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plot.R
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plot.R
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#' Plot Spline Spatial Temporal Aggregated Predictors
#'
#' Plots the smooth curve on a grid over the range of the stap smooth predictor
#' If no stap term is selected, the first stap component is plotted by default.
#' @export
#' @param x sstapreg object
#' @param stap_term optional string for name of BEF smooth function to plot.
#' Alternatively plots first BEF smooth function
#' @param p probability mass contained within uncertainty interval
#' @param grid by default is NULL corresponding to a .1 step grid from the min-max of the covariate space
#' @param ... ignored
#'
plot.sstapreg <- function(x,stap_term = NULL, p = 0.95, grid = NULL,...){
# to pass R CMD Check
Distance <- Time <- Median <- Parameters <-
Grid <- Lower <- Upper <- . <- .data <- NULL
spec <- x$specification
if(is.null(stap_term)){
ix <- 1
stap_term <- spec$term[ix]
component <- get_component(spec,stap_term)
}
else if(stap_term %in% spec$term){
ix <- which(spec$term==stap_term)
component <- get_component(spec,stap_term)
}
else
stop("stap_term must be NULL or one of the stap terms in the model object")
beta <- as.matrix(x$stapfit)
gd_eta <- get_stap(spec,stap_term,component,beta,x$family,grid)
gd <- gd_eta$grid
eta <- gd_eta$eta
pltdf <- get_pltdf(gd,eta,p,component)
if(component %in% c("Distance","Time")){
pltdf %>% ggplot2::ggplot(ggplot2::aes(x = .data[[component]], y = Median )) +
ggplot2::geom_line() +
ggplot2::geom_ribbon(ggplot2::aes(ymin=Lower,ymax=Upper),alpha=0.3) +
ggplot2::theme_bw() +
ggplot2::geom_hline(ggplot2::aes(yintercept = 0),
linetype=2,color='red') +
ggplot2::xlab(component) +
ggplot2::ggtitle(stap_term) +
ggplot2::ylab("") -> pl
}else{
pltdf %>% ggplot2::ggplot(ggplot2::aes(x=Distance,y=Time,z=Median)) +
ggplot2::theme_bw() +
ggplot2::geom_contour() ->pl
}
if(has_bw(spec,stap_term)){
pltdf2 <- get_pltdf(gd,gd_eta$eta_within,p,component) %>%
dplyr::mutate(Parameters = "Within")
pltdf %>% dplyr::mutate(Parameters=="Between") %>%
rbind(.,pltdf2) -> pltdf
if(component %in% c("Distance","Time")){
pltdf %>% ggplot2::ggplot(ggplot2::aes(x=.data[[component]],y=Median)) +
ggplot2::geom_ribbon(ggplot2::aes(ymin=Lower,ymax=Upper),alpha=0.3) +
ggplot2::theme_bw() +
ggplot2::theme(strip.background=ggplot2::element_blank()) +
ggplot2::facet_wrap(~Parameters) -> pl2
}else{
pltdf %>% ggplot2::ggplot(ggplot2::aes(x=Distance,y=Time,z=Median)) +
ggplot2::geom_contour() +
ggplot2::theme_bw() +
ggplot2::theme(strip.background=ggplot2::element_blank()) +
ggplot2::facet_wrap(~Parameters) -> pl2
}
return(pl2)
}
return(pl)
}
#' Spatial-Temporal Effects DataFrame
#'
#' Returns a dataframe with the betas evaluated at either a default or given grid points
#' If no stap term is selected, the first stap component is plotted by default.
#' @export
#' @param x sstapreg object
#' @param stap_term optional string for name of BEF smooth function to plot.
#' Alternatively plots first BEF smooth function
#' @param p probability mass contained within uncertainty interval
#' @param grid by default is NULL corresponding to a .1 step grid from the min-max of the covariate space
plotdf <- function(x,stap_term = NULL, p = 0.95, grid = NULL)
UseMethod("plotdf")
#' @describeIn plotdf
#' @export
plotdf.sstapreg <- function(x,stap_term = NULL, p = 0.95, grid = NULL){
# to pass R CMD Check
Distance <- Time <- Median <- Parameters <-
Grid <- Lower <- Upper <- . <- .data <- NULL
spec <- x$specification
if(is.null(stap_term)){
ix <- 1
stap_term <- spec$term[ix]
component <- get_component(spec,stap_term)
}
else if(stap_term %in% spec$term){
ix <- which(spec$term==stap_term)
component <- get_component(spec,stap_term)
}
else
stop("stap_term must be NULL or one of the stap terms in the model object")
beta <- as.matrix(x$stapfit)
gd_eta <- get_stap(spec,stap_term,component,beta,x$family,grid)
gd <- gd_eta$grid
eta <- gd_eta$eta
pltdf <- get_pltdf(gd,eta,p,component)
return(pltdf)
}
#' 3D plots for rsstap models
#'
#' @export
#' @param x sstapreg object
#' @param stap_term string argument for which \code{stap()} bef term to plot
#' @param grid optional grid argument by default is NULL corresponding to a .1 step grid from the min-max of the covariate space
#'
plot3D <- function(x,stap_term = NULL,grid = NULL)
UseMethod("plot3D")
#'
#' @describeIn plot3D 3d stap plot
#' @export
#'
plot3D.sstapreg <- function(x,stap_term = NULL, grid = NULL){
spec <- x$specification
if(!has_any_staps(spec))
stop("Model has no stap terms specified")
if(is.null(stap_term)){
ix <- which(spec$component=="Distance-Time")[1]
stap_term <- spec$term[ix]
}
else if(stap_term %in% spec$term){
## check term is a stap_term
stopifnot(get_component(spec,stap_term)=="Distance-Time")
}else{
stop("Term specified is not included in model")
}
beta <- as.matrix(x$stapfit)
gd_eta <- get_stap(spec,stap_term,"Distance-Time",beta,x$family,grid)
gd <- gd_eta$grid
eta <- gd_eta$eta
dplyr::tibble(Distance = gd$Distance,
Time = gd$Time,
Lower = apply(eta,1,function(x) quantile(x,0.025)),
Exposure = apply(eta,1,median),
Upper = apply(eta,1,function(x) quantile(x,0.975))
) -> pltdf
pl <- plotly::plot_ly(pltdf,x = ~Distance, y = ~Time, z = ~Exposure,
mode = "markers",
type ='scatter3d')
if(has_bw(spec,stap_term)){
dplyr::tibble(Distance = gd$Distance,
Time = gd$Time,
Lower = apply(gd_eta$eta_within,1,function(x) quantile(x,0.025)),
Exposure = apply(gd_eta$eta_within,1,median),
Upper = apply(gd_eta$eta_within,1,function(x) quantile(x,0.975))
) -> pltdf
pl2 <- plotly::plot_ly(pltdf,x = ~Distance, y = ~Time, z = ~Exposure,
mode = "markers",
type ='scatter3d')
return((list(Between=pl,Within=pl2)))
}
return(pl)
}
#' Posterior Predictive Checks
#'
#' @export
#' @keywords internal
#' @param x a sstapreg object
#' @param num_reps number of yhat samples to plot
#'
ppc <- function(x,num_reps = 20)
UseMethod("ppc")
#' Posterior Predictive Checks
#'
#' @export
#' @describeIn ppc
#'
ppc.sstapreg <- function(x,num_reps = 20){
Samples <- Parameter <- iteration_ix <- NULL
samp <- sample(1:nsamples(x),size=num_reps)
if(is.matrix(x$model$y))
y <- x$model$y[,1] / rowSums(x$model$y)
else
y <- x$model$y
yhatmat <- posterior_predict(x,'response')
yhatmat <- yhatmat[samp,]
colnames(yhatmat) <- paste0("yhat_",colnames(yhatmat))
pltdf <- dplyr::as_tibble(yhatmat,silent=TRUE) %>%
dplyr::mutate(iteration_ix = 1:dplyr::n()) %>%
tidyr::pivot_longer(dplyr::contains('yhat'),
names_to = "Parameter",
values_to="Samples") %>%
dplyr::mutate(Parameter = 'yrep')
pltdf <- rbind(pltdf,
dplyr::tibble(iteration_ix = 0, Parameter='y',Samples= y ))
p <- pltdf %>%
ggplot2::ggplot(ggplot2::aes(x=Samples,color=Parameter,group=iteration_ix)) +
ggplot2::geom_density() + ggplot2::theme_bw()+ ggplot2::theme(legend.title=ggplot2::element_blank()) +
ggplot2::scale_colour_manual(values=c("black","grey")) +
ggplot2::xlab("y") + ggplot2::ylab("")
return(p)
}
#' Plot Cross-Sections
#'
#' @export
#' @keywords internal
#' @param x a sstapreg object
#' @param stap_term name of stap term to plot
#' @param component one of c("Distance","Time")
#' @param fixed_val vector that contains fixed values for whichever component was not specified
#' @param p probability_interval
#' @param optional grid by default is NULL corresponding to a .1 step grid from the min-max of the covariate space
#'
plot_xsection <- function(x,stap_term = NULL, component = "Distance",fixed_val = 1, p = 0.95,grid = NULL)
UseMethod("plot_xsection")
#' Plot Cross-Sections
#'
#' @export
#' @describeIn plot_xsection
#'
plot_xsection.sstapreg <- function(x,stap_term = NULL, component = "Distance",fixed_val =1 , p = 0.95,grid = NULL){
Distance <- Time <- Median <- Grid <- Lower <- Upper <- . <- .data <- NULL
check_p(p)
spec <- x$specification
if(!has_any_staps(spec))
stop("Model has no stap terms specified")
if(is.null(stap_term)){
ix <- which(spec$component=="Distance-Time")[1]
stap_term <- spec$term[ix]
}
else if(stap_term %in% spec$term){
## check term is a stap_term
stopifnot(get_component(spec,stap_term)=="Distance-Time")
}else{
stop("Term specified is not included in model")
}
beta <- as.matrix(x$stapfit)
gd_eta <- get_stap(spec,stap_term,"Distance-Time",beta,x$family,grid)
gd <- gd_eta$grid
eta <- gd_eta$eta
l <- .5 - p/2
u <- .5 + p/2
ocomp <- switch(component,
"Distance"="Time",
"Time"="Distance")
lbl <- paste0(ocomp, " fixed at ", fixed_val)
ics <- which(gd[,ocomp]==fixed_val)
gd <- gd[ics,]
eta <- eta[ics,]
dplyr::tibble(Distance = gd$Distance,
Time = gd$Time,
Lower = apply(eta,1,function(x) quantile(x,l)),
Median = apply(eta,1,median),
Upper = apply(eta,1,function(x) quantile(x,u))
) -> pltdf
if(has_bw(spec,stap_term)){
dplyr::tibble(Distance = gd$Distance,
Time = gd$Time,
Lower = apply(gd_eta$eta_within[ics,],1,function(x) quantile(x,l)),
Median = apply(gd_eta$eta_within[ics,],1,median),
Upper = apply(gd_eta$eta_within[ics,],1,function(x) quantile(x,u)),
Parameters = "within") -> pltdf2
pltdf %>% dplyr::mutate(Parameters = "between") %>% rbind(.,pltdf2) -> pltdf
pltdf %>% ggplot2::ggplot(ggplot2::aes(x=.data[[component]],y=Median)) +
ggplot2::geom_line() +
ggplot2::geom_ribbon(ggplot2::aes(ymin=Lower,ymax=Upper),alpha=0.3) +
ggplot2::theme_bw() +
ggplot2::theme(strip.background=ggplot2::element_blank()) +
ggplot2::labs(subtitle = lbl) +
ggplot2::facet_wrap(~Parameters) -> pl2
return(pl2)
}
pltdf %>% ggplot2::ggplot(ggplot2::aes(x = .data[[component]], y = Median )) +
ggplot2::geom_line() +
ggplot2::geom_ribbon(ggplot2::aes(ymin=Lower,ymax=Upper),alpha=0.3) +
ggplot2::theme_bw() +
ggplot2::geom_hline(ggplot2::aes(yintercept = 0),
linetype=2,color='red') +
ggplot2::xlab(component) +
ggplot2::labs(subtitle = lbl) +
ggplot2::ylab("") ->pl
return(pl)
}
# Internal ---------------------------------------------
check_p <- function(p){
stopifnot(p<1 && p>0)
}
get_pltdf <- function(gd,eta,p,component){
check_p(p)
l <- .5 - p/2
u <- .5 + p/2
pltdf <- dplyr::tibble(Lower = apply(eta,1,function(x) quantile(x,l)),
Median = apply(eta,1,median),
Upper = apply(eta,1,function(x) quantile(x,u)))
if(component == "Distance-Time"){
pltdf$Time <- gd$Time
pltdf$Distance <- gd$Distance
}else if(component == "Distance")
pltdf$Distance <- gd$Distance
else
pltdf$Time <- gd$Time
return(pltdf)
}