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

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

data(data_LOGIT)

matplot(
  t(data_LOGIT[, 12:21]),t(data_LOGIT[, 2:11]),
  pch = 1, type='b', col="black", lty=1,
  xlab = "Times", ylab = "Values", main = "Plot of the individual's trajectories")

## ----message = FALSE----------------------------------------------------------
solL <- trajeR(
  Y = data_LOGIT[,2:11], A = data_LOGIT[,12:21],
  ng = 3, degre = c(0,3,4),
  Model = "LOGIT", Method = "L",
  hessian = TRUE
  )

solL

## ----message = FALSE----------------------------------------------------------
#EM
solEM <- trajeR(Y = data_LOGIT[,2:11], A = data_LOGIT[,12:21],
               ng = 3, degre = c(0,3,4), 
               Model = "LOGIT", Method = "EM", hessian = TRUE, itermax = 300) 
#EMIRLS
solEMIRLS <- trajeR(Y = data_LOGIT[,2:11], A = data_LOGIT[,12:21],
                    ng = 3, degre=c(0,3,4),
                    Model = "LOGIT", Method = "EMIRLS", hessian = TRUE,
                    itermax = 300)

solEM
solEMIRLS

## -----------------------------------------------------------------------------
solLRisk <- trajeR(Y = data_LOGIT[,2:11], A = data_LOGIT[,12:21], Risk = data_LOGIT[,22:23],
                  ng = 3, degre = c(0,3,4),
                  Model = "LOGIT", Method = "L", hessian = TRUE,
                  itermax = 300)

solLRisk

## -----------------------------------------------------------------------------
plotrajeR(solLRisk)

## -----------------------------------------------------------------------------
# colour's defintion
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)
vcol <- c(cols1, cols2)

plotrajeR(solLRisk, Y = data_LOGIT[,2:11], A = data_LOGIT[,12:21], dec = 5, col = vcol)

## -----------------------------------------------------------------------------
solLTCOV <- trajeR(
  Y = data_LOGIT[,2:11], A =data_LOGIT[,12:21], TCOV = data_LOGIT[,24:33],
  ng = 3, degre = c(0,3,4),
  Model = "LOGIT", Method = "L", hessian = TRUE,
  itermax = 300
  )

solEMTCOV <- trajeR(
  Y = data_LOGIT[,2:11], A = data_LOGIT[,12:21], TCOV = data_LOGIT[,24:33],
  ng = 3, degre = c(0,3,4),
  Model = "LOGIT", Method = "EM", hessian = TRUE,
  itermax = 300
  )

solEMIRLSTCOV <- trajeR(
  Y = data_LOGIT[,2:11], A = data_LOGIT[,12:21], TCOV = data_LOGIT[,24:33],
  ng = 3, degre = c(0,3,4),
  Model = "LOGIT", Method = "EMIRLS", hessian = FALSE,
  itermax = 300
  )

solLTCOV
solEMTCOV
solEMIRLSTCOV

plotrajeR(solLTCOV, col = vcol)

## -----------------------------------------------------------------------------
plotrajeR(solLTCOV, col = vcol, plotcov = c(0,0,0,0,0,1,1,1,1,1))