## ------------------------------------- ##
## Verify working results
## ------------------------------------- ##
test_that("Joint data generation, no error", {
    a <- c(0,0,0,1,1,1)
    b <- c(1,1,1,2,2,2)
    c <- c(0,1,2,2,1,0)
    d <- c(1,1,0,0,1,1)
    e <- c(0,1,1,1,0,0)
    df <- data.table('t0'=a,'t1'=b,'e0'=c,'e1'=d,'fac'=e)
    time1 <- "t0"
    time2 <- "t1"
    df$pyr <- df$t1 - df$t0
    pyr <- "pyr"
    events <- c('e0','e1')
    names_e0 <- c('fac')
    names_e1 <- c('fac')
    names_shared <- c('t0','t0')
    Term_n_e0 <- c(0)
    Term_n_e1 <- c(0)
    Term_n_shared <- c(0,0)
    tform_e0 <- c("loglin")
    tform_e1 <- c("loglin")
    tform_shared <- c("quad_slope","loglin_top")
    keep_constant_e0 <- c(0)
    keep_constant_e1 <- c(0)
    keep_constant_shared <- c(0,0)
    a_n_e0 <- c(-0.1)
    a_n_e1 <- c(0.1)
    a_n_shared <- c(0.001, -0.02)
    name_list <- list('shared'=names_shared,'e0'=names_e0,'e1'=names_e1)
    Term_n_list <- list('shared'=Term_n_shared,'e0'=Term_n_e0,'e1'=Term_n_e1)
    tform_list <- list('shared'=tform_shared,'e0'=tform_e0,'e1'=tform_e1)
    keep_constant_list <- list('shared'=keep_constant_shared, 'e0'=keep_constant_e0,'e1'=keep_constant_e1)
    a_n_list <- list('shared'=a_n_shared,'e0'=a_n_e0,'e1'=a_n_e1)
    #
    expect_no_error(Joint_Multiple_Events(df, events, name_list, Term_n_list, tform_list, keep_constant_list, a_n_list))
})
test_that("Joint data generation fill defaults, no error", {
    a <- c(0,0,0,1,1,1)
    b <- c(1,1,1,2,2,2)
    c <- c(0,1,2,2,1,0)
    d <- c(1,1,0,0,1,1)
    e <- c(0,1,1,1,0,0)
    df <- data.table('t0'=a,'t1'=b,'e0'=c,'e1'=d,'fac'=e)
    time1 <- "t0"
    time2 <- "t1"
    df$pyr <- df$t1 - df$t0
    pyr <- "pyr"
    events <- c('e0','e1')
    names_e0 <- c('fac')
    names_e1 <- c('fac')
    names_shared <- c('t0','t0')
    Term_n_e0 <- c(0)
    Term_n_e1 <- c(0)
    Term_n_shared <- c(0,0)
    tform_e0 <- c("loglin")
    tform_e1 <- c("loglin")
    tform_shared <- c("quad_slope","loglin_top")
    keep_constant_e0 <- c(0)
    keep_constant_e1 <- c(0)
    keep_constant_shared <- c(0,0)
    a_n_e0 <- c(-0.1)
    a_n_e1 <- c(0.1)
    a_n_shared <- c(0.001, -0.02)
    name_list <- list('shared'=names_shared,'e0'=names_e0,'e1'=names_e1)
    Term_n_list <- list('shared'=Term_n_shared,'e0'=Term_n_e0,'e1'=Term_n_e1)
    tform_list <- list('shared'=tform_shared,'e0'=tform_e0,'e1'=tform_e1)
    keep_constant_list <- list('shared'=keep_constant_shared, 'e0'=keep_constant_e0,'e1'=keep_constant_e1)
    a_n_list <- list('shared'=a_n_shared,'e0'=a_n_e0,'e1'=a_n_e1)
    #
    expect_no_error(Joint_Multiple_Events(df, events, name_list, list(), list(), list(), list()))
    val <- Joint_Multiple_Events(df, events, name_list, list(), list(), list(), list())
    expect_equal(val$Term_n, rep(0,4))
    expect_equal(val$tform, rep('loglin',4))
    expect_equal(val$keep_constant, rep(0,4))
    expect_equal(val$a_n, rep(0,4))
})
test_that("Joint data generation, check results", {
    a <- c(0,0,0,1,1,1)
    b <- c(1,1,1,2,2,2)
    c <- c(0,1,2,2,1,0)
    d <- c(1,1,0,0,1,1)
    e <- c(0,1,1,1,0,0)
    df <- data.table('t0'=a,'t1'=b,'e0'=c,'e1'=d,'fac'=e)
    time1 <- "t0"
    time2 <- "t1"
    df$pyr <- df$t1 - df$t0
    pyr <- "pyr"
    events <- c('e0','e1')
    names_e0 <- c('fac')
    names_e1 <- c('fac')
    names_shared <- c('t0','t0')
    Term_n_e0 <- c(0)
    Term_n_e1 <- c(0)
    Term_n_shared <- c(0,0)
    tform_e0 <- c("loglin")
    tform_e1 <- c("loglin")
    tform_shared <- c("quad_slope","loglin_top")
    keep_constant_e0 <- c(0)
    keep_constant_e1 <- c(0)
    keep_constant_shared <- c(0,0)
    a_n_e0 <- c(-0.1)
    a_n_e1 <- c(0.1)
    a_n_shared <- c(0.001, -0.02)
    name_list <- list('shared'=names_shared,'e0'=names_e0,'e1'=names_e1)
    Term_n_list <- list('shared'=Term_n_shared,'e0'=Term_n_e0,'e1'=Term_n_e1)
    tform_list <- list('shared'=tform_shared,'e0'=tform_e0,'e1'=tform_e1)
    keep_constant_list <- list('shared'=keep_constant_shared, 'e0'=keep_constant_e0,'e1'=keep_constant_e1)
    a_n_list <- list('shared'=a_n_shared,'e0'=a_n_e0,'e1'=a_n_e1)
    #
    val <- Joint_Multiple_Events(df, events, name_list, Term_n_list, tform_list, keep_constant_list, a_n_list)
    expect_equal(val$names, c("t0", "t0", "fac_e0", "fac_e1"))
    expect_equal(names(val$df),c('t0', 't1', 'events', 'e0', 'e1', 'fac', 'pyr', 'fac_e0', 'fac_e1'))
})
test_that("Joint data regression, no error", {
    a <- c(0,0,0,1,1,1)
	b <- c(1,1,1,2,2,2)
	c <- c(0,1,2,2,1,0)
	d <- c(1,1,0,0,1,1)
	e <- c(0,1,1,1,0,0)
	f <- c(0,1,0,0,1,1)
	df <- data.table('t0'=a,'t1'=b,'e0'=c,'e1'=d,'fac'=e)
	time1 <- "t0"
	time2 <- "t1"
	df$pyr <- df$t1 - df$t0
	pyr <- "pyr"
	events <- c('e0','e1')
	names_e0 <- c('fac')
	names_e1 <- c('fac')
	names_shared <- c('t0','t0')
	Term_n_e0 <- c(0)
	Term_n_e1 <- c(0)
	Term_n_shared <- c(0,0)
	tform_e0 <- c("loglin")
	tform_e1 <- c("loglin")
	tform_shared <- c("quad_slope","loglin_top")
	keep_constant_e0 <- c(0)
	keep_constant_e1 <- c(0)
	keep_constant_shared <- c(0,0)
	a_n_e0 <- c(-0.1)
	a_n_e1 <- c(0.1)
	a_n_shared <- c(0.001, -0.02)
	name_list <- list('shared'=names_shared,'e0'=names_e0,'e1'=names_e1)
	Term_n_list <- list('shared'=Term_n_shared,'e0'=Term_n_e0,'e1'=Term_n_e1)
	tform_list <- list('shared'=tform_shared,'e0'=tform_e0,'e1'=tform_e1)
	keep_constant_list <- list('shared'=keep_constant_shared,
		                       'e0'=keep_constant_e0,'e1'=keep_constant_e1)
	a_n_list <- list('shared'=a_n_shared,'e0'=a_n_e0,'e1'=a_n_e1)

	der_iden <- 0
	modelform <- "M"
	fir <- 0
	control <- list("Ncores"=2,'lr' = 0.75,'maxiter' = 2,'halfmax' = 5,'epsilon' = 1e-3,
	   'dbeta_max' = 0.5,'deriv_epsilon' = 1e-3, 'abs_max'=1.0,'change_all'=TRUE,
	   'dose_abs_max'=100.0,'verbose'=FALSE, 'ties'='breslow','double_step'=1)
	guesses_control <- list("maxiter"=10,"guesses"=10,"lin_min"=0.001,"lin_max"=1,
		"loglin_min"=-1,"loglin_max"=1, "lin_method"="uniform","loglin_method"="uniform",
		 strata=FALSE)
	Strat_Col <- 'f'
	expect_no_error(RunPoissonRegression_Joint_Omnibus(df, pyr, events, name_list, Term_n_list,
		                                    tform_list, keep_constant_list, a_n_list,
		                                    modelform, fir, der_iden, control,Strat_Col)
    )
})
test_that("Joint data regression, check results", {
    a <- c(0,0,0,1,1,1)
	b <- c(1,1,1,2,2,2)
	c <- c(0,1,2,2,1,0)
	d <- c(1,1,0,0,1,1)
	e <- c(0,1,1,1,0,0)
	f <- c(0,1,0,0,1,1)
	df <- data.table('t0'=a,'t1'=b,'e0'=c,'e1'=d,'fac'=e)
	time1 <- "t0"
	time2 <- "t1"
	df$pyr <- df$t1 - df$t0
	pyr <- "pyr"
	events <- c('e0','e1')
	names_e0 <- c('fac')
	names_e1 <- c('fac')
	names_shared <- c('t0','t0')
	Term_n_e0 <- c(0)
	Term_n_e1 <- c(0)
	Term_n_shared <- c(0,0)
	tform_e0 <- c("loglin")
	tform_e1 <- c("loglin")
	tform_shared <- c("quad_slope","loglin_top")
	keep_constant_e0 <- c(0)
	keep_constant_e1 <- c(0)
	keep_constant_shared <- c(0,0)
	a_n_e0 <- c(-0.1)
	a_n_e1 <- c(0.1)
	a_n_shared <- c(0.001, -0.02)
	name_list <- list('shared'=names_shared,'e0'=names_e0,'e1'=names_e1)
	Term_n_list <- list('shared'=Term_n_shared,'e0'=Term_n_e0,'e1'=Term_n_e1)
	tform_list <- list('shared'=tform_shared,'e0'=tform_e0,'e1'=tform_e1)
	keep_constant_list <- list('shared'=keep_constant_shared,
		                       'e0'=keep_constant_e0,'e1'=keep_constant_e1)
	a_n_list <- list('shared'=a_n_shared,'e0'=a_n_e0,'e1'=a_n_e1)

	der_iden <- 0
	modelform <- "M"
	fir <- 0
	control <- list("Ncores"=2,'lr' = 0.75,'maxiter' = 10,'halfmax' = 5,'epsilon' = 1e-3,
	   'dbeta_max' = 0.5,'deriv_epsilon' = 1e-3, 'abs_max'=1.0,'change_all'=TRUE,
	   'dose_abs_max'=100.0,'verbose'=FALSE, 'ties'='breslow','double_step'=1)
	guesses_control <- list("maxiter"=10,"guesses"=10,"lin_min"=0.001,"lin_max"=1,
		"loglin_min"=-1,"loglin_max"=1, "lin_method"="uniform","loglin_method"="uniform",
		 strata=FALSE)
	Strat_Col <- 'f'
	e <- RunPoissonRegression_Joint_Omnibus(df, pyr, events, name_list, Term_n_list,
		                                    tform_list, keep_constant_list, a_n_list,
		                                    modelform, fir, der_iden, control,Strat_Col)
    expect_equal(e$beta_0, c(0.5742600, -1.0349816, -0.0200000, -0.1647421),tolerance=1e-2)
    expect_equal(e$Converged,TRUE)
})

## ------------------------------------- ##
## Verify errors results
## ------------------------------------- ##
test_that("Joint data generation, incorrect length error", {
    a <- c(0,0,0,1,1,1)
    b <- c(1,1,1,2,2,2)
    c <- c(0,1,2,2,1,0)
    d <- c(1,1,0,0,1,1)
    e <- c(0,1,1,1,0,0)
    df <- data.table('t0'=a,'t1'=b,'e0'=c,'e1'=d,'fac'=e)
    time1 <- "t0"
    time2 <- "t1"
    df$pyr <- df$t1 - df$t0
    pyr <- "pyr"
    events <- c('e0','e1')
    names_e0 <- c('fac')
    names_e1 <- c('fac')
    names_shared <- c('t0','t0')
    Term_n_e0 <- c(0)
    Term_n_e1 <- c(0)
    Term_n_shared <- c(0,0)
    tform_e0 <- c("loglin")
    tform_e1 <- c("loglin")
    tform_shared <- c("quad_slope","loglin_top")
    keep_constant_e0 <- c(0)
    keep_constant_e1 <- c(0)
    keep_constant_shared <- c(0,0)
    a_n_e0 <- c(-0.1)
    a_n_e1 <- c(0.1)
    a_n_shared <- c(0.001, -0.02)
    #
    name_list <- list('shared'=names_shared,'e0'=names_e0,'e1'=names_e1)
    Term_n_list <- list('shared'=Term_n_shared,'e0'=Term_n_e0,'e1'=Term_n_e1)
    tform_list <- list('shared'=tform_shared,'e0'=tform_e0,'e1'=tform_e1)
    keep_constant_list <- list('shared'=keep_constant_shared, 'e0'=keep_constant_e0,'e1'=keep_constant_e1)
    a_n_list <- list('shared'=a_n_shared,'e0'=a_n_e0,'e1'=a_n_e1)
    #
    Term_n_list <- list('shared'=Term_n_shared,'e0'=Term_n_e0,'e1'=c(1,1,1,1,1,1))
    expect_error(Joint_Multiple_Events(df, events, name_list, Term_n_list, tform_list, keep_constant_list, a_n_list))
    #
    Term_n_list <- list('shared'=Term_n_shared,'e0'=Term_n_e0,'e1'=Term_n_e1)
    tform_list <- list('shared'=tform_shared,'e0'=tform_e0,'e1'=c(1,1,1,1,1,1))
    expect_error(Joint_Multiple_Events(df, events, name_list, Term_n_list, tform_list, keep_constant_list, a_n_list))
    #
    tform_list <- list('shared'=tform_shared,'e0'=tform_e0,'e1'=tform_e1)
    keep_constant_list <- list('shared'=keep_constant_shared, 'e0'=keep_constant_e0,'e1'=c(1,1,1,1,1,1))
    expect_error(Joint_Multiple_Events(df, events, name_list, Term_n_list, tform_list, keep_constant_list, a_n_list))
    #
    keep_constant_list <- list('shared'=keep_constant_shared, 'e0'=keep_constant_e0,'e1'=keep_constant_e1)
    a_n_list <- list('shared'=a_n_shared,'e0'=a_n_e0,'e1'=c(1,1,1,1,1,1))
    expect_error(Joint_Multiple_Events(df, events, name_list, Term_n_list, tform_list, keep_constant_list, a_n_list))
})