1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
|
##' Spaghetti plot for longitudinal data
##'
##' @title Spaghetti plot
##' @param formula Formula (response ~ time)
##' @param data data.frame
##' @param id Id variable
##' @param group group variable
##' @param type Type (line 'l', stair 's', ...)
##' @param lty Line type
##' @param pch Colour
##' @param col Colour
##' @param alpha transparency (0-1)
##' @param lwd Line width
##' @param level Confidence level
##' @param trend.formula Formula for trendline
##' @param tau Quantile to estimate (trend)
##' @param trend.lty Trend line type
##' @param trend.join Trend polygon
##' @param trend.delta Length of limit bars
##' @param trend Add trend line
##' @param trend.col Colour of trend line
##' @param trend.alpha Transparency
##' @param trend.lwd Trend line width
##' @param trend.jitter Jitter amount
##' @param legend Legend
##' @param by make separate plot for each level in 'by' (formula, name of column, or vector)
##' @param xlab Label of X-axis
##' @param ylab Label of Y-axis
##' @param add Add to existing device
##' @param ... Additional arguments to lower level arguments
##' @author Klaus K. Holst
##' @export
##' @examples
##' if (interactive() & requireNamespace("mets")) {
##' K <- 5
##' y <- "y"%++%seq(K)
##' m <- lvm()
##' regression(m,y=y,x=~u) <- 1
##' regression(m,y=y,x=~s) <- seq(K)-1
##' regression(m,y=y,x=~x) <- "b"
##' N <- 50
##' d <- sim(m,N); d$z <- rbinom(N,1,0.5)
##' dd <- mets::fast.reshape(d); dd$num <- dd$num+3
##' spaghetti(y~num,dd,id="id",lty=1,col=Col(1,.4),
##' trend.formula=~factor(num),trend=TRUE,trend.col="darkblue")
##' dd$num <- dd$num+rnorm(nrow(dd),sd=0.5) ## Unbalance
##' spaghetti(y~num,dd,id="id",lty=1,col=Col(1,.4),
##' trend=TRUE,trend.col="darkblue")
##' spaghetti(y~num,dd,id="id",lty=1,col=Col(1,.4),
##' trend.formula=~num+I(num^2),trend=TRUE,trend.col="darkblue")
##' }
spaghetti <- function(formula,data=NULL,id="id",group=NULL,
type="o",lty=1,pch=NA,col=1:10,alpha=0.3,lwd=1,
level=0.95,
trend.formula=formula,tau=NULL,
trend.lty=1,trend.join=TRUE,trend.delta=0.2,
trend=!is.null(tau),trend.col=col,
trend.alpha=0.2,trend.lwd=3,
trend.jitter=0,
legend=NULL, by=NULL,
xlab="Time",ylab="",add=FALSE,...) {
if (!lava.options()$cluster.index) stop("mets not available? Check 'lava.options()cluster.index'.")
if (!is.null(by)) {
if (is.character(by) && length(by==1)) {
by <- data[,by]
} else if (inherits(by,"formula")) {
##by <- model.matrix(update(by,~-1+.), model.frame(~.,data,na.action=na.pass))
by <- model.frame(by,data,na.action=na.pass)
}
cl <- match.call(expand.dots=TRUE)
cl$by <- NULL
datasets <- split(data,by)
res <- c()
for (d in datasets) {
cl$data <- d
res <- c(res, eval(cl,parent.frame()))
}
return(invisible(res))
}
if (!is.null(group)) {
if (is.character(group) && length(group==1)) {
M <- data[,group]
} else if (inherits(group,"formula")) {
##M <- model.matrix(update(group,~-1+.),data)
M <- model.frame(group,data,na.action=na.pass)
} else {
M <- group
}
if (!add) plot(formula,data=data,xlab=xlab,ylab=ylab,...,type="n")
dd <- split(data,M)
K <- length(dd)
if (length(type)<K) type <- rep(type,K)
if (length(col)<K) col <- rep(col,K)
if (length(pch)<K) pch <- rep(pch,K)
if (length(lty)<K) lty <- rep(lty,K)
if (length(lwd)<K) lwd <- rep(lwd,K)
if (length(alpha)<K) alpha <- rep(alpha,K)
if (length(trend)<K) trend <- rep(trend,K)
if (length(trend.col)<K) trend.col <- rep(trend.col,K)
if (length(trend.lty)<K) trend.lty <- rep(trend.lty,K)
if (length(trend.alpha)<K) trend.alpha <- rep(trend.alpha,K)
if (length(trend.lwd)<K) trend.lwd <- rep(trend.lwd,K)
for (i in seq_len(K)) {
spaghetti(formula,data=dd[[i]],id=id,type=type[i],
lty=lty[i],pch=pch[i],col=col[i],lwd=lwd[i],
alpha=alpha[i],
group=NULL,
trend=trend[i],tau=tau,
trend.col=trend.col[i],
trend.alpha=trend.alpha[i],
trend.lwd=trend.lwd[i],
trend.lty=trend.lty[i],
trend.delta=trend.delta,
trend.formula=trend.formula,
add=TRUE,...)
}
if (!is.null(legend)) {
graphics::legend(legend,names(dd),lwd=lwd,col=col,lty=lty)
}
return(invisible(NULL))
}
if (inherits(id,"formula")) id <- all.vars(id)
if (inherits(group,"formula")) group <- all.vars(group)
if (is.character(id) && length(id)==1) Id <- data[,id]
y <- getoutcome(formula)
x <- attributes(y)$x
Idx <- function(vname,widenames) {
idx <- which(unlist(lapply(widenames,function(x)
length(grep(paste0(vname,"[0-9]+$"),x))>0)))
nn <- widenames[idx]
ord <- order(char2num(unlist(lapply(nn,function(x) gsub(vname,"",x)))))
idx[ord]
}
if (!requireNamespace("mets",quietly=TRUE)) stop("'mets' package required")
if (length(x)==0) {
data <- data[,c(id,y),drop=FALSE]
wide <- mets::fast.reshape(data,id=id,varying=y,...)
yidx <- Idx(y,names(wide))
Y <- wide[,yidx,drop=FALSE]
X <- NULL
matplot(t(Y),type=type,lty=lty,pch=pch,lwd=lwd,col=Col(col[1],alpha[1]),xlab=xlab,ylab=ylab,...)
} else {
data <- data[,c(id,x,y),drop=FALSE]
wide <- mets::fast.reshape(data[order(data[,id],data[,x]),],id=id,varying=c(y,x),...)
yidx <- Idx(y,names(wide))
xidx <- Idx(x,names(wide))
Y <- wide[,yidx,drop=FALSE]
X <- wide[,xidx,drop=FALSE]
matplot(t(X),t(Y),type=type,pch=pch,lty=lty,lwd=lwd,col=Col(col[1],alpha[1]),xlab=xlab,ylab=ylab,add=add,...)
if (trend) {
if (is.numeric(trend.formula)) {
trend.formula <- sort(trend.formula)
tf <- toformula(y,"1")
res <- c()
if (!is.null(tau)) {
if (length(trend.alpha)<length(tau)) trend.alpha <- rep(trend.alpha,length(tau))
if (length(trend.lty)<length(tau)) trend.lty <- rep(trend.lty,length(tau))
if (length(trend.col)<length(tau)) trend.col <- rep(trend.col,length(tau))
if (length(trend.lwd)<length(tau)) trend.lwd <- rep(trend.lwd,length(tau))
}
for (i in trend.formula) {
data0 <- data[data[,x]==i,,drop=FALSE]
newdata <- data.frame(i); names(newdata) <- x
if (!is.null(tau)) {
##if (!require(quantreg)) stop("Install 'quantreg'")
suppressWarnings(r1 <- quantreg::rq(tf,data=data0,tau=tau))
pr <- predict(r1,newdata=newdata,level=level)
res <- rbind(res,pr)
} else {
l1 <- lm(tf,data0)
pr <- predict(l1,newdata=newdata,interval="confidence",level=level)
res <- rbind(res,pr)
}
}
if (!is.null(tau)) {
for (j in seq_len(ncol(res))) {
if (trend.join) lines(trend.formula,res[,j],col=trend.col[j],lwd=trend.lwd[j],lty=trend.lty[j],...)
if (trend.delta>0) confband(trend.formula,res[,j],line=FALSE,col=trend.col[j],lty=trend.lty[j],lwd=trend.lwd[j],delta=trend.delta,...)
}
} else {
confband(trend.formula,res[,2],res[,3],res[,1],col=Col(trend.col,trend.alpha),lty=trend.lty,lwd=trend.lwd,polygon=trend.join,...)
}
} else {
tf <- getoutcome(trend.formula)
if (is.list(tf)) {
trend.formula <- update(trend.formula,toformula(y,"."))
}
if (!is.null(tau)) {
##if (!require(quantreg)) stop("Install 'quantreg'")
suppressWarnings(r1 <- quantreg::rq(trend.formula,data=data,tau=tau))
newdata <- data.frame(seq(min(X,na.rm=TRUE),max(X,na.rm=TRUE),length.out=100))
names(newdata) <- x
pr <- predict(r1,newdata=newdata,interval="confidence",level=level)
##confband(xx,pr[,3],pr[,2],polygon=TRUE,col=Col(trend.col,trend.alpha),border=FALSE)
for (i in seq_along(tau))
lines(newdata[,1],pr[,i],col=trend.col,lwd=trend.lwd,lty=trend.lty)
} else {
l1. <- lm(trend.formula,data)
l1 <- estimate(l1.,id=data[,id],level=level)
xy <- plotConf(l1.,vcov=vcov(l1),data=data,partres=FALSE,plot=FALSE,level=level,...)
xx <- xy$x
pr <- xy$predict$fit
if (is.factor(xx)) {
xx <- char2num(as.character(xx))
if (trend.jitter>0) xx <- jitter(xx,trend.jitter)
confband(xx,pr[,3],pr[,2],pr[,1],col=trend.col,lwd=2)
} else {
confband(xx,pr[,3],pr[,2],polygon=TRUE,col=Col(trend.col,trend.alpha),border=FALSE)
lines(xx,pr[,1],col=trend.col,lwd=trend.lwd,lty=trend.lty)
}
}
}
}
}
return(invisible(list(Y,X)))
}
|
