Nothing
##
## relrisk.ppm.R
##
## $Revision: 1.9 $ $Date: 2019/01/08 07:44:07 $
##
relrisk.ppm <- local({
relrisk.ppm <- function(X, ..., at=c("pixels", "points"),
relative=FALSE, se=FALSE,
casecontrol=TRUE, control=1, case,
ngrid=NULL, window=NULL) {
stopifnot(is.ppm(X))
stopifnot(is.multitype(X))
control.given <- !missing(control)
case.given <- !missing(case)
at <- match.arg(at)
if(!relative && (control.given || case.given)) {
aa <- c("control", "case")[c(control.given, case.given)]
nn <- length(aa)
warning(paste(ngettext(nn, "Argument", "Arguments"),
paste(sQuote(aa), collapse=" and "),
ngettext(nn, "was", "were"),
"ignored, because relative=FALSE"))
}
model <- X
Y <- data.ppm(model)
types <- levels(marks(Y))
ntypes <- length(types)
# np <- length(coef(model))
## compute probabilities or risks
if(ntypes == 2 && casecontrol) {
if(control.given || !case.given) {
stopifnot(length(control) == 1)
if(is.numeric(control)) {
icontrol <- control <- as.integer(control)
stopifnot(control %in% 1:2)
} else if(is.character(control)) {
icontrol <- match(control, types)
if(is.na(icontrol)) stop(paste("No points have mark =", control))
} else
stop(paste("Unrecognised format for argument", sQuote("control")))
if(!case.given)
icase <- 3 - icontrol
}
if(case.given) {
stopifnot(length(case) == 1)
if(is.numeric(case)) {
icase <- case <- as.integer(case)
stopifnot(case %in% 1:2)
} else if(is.character(case)) {
icase <- match(case, types)
if(is.na(icase)) stop(paste("No points have mark =", case))
} else stop(paste("Unrecognised format for argument", sQuote("case")))
if(!control.given)
icontrol <- 3 - icase
}
switch(at,
pixels= {
## estimate is a single image
## compute images of intensities of each mark
lambda.each <- predict(model, ngrid=ngrid, window=window)
if(!relative) {
## compute probabilities..
## total intensity (image)
lambda.all <- im.apply(lambda.each, sum, check=FALSE)
## WAS: lambda.all <- Reduce("+", lambda.each)
if(!se) {
result <- lambda.each[[icase]]/lambda.all
result <- killglitches(result)
} else {
probs <- lapply(lambda.each, "/", e2=lambda.all)
probs <- as.solist(lapply(probs, killglitches))
estimate <- probs[[icase]]
SE <- SEprobPixels(model, probs)[[icase]]
SE <- killglitches(SE)
result <- list(estimate=estimate, SE=SE)
}
} else {
## relative risks
lambda.ctrl <- lambda.each[[icontrol]]
if(!se) {
result <- lambda.each[[icase]]/lambda.ctrl
result <- killglitches(result)
} else {
risks <- lapply(lambda.each, "/", e2=lambda.ctrl)
risks <- as.solist(lapply(risks, killglitches))
estimate <- risks[[icase]]
SE <- SErelriskPixels(model, risks, icontrol)[[icase]]
SE <- killglitches(SE)
result <- list(estimate=estimate, SE=SE)
}
}
},
points={
## compute intensities of each type
Ycase <- unmark(Y) %mark% factor(types[icase], levels=types)
Yctrl <- unmark(Y) %mark% factor(types[icontrol], levels=types)
lambda.case <- predict(model, locations=Ycase)
lambda.ctrl <- predict(model, locations=Yctrl)
if(!relative) {
## compute probabilities
## total intensity
lambda.all <- lambda.case + lambda.ctrl
prob.case <- lambda.case/lambda.all
if(!se) {
result <- prob.case
} else {
probs <- matrix(, length(prob.case), 2)
probs[,icase] <- prob.case
probs[,icontrol] <- 1 - prob.case
SE <- SEprobPoints(model, probs)[,icase]
result <- list(estimate=prob.case, SE=SE)
}
} else {
## compute relative risks
risk.case <- lambda.case/lambda.ctrl
if(!se) {
result <- risk.case
} else {
risks <- matrix(, length(risk.case), 2)
risks[,icase] <- risk.case
risks[,icontrol] <- 1
SE <- SErelriskPoints(model, risks, icontrol)[,icase]
result <- list(estimate=risk.case, SE=SE)
}
}
})
} else {
## several types
if(relative) {
## need 'control' type
stopifnot(length(control) == 1)
if(is.numeric(control)) {
icontrol <- control <- as.integer(control)
stopifnot(control %in% 1:ntypes)
} else if(is.character(control)) {
icontrol <- match(control, types)
if(is.na(icontrol)) stop(paste("No points have mark =", control))
} else
stop(paste("Unrecognised format for argument", sQuote("control")))
}
switch(at,
pixels={
## estimate is a list of images
## Compute images of intensities of each type
lambda.each <- predict(model, ngrid=ngrid, window=window)
if(!relative) {
## compute probabilities...
## image of total intensity
lambda.all <- im.apply(lambda.each, sum, check=FALSE)
## WAS: lambda.all <- Reduce("+", lambda.each)
probs <- lapply(lambda.each, "/", e2=lambda.all)
probs <- as.solist(lapply(probs, killglitches))
if(!se) {
result <- probs
} else {
SE <- SEprobPixels(model, probs)
SE <- as.solist(lapply(SE, killglitches))
result <- list(estimate=probs, SE=SE)
}
} else {
## compute relative risks
risks <- lapply(lambda.each, "/",
e2=lambda.each[[icontrol]])
risks <- as.solist(lapply(risks, killglitches))
if(!se) {
result <- risks
} else {
SE <- SErelriskPixels(model, risks, icontrol)
SE <- as.solist(lapply(SE, killglitches))
result <- list(estimate=risks, SE=SE)
}
}
},
points = {
## matrix of intensities of each type at each point
## rows=locations, cols=types
lambda.each <- sapply(types,
predictfortype,
loc=unmark(Y), model=model, types=types)
if(!relative) {
## compute probabilities
lambda.all <- rowSums(lambda.each)
probs <- lambda.each/lambda.all
if(!se) {
result <- probs
} else {
SE <- SEprobPoints(model, probs)
result <- list(estimate=probs, SE=SE)
}
} else {
## compute relative risks
risks <- lambda.each/lambda.each[,icontrol]
if(!se) {
result <- risks
} else {
SE <- SErelriskPoints(model, risks, icontrol)
result <- list(estimate=risks, SE=SE)
}
}
})
}
return(result)
}
modmats <- function(model) {
# model matrices for data locations for each possible mark
QM <- quad.ppm(model)
Y <- QM$data
suppressWarnings({
QR <- quadscheme.replicated(Y, unmark(Y[FALSE]))
})
sourceid <- QR$param$sourceid
## canonical covariates
mm <- model.matrix(model, Q=QR)
## mm is a matrix with one column for canonical covariate
## and one row for each marked point in QR.
mm <- cbind(data.frame(".s"=sourceid, ".m"=marks(QR)), mm)
## Split by marks
ss <- split(mm, mm$.m)
## Reorganise into compatible matrices
zz <- lapply(ss, reorg)
return(zz)
}
reorg <- function(x) {
z <- x
rownames(z) <- NULL
z[x$.s, ] <- z
return(z[,-(1:2), drop=FALSE])
}
SErelriskPoints <- function(model, riskvalues, icontrol) {
## riskvalues is a matrix with rows=data locations, cols=types
types <- colnames(riskvalues)
ntypes <- length(types)
##
S.um <- modmats(model)
S.um <- lapply(S.um, as.matrix)
## S.um is a list of matrices, one for each possible type,
## each matrix having one row per data location
dS.um <- lapply(S.um, "-", e2=S.um[[icontrol]])
R.um <- mapply("*",
dS.um,
as.list(as.data.frame(riskvalues)),
SIMPLIFY=FALSE)
## likewise R.um is a list of matrices
##
vc <- vcov(model)
VAR <- lapply(R.um, quadform, v=vc)
VAR <- do.call(cbind, VAR)
SE <- sqrt(VAR)
colnames(SE) <- types
return(SE)
}
msubtract <- function(z1, z2) mapply("-", e1=z1, e2=z2, SIMPLIFY=FALSE)
mmultiply <- function(z1, z2) solapply(z1, "*", e2=z2)
SErelriskPixels <- function(model, riskvalues, icontrol) {
## riskvalues is an imlist
types <- names(riskvalues)
ntypes <- length(types)
## canonical covariates
S.um <- model.images(model)
## S.um is a hyperframe with one column for each mark value
## and one row for each canonical covariate
dS.um <- lapply(S.um, msubtract,
z2=S.um[,icontrol,drop=TRUE])
R.um <- mapply(mmultiply,
z1=dS.um,
z2=riskvalues,
SIMPLIFY=FALSE)
VAR <- vector(mode="list", length=ntypes)
ntypes <- length(types)
vc <- vcov(model)
ncoef <- nrow(vc)
for(type in 1:ntypes) {
v <- 0
Rum <- R.um[[type]]
for(i in 1:ncoef) {
for(j in 1:ncoef) {
v <- v + Rum[[i]] * vc[i,j] * Rum[[j]]
}
}
VAR[[type]] <- v
}
names(VAR) <- types
VAR <- as.solist(VAR)
SE <- as.solist(lapply(VAR, sqrt))
return(SE)
}
SEprobPixels <- function(model, probvalues) {
## probvalues is an imlist
types <- names(probvalues)
ntypes <- length(types)
## canonical covariates
S.um <- model.images(model)
## S.um is a hyperframe with one column for each mark value
## and one row for each canonical covariate
ncoef <- length(coef(model))
Sbar.u <- vector(mode="list", length=ncoef)
for(k in 1:ncoef) {
A <- mapply("*", e1=S.um[k,,drop=TRUE], e2=probvalues, SIMPLIFY=FALSE)
Sbar.u[[k]] <- im.apply(A, sum)
}
## Sbar.u is a list of images, one for each canonical covariate
Sdif.um <- lapply(as.list(S.um),
msubtract,
z2=Sbar.u)
## Sdif.um is a list of lists of images.
## List of length ntypes,
## each entry being an imlist of length ncoef
P.um <- mapply(mmultiply,
Sdif.um,
probvalues,
SIMPLIFY=FALSE)
## P.um is same format as Sdif.um
vc <- vcov(model)
ncoef <- nrow(vc)
VAR <- vector(mode="list", length=ntypes)
for(m in 1:ntypes) {
v <- 0
Pum <- P.um[[m]]
for(i in 1:ncoef) {
for(j in 1:ncoef) {
v <- v + Pum[[i]] * vc[i,j] * Pum[[j]]
}
}
VAR[[m]] <- v
}
names(VAR) <- types
VAR <- as.solist(VAR)
SE <- as.solist(lapply(VAR, sqrt))
}
SEprobPoints <- function(model, probvalues) {
## probvalues is a matrix with row=location and column=type
types <- colnames(probvalues)
ntypes <- length(types)
## canonical covariates
S.um <- modmats(model)
S.um <- lapply(S.um, as.matrix)
## S.um is a list of matrices, one for each possible type,
## each matrix having rows=locations and cols=covariates
## Weight each matrix by its mark probabilities
SW <- mapply("*",
e1=S.um,
e2=as.list(as.data.frame(probvalues)),
SIMPLIFY=FALSE)
## average them
Sbar.u <- Reduce("+", SW)
## Sbar.u is a matrix with rows=locations and cols=covariates
Sdif.um <- lapply(S.um, "-", e2=Sbar.u)
## Sdif.um is a list of matrices like S.um
P.um <- mapply("*",
e1=Sdif.um,
e2=as.list(as.data.frame(probvalues)),
SIMPLIFY=FALSE)
## P.um likewise
vc <- vcov(model)
VAR <- lapply(P.um, quadform, v=vc)
VAR <- do.call(cbind, VAR)
SE <- sqrt(VAR)
colnames(SE) <- types
return(SE)
}
predictfortype <- function(type, model, types, loc) {
predict(model, locations=loc %mark% factor(type, levels=types))
}
killglitches <- function(z, eps=.Machine$double.eps) {
ra <- range(z, finite=TRUE)
if(max(abs(ra)) < eps) {
z[] <- 0
return(z)
}
if(diff(ra) < eps)
z[] <- mean(z, na.rm=TRUE)
return(z)
}
relrisk.ppm
})
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