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`slope` <- function(ogg, parm, conf.level=0.95, rev.sgn=FALSE, APC=FALSE, .vcov=NULL, .coef=NULL, use.t=NULL,
by=NULL, interc=TRUE, level=0, ..., digits = max(4, getOption("digits") - 2)){
# se e' un "newsegmented"
# if(!is.null(ogg$R.slope)) {
# covv<-old.coef.var(ogg)
# ogg$coefficients<- covv$b
# covv<- covv$cov
# ogg$psi<-old.psi(ogg)
# ogg$nameUV<-old.nomi(ogg)
# } else {
# covv<-try(vcov(ogg,...), silent=TRUE)
# }
slopeM<-function(obj, by=NULL, conf.level=0.95, vcov.=NULL, level=level, ... ){
#=========>> da provare con by con piu' termini e se leftSlope=0
#obj: the segmented.lme object
#by: a named list indicating covariate names and corresponding values affecting the fitted segmented relationship.
# Example: by=list(group="2",z2=.2)
#conf.level: for pointwise CI..
#withI: if TRUE, the fitted lines are plotted with intercept (if included in the model)
#vcov.: the fixed effect cov matrix. If NULL is computed by vcov.segmented.lme
#drop.var: possible coefficient names to be removed before computing the segmented relationship (E.g. the group-specific intercept..)
#obj[[1]] -> obj$lme.fit
#obj[[2]] -> obj$lme.fit.noG
#------------------
V<- if(is.null(vcov.)) vcov.segmented.lme(obj) else vcov. #object$lme.fit$varFix
if(!is.null(by) && !is.list(by)) stop("if provided, 'by' should be a (named) list of scalars")
Z<-obj$Z
nomeZ<-obj$namesGZ$nameZ
beta.noG<- fixef(obj$lme.fit.noG)
beta.all<-fixef(obj$lme.fit)
#browser()
beta.G<-beta.all[setdiff(names(fixef(obj$lme.fit)), names(beta.noG))]
nomiCoef<-names(beta.noG)
if(!is.null(by)) {
a<-by
#isZero<-sapply(a, function(x) x==0)
if(!all(sapply(a, length)==1)) stop("vectors in 'by' are not allowed")
nomiOK<-const<-idList<-vector("list", length(a))
values<-vector(,length(a))
for(i in 1:length(a)) {
nomiOK[i]<-nomeOK <- if(is.character(a[[i]])) paste(names(a[i]),a[[i]], sep="") else names(a[i])
#replace 0
if(a[[i]]==0) a[[i]]<- 1e-16
#per la left slope
bLeftSlope<-c(beta.noG[paste(obj$namesGZ$nameZ,":",nomeOK, sep="")],
beta.noG[paste(nomeOK, ":", obj$namesGZ$nameZ, sep="")])
bLeftSlope<-bLeftSlope[!is.na(bLeftSlope)]
if(!is.character(a[[i]])) bLeftSlope<-bLeftSlope*a[[i]]
if(length(bLeftSlope)<=0) bLeftSlope<-NA
#per la slope-diff
bU<-beta.noG[paste("U", nomeOK, sep=".")]
if(!is.character(a[[i]])) bU <-bU*a[[i]]
const[[i]]<-c(bLeftSlope, bU)
const[[i]]<- ifelse(is.na(const[[i]]),0,const[[i]])
idList[[i]]<-names(c(bLeftSlope, bU))
values[i]<-ifelse(is.character(a[[i]]),1,a[[i]])
}
#browser()
const<-matrix(unlist(const),2, byrow=FALSE)
colnames(const)<-names(by)
nomiNOdiff <- names(which(colSums(const)==0))
if(length(nomiNOdiff)>0) warning("The value of", paste(" '", paste(nomiNOdiff, collapse=" and "),"' ",sep=""),
"supplied in 'by' does not modify the baseline slopes estimates", call. = FALSE)
nomiCoef<- c(nomeZ, "U", unlist(idList))
##########################################
} else { #se 'by' e' NULL
const<-matrix(0,2,1)
nomiCoef<- c(nomeZ, "U")
values<-c(1,1)
}
##########################################
#browser()
final.names<-setdiff(nomiCoef, c("G0",obj$namesGZ$nomiG,""))
final.names<-final.names[!is.na(final.names)]
#prepara la matrice del disegno..
X<-matrix(1, 2, 2) #SOLO un breakpoint, quindi 2 segmenti..
X[row(X)<col(X)]<-0
Ident<-diag(ncol(X))
M<-vector("list", length=ncol(const))
for(j in 1:ncol(const)) M[[j]]<-values[j]*Ident[, which(const[,j]!=0), drop=FALSE]
M<-cbind(Ident, do.call("cbind", M))
XX<- X%*%M
r<- drop(XX %*% beta.noG[final.names])
V<-V[final.names,final.names]
SE.fit<-sqrt(rowSums((XX %*% V) * XX)) #sqrt(diag(X%*%Var%*%t(X)))
zalpha<- -qnorm((1-conf.level)/2)
ci<-cbind(r-zalpha*SE.fit, r+zalpha*SE.fit)
#colnames(ci)<-paste("CI", "(", conf.level * 100,"%", ")", c(".low", ".up"), sep = "")
colnames(ci)<-paste(" ", conf.level, c(".low", ".up"), sep = "")
ris<-cbind("Est."=r, "St.Err"=SE.fit, "t value"=r/SE.fit, ci)
rownames(ris)<-c("leftSlope", "rightSlope")
#ris
# rev.sgn=FALSE
# if(rev.sgn){
# ris<-cbind(-ris[nrow(ris):1,1],ris[nrow(ris):1,2],-ris[nrow(ris):1,3],
# -ris[nrow(ris):1,5],-ris[nrow(ris):1,4])}
if(level>0){
re<-ranef(obj[['lme.fit.noG']])
re.left<- if(obj$namesGZ$nameZ%in%colnames(re)) re[,obj$namesGZ$nameZ] else rep(0, nrow(re))
re.right<- if("U"%in%colnames(re)) re.left+re[,"U"] else re.left
ris<- data.frame("leftSlope"=re.left+ris["leftSlope","Est."], "rightSlope"=re.right+ris["rightSlope","Est."])
rownames(ris)<-rownames(re)
}
ris
}
#se metti la linea sotto, poi NON funziona con oggetti che provengono da segmented.default
#if(!inherits(ogg, "stepmented") || !inherits(ogg, "segmented") || !inherits(ogg, "segmented.lme")) stop("slope() works only for..")
if(inherits(ogg, "stepmented")){
covv <- if(is.null(.vcov)) vcov(ogg, ...) else .vcov
estcoef<- if(is.null(.coef)) coef(ogg) else .coef
if(length(estcoef)==0) stop("No coefficient in the object fit?")
if(!all(dim(covv)==c(length(estcoef), length(estcoef)))) stop("dimension of cov matrix and estimated coeffs do not match", call. = FALSE)
nomepsi<-rownames(ogg$psi) #OK
nomeU<-ogg$nameUV$U
nomeZ<-ogg$nameUV$Z
if(missing(parm)) {
nomeZ<- ogg$nameUV$Z
} else {
if(! all(parm %in% ogg$nameUV$Z)) {
stop("invalid parm") } else {nomeZ<-parm}
}
nomi<-names(estcoef)
index<-vector(mode = "list", length = length(nomeZ))
for(i in 1:length(nomeZ)) {
idU <- ogg$nameUV$U[endsWith(ogg$nameUV$U, paste(".", nomeZ[i], sep = ""))]
if (interc && "(Intercept)" %in% nomi) idU <- c("(Intercept)", idU)
index[[i]]<- idU
}
if(!is.null(use.t)){
k0<- if(use.t) abs(qt((1-conf.level)/2,df=ogg$df.residual)) else abs(qnorm((1-conf.level)/2))
} else {
k0<-if(inherits(ogg, "lm", which=TRUE)==2) abs(qt((1-conf.level)/2,df=ogg$df.residual)) else abs(qnorm((1-conf.level)/2))
}
#k<-if("lm"%in%class(ogg)) abs(qt((1-conf.level)/2,df=ogg$df.residual)) else abs(qnorm((1-conf.level)/2))
Ris<-list()
#digits <- max(3, getOption("digits") - 3)
for(i in 1:length(index)){
#ind<-as.numeric(na.omit(unlist(index[[i]])))
ind<- match(na.omit(unlist(index[[i]])),nomi)
M<-matrix(1,length(ind),length(ind))
M[row(M)<col(M)]<-0
cof<-estcoef[ind]
cof.out<-M%*%cof
if(!inherits(covv, "try-error")){
cov.ok<-covv[ind,ind]
cov.out<-M%*%cov.ok%*%t(M)
se.out<-sqrt(diag(cov.out))
k<-k0*se.out
ris<-cbind(cof.out,se.out,(cof.out/se.out),(cof.out-k),(cof.out+k))
} else {
ris<-cbind(cof.out, NA, NA, NA,NA)
}
cin<-paste("CI","(",conf.level*100,"%",")",c(".l",".u"),sep="")
#se la left slope e' nulla... per stepmented NON vale!
#if(!nomeZ[i]%in%nomi){
# ris<-rbind(c(0,rep(NA,(ncol(ris)-1))),ris)
#}
if(!interc || !("(Intercept)"%in%nomi) ){
ris<-rbind(c(0,rep(NA,(ncol(ris)-1))),ris)
}
nomeT<-if("lm"%in%class(ogg)) "t value" else "z value"
dimnames(ris)<-list(paste("level", 1:nrow(ris), sep=""),c("Est.","St.Err.",nomeT,cin[1],cin[2]))
Ris[[nomeZ[i]]]<- signif(ris,digits)
} #end loop i
return(Ris)
} else {
if(length(ogg)==2 && all(sapply(ogg, function(.x)inherits(.x, "segmented") ))){
obj1<-ogg[[1]]
obj2<-ogg[[2]]
os1 <- slope(obj1,conf.level=conf.level,...)[[1]]
os2 <- slope(obj2,conf.level=conf.level,...)[[1]]
K<-min(length(os1[,1]),length(os2[,1]))
estdiff<-zvalue<-pvalue<-rep(NA,K)
for(id in 1:K){
est1<- os1[id,1]
se1 <- os1[id,2]
est2<- os2[id,1]
se2<- os2[id,1]
estdiff[id]<-abs(est1-est2)
zvalue[id] <-(est1-est2)/sqrt(se1^2+se2^2)
pvalue[id] <-2*(1-pnorm(abs(est1-est2)))
}
r<-cbind("|est diff|"=estdiff, "p-value"=signif(pvalue,3))
rownames(r)<-paste("slope",1:K,sep="")
#if(msg)
cat("Comparing 'matched' slopes for two segmented fits\n")
r
} else {
#if(length(ogg)>2 && (inherits(ogg, "segmented") || inherits(ogg, "segmented.lme"))){
if(class(ogg)[1]=="segmented.lme"){
a<-slopeM(ogg, conf.level=conf.level, vcov.=.vcov, by=by, level=level, ...)
return(a)
} else {
covv <- if(is.null(.vcov)) vcov(ogg, ...) else .vcov
if(is.null(.coef)) {
estcoef<- coef(ogg)
if(is.null(estcoef)) estcoef <- ogg$coef
if(is.null(estcoef)) stop("No coeffs in the fit? Please use '.coef'")
} else {
estcoef<- .coef
}
#browser()
if(length(estcoef)==0) stop("No coefficient in the object fit?")
if(!all(dim(covv)==c(length(estcoef), length(estcoef)))) stop("dimension of cov matrix and estimated coeffs do not match", call. = FALSE)
nomepsi<-rownames(ogg$psi) #OK
nomeU<-ogg$nameUV$U
nomeZ<-ogg$nameUV$Z
if(missing(parm)) {
nomeZ<- ogg$nameUV$Z
if(length(rev.sgn)==1) rev.sgn<-rep(rev.sgn,length(nomeZ))
} else {
if(! all(parm %in% ogg$nameUV$Z)) {
stop("invalid parm") } else {nomeZ<-parm}
}
if(length(rev.sgn)!=length(nomeZ)) rev.sgn<-rep(rev.sgn, length.out=length(nomeZ))
nomi<-names(estcoef)
index<-vector(mode = "list", length = length(nomeZ))
for(i in 1:length(nomeZ)) {
index[[i]]<- match(c(nomeZ[i],ogg$nameUV$U[grep(nomeZ[i], ogg$nameUV$U)]), names(estcoef),0)
n.psi.est.i <- length(ogg$nameUV$V[grep(nomeZ[i], ogg$nameUV$V)])
if(length(ogg$indexU[[nomeZ[i]]])!=n.psi.est.i){ #se ci sono anche psi fissi
if(!is.null(ogg$constr)){
stop("slope() does not work with constraints and fixed psi")
} else {
index[[i]]<-match(c(nomeZ[i], names(ogg$indexU[[nomeZ[i]]])), nomi, 0)
}
}
}
if(!is.null(use.t)){
k0<- if(use.t) abs(qt((1-conf.level)/2,df=ogg$df.residual)) else abs(qnorm((1-conf.level)/2))
} else {
k0<-if(inherits(ogg, "lm", which=TRUE)==2) abs(qt((1-conf.level)/2,df=ogg$df.residual)) else abs(qnorm((1-conf.level)/2))
}
#k<-if("lm"%in%class(ogg)) abs(qt((1-conf.level)/2,df=ogg$df.residual)) else abs(qnorm((1-conf.level)/2))
Ris<-list()
#digits <- max(3, getOption("digits") - 3)
rev.sgn<-rep(rev.sgn, length.out=length(nomeZ))
#browser()
for(i in 1:length(index)){
ind<- index[[i]] #as.numeric(unlist(index[[i]]))
ind<-ind[ind!=0]
cof<-estcoef[ind]
if(is.null(ogg$constr)){
M<-matrix(1,length(ind),length(ind))
M[row(M)<col(M)]<-0
cof.out<-M%*%cof
} else {
M<-ogg$constr$RList[[match(nomeZ[i], ogg$nameUV$Z,0)]]
cof.out <- M%*%cof
}
if(!inherits(covv, "try-error")){
cov.ok<-covv[ind,ind]
cov.out<-M%*%cov.ok%*%t(M)
se.out<-sqrt(diag(cov.out))
k<-k0*se.out
ris<-cbind(cof.out,se.out,(cof.out/se.out),(cof.out-k),(cof.out+k))
} else {
ris<-cbind(cof.out, NA, NA, NA,NA)
}
cin<-paste("CI","(",conf.level*100,"%",")",c(".l",".u"),sep="")
#se la left slope e' nulla....
#if(identical(length(ind),length(grep(paste("\\.",nomeZ[i],"$",sep=""), nomeU)))){
if(is.null(ogg$constr) && !nomeZ[i]%in%nomi){
ris<-rbind(c(0,rep(NA,(ncol(ris)-1))),ris)
}
if(rev.sgn[i]){
ris<-cbind(-ris[nrow(ris):1,1],ris[nrow(ris):1,2],-ris[nrow(ris):1,3],
-ris[nrow(ris):1,5],-ris[nrow(ris):1,4])
}
nomeT<-if("lm"%in%class(ogg)) "t value" else "z value"
dimnames(ris)<-list(paste("slope", 1:nrow(ris), sep=""),c("Est.","St.Err.",nomeT,cin[1],cin[2]))
if(APC) ris<-100*(exp(ris[,c(1,4,5)])-1)
Ris[[nomeZ[i]]]<- signif(ris,digits)
} #end loop i
#if(!missing(parm)){
# if(!all(parm %in% ogg$nameUV[[3]])) stop("invalid parm") else Ris<-Ris[parm]}
return(Ris)
}
}
}
}
# else {
# obj1<-ogg[[1]]
# obj2<-ogg[[2]]
# os1 <- slope(obj1,conf.level=conf.level,...)[[1]]
# os2 <- slope(obj2,conf.level=conf.level,...)[[1]]
# K<-min(length(os1[,1]),length(os2[,1]))
# estdiff<-zvalue<-pvalue<-rep(NA,K)
# for(id in 1:K){
# est1<- os1[id,1]
# se1 <- os1[id,2]
# est2<- os2[id,1]
# se2<- os2[id,1]
# estdiff[id]<-abs(est1-est2)
# zvalue[id] <-(est1-est2)/sqrt(se1^2+se2^2)
# pvalue[id] <-2*(1-pnorm(abs(est1-est2)))
# }
# r<-cbind("|est diff|"=estdiff, "p-value"=signif(pvalue,3))
# rownames(r)<-paste("slope",1:K,sep="")
# #if(msg)
# cat("Comparing 'matched' slopes for two segmented fits\n")
# r
# }
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