From a129cefac73cd4d95381df3cfaf2599560c55448 Mon Sep 17 00:00:00 2001 From: Sergey Kucheryavskiy Date: Thu, 3 Jan 2019 09:40:53 +0100 Subject: [PATCH] Help files were re-created. --- DESCRIPTION | 3 ++- NAMESPACE | 2 ++ R/pca.R | 4 +++- R/pls.R | 4 +++- man/getRegcoeffs.pls.Rd | 7 ++++--- man/ipls.Rd | 7 ++++--- man/ldecomp.getDistances.Rd | 3 ++- man/mdaplot.Rd | 9 +++++---- man/mdaplot.getAxesLim.Rd | 4 ++-- man/mdaplot.plotAxes.Rd | 6 +++--- man/mdaplot.showLines.Rd | 3 ++- man/mdaplot.showRegressionLine.Rd | 4 ++-- man/mdaplotg.Rd | 15 ++++++++------- man/pca.Rd | 7 ++++--- man/pca.cal.Rd | 4 ++-- man/pca.mvreplace.Rd | 4 ++-- man/plot.randtest.Rd | 4 ++-- man/plot.regcoeffs.Rd | 6 +++--- man/plotCooman.simcamres.Rd | 4 ++-- man/plotCumVariance.ldecomp.Rd | 4 ++-- man/plotModelDistance.simcam.Rd | 4 ++-- man/plotPerformance.classmodel.Rd | 6 +++--- man/plotPredictions.plsres.Rd | 4 ++-- man/plotPredictions.regres.Rd | 6 +++--- man/plotRMSE.ipls.Rd | 14 +++++++------- man/plotRMSE.regres.Rd | 3 ++- man/plotResiduals.pcares.Rd | 4 ++-- man/plotResiduals.simcares.Rd | 6 +++--- man/plotScores.pca.Rd | 6 +++--- man/plotSelection.ipls.Rd | 5 +++-- man/plotSelectivityRatio.pls.Rd | 4 ++-- man/plotVariance.ldecomp.Rd | 4 ++-- man/plotVariance.pca.Rd | 4 ++-- man/plotVariance.pls.Rd | 7 ++++--- man/plotXCumVariance.plsres.Rd | 3 ++- man/plotXResiduals.pls.Rd | 4 ++-- man/plotXScores.plsres.Rd | 3 ++- man/plotYCumVariance.plsres.Rd | 3 ++- man/plotYResiduals.regres.Rd | 4 ++-- man/pls.Rd | 9 ++++++--- man/pls.cal.Rd | 5 +++-- man/plsda.Rd | 5 +++-- man/prep.autoscale.Rd | 9 +++++++-- man/randtest.Rd | 3 ++- man/selectCompNum.Rd | 4 +++- man/selectCompNum.pca.Rd | 4 +++- man/selectCompNum.pls.Rd | 13 +++++++++++-- man/setResLimits.pca.Rd | 3 ++- man/summary.regcoeffs.Rd | 3 ++- 49 files changed, 151 insertions(+), 105 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1aa49a6..5eca34e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -6,11 +6,12 @@ Author: Sergey Kucheryavskiy Maintainer: Sergey Kucheryavskiy Description: Package implements projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics. +Encoding: UTF-8 License: MIT + file LICENSE Imports: methods, graphics, grDevices, stats -RoxygenNote: 6.0.1 +RoxygenNote: 6.1.1 Suggests: testthat diff --git a/NAMESPACE b/NAMESPACE index 038c6fe..1674d5e 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -130,6 +130,8 @@ S3method(summary,simca) S3method(summary,simcam) S3method(summary,simcamres) S3method(summary,simcares) +export(classres) +export(crossval) export(erfinv) export(getCalibrationData) export(getConfusionMatrix) diff --git a/R/pca.R b/R/pca.R index d1b5741..c996eb1 100755 --- a/R/pca.R +++ b/R/pca.R @@ -222,12 +222,14 @@ getCalibrationData.pca = function(obj, ...) { #' PCA model (object of class \code{pca}) #' @param ncomp #' number of components to select +#' @param ... +#' other parameters if any #' #' @return #' the same model with selected number of components #' #' @export -selectCompNum.pca = function(model, ncomp) { +selectCompNum.pca = function(model, ncomp, ...) { if (ncomp < 1 || ncomp > model$ncomp) stop('Wrong number of selected components!') diff --git a/R/pls.R b/R/pls.R index 46220cd..bb598ad 100755 --- a/R/pls.R +++ b/R/pls.R @@ -801,6 +801,8 @@ pls.crossval = function(model, x, y, cv, center, scale, method, jack.knife = T) #' @param selcrit #' criterion for selecting optimal number of components (\code{'min'} for #' first local minimum of RMSECV and \code{'wold'} for Wold's rule.) +#' @param ... +#' other parameters if any #' #' @return #' the same model with selected number of components @@ -813,7 +815,7 @@ pls.crossval = function(model, x, y, cv, center, scale, method, jack.knife = T) #' See examples in help for \code{\link{pls}} function. #' #' @export -selectCompNum.pls = function(model, ncomp = NULL, selcrit = model$ncomp.selcrit) { +selectCompNum.pls = function(model, ncomp = NULL, selcrit = model$ncomp.selcrit, ...) { if (!is.null(ncomp)) { # user defined number of components if (ncomp > model$ncomp || ncomp < 0) diff --git a/man/getRegcoeffs.pls.Rd b/man/getRegcoeffs.pls.Rd index 7c64109..0d3babe 100644 --- a/man/getRegcoeffs.pls.Rd +++ b/man/getRegcoeffs.pls.Rd @@ -4,8 +4,8 @@ \alias{getRegcoeffs.pls} \title{Regression coefficients for PLS model'} \usage{ -\method{getRegcoeffs}{pls}(obj, ncomp = NULL, ny = NULL, full = FALSE, - alpha = obj$coeffs.alpha, ...) +\method{getRegcoeffs}{pls}(obj, ncomp = NULL, ny = NULL, + full = FALSE, alpha = obj$coeffs.alpha, ...) } \arguments{ \item{obj}{a PLS model (object of class \code{pls})} @@ -14,7 +14,8 @@ \item{ny}{if y is multivariate which variables you want to see the coefficients for} -\item{full}{if TRUE the method also shows p-values and t-values as well as confidence intervals for the coefficients (if available)} +\item{full}{if TRUE the method also shows p-values and t-values as well as confidence intervals for the +coefficients (if available)} \item{alpha}{significance level for confidence intervals (a number between 0 and 1, e.g. for 95\% alpha = 0.05)} diff --git a/man/ipls.Rd b/man/ipls.Rd index 9c1af51..1db67aa 100644 --- a/man/ipls.Rd +++ b/man/ipls.Rd @@ -5,9 +5,10 @@ \title{Variable selection with interval PLS} \usage{ ipls(x, y, glob.ncomp = 10, center = T, scale = F, cv = 10, - exclcols = NULL, exclrows = NULL, int.ncomp = 10, int.num = NULL, - int.width = NULL, int.limits = NULL, int.niter = NULL, - ncomp.selcrit = "min", method = "forward", silent = F) + exclcols = NULL, exclrows = NULL, int.ncomp = glob.ncomp, + int.num = NULL, int.width = NULL, int.limits = NULL, + int.niter = NULL, ncomp.selcrit = "min", method = "forward", + silent = F) } \arguments{ \item{x}{a matrix with predictor values} diff --git a/man/ldecomp.getDistances.Rd b/man/ldecomp.getDistances.Rd index 1a5504c..97666c8 100644 --- a/man/ldecomp.getDistances.Rd +++ b/man/ldecomp.getDistances.Rd @@ -4,7 +4,8 @@ \alias{ldecomp.getDistances} \title{Residuals distances for linear decomposition} \usage{ -ldecomp.getDistances(scores, loadings, residuals, tnorm = NULL, cal = FALSE) +ldecomp.getDistances(scores, loadings, residuals, tnorm = NULL, + cal = FALSE) } \arguments{ \item{scores}{matrix with scores (T).} diff --git a/man/mdaplot.Rd b/man/mdaplot.Rd index e684942..b061293 100644 --- a/man/mdaplot.Rd +++ b/man/mdaplot.Rd @@ -9,10 +9,11 @@ mdaplot(data = NULL, plot.data = NULL, type = "p", pch = 16, xlim = NULL, ylim = NULL, colmap = "default", labels = NULL, main = NULL, xlab = NULL, ylab = NULL, show.labels = F, show.colorbar = T, show.lines = F, show.grid = T, show.axes = T, - xticks = NULL, yticks = NULL, xticklabels = NULL, yticklabels = NULL, - xlas = 0, ylas = 0, lab.col = "darkgray", lab.cex = 0.65, - show.excluded = FALSE, col.excluded = "#E0E0E0", nbins = 256, - colramp = mdaplot.getColors, force.x.values = NA, opacity = 1, ...) + xticks = NULL, yticks = NULL, xticklabels = NULL, + yticklabels = NULL, xlas = 0, ylas = 0, lab.col = "darkgray", + lab.cex = 0.65, show.excluded = FALSE, col.excluded = "#E0E0E0", + nbins = 256, colramp = mdaplot.getColors, force.x.values = NA, + opacity = 1, ...) } \arguments{ \item{data}{a vector, matrix or a data.frame with data values.} diff --git a/man/mdaplot.getAxesLim.Rd b/man/mdaplot.getAxesLim.Rd index efe238e..f3cbdfa 100644 --- a/man/mdaplot.getAxesLim.Rd +++ b/man/mdaplot.getAxesLim.Rd @@ -5,8 +5,8 @@ \title{Calculate axes limits} \usage{ mdaplot.getAxesLim(x.values, y.values, lower = NULL, upper = NULL, - show.colorbar = F, show.lines = F, legend = NULL, show.legend = F, - legend.position = "topright", show.labels = F) + show.colorbar = F, show.lines = F, legend = NULL, + show.legend = F, legend.position = "topright", show.labels = F) } \arguments{ \item{x.values}{a vector with x values.} diff --git a/man/mdaplot.plotAxes.Rd b/man/mdaplot.plotAxes.Rd index b336f73..62960ef 100644 --- a/man/mdaplot.plotAxes.Rd +++ b/man/mdaplot.plotAxes.Rd @@ -4,9 +4,9 @@ \alias{mdaplot.plotAxes} \title{Create axes plane} \usage{ -mdaplot.plotAxes(xticklabels = NULL, yticklabels = NULL, xticks = NULL, - yticks = NULL, lim = NULL, main = NULL, xlab = NULL, ylab = NULL, - xlas = 0, ylas = 0) +mdaplot.plotAxes(xticklabels = NULL, yticklabels = NULL, + xticks = NULL, yticks = NULL, lim = NULL, main = NULL, + xlab = NULL, ylab = NULL, xlas = 0, ylas = 0) } \arguments{ \item{xticklabels}{labels for x ticks} diff --git a/man/mdaplot.showLines.Rd b/man/mdaplot.showLines.Rd index 9eb9610..b554fb9 100644 --- a/man/mdaplot.showLines.Rd +++ b/man/mdaplot.showLines.Rd @@ -4,7 +4,8 @@ \alias{mdaplot.showLines} \title{Plot lines} \usage{ -mdaplot.showLines(point, lty = 2, lwd = 0.75, col = rgb(0.2, 0.2, 0.2)) +mdaplot.showLines(point, lty = 2, lwd = 0.75, col = rgb(0.2, 0.2, + 0.2)) } \arguments{ \item{point}{vector with two values: x coordinate for vertical point y for horizontal} diff --git a/man/mdaplot.showRegressionLine.Rd b/man/mdaplot.showRegressionLine.Rd index a4517e5..a99d36c 100644 --- a/man/mdaplot.showRegressionLine.Rd +++ b/man/mdaplot.showRegressionLine.Rd @@ -4,8 +4,8 @@ \alias{mdaplot.showRegressionLine} \title{Regression line for data points} \usage{ -mdaplot.showRegressionLine(data, lty = 1, lwd = 1, colmap = "default", - col = NULL) +mdaplot.showRegressionLine(data, lty = 1, lwd = 1, + colmap = "default", col = NULL) } \arguments{ \item{data}{data values} diff --git a/man/mdaplotg.Rd b/man/mdaplotg.Rd index 9f7b746..78929b4 100644 --- a/man/mdaplotg.Rd +++ b/man/mdaplotg.Rd @@ -4,13 +4,14 @@ \alias{mdaplotg} \title{Plotting function for several sets of objects} \usage{ -mdaplotg(data, groupby = NULL, type = "p", pch = 16, lty = 1, lwd = 1, - bwd = 0.8, legend = NULL, xlab = NULL, ylab = NULL, main = NULL, - labels = NULL, ylim = NULL, xlim = NULL, colmap = "default", - legend.position = "topright", show.legend = T, show.labels = F, - show.lines = F, show.grid = T, xticks = NULL, xticklabels = NULL, - yticks = NULL, yticklabels = NULL, show.excluded = FALSE, - lab.col = "darkgray", lab.cex = 0.65, xlas = 1, ylas = 1, ...) +mdaplotg(data, groupby = NULL, type = "p", pch = 16, lty = 1, + lwd = 1, bwd = 0.8, legend = NULL, xlab = NULL, ylab = NULL, + main = NULL, labels = NULL, ylim = NULL, xlim = NULL, + colmap = "default", legend.position = "topright", show.legend = T, + show.labels = F, show.lines = F, show.grid = T, xticks = NULL, + xticklabels = NULL, yticks = NULL, yticklabels = NULL, + show.excluded = FALSE, lab.col = "darkgray", lab.cex = 0.65, + xlas = 1, ylas = 1, ...) } \arguments{ \item{data}{a matrix, data frame or a list with data values (see details below).} diff --git a/man/pca.Rd b/man/pca.Rd index 2a6e76c..5907c5a 100644 --- a/man/pca.Rd +++ b/man/pca.Rd @@ -4,9 +4,10 @@ \alias{pca} \title{Principal Component Analysis} \usage{ -pca(x, ncomp = 15, center = T, scale = F, cv = NULL, exclrows = NULL, - exclcols = NULL, x.test = NULL, method = "svd", rand = NULL, - lim.type = "jm", alpha = 0.05, gamma = 0.01, info = "") +pca(x, ncomp = 15, center = T, scale = F, cv = NULL, + exclrows = NULL, exclcols = NULL, x.test = NULL, method = "svd", + rand = NULL, lim.type = "jm", alpha = 0.05, gamma = 0.01, + info = "") } \arguments{ \item{x}{a numerical matrix with calibration data.} diff --git a/man/pca.cal.Rd b/man/pca.cal.Rd index 4341ea5..78d0688 100644 --- a/man/pca.cal.Rd +++ b/man/pca.cal.Rd @@ -4,8 +4,8 @@ \alias{pca.cal} \title{PCA model calibration} \usage{ -pca.cal(x, ncomp, center, scale, method, exclcols = NULL, exclrows = NULL, - cv, rand, lim.type, alpha, gamma, info) +pca.cal(x, ncomp, center, scale, method, exclcols = NULL, + exclrows = NULL, cv, rand, lim.type, alpha, gamma, info) } \arguments{ \item{x}{matrix with data values} diff --git a/man/pca.mvreplace.Rd b/man/pca.mvreplace.Rd index f4b32c6..7be265f 100644 --- a/man/pca.mvreplace.Rd +++ b/man/pca.mvreplace.Rd @@ -4,8 +4,8 @@ \alias{pca.mvreplace} \title{Replace missing values in data} \usage{ -pca.mvreplace(x, center = T, scale = F, maxncomp = 7, expvarlim = 0.95, - covlim = 10^-6, maxiter = 100) +pca.mvreplace(x, center = T, scale = F, maxncomp = 7, + expvarlim = 0.95, covlim = 10^-6, maxiter = 100) } \arguments{ \item{x}{a matrix with data, containing missing values.} diff --git a/man/plot.randtest.Rd b/man/plot.randtest.Rd index 8b00ea4..2d15577 100644 --- a/man/plot.randtest.Rd +++ b/man/plot.randtest.Rd @@ -4,8 +4,8 @@ \alias{plot.randtest} \title{Plot for randomization test results} \usage{ -\method{plot}{randtest}(x, main = "Alpha", xlab = "Components", ylab = "", - ...) +\method{plot}{randtest}(x, main = "Alpha", xlab = "Components", + ylab = "", ...) } \arguments{ \item{x}{results of randomization test (object of class `randtest`)} diff --git a/man/plot.regcoeffs.Rd b/man/plot.regcoeffs.Rd index 5e92382..bd4f9d3 100644 --- a/man/plot.regcoeffs.Rd +++ b/man/plot.regcoeffs.Rd @@ -4,9 +4,9 @@ \alias{plot.regcoeffs} \title{Regression coefficients plot} \usage{ -\method{plot}{regcoeffs}(x, ncomp = 1, ny = 1, type = NULL, col = NULL, - main = NULL, ylab = NULL, show.line = T, show.ci = T, alpha = 0.05, - ...) +\method{plot}{regcoeffs}(x, ncomp = 1, ny = 1, type = NULL, + col = NULL, main = NULL, ylab = NULL, show.line = T, + show.ci = T, alpha = 0.05, ...) } \arguments{ \item{x}{regression coefficients object (class \code{regcoeffs})} diff --git a/man/plotCooman.simcamres.Rd b/man/plotCooman.simcamres.Rd index 6e37658..0a609f0 100644 --- a/man/plotCooman.simcamres.Rd +++ b/man/plotCooman.simcamres.Rd @@ -5,8 +5,8 @@ \title{Cooman's plot for SIMCAM results} \usage{ \method{plotCooman}{simcamres}(obj, nc = c(1, 2), type = "p", - main = "Cooman's plot", xlab = NULL, ylab = NULL, show.limits = T, - legend = NULL, ...) + main = "Cooman's plot", xlab = NULL, ylab = NULL, + show.limits = T, legend = NULL, ...) } \arguments{ \item{obj}{SIMCAM results (object of class \code{simcamres})} diff --git a/man/plotCumVariance.ldecomp.Rd b/man/plotCumVariance.ldecomp.Rd index a2bb956..a66aee6 100644 --- a/man/plotCumVariance.ldecomp.Rd +++ b/man/plotCumVariance.ldecomp.Rd @@ -6,8 +6,8 @@ \usage{ \method{plotCumVariance}{ldecomp}(obj, type = "b", main = "Cumulative variance", xlab = "Components", - ylab = "Explained variance, \%", show.labels = F, labels = "values", - ...) + ylab = "Explained variance, \%", show.labels = F, + labels = "values", ...) } \arguments{ \item{obj}{object of \code{ldecomp} class.} diff --git a/man/plotModelDistance.simcam.Rd b/man/plotModelDistance.simcam.Rd index 10ebbc3..5b2c3ff 100644 --- a/man/plotModelDistance.simcam.Rd +++ b/man/plotModelDistance.simcam.Rd @@ -4,8 +4,8 @@ \alias{plotModelDistance.simcam} \title{Modelling distance plot for SIMCAM model} \usage{ -\method{plotModelDistance}{simcam}(obj, nc = 1, type = "h", main = NULL, - xlab = "Models", ylab = "", ...) +\method{plotModelDistance}{simcam}(obj, nc = 1, type = "h", + main = NULL, xlab = "Models", ylab = "", ...) } \arguments{ \item{obj}{a SIMCAM model (object of class \code{simcam})} diff --git a/man/plotPerformance.classmodel.Rd b/man/plotPerformance.classmodel.Rd index f296b8d..d8f48bc 100644 --- a/man/plotPerformance.classmodel.Rd +++ b/man/plotPerformance.classmodel.Rd @@ -4,9 +4,9 @@ \alias{plotPerformance.classmodel} \title{Performance plot for classification model} \usage{ -\method{plotPerformance}{classmodel}(obj, nc = NULL, param = "specificity", - type = "h", main = NULL, xlab = "Components", ylab = "", ylim = c(0, - 1.15), ...) +\method{plotPerformance}{classmodel}(obj, nc = NULL, + param = "specificity", type = "h", main = NULL, + xlab = "Components", ylab = "", ylim = c(0, 1.15), ...) } \arguments{ \item{obj}{classification model (object of class \code{plsda}, \code{simca}, etc.).} diff --git a/man/plotPredictions.plsres.Rd b/man/plotPredictions.plsres.Rd index a42cdce..d695b3c 100644 --- a/man/plotPredictions.plsres.Rd +++ b/man/plotPredictions.plsres.Rd @@ -4,8 +4,8 @@ \alias{plotPredictions.plsres} \title{Predictions plot for PLS results} \usage{ -\method{plotPredictions}{plsres}(obj, ny = 1, ncomp = NULL, main = NULL, - ...) +\method{plotPredictions}{plsres}(obj, ny = 1, ncomp = NULL, + main = NULL, ...) } \arguments{ \item{obj}{PLS results (object of class \code{plsres})} diff --git a/man/plotPredictions.regres.Rd b/man/plotPredictions.regres.Rd index b736d52..8760258 100644 --- a/man/plotPredictions.regres.Rd +++ b/man/plotPredictions.regres.Rd @@ -4,9 +4,9 @@ \alias{plotPredictions.regres} \title{Predictions plot for regression results} \usage{ -\method{plotPredictions}{regres}(obj, ny = 1, ncomp = NULL, show.line = T, - show.stat = F, stat.col = "#606060", stat.cex = 0.85, axes.equal = T, - col = mdaplot.getColors(1), ...) +\method{plotPredictions}{regres}(obj, ny = 1, ncomp = NULL, + show.line = T, show.stat = F, stat.col = "#606060", + stat.cex = 0.85, axes.equal = T, col = mdaplot.getColors(1), ...) } \arguments{ \item{obj}{regression results (object of class \code{regres})} diff --git a/man/plotRMSE.ipls.Rd b/man/plotRMSE.ipls.Rd index 17c6698..32d3299 100644 --- a/man/plotRMSE.ipls.Rd +++ b/man/plotRMSE.ipls.Rd @@ -4,8 +4,9 @@ \alias{plotRMSE.ipls} \title{RMSE development plot} \usage{ -\method{plotRMSE}{ipls}(obj, glob.ncomp = NULL, main = "RMSE development", - xlab = "Iterations", ylab = "RMSECV", xlim = NULL, ylim = NULL, ...) +\method{plotRMSE}{ipls}(obj, glob.ncomp = NULL, + main = "RMSE development", xlab = "Iterations", ylab = "RMSECV", + xlim = NULL, ylim = NULL, ...) } \arguments{ \item{obj}{iPLS results (object of class ipls)} @@ -29,11 +30,10 @@ Shows how RMSE develops for each iteration of iPLS selection algorithm } \details{ -The plot shows RMSE values obtained at each iteration of the iPLS selection -algorithm as bars. The first bar correspond to the global model with all variables -included, second - to the model obtained at the first iteration and so on. Number -at the bottom of each bar corresponds to the interval included or excluded at the -particular iteration. The selected intervals are shown with green color. +The plot shows RMSE values obtained at each iteration of the iPLS algorithm as bars. The first +bar correspond to the global model with all variables included, second - to the model obtained +at the first iteration and so on. Number at the bottom of each bar corresponds to the interval +included or excluded at the particular iteration. } \seealso{ \code{\link{summary.ipls}}, \code{\link{plotSelection.ipls}} diff --git a/man/plotRMSE.regres.Rd b/man/plotRMSE.regres.Rd index a7bb5bb..e76c870 100644 --- a/man/plotRMSE.regres.Rd +++ b/man/plotRMSE.regres.Rd @@ -4,7 +4,8 @@ \alias{plotRMSE.regres} \title{RMSE plot for regression results} \usage{ -\method{plotRMSE}{regres}(obj, ny = 1, type = "b", labels = "values", ...) +\method{plotRMSE}{regres}(obj, ny = 1, type = "b", labels = "values", + ...) } \arguments{ \item{obj}{regression results (object of class \code{regres})} diff --git a/man/plotResiduals.pcares.Rd b/man/plotResiduals.pcares.Rd index d1c73ea..050ae9b 100644 --- a/man/plotResiduals.pcares.Rd +++ b/man/plotResiduals.pcares.Rd @@ -6,8 +6,8 @@ \usage{ \method{plotResiduals}{pcares}(obj, ncomp = NULL, main = NULL, xlab = NULL, ylab = NULL, show.labels = F, show.limits = T, - norm = F, xlim = NULL, ylim = NULL, lim.col = c("#333333", "#333333"), - lim.lwd = c(1, 1), lim.lty = c(2, 3), ...) + norm = F, xlim = NULL, ylim = NULL, lim.col = c("#333333", + "#333333"), lim.lwd = c(1, 1), lim.lty = c(2, 3), ...) } \arguments{ \item{obj}{object of \code{ldecomp} class.} diff --git a/man/plotResiduals.simcares.Rd b/man/plotResiduals.simcares.Rd index 0b47a9a..ab3d298 100644 --- a/man/plotResiduals.simcares.Rd +++ b/man/plotResiduals.simcares.Rd @@ -5,9 +5,9 @@ \title{Residuals plot for SIMCA results} \usage{ \method{plotResiduals}{simcares}(obj, ncomp = NULL, main = NULL, - xlab = NULL, ylab = NULL, norm = F, show.limits = T, legend = NULL, - lim.col = c("#c0a0a0", "#906060"), lim.lwd = c(1, 1), lim.lty = c(2, 3), - ...) + xlab = NULL, ylab = NULL, norm = F, show.limits = T, + legend = NULL, lim.col = c("#c0a0a0", "#906060"), lim.lwd = c(1, + 1), lim.lty = c(2, 3), ...) } \arguments{ \item{obj}{SIMCA results (object of class \code{simcares})} diff --git a/man/plotScores.pca.Rd b/man/plotScores.pca.Rd index d20d5c3..00fac45 100644 --- a/man/plotScores.pca.Rd +++ b/man/plotScores.pca.Rd @@ -4,9 +4,9 @@ \alias{plotScores.pca} \title{Scores plot for PCA} \usage{ -\method{plotScores}{pca}(obj, comp = c(1, 2), type = "p", main = "Scores", - xlab = NULL, ylab = NULL, show.labels = F, show.legend = NULL, - cgroup = NULL, show.axes = TRUE, ...) +\method{plotScores}{pca}(obj, comp = c(1, 2), type = "p", + main = "Scores", xlab = NULL, ylab = NULL, show.labels = F, + show.legend = NULL, cgroup = NULL, show.axes = TRUE, ...) } \arguments{ \item{obj}{a PCA model (object of class \code{pca})} diff --git a/man/plotSelection.ipls.Rd b/man/plotSelection.ipls.Rd index dae1574..17ffb00 100644 --- a/man/plotSelection.ipls.Rd +++ b/man/plotSelection.ipls.Rd @@ -4,8 +4,9 @@ \alias{plotSelection.ipls} \title{iPLS performance plot} \usage{ -\method{plotSelection}{ipls}(obj, glob.ncomp = NULL, main = "iPLS results", - xlab = obj$xaxis.name, ylab = "RMSECV", xlim = NULL, ylim = NULL, ...) +\method{plotSelection}{ipls}(obj, glob.ncomp = NULL, + main = "iPLS results", xlab = obj$xaxis.name, ylab = "RMSECV", + xlim = NULL, ylim = NULL, ...) } \arguments{ \item{obj}{iPLS results (object of class ipls)} diff --git a/man/plotSelectivityRatio.pls.Rd b/man/plotSelectivityRatio.pls.Rd index febe11d..ca9bbae 100644 --- a/man/plotSelectivityRatio.pls.Rd +++ b/man/plotSelectivityRatio.pls.Rd @@ -4,8 +4,8 @@ \alias{plotSelectivityRatio.pls} \title{Selectivity ratio plot for PLS model} \usage{ -\method{plotSelectivityRatio}{pls}(obj, ncomp = NULL, ny = 1, type = "l", - main = NULL, ylab = "", ...) +\method{plotSelectivityRatio}{pls}(obj, ncomp = NULL, ny = 1, + type = "l", main = NULL, ylab = "", ...) } \arguments{ \item{obj}{a PLS model (object of class \code{pls})} diff --git a/man/plotVariance.ldecomp.Rd b/man/plotVariance.ldecomp.Rd index 53b075a..5086811 100644 --- a/man/plotVariance.ldecomp.Rd +++ b/man/plotVariance.ldecomp.Rd @@ -5,8 +5,8 @@ \title{Explained variance plot for linear decomposition} \usage{ \method{plotVariance}{ldecomp}(obj, type = "b", main = "Variance", - xlab = "Components", ylab = "Explained variance, \%", show.labels = F, - labels = "values", ...) + xlab = "Components", ylab = "Explained variance, \%", + show.labels = F, labels = "values", ...) } \arguments{ \item{obj}{object of \code{ldecomp} class.} diff --git a/man/plotVariance.pca.Rd b/man/plotVariance.pca.Rd index 5355772..ffffcdf 100644 --- a/man/plotVariance.pca.Rd +++ b/man/plotVariance.pca.Rd @@ -5,8 +5,8 @@ \title{Explained variance plot for PCA} \usage{ \method{plotVariance}{pca}(obj, type = "b", variance = "expvar", - main = "Variance", xlab = "Components", ylab = "Explained variance, \%", - show.legend = T, ...) + main = "Variance", xlab = "Components", + ylab = "Explained variance, \%", show.legend = T, ...) } \arguments{ \item{obj}{a PCA model (object of class \code{pca})} diff --git a/man/plotVariance.pls.Rd b/man/plotVariance.pls.Rd index 8cd5724..e782518 100644 --- a/man/plotVariance.pls.Rd +++ b/man/plotVariance.pls.Rd @@ -4,9 +4,10 @@ \alias{plotVariance.pls} \title{Variance plot for PLS} \usage{ -\method{plotVariance}{pls}(obj, decomp = "xdecomp", variance = "expvar", - type = "b", main = "X variance", xlab = "Components", - ylab = "Explained variance, \%", labels = "values", ...) +\method{plotVariance}{pls}(obj, decomp = "xdecomp", + variance = "expvar", type = "b", main = "X variance", + xlab = "Components", ylab = "Explained variance, \%", + labels = "values", ...) } \arguments{ \item{obj}{a PLS model (object of class \code{pls})} diff --git a/man/plotXCumVariance.plsres.Rd b/man/plotXCumVariance.plsres.Rd index f6083a0..42edf37 100644 --- a/man/plotXCumVariance.plsres.Rd +++ b/man/plotXCumVariance.plsres.Rd @@ -4,7 +4,8 @@ \alias{plotXCumVariance.plsres} \title{Explained cumulative X variance plot for PLS results} \usage{ -\method{plotXCumVariance}{plsres}(obj, main = "X cumulative variance", ...) +\method{plotXCumVariance}{plsres}(obj, main = "X cumulative variance", + ...) } \arguments{ \item{obj}{PLS results (object of class \code{plsres})} diff --git a/man/plotXResiduals.pls.Rd b/man/plotXResiduals.pls.Rd index e13cbfd..8256b80 100644 --- a/man/plotXResiduals.pls.Rd +++ b/man/plotXResiduals.pls.Rd @@ -4,8 +4,8 @@ \alias{plotXResiduals.pls} \title{X residuals plot for PLS} \usage{ -\method{plotXResiduals}{pls}(obj, ncomp = NULL, main = NULL, xlab = "T2", - ylab = "Squared residual distance (Q)", ...) +\method{plotXResiduals}{pls}(obj, ncomp = NULL, main = NULL, + xlab = "T2", ylab = "Squared residual distance (Q)", ...) } \arguments{ \item{obj}{a PLS model (object of class \code{pls})} diff --git a/man/plotXScores.plsres.Rd b/man/plotXScores.plsres.Rd index 6085580..3aca554 100644 --- a/man/plotXScores.plsres.Rd +++ b/man/plotXScores.plsres.Rd @@ -4,7 +4,8 @@ \alias{plotXScores.plsres} \title{X scores plot for PLS results} \usage{ -\method{plotXScores}{plsres}(obj, comp = c(1, 2), main = "X scores", ...) +\method{plotXScores}{plsres}(obj, comp = c(1, 2), main = "X scores", + ...) } \arguments{ \item{obj}{PLS results (object of class \code{plsres})} diff --git a/man/plotYCumVariance.plsres.Rd b/man/plotYCumVariance.plsres.Rd index dedb67d..09f448b 100644 --- a/man/plotYCumVariance.plsres.Rd +++ b/man/plotYCumVariance.plsres.Rd @@ -4,7 +4,8 @@ \alias{plotYCumVariance.plsres} \title{Explained cumulative Y variance plot for PLS results} \usage{ -\method{plotYCumVariance}{plsres}(obj, main = "Y cumulative variance", ...) +\method{plotYCumVariance}{plsres}(obj, main = "Y cumulative variance", + ...) } \arguments{ \item{obj}{PLS results (object of class \code{plsres})} diff --git a/man/plotYResiduals.regres.Rd b/man/plotYResiduals.regres.Rd index 2c93ee8..be7ae5c 100644 --- a/man/plotYResiduals.regres.Rd +++ b/man/plotYResiduals.regres.Rd @@ -4,8 +4,8 @@ \alias{plotYResiduals.regres} \title{Residuals plot for regression results} \usage{ -\method{plotYResiduals}{regres}(obj, ny = 1, ncomp = NULL, show.line = T, - ...) +\method{plotYResiduals}{regres}(obj, ny = 1, ncomp = NULL, + show.line = T, ...) } \arguments{ \item{obj}{regression results (object of class \code{regres})} diff --git a/man/pls.Rd b/man/pls.Rd index 8d0b310..4c40bd0 100644 --- a/man/pls.Rd +++ b/man/pls.Rd @@ -55,11 +55,14 @@ Returns an object of \code{pls} class with following fields: \item{weights }{matrix with PLS weights.} \item{selratio }{array with selectivity ratio values.} \item{vipscores }{matrix with VIP scores values.} -\item{coeffs }{object of class \code{\link{regcoeffs}} with regression coefficients calculated for each component.} +\item{coeffs }{object of class \code{\link{regcoeffs}} with regression coefficients calculated +for each component.} \item{info }{information about the model, provided by user when build the model.} \item{calres }{an object of class \code{\link{plsres}} with PLS results for a calibration data.} -\item{testres }{an object of class \code{\link{plsres}} with PLS results for a test data, if it was provided.} -\item{cvres }{an object of class \code{\link{plsres}} with PLS results for cross-validation, if this option was chosen.} +\item{testres }{an object of class \code{\link{plsres}} with PLS results for a test data, if it +was provided.} +\item{cvres }{an object of class \code{\link{plsres}} with PLS results for cross-validation, if +this option was chosen.} } \description{ \code{pls} is used to calibrate, validate and use of partial least squares (PLS) diff --git a/man/pls.cal.Rd b/man/pls.cal.Rd index 085c924..8940038 100644 --- a/man/pls.cal.Rd +++ b/man/pls.cal.Rd @@ -4,8 +4,9 @@ \alias{pls.cal} \title{PLS model calibration} \usage{ -pls.cal(x, y, ncomp, center, scale, method, cv, alpha, coeffs.ci, coeffs.alpha, - info, light, exclcols = NULL, exclrows = NULL, ncomp.selcrit) +pls.cal(x, y, ncomp, center, scale, method, cv, alpha, coeffs.ci, + coeffs.alpha, info, light, exclcols = NULL, exclrows = NULL, + ncomp.selcrit) } \arguments{ \item{x}{a matrix with x values (predictors)} diff --git a/man/plsda.Rd b/man/plsda.Rd index 05c6e6b..2b90311 100644 --- a/man/plsda.Rd +++ b/man/plsda.Rd @@ -6,8 +6,9 @@ \usage{ plsda(x, c, ncomp = 15, center = T, scale = F, cv = NULL, exclcols = NULL, exclrows = NULL, x.test = NULL, c.test = NULL, - method = "simpls", alpha = 0.05, coeffs.ci = NULL, coeffs.alpha = 0.1, - info = "", light = F, ncomp.selcrit = "min", classname = NULL) + method = "simpls", alpha = 0.05, coeffs.ci = NULL, + coeffs.alpha = 0.1, info = "", light = F, ncomp.selcrit = "min", + classname = NULL) } \arguments{ \item{x}{matrix with predictors.} diff --git a/man/prep.autoscale.Rd b/man/prep.autoscale.Rd index 7aad067..c83d8b4 100644 --- a/man/prep.autoscale.Rd +++ b/man/prep.autoscale.Rd @@ -4,7 +4,7 @@ \alias{prep.autoscale} \title{Autoscale values} \usage{ -prep.autoscale(data, center = T, scale = F, max.cov = 0.1) +prep.autoscale(data, center = T, scale = F, max.cov = 0) } \arguments{ \item{data}{a matrix with data values} @@ -13,11 +13,16 @@ prep.autoscale(data, center = T, scale = F, max.cov = 0.1) \item{scale}{a logical value or vector with numbers for weighting} -\item{max.cov}{columns that have coefficient of variation (in percent) below `max.cv` will not be scaled} +\item{max.cov}{columns that have coefficient of variation (in percent) below or equal to `max.cov` will not be scaled} } \value{ data matrix with processed values } \description{ Autoscale (mean center and standardize) values in columns of data matrix. + +The use of `max.cov` allows to avoid overestimation of inert variables, which vary +very little. Note, that the `max.cov` value is already in percent, e.g. if `max.cov = 0.1` it +will compare the coefficient of variation of every variable with 0.1% (not 1%). If you do not +want to use this option simply keep `max.cov = 0`. } diff --git a/man/randtest.Rd b/man/randtest.Rd index e28f6ee..ee054ca 100644 --- a/man/randtest.Rd +++ b/man/randtest.Rd @@ -5,7 +5,8 @@ \title{Randomization test for PLS regression} \usage{ randtest(x, y, ncomp = 15, center = T, scale = F, nperm = 1000, - sig.level = 0.05, silent = TRUE, exclcols = NULL, exclrows = NULL) + sig.level = 0.05, silent = TRUE, exclcols = NULL, + exclrows = NULL) } \arguments{ \item{x}{matrix with predictors.} diff --git a/man/selectCompNum.Rd b/man/selectCompNum.Rd index c8a079b..1752ac3 100644 --- a/man/selectCompNum.Rd +++ b/man/selectCompNum.Rd @@ -4,12 +4,14 @@ \alias{selectCompNum} \title{Select optimal number of components for a model} \usage{ -selectCompNum(model, ncomp) +selectCompNum(model, ncomp = NULL, ...) } \arguments{ \item{model}{a model object} \item{ncomp}{number of components to select} + +\item{...}{other arguments} } \description{ Generic function for selecting number of components for multivariate models (e.g. PCA, PLS, ...) diff --git a/man/selectCompNum.pca.Rd b/man/selectCompNum.pca.Rd index 4d0f888..1b8bf5c 100644 --- a/man/selectCompNum.pca.Rd +++ b/man/selectCompNum.pca.Rd @@ -4,12 +4,14 @@ \alias{selectCompNum.pca} \title{Select optimal number of components for PCA model} \usage{ -\method{selectCompNum}{pca}(model, ncomp) +\method{selectCompNum}{pca}(model, ncomp, ...) } \arguments{ \item{model}{PCA model (object of class \code{pca})} \item{ncomp}{number of components to select} + +\item{...}{other parameters if any} } \value{ the same model with selected number of components diff --git a/man/selectCompNum.pls.Rd b/man/selectCompNum.pls.Rd index 1d852ed..c4150ad 100644 --- a/man/selectCompNum.pls.Rd +++ b/man/selectCompNum.pls.Rd @@ -4,12 +4,18 @@ \alias{selectCompNum.pls} \title{Select optimal number of components for PLS model} \usage{ -\method{selectCompNum}{pls}(model, ncomp = NULL) +\method{selectCompNum}{pls}(model, ncomp = NULL, + selcrit = model$ncomp.selcrit, ...) } \arguments{ \item{model}{PLS model (object of class \code{pls})} \item{ncomp}{number of components to select} + +\item{selcrit}{criterion for selecting optimal number of components (\code{'min'} for +first local minimum of RMSECV and \code{'wold'} for Wold's rule.)} + +\item{...}{other parameters if any} } \value{ the same model with selected number of components @@ -18,6 +24,9 @@ the same model with selected number of components Allows user to select optimal number of components for PLS model } \details{ -If number of components is not specified, the Wold's R criterion is used. +If number of components is not specified, the cross-validation statistics will be used. It can +be either first local minimum of RMSECV (`selcrit='min'`) or Wold's rule (`selcrit='wold'`) +based on ratio of PRESS values and threshold of 0.95. + See examples in help for \code{\link{pls}} function. } diff --git a/man/setResLimits.pca.Rd b/man/setResLimits.pca.Rd index a05fdb4..cee547d 100644 --- a/man/setResLimits.pca.Rd +++ b/man/setResLimits.pca.Rd @@ -4,7 +4,8 @@ \alias{setResLimits.pca} \title{Set statistical limits for Q and T2 residuals for PCA model} \usage{ -\method{setResLimits}{pca}(obj, alpha = obj$alpha, gamma = obj$gamma, ...) +\method{setResLimits}{pca}(obj, alpha = obj$alpha, gamma = obj$gamma, + ...) } \arguments{ \item{obj}{object with PCA model} diff --git a/man/summary.regcoeffs.Rd b/man/summary.regcoeffs.Rd index 94ac6d0..d21b9cd 100644 --- a/man/summary.regcoeffs.Rd +++ b/man/summary.regcoeffs.Rd @@ -4,7 +4,8 @@ \alias{summary.regcoeffs} \title{Summary method for regcoeffs object} \usage{ -\method{summary}{regcoeffs}(object, ncomp = 1, ny = 1, alpha = 0.05, ...) +\method{summary}{regcoeffs}(object, ncomp = 1, ny = 1, alpha = 0.05, + ...) } \arguments{ \item{object}{object of class \code{regcoeffs}}