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quantiles in predict function #27

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quantiles in predict function #27

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bb56394
return various quantiles for uncertainty quantification in prediction
sastoudt Apr 9, 2019
dd3ae51
clean up
sastoudt Apr 9, 2019
f17937e
fix redundancy and missing return quantile
sastoudt Apr 9, 2019
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91 changes: 86 additions & 5 deletions R/predict.hmsc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -496,22 +496,103 @@ predict.hmsc<-function(object, newdata, type = c("response","link"), conditional
### Apply inverse link function
if(type=="response"){
if(any(class(object)=="probit")){
result<-pnorm(apply(res,1:2, mean))
#result<-pnorm(apply(res,1:2, mean))
mu <- apply(res, 1:2, mean)
q025 <- apply(res, 1:2, function(x) {
pnorm(quantile(x, .025))
})
q05 <- apply(res, 1:2, function(x) {
pnorm(quantile(x, .05))
})
q10 <- apply(res, 1:2, function(x) {
pnorm(quantile(x, .1))
})
q90 <- apply(res, 1:2, function(x) {
pnorm(quantile(x, .9))
})
q95 <- apply(res, 1:2, function(x) {
pnorm(quantile(x, .95))
})
q975 <- apply(res, 1:2, function(x) {
pnorm(quantile(x, .975))
})
result <- list(mu = mu, q025 = q025, q05=q05, q10 = q10, q90 = q90, q95 = q95, q975 = q975)
}

if(any(class(object)=="gaussian")){
result<-apply(res,1:2, mean)
#result<-apply(res,1:2, mean)
mu <- apply(res, 1:2, mean)
q025 <- apply(res, 1:2, function(x) {
quantile(x, .025)
})
q05 <- apply(res, 1:2, function(x) {
quantile(x, .05)
})
q10 <- apply(res, 1:2, function(x) {
quantile(x, .1)
})
q90 <- apply(res, 1:2, function(x) {
quantile(x, .9)
})
q95 <- apply(res, 1:2, function(x) {
quantile(x, .95)
})
q975 <- apply(res, 1:2, function(x) {
quantile(x, .975)
})
result <- list(mu = mu, q025 = q025, q05=q05, q10 = q10, q90 = q90, q95 = q95, q975 = q975)
}

if(any(class(object)=="poisson" | any(class(object)=="overPoisson"))){
result<-exp(apply(res,1:2, mean))
#result<-exp(apply(res,1:2, mean))
mu <- apply(res, 1:2, mean)
q025 <- apply(res, 1:2, function(x) {
exp(quantile(x, .025))
})
q05 <- apply(res, 1:2, function(x) {
exp(quantile(x, .05))
})
q10 <- apply(res, 1:2, function(x) {
exp(quantile(x, .1))
})
q90 <- apply(res, 1:2, function(x) {
exp(quantile(x, .9))
})
q95 <- apply(res, 1:2, function(x) {
exp(quantile(x, .95))
})
q975 <- apply(res, 1:2, function(x) {
exp(quantile(x, .975))
})
result <- list(mu = mu, q025 = q025, q05=q05, q10 = q10, q90 = q90, q95 = q95, q975 = q975)
}
}

if(type=="link"){
result<-apply(res,1:2, mean)
#result<-apply(res,1:2, mean)
mu <- apply(res, 1:2, mean)
q025 <- apply(res, 1:2, function(x) {
quantile(x, .025)
})
q05 <- apply(res, 1:2, function(x) {
quantile(x, .05)
})
q10 <- apply(res, 1:2, function(x) {
quantile(x, .1)
})
q90 <- apply(res, 1:2, function(x) {
quantile(x, .9)
})
q95 <- apply(res, 1:2, function(x) {
quantile(x, .95)
})
q975 <- apply(res, 1:2, function(x) {
quantile(x, .975)
})
result <- list(mu = mu, q025 = q025, q05=q05, q10 = q10, q90 = q90, q95 = q95, q975 = q975)
}
colnames(result)<-colnames(Y)
#colnames(result)<-colnames(Y)
## the colnames match without this
}else{
### Apply inverse link function
if(type=="response"){
Expand Down