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

options(rmarkdown.html_vignette.check_title = FALSE)
oldpar <- par(no.readonly = TRUE)

## -----------------------------------------------------------------------------
library(PlotNormTest)

## ----The Cork dataset---------------------------------------------------------
cork <- matrix(c(
  72, 66, 76, 77,
  60, 53, 66, 63,
  56, 57, 64, 58,
  41, 29, 36, 38,
  32, 32, 35, 36,
  30, 35, 34, 26,
  39, 39, 31, 27,
  42, 43, 31, 25,
  37, 40, 31, 25,
  33, 29, 27, 36,
  32, 30, 34, 28,
  63, 45, 74, 63,
  54, 46, 60, 52,
  47, 51, 52, 43,
  91, 79, 100, 75,
  56, 68, 47, 50,
  79, 65, 70, 61,
  81, 80, 68, 58,
  78, 55, 67, 60,
  46, 38, 37, 38,
  39, 35, 34, 37,
  32, 30, 30, 32,
  60, 50, 67, 54,
  35, 37, 48, 39,
  39, 36, 39, 31,
  50, 34, 37, 40,
  43, 37, 39, 50,
  48, 54, 57, 43
), nrow = 28, ncol = 4, byrow = T)
colnames(cork) <- c("North", "East", "South", "West")

head(cork)

## ----fig.width=6, fig.height=6, fig.align='center'----------------------------
library(ggplot2)
# Score function
lapply(1:4,  FUN = function(mycol) {
  re <- PlotNormTest::cox(matrix(sort(cork[, mycol])), x.dist = 0.0001)
  a <- re$a[, 1]
  p <- ggplot(data.frame(x = re$x, a = a), aes(x = x, y = a)) + 
    geom_point(color = "steelblue3", shape = 19, size = 1.5) + 
    ggtitle(paste("Score plot: ", colnames(cork)[mycol])) +
    coord_fixed() + xlab("y")+ 
    ylab("Score function") + 
    theme_bw() + 
    theme(aspect.ratio = 1/1, panel.grid = element_blank(),
          axis.line = element_line(colour = "black"), 
          axis.text=element_text(size=12),
          axis.title=element_text(size=14,face="bold"), 
          legend.background = element_rect( 
            size=0.5, linetype="solid"), 
          legend.text = element_text(size=12))
  p
  
}
)

## ----fig.width=6, fig.height=6, fig.align='center'----------------------------
# T3 
lapply(1:4,  FUN = function(mycol) {
  x <- cork[, mycol]
  par(cex.axis = 1.2, cex.lab = 1.2,
               mar = c(4, 4.2, 2,1), cex.main = 1.2)
  PlotNormTest::dhCGF_plot1D(x, method = "T3") 
  namex <- colnames(cork)[mycol]
  title(main = bquote(T[3]~"plot: "~.(namex)), adj = 0)
}
)


## ----fig.width=6, fig.height=6, fig.align='center'----------------------------
# T4
 par(cex.axis = 1.2, cex.lab = 1.2,
             mar = c(4, 4.2, 2,1), cex.main = 1.2)
lapply(1:4,  FUN = function(mycol) {
  x <- cork[, mycol]
  PlotNormTest::dhCGF_plot1D(x, method = "T4") 
  namex <- colnames(cork)[mycol]
  title(main = bquote(T[4]~"plot: "~.(namex)), adj = 0)
}
)

## ----fig.width=6, fig.height=6, fig.align='center'----------------------------
df <- Multi.to.Uni(cork)
# Cox
score_plot1D(df$x.new, ori.index = df$ind, x.dist = .001)$plot +
  theme(legend.position = "none")+ xlab("y") +
  ggtitle("Score plot")+
  ylab("Score function")

#T3 and T4
par(cex.axis = 1.2, cex.lab = 1.2, mar = c(4, 4.2, 2,1), cex.main = 1.2)
PlotNormTest::dhCGF_plot1D(df$x.new, method = "T3")
par(cex.axis = 1.2, cex.lab = 1.2, mar = c(4, 4.2, 2,1), cex.main = 1.2)
dhCGF_plot1D(df$x.new, method = "T4")

## ----fig.width=6, fig.height=6, fig.align='center'----------------------------
par(cex.axis = 1.2, cex.lab = 1.2, mar = c(4, 4.2, 2,1), cex.main = 1.2)
PlotNormTest::d3hCGF_plot(cork)

## ----fig.width=6, fig.height=6, fig.align='center'----------------------------
par(cex.axis = 1.2, cex.lab = 1.2, mar = c(4, 4.2, 2,1), cex.main = 1.2)
PlotNormTest::d4hCGF_plot(cork)

## ----Change par back to default, include = FALSE------------------------------
par(oldpar)