## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

## ----setup, echo=FALSE, warning=FALSE, message=FALSE--------------------------
#  library(devtools)
#  #devtools::install_github('jagm03/kernstadapt', force = T)
#  library(kernstadapt)
#  library(ggplot2)

## ----,fig.height = 3, fig.width= 5, fig.align="center"------------------------
#  # Setting a simulation of temporal point pattern with a hotspot
#  # intensity for Nt points
#  Nt <- 2000
#  y1 <- rnorm(Nt, 10, 0.1)
#  
#  # fixed bandwidth estimate
#  classic.dens <- density.default(y1, from = min(y1), to = max(y1))
#  classic.dens$y <- classic.dens$y * Nt
#  adapt.dens <- dens.par.temp(y1, at = "bins", dimt = 512)
#  true.dens <- Nt * dnorm(classic.dens$x, 10, 0.1)
#  
#  ##ISE
#  ISE.adapt <- (sum(adapt.dens$y - true.dens) ^ 2) * diff(adapt.dens$x[1:2])
#  ISE.classic <- (sum(classic.dens$y - true.dens) ^ 2) * diff(adapt.dens$x[1:2])
#  
#  PD <- data.frame(x = rep(adapt.dens$x, 3),
#                   intensity = c(classic.dens$y, adapt.dens$y, true.dens),
#                   estimator = factor(rep(1:3, rep(512,3)), levels = 1:3,
#                                 labels = c("classical", "adaptive", "true")))
#  ggplot(data = PD, aes(x = x, y = intensity, group = estimator, colour = estimator)) +
#    geom_path() + theme(axis.title.x = element_blank())

## ----fig.height = 3.5, fig.width= 7, fig.align="center"-----------------------
#  # Setting a simulation of a high clustered temporal point pattern
#  # Probability density function
#  fdens.x <- function(x) (dbeta(x %% 4, 2, 2))
#  # intensity for Nt points
#  Nt <- 2000
#  x <- runif(Nt, 0, 10)
#  # temporal point pattern
#  y <- sample(x, replace = T, prob = fdens.x(x))
#  # fixed bandwidth estimate
#  classic.dens <- density.default(y, from = min(y), to = max(y))
#  classic.dens$y <- classic.dens$y * Nt
#  # Global bandwidth (we give such a refined one because of the high clustering)
#  bw0 <- bw.nrd0(y) / 4
#  # Abram's bandwidth
#  bw1 <- bw.abram.temp(y, h0 = bw0, trim = 2)
#  # Adaptive intensity
#  adapt.dens <- dens.par.temp(y, bw = bw1, at = "bins", dimt = 512)
#  true.dens <- Nt * fdens.x(adapt.dens$x)
#  
#  ##ISE
#  ISE.adapt <- (sum(adapt.dens$y - true.dens) ^ 2) * diff(adapt.dens$x[1:2])
#  ISE.classic <- (sum(classic.dens$y - true.dens) ^ 2) * diff(adapt.dens$x[1:2])
#  
#  PD <- data.frame(x = rep(adapt.dens$x, 3),
#                   intensity = c(classic.dens$y, adapt.dens$y, true.dens),
#                   estimator = factor(rep(1:3, rep(512,3)), levels = 1:3,
#                                 labels = c("classical", "adaptive", "true")))
#  ggplot(data = PD, aes(x = x, y = intensity, group = estimator, colour = estimator)) +
#    geom_line() + theme(axis.title.x = element_blank())

## ----,fig.height = 5, fig.width= 7, fig.align="center"------------------------
#  # Load aegiss data-set and plotting
#  data(aegiss)
#  plot(aegiss, bg = rainbow(512), pch = 21, cex = 1,
#       main = "Gastrointestinal desease cases in Hampshire")

## ----,fig.height = 3, fig.width= 5.5, fig.align="center"----------------------
#  # Fixed bandwidth estimate
#  ti <- aegiss$marks
#  Nt <- aegiss$n
#  # Classical estimate
#  classic.dens <- density.default(ti, from = min(ti), to = max(ti))
#  classic.dens$y <- classic.dens$y * Nt
#  # Adaptive estimate
#  adapt.dens <- dens.par.temp(ti, at = "bins", dimt = 512)
#  
#  aegissD <- data.frame(x = rep(adapt.dens$x, 2),
#                   intensity = c(classic.dens$y, adapt.dens$y),
#                   estimator = factor(rep(1:2, rep(512,2)), levels = 1:2,
#                                 labels = c("classical", "adaptive")))
#  ggplot(data = aegissD, aes(x = x, y = intensity,
#                             group = estimator, colour = estimator)) +
#    geom_line() + theme(axis.title.x = element_blank())