1\name{plotrcim0} 2\alias{plotrcim0} 3%- Also NEED an '\alias' for EACH other topic documented here. 4\title{ Main Effects Plot for a Row-Column Interaction Model (RCIM) 5 6} 7\description{ 8 Produces a main effects plot for Row-Column Interaction 9 Models (RCIMs). 10 11} 12\usage{ 13 plotrcim0(object, centered = TRUE, which.plots = c(1, 2), 14 hline0 = TRUE, hlty = "dashed", hcol = par()$col, hlwd = par()$lwd, 15 rfirst = 1, cfirst = 1, 16 rtype = "h", ctype = "h", 17 rcex.lab = 1, rcex.axis = 1, rtick = FALSE, 18 ccex.lab = 1, ccex.axis = 1, ctick = FALSE, 19 rmain = "Row effects", rsub = "", 20 rxlab = "", rylab = "Row effects", 21 cmain = "Column effects", csub = "", 22 cxlab= "", cylab = "Column effects", 23 rcol = par()$col, ccol = par()$col, 24 no.warning = FALSE, ...) 25 26} 27\arguments{ 28\item{object}{ 29 An \code{\link{rcim}} object. 30 This should be of rank-0, i.e., main effects only and no 31 interactions. 32 33 34} 35\item{which.plots}{ 36 Numeric, describing which plots are to be plotted. 37 The row effects plot is 1 and the column effects plot is 2. 38 Set the value \code{0}, say, for no plots at all. 39 40 41} 42\item{centered}{ 43 Logical. 44 If \code{TRUE} then the row and column effects are centered 45 (but not scaled) by \code{\link[base]{scale}}. 46 If \code{FALSE} then the raw effects are used (of which 47 the first are zero by definition). 48 49 50} 51\item{hline0, hlty, hcol, hlwd}{ 52 \code{hline0} is logical. If \code{TRUE} then a horizontal line is 53 plotted at 0 and the other arguments describe this line. 54 Probably having \code{hline0 = TRUE} only makes sense when 55 \code{centered = TRUE}. 56 57 58} 59\item{rfirst, cfirst}{ 60 \code{rfirst} is the level of row that is placed first in the 61 row effects plot, etc. 62 63 64} 65\item{rmain, cmain}{ 66 Character. 67 \code{rmain} is the main label in the row effects plot, etc. 68 69 70} 71\item{rtype, ctype, rsub, csub}{ 72 See the \code{type} and \code{sub} arguments of 73 \code{\link[graphics]{plot.default}}. 74 75 76 77% 20201020; trying \code{\link[graphics]{plot.default}}. 78 79 80% 20200427; all \code{\link[graphics:plot]{plot}} changed to 81% \code{\link[base:plot]{plot}}, because of R.4.0.0. 82 83 84 85 86} 87%\item{rlabels, clabels}{ 88% rlabels = FALSE, clabels = FALSE, 89% Currently not functioning properly. 90% zz. 91% See \code{labels} argument of 92% \code{\link[base:plot]{plot}}. 93% 94%} 95\item{rxlab, rylab, cxlab, cylab}{ 96 Character. 97 For the row effects plot, 98 \code{rxlab} is \code{xlab} and 99 \code{rylab} is \code{ylab}; 100 see \code{\link[graphics:par]{par}}. 101 Ditto for \code{cxlab} and \code{cylab} for the column effects plot. 102 103 104} 105\item{rcex.lab, ccex.lab}{ 106 Numeric. 107 \code{rcex.lab} is \code{cex} for the row effects plot label, 108 etc. 109 110 111} 112\item{rcex.axis, ccex.axis}{ 113 Numeric. 114 \code{rcex.axis} is the \code{cex} argument for the row effects axis label, 115 etc. 116 117 118} 119 120\item{rtick, ctick}{ 121 Logical. 122 If \code{rtick = TRUE} then add ticks to the row effects plot, etc. 123 124 125} 126\item{rcol, ccol}{ 127 \code{rcol} give a colour for the row effects plot, 128 etc. 129 130 131} 132\item{no.warning}{ 133 Logical. If \code{TRUE} then no warning is issued if the 134 model is not rank-0. 135 136 137} 138%\item{llwd}{ 139% Fed into \code{lwd} of \code{\link[graphics:par]{par}}. 140% 141%} 142%\item{rlas, clas}{ 143% Fed into \code{las} of \code{\link[graphics:par]{par}}. 144% 145%} 146%\item{main}{ 147% Character. A common title. 148% 149%} 150%\item{type}{ 151% Fed into \code{type} of \code{\link[base:plot]{plot}}. 152% 153%} 154\item{...}{ 155 Arguments fed into 156 \code{\link[graphics]{plot.default}}, etc. 157 158 159 160% 20201026: was 161% Arguments fed into both \code{\link[base:plot]{plot}} calls. 162 163 164 165 166} 167 168} 169\details{ 170 This function plots the row and column effects of a rank-0 RCIM. 171 As the result is a main effects plot of a regression analysis, its 172 interpretation when \code{centered = FALSE} is relative 173 to the baseline (reference level) of a row and column, and 174 should also be considered in light of the link function used. 175 Many arguments that start with \code{"r"} refer to the row 176 effects plot, and \code{"c"} for the column 177 effects plot. 178 179 180} 181\value{ 182 The original object with the \code{post} slot 183 assigned additional information from the plot. 184 185 186} 187 188 189 190\note{ 191 This function should be only used to plot the object of rank-0 RCIM. 192 If the rank is positive then it will issue a warning. 193 194 195 Using an argument \code{ylim} will mean the row and column 196 effects are plotted on a common scale; 197 see \code{\link[graphics]{plot.window}}. 198 199 200% This function is not finished yet. 201% There may be several bugs! 202 203} 204 205 206\author{ 207 T. W. Yee, 208 A. F. Hadi. 209 210} 211 212%\section{Warning}{ 213% 214%} 215 216 217\seealso{ 218 \code{\link{moffset}} 219 \code{\link{Rcim}}, 220 \code{\link{rcim}}. 221 222 223 224} 225\examples{ 226alcoff.e <- moffset(alcoff, "6", "Mon", postfix = "*") # Effective day 227fit0 <- rcim(alcoff.e, family = poissonff) 228\dontrun{par(oma = c(0, 0, 4, 0), mfrow = 1:2) # For all plots below too 229ii <- plot(fit0, rcol = "blue", ccol = "orange", 230 lwd = 4, ylim = c(-2, 2), # A common ylim 231 cylab = "Effective daily effects", rylab = "Hourly effects", 232 rxlab = "Hour", cxlab = "Effective day") 233ii@post # Endowed with additional information 234} 235 236# Negative binomial example 237\dontrun{ 238fit1 <- rcim(alcoff.e, negbinomial, trace = TRUE) 239plot(fit1, ylim = c(-2, 2)) } 240 241# Univariate normal example 242fit2 <- rcim(alcoff.e, uninormal, trace = TRUE) 243\dontrun{ plot(fit2, ylim = c(-200, 400)) } 244 245# Median-polish example 246\dontrun{ 247fit3 <- rcim(alcoff.e, alaplace1(tau = 0.5), maxit = 1000, trace = FALSE) 248plot(fit3, ylim = c(-200, 250)) } 249 250# Zero-inflated Poisson example on "crashp" (no 0s in alcoff) 251\dontrun{ 252cbind(rowSums(crashp)) # Easy to see the data 253cbind(colSums(crashp)) # Easy to see the data 254fit4 <- rcim(Rcim(crashp, rbaseline = "5", cbaseline = "Sun"), 255 zipoissonff, trace = TRUE) 256plot(fit4, ylim = c(-3, 3)) } 257} 258