -6,8 +6,8 @@ \usage{ \method{autoplot}{density}(object, p = NULL, colour = "#000000", linetype = NULL, fill = NULL, alpha = NULL, xlim = c(NA, NA), - ylim = c(NA, NA), log = "", main = NULL, xlab = NULL, ylab = NULL, - asp = NULL, ...) + ylim = c(NA, NA), log = "", main = NULL, xlab = NULL, + ylab = NULL, asp = NULL, ...) } \arguments{ \item{object}{\code{stats::density} instance} diff --git a/man/autoplot.forecast.Rd b/man/autoplot.forecast.Rd index 7eee4c7..eaa5dbb 100644 --- a/man/autoplot.forecast.Rd +++ b/man/autoplot.forecast.Rd @@ -5,11 +5,11 @@ \title{Autoplot \code{forecast::forecast}} \usage{ \method{autoplot}{forecast}(object, is.date = NULL, ts.connect = TRUE, - predict.geom = "line", predict.colour = "#0000FF", predict.size = NULL, - predict.linetype = NULL, predict.alpha = NULL, predict.fill = NULL, - predict.shape = NULL, conf.int = TRUE, conf.int.colour = "#0000FF", - conf.int.linetype = "none", conf.int.fill = "#000000", - conf.int.alpha = 0.3, ...) + predict.geom = "line", predict.colour = "#0000FF", + predict.size = NULL, predict.linetype = NULL, predict.alpha = NULL, + predict.fill = NULL, predict.shape = NULL, conf.int = TRUE, + conf.int.colour = "#0000FF", conf.int.linetype = "none", + conf.int.fill = "#000000", conf.int.alpha = 0.3, ...) } \arguments{ \item{object}{\code{forecast::forecast} instance} diff --git a/man/autoplot.glmnet.Rd b/man/autoplot.glmnet.Rd index ada26a6..908955d 100644 --- a/man/autoplot.glmnet.Rd +++ b/man/autoplot.glmnet.Rd @@ -5,12 +5,12 @@ \title{Autoplot \code{glmnet::glmnet}} \usage{ \method{autoplot}{glmnet}(object, xvar = c("norm", "lambda", "dev"), - label.n = 7, label = TRUE, label.label = "Df", label.colour = NULL, - label.alpha = NULL, label.size = NULL, label.angle = NULL, - label.family = NULL, label.fontface = NULL, label.lineheight = NULL, - label.hjust = NULL, label.vjust = NULL, xlim = c(NA, NA), ylim = c(NA, - NA), log = "", main = NULL, xlab = NULL, ylab = "Coefficients", - asp = NULL, ...) + label.n = 7, label = TRUE, label.label = "Df", + label.colour = NULL, label.alpha = NULL, label.size = NULL, + label.angle = NULL, label.family = NULL, label.fontface = NULL, + label.lineheight = NULL, label.hjust = NULL, label.vjust = NULL, + xlim = c(NA, NA), ylim = c(NA, NA), log = "", main = NULL, + xlab = NULL, ylab = "Coefficients", asp = NULL, ...) } \arguments{ \item{object}{\code{glmnet::glmnet} instance} diff --git a/man/autoplot.list.Rd b/man/autoplot.list.Rd index 468948a..d171443 100644 --- a/man/autoplot.list.Rd +++ b/man/autoplot.list.Rd @@ -4,8 +4,8 @@ \alias{autoplot.list} \title{Autoplot list} \usage{ -\method{autoplot}{list}(object, data = NULL, nrow = NULL, ncol = NULL, - scales = "free_y", ...) +\method{autoplot}{list}(object, data = NULL, nrow = NULL, + ncol = NULL, scales = "free_y", ...) } \arguments{ \item{object}{\code{list} instance} diff --git a/man/autoplot.lm.Rd b/man/autoplot.lm.Rd index 0207787..6f82505 100644 --- a/man/autoplot.lm.Rd +++ b/man/autoplot.lm.Rd @@ -12,7 +12,8 @@ label.lineheight = NULL, label.hjust = NULL, label.vjust = NULL, label.repel = FALSE, label.n = 3, smooth.colour = "#0000FF", smooth.linetype = "solid", ad.colour = "#888888", - ad.linetype = "dashed", ad.size = 0.2, nrow = NULL, ncol = NULL, ...) + ad.linetype = "dashed", ad.size = 0.2, nrow = NULL, ncol = NULL, + ...) } \arguments{ \item{object}{\code{stats::lm} instance} diff --git a/man/autoplot.map.Rd b/man/autoplot.map.Rd index 0a13637..1ae524c 100644 --- a/man/autoplot.map.Rd +++ b/man/autoplot.map.Rd @@ -4,10 +4,11 @@ \alias{autoplot.map} \title{Autoplot \code{maps::map}} \usage{ -\method{autoplot}{map}(object, p = NULL, geom = "path", group = "group", - colour = "black", size = NULL, linetype = NULL, alpha = NULL, - fill = NULL, shape = NULL, xlim = c(NA, NA), ylim = c(NA, NA), - log = "", main = NULL, xlab = "", ylab = "", asp = NULL, ...) +\method{autoplot}{map}(object, p = NULL, geom = "path", + group = "group", colour = "black", size = NULL, linetype = NULL, + alpha = NULL, fill = NULL, shape = NULL, xlim = c(NA, NA), + ylim = c(NA, NA), log = "", main = NULL, xlab = "", ylab = "", + asp = NULL, ...) } \arguments{ \item{object}{\code{maps::map} instance} diff --git a/man/autoplot.matrix.Rd b/man/autoplot.matrix.Rd index cf6947a..8cc9495 100644 --- a/man/autoplot.matrix.Rd +++ b/man/autoplot.matrix.Rd @@ -10,8 +10,9 @@ label.colour = colour, label.alpha = NULL, label.size = NULL, label.angle = NULL, label.family = NULL, label.fontface = NULL, label.lineheight = NULL, label.hjust = NULL, label.vjust = NULL, - label.repel = FALSE, scale = NULL, xlim = c(NA, NA), ylim = c(NA, NA), - log = "", main = NULL, xlab = NULL, ylab = NULL, asp = NULL, ...) + label.repel = FALSE, scale = NULL, xlim = c(NA, NA), ylim = c(NA, + NA), log = "", main = NULL, xlab = NULL, ylab = NULL, + asp = NULL, ...) } \arguments{ \item{object}{\code{base::matrix} instance} diff --git a/man/autoplot.spec.Rd b/man/autoplot.spec.Rd index 2d17cf2..16376e6 100644 --- a/man/autoplot.spec.Rd +++ b/man/autoplot.spec.Rd @@ -5,7 +5,8 @@ \title{Autoplot \code{stats::spec}} \usage{ \method{autoplot}{spec}(object, xlim = c(NA, NA), ylim = c(NA, NA), - log = "y", main = NULL, xlab = NULL, ylab = NULL, asp = NULL, ...) + log = "y", main = NULL, xlab = NULL, ylab = NULL, asp = NULL, + ...) } \arguments{ \item{object}{\code{stats::spec} instance} diff --git a/man/autoplot.stepfun.Rd b/man/autoplot.stepfun.Rd index 38a48d4..5dd80fa 100644 --- a/man/autoplot.stepfun.Rd +++ b/man/autoplot.stepfun.Rd @@ -6,8 +6,8 @@ \usage{ \method{autoplot}{stepfun}(object, colour = NULL, size = NULL, linetype = NULL, alpha = NULL, shape = 1, xlim = c(NA, NA), - ylim = c(NA, NA), log = "", main = NULL, xlab = NULL, ylab = NULL, - asp = NULL, ...) + ylim = c(NA, NA), log = "", main = NULL, xlab = NULL, + ylab = NULL, asp = NULL, ...) } \arguments{ \item{object}{\code{stats::stepfun} instance} diff --git a/man/autoplot.survfit.Rd b/man/autoplot.survfit.Rd index 0aa615e..aa5e30a 100644 --- a/man/autoplot.survfit.Rd +++ b/man/autoplot.survfit.Rd @@ -13,9 +13,9 @@ conf.int.alpha = 0.3, censor = TRUE, censor.colour = NULL, censor.size = 3, censor.alpha = NULL, censor.shape = "+", facets = FALSE, nrow = NULL, ncol = 1, grid = FALSE, - strip_swap = FALSE, scales = "free_y", xlim = c(NA, NA), ylim = c(NA, - NA), log = "", main = NULL, xlab = NULL, ylab = NULL, asp = NULL, - ...) + strip_swap = FALSE, scales = "free_y", xlim = c(NA, NA), + ylim = c(NA, NA), log = "", main = NULL, xlab = NULL, + ylab = NULL, asp = NULL, ...) } \arguments{ \item{object}{\code{survival::survfit} instance} diff --git a/man/autoplot.ts.Rd b/man/autoplot.ts.Rd index 16769d0..26e4d08 100644 --- a/man/autoplot.ts.Rd +++ b/man/autoplot.ts.Rd @@ -12,12 +12,13 @@ \method{autoplot}{ts}(object, columns = NULL, group = NULL, is.date = NULL, index.name = "Index", p = NULL, ts.scale = FALSE, stacked = FALSE, facets = TRUE, nrow = NULL, ncol = 1, - scales = "free_y", ts.geom = "line", ts.colour = NULL, ts.size = NULL, - ts.linetype = NULL, ts.alpha = NULL, ts.fill = NULL, ts.shape = NULL, - geom = ts.geom, colour = ts.colour, size = ts.size, - linetype = ts.linetype, alpha = ts.alpha, fill = ts.fill, - shape = ts.shape, xlim = c(NA, NA), ylim = c(NA, NA), log = "", - main = NULL, xlab = "", ylab = "", asp = NULL, ...) + scales = "free_y", ts.geom = "line", ts.colour = NULL, + ts.size = NULL, ts.linetype = NULL, ts.alpha = NULL, + ts.fill = NULL, ts.shape = NULL, geom = ts.geom, + colour = ts.colour, size = ts.size, linetype = ts.linetype, + alpha = ts.alpha, fill = ts.fill, shape = ts.shape, xlim = c(NA, + NA), ylim = c(NA, NA), log = "", main = NULL, xlab = "", + ylab = "", asp = NULL, ...) } \arguments{ \item{object}{time-series-like instance} diff --git a/man/autoplot.tsmodel.Rd b/man/autoplot.tsmodel.Rd index f5d8fa7..94cc45e 100644 --- a/man/autoplot.tsmodel.Rd +++ b/man/autoplot.tsmodel.Rd @@ -11,9 +11,10 @@ \usage{ \method{autoplot}{tsmodel}(object, data = NULL, predict = NULL, is.date = NULL, ts.connect = TRUE, fitted.geom = "line", - fitted.colour = "#FF0000", fitted.size = NULL, fitted.linetype = NULL, - fitted.alpha = NULL, fitted.fill = NULL, fitted.shape = NULL, - predict.geom = "line", predict.colour = "#0000FF", predict.size = NULL, + fitted.colour = "#FF0000", fitted.size = NULL, + fitted.linetype = NULL, fitted.alpha = NULL, fitted.fill = NULL, + fitted.shape = NULL, predict.geom = "line", + predict.colour = "#0000FF", predict.size = NULL, predict.linetype = NULL, predict.alpha = NULL, predict.fill = NULL, predict.shape = NULL, conf.int = TRUE, conf.int.colour = "#0000FF", conf.int.linetype = "none", conf.int.fill = "#000000", diff --git a/man/autoplot.varprd.Rd b/man/autoplot.varprd.Rd index e54ae6b..cb9e9d0 100644 --- a/man/autoplot.varprd.Rd +++ b/man/autoplot.varprd.Rd @@ -5,11 +5,12 @@ \title{Autoplot \code{vars::varprd}} \usage{ \method{autoplot}{varprd}(object, is.date = NULL, ts.connect = TRUE, - scales = "free_y", predict.geom = "line", predict.colour = "#0000FF", - predict.size = NULL, predict.linetype = NULL, predict.alpha = NULL, - predict.fill = NULL, predict.shape = NULL, conf.int = TRUE, - conf.int.colour = "#0000FF", conf.int.linetype = "none", - conf.int.fill = "#000000", conf.int.alpha = 0.3, ...) + scales = "free_y", predict.geom = "line", + predict.colour = "#0000FF", predict.size = NULL, + predict.linetype = NULL, predict.alpha = NULL, predict.fill = NULL, + predict.shape = NULL, conf.int = TRUE, conf.int.colour = "#0000FF", + conf.int.linetype = "none", conf.int.fill = "#000000", + conf.int.alpha = 0.3, ...) } \arguments{ \item{object}{\code{vars::varpred} instance} diff --git a/man/fortify.ts.Rd b/man/fortify.ts.Rd index 923c040..0739337 100644 --- a/man/fortify.ts.Rd +++ b/man/fortify.ts.Rd @@ -4,9 +4,9 @@ \alias{fortify.ts} \title{Convert time-series-like to data.frame} \usage{ -\method{fortify}{ts}(model, data = NULL, columns = NULL, is.date = NULL, - index.name = "Index", data.name = "Data", scale = FALSE, melt = FALSE, - ...) +\method{fortify}{ts}(model, data = NULL, columns = NULL, + is.date = NULL, index.name = "Index", data.name = "Data", + scale = FALSE, melt = FALSE, ...) } \arguments{ \item{model}{time-series-like instance} diff --git a/man/ggbiplot.Rd b/man/ggbiplot.Rd index 0375af3..0fa02d0 100644 --- a/man/ggbiplot.Rd +++ b/man/ggbiplot.Rd @@ -8,18 +8,19 @@ ggbiplot(plot.data, loadings.data = NULL, colour = NULL, size = NULL, linetype = NULL, alpha = NULL, fill = NULL, shape = NULL, label = FALSE, label.label = "rownames", label.colour = colour, label.alpha = NULL, label.size = NULL, label.angle = NULL, - label.family = NULL, label.fontface = NULL, label.lineheight = NULL, - label.hjust = NULL, label.vjust = NULL, label.repel = FALSE, - loadings = FALSE, loadings.colour = "#FF0000", loadings.label = FALSE, - loadings.label.label = "rownames", loadings.label.colour = "#FF0000", - loadings.label.alpha = NULL, loadings.label.size = NULL, - loadings.label.angle = NULL, loadings.label.family = NULL, - loadings.label.fontface = NULL, loadings.label.lineheight = NULL, - loadings.label.hjust = NULL, loadings.label.vjust = NULL, - loadings.label.repel = FALSE, label.show.legend = NA, frame = FALSE, - frame.type = NULL, frame.colour = colour, frame.level = 0.95, - frame.alpha = 0.2, xlim = c(NA, NA), ylim = c(NA, NA), log = "", - main = NULL, xlab = NULL, ylab = NULL, asp = NULL, ...) + label.family = NULL, label.fontface = NULL, + label.lineheight = NULL, label.hjust = NULL, label.vjust = NULL, + label.repel = FALSE, loadings = FALSE, loadings.colour = "#FF0000", + loadings.label = FALSE, loadings.label.label = "rownames", + loadings.label.colour = "#FF0000", loadings.label.alpha = NULL, + loadings.label.size = NULL, loadings.label.angle = NULL, + loadings.label.family = NULL, loadings.label.fontface = NULL, + loadings.label.lineheight = NULL, loadings.label.hjust = NULL, + loadings.label.vjust = NULL, loadings.label.repel = FALSE, + label.show.legend = NA, frame = FALSE, frame.type = NULL, + frame.colour = colour, frame.level = 0.95, frame.alpha = 0.2, + xlim = c(NA, NA), ylim = c(NA, NA), log = "", main = NULL, + xlab = NULL, ylab = NULL, asp = NULL, ...) } \arguments{ \item{plot.data}{data.frame} diff --git a/man/ggdistribution.Rd b/man/ggdistribution.Rd index 2c62407..30acfd5 100644 --- a/man/ggdistribution.Rd +++ b/man/ggdistribution.Rd @@ -4,8 +4,8 @@ \alias{ggdistribution} \title{Plot distribution} \usage{ -ggdistribution(func, x, p = NULL, colour = "#000000", linetype = NULL, - fill = NULL, alpha = NULL, ...) +ggdistribution(func, x, p = NULL, colour = "#000000", + linetype = NULL, fill = NULL, alpha = NULL, ...) } \arguments{ \item{func}{PDF or CDF function} diff --git a/man/ggfreqplot.Rd b/man/ggfreqplot.Rd index fa23af0..7ba4c37 100644 --- a/man/ggfreqplot.Rd +++ b/man/ggfreqplot.Rd @@ -7,7 +7,8 @@ ggfreqplot(data, freq = NULL, nrow = NULL, ncol = NULL, conf.int = FALSE, conf.int.colour = "#0000FF", conf.int.linetype = "dashed", conf.int.fill = NULL, - conf.int.alpha = 0.3, conf.int.value = 0.95, facet.labeller = NULL, ...) + conf.int.alpha = 0.3, conf.int.value = 0.95, facet.labeller = NULL, + ...) } \arguments{ \item{data}{\code{stats::ts} instance} diff --git a/man/ggmultiplot-class.Rd b/man/ggmultiplot-class.Rd index c84dcc9..9a24c50 100644 --- a/man/ggmultiplot-class.Rd +++ b/man/ggmultiplot-class.Rd @@ -4,7 +4,6 @@ \name{ggmultiplot-class} \alias{ggmultiplot-class} \alias{length,ggmultiplot-method} -\alias{[,ggmultiplot,ANY,ANY-method} \alias{[,ggmultiplot-method} \alias{[[,ggmultiplot-method} \alias{[<-,ggmultiplot-method} @@ -13,7 +12,7 @@ \usage{ \S4method{length}{ggmultiplot}(x) -\S4method{[}{ggmultiplot,ANY,ANY}(x, i, j, ..., drop = TRUE) +\S4method{[}{ggmultiplot}(x, i, j, ..., drop = TRUE) \S4method{[[}{ggmultiplot}(x, i, j, ..., drop) diff --git a/man/ggtsdiag.Rd b/man/ggtsdiag.Rd index f769975..08dbaad 100644 --- a/man/ggtsdiag.Rd +++ b/man/ggtsdiag.Rd @@ -7,7 +7,8 @@ ggtsdiag(object, gof.lag = 10, conf.int = TRUE, conf.int.colour = "#0000FF", conf.int.linetype = "dashed", conf.int.fill = NULL, conf.int.alpha = 0.3, ad.colour = "#888888", - ad.linetype = "dashed", ad.size = 0.2, nrow = NULL, ncol = 1, ...) + ad.linetype = "dashed", ad.size = 0.2, nrow = NULL, ncol = 1, + ...) } \arguments{ \item{object}{A fitted time-series model}