## -----------------------------------------------------------------------------
library(trajeR)

data("data_ZIP")

matplot(
  t(data_ZIP[, 7:11]),
  t(data_ZIP[, 2:6]),
  pch = 1,
  type = 'b',
  col = "black",
  lty = 1,
  xlab = "Times",
  ylab = "Values",
  main = "Plot of the individual's trajectories"
)

## ----message = FALSE----------------------------------------------------------
# Likelihood
solL <- trajeR(
  Y = data_ZIP[, 2:6],
  A = data_ZIP[, 7:11],
  ng = 2,
  degre = c(2, 2),
  degre.nu = c(1, 1),
  Model = "ZIP",
  Method = "L",
  hessian = TRUE
)
solL

## ----message = FALSE----------------------------------------------------------
# EM
solEM <- trajeR(
  Y = data_ZIP[, 2:6],
  A = data_ZIP[, 7:11],
  ng = 2,
  degre = c(2, 2),
  degre.nu = c(1, 1),
  Model = "ZIP",
  Method = "EM",
  hessian = TRUE
)
solEMIRLS <- trajeR(
  Y = data_ZIP[, 2:6],
  A = data_ZIP[, 7:11],
  ng = 2,
  degre = c(2, 2),
  degre.nu = c(1, 1),
  Model = "ZIP",
  Method = "EMIRLS",
  hessian = TRUE
)

## ----echo = FALSE-------------------------------------------------------------
library(kableExtra)
t1 <- solL$tab[, 1:2]
t1[11:12, 1] <- exp(t1[11:12, 1]) / sum(exp(t1[11:12, 1]))
t2 <- solEM$tab[, 1:2]
t2[12, 2] <- t2[11, 2]
t3 <- solEMIRLS$tab[, 1:2]
t3[12, 2] <- t3[11, 2]
tab <- round(cbind(t1, t2, t3), 5)
colnames(tab) <- c("parameters", "sd", "parameters", "sd", "parameters", "sd")

kable(tab, "html", booktabs = T, escape = FALSE, align = "r") %>%
  kable_styling() %>%
  add_header_above(c("SolL" = 2, "SolEM" = 2, "SolEMIRLS" = 2)) %>%
  pack_rows("Beta 1", 1, 3) %>%
  pack_rows("Beta 2", 4, 6) %>%
  pack_rows("Nu 1", 7, 8) %>%
  pack_rows("Nu 2", 9, 10) %>%
  pack_rows("Pi", 11, 12)

## -----------------------------------------------------------------------------
plotrajeR(solL)

## -----------------------------------------------------------------------------
# colour's defintion
trans <- "70"
col1 <- "#034569"
col1.1 <- paste0("#64AAD0", trans)
col2 <- "#750062"
col2.1 <- paste0("#D962C7", trans)
cols1 <- c(col1.1, col2.1)
cols2 <- c(col1, col2)
vcol <- c(cols1, cols2)

plotrajeR(solEM, Y = data_ZIP[, 2:6], A = data_ZIP[, 7:11], dec = 5, col = vcol)

## ----message = FALSE----------------------------------------------------------
solLRisk <- trajeR(
  Y = data_ZIP[, 2:6],
  A = data_ZIP[, 7:11],
  Risk = data_ZIP[, 12],
  ng = 2,
  degre = c(2, 2),
  degre.nu = c(1, 1),
  Model = "ZIP",
  Method = "L",
  hessian = TRUE
)
solLRisk

## ----message = FALSE----------------------------------------------------------
solEMRisk <- trajeR(
  Y = data_ZIP[, 2:6],
  A = data_ZIP[, 7:11],
  Risk = data_ZIP[, 12],
  ng = 2,
  degre = c(2, 2),
  degre.nu = c(1, 1),
  Model = "ZIP",
  Method = "EM",
  hessian = TRUE
)
solEMIRLSRisk <- trajeR(
  Y = data_ZIP[, 2:6],
  A = data_ZIP[, 7:11],
  Risk = data_ZIP[, 12],
  ng = 2,
  degre = c(2, 2),
  degre.nu = c(1, 1),
  Model = "ZIP",
  Method = "EMIRLS",
  hessian = TRUE
)

## ----echo = FALSE-------------------------------------------------------------
t1 <- solLRisk$tab[, 1:2]
t1 <- round(t1, 5)
t2 <- solEMRisk$tab[, 1:2]
t2[, 1] <- round(t2[, 1], 5)
t3 <- round(solEMIRLSRisk$tab[, 1:2], 5)
tab <- cbind(t1, t2, t3)
tab[11:14, 1] <- tab[11:12, 1] - tab[11:14, 1]
tab[11:14, 5] <- tab[11:12, 5] - tab[11:14, 5]
#tab=tab[-11,]
colnames(tab) <- c("parameters", "sd", "parameters", "sd", "parameters", "sd")

kable(tab, "html", booktabs = T, escape = FALSE, align = "r") %>%
  kable_styling() %>%
  add_header_above(c("SolLRisk" = 2, "SolEMRisk" = 2, "SolEMIRLSRisk" = 2)) %>%
  pack_rows("Beta 1", 1, 3) %>%
  pack_rows("Beta 2", 4, 6) %>%
  pack_rows("Nu 1", 7, 8) %>%
  pack_rows("Nu 2", 9, 10) %>%
  pack_rows("Theta", 11, 14)

## ----message = FALSE----------------------------------------------------------
solLTCOV <- trajeR(
  Y = data_ZIP[, 2:6],
  A = data_ZIP[, 7:11],
  TCOV = data_ZIP[, 13:17],
  ng = 2,
  degre = c(2, 2),
  degre.nu = c(1, 1),
  Model = "ZIP",
  Method = "L",
  hessian = TRUE
)
solLTCOV 

## ----message = FALSE----------------------------------------------------------
solEMTCOV <- trajeR(
  Y = data_ZIP[, 2:6],
  A = data_ZIP[, 7:11],
  TCOV = data_ZIP[, 13:17],
  ng = 2,
  degre = c(2, 2),
  degre.nu = c(1, 1),
  Model = "ZIP",
  Method = "EM",
  hessian = TRUE
)
solEMIRLSTCOV <- trajeR(
  Y = data_ZIP[, 2:6],
  A = data_ZIP[, 7:11],
  TCOV = data_ZIP[, 13:17],
  ng = 2,
  degre = c(2, 2),
  degre.nu = c(1, 1),
  Model = "ZIP",
  Method = "EMIRLS",
  hessian = TRUE
)

## ----echo = FALSE-------------------------------------------------------------
t1 <- solLTCOV$tab[, 1]
t1[13:14] <- exp(t1[13:14]) / sum(exp(t1[13:14]))
t2 <- solEMTCOV$tab[, 1]
t3 <- solEMIRLSTCOV$tab[, 1]
tab <- round(cbind(t1, t2, t3), 5)
colnames(tab) <- c("SolLTCOV", "SolEMTCOV", "SoEMIRLSTCOV")

kable(tab, "html", booktabs = T, escape = FALSE, align = "r") %>%
  kable_styling() %>%
  pack_rows("Beta 1", 1, 3) %>%
  pack_rows("Beta 2", 4, 6) %>%
  pack_rows("Nu 1", 7, 8) %>%
  pack_rows("Nu 2", 9, 10) %>%
  pack_rows("Pi", 13, 14) %>%
  pack_rows("TCOV", 11, 12)

## ----message = FALSE----------------------------------------------------------
trans <- "70"
col1 <- "#034569"
col1.1 <- paste0("#64AAD0", trans)
col2 <- "#750062"
col2.1 <- paste0("#D962C7", trans)
col3 <- "#A68900"
col3.1 <- paste0("#FFE773", trans)
cols1 <- c(col1.1, col2.1, col3.1)
cols2 <- c(col1, col2, col3)
cols1 <- c(col1.1, col2.1)
cols2 <- c(col1, col2)
vcol <- c(cols1, cols2)
plotrajeR(
  solLTCOV,
  Y = data_ZIP[, 2:6],
  A = data_ZIP[, 7:11],
  TCOV = data_ZIP[, 13:17],
  col = vcol,
  plotcov = c(1, 1, 0, 0, 1, 0, 0, 1, 1, 1),
  mean = TRUE,
  alpha = 0.75
)