######################
## PLOTTING CHECKS
######################

test_that( "Coxph plot time column missing", {
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(0,1,0,0,0,1,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a_bad"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv",paste(tempfile(), "run",sep="" )), "martingale"=FALSE, "surv_curv"=FALSE, "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
})
test_that( "Coxph plot no events", {
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(0,0,0,0,0,0,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv", "run" ), "martingale"=FALSE, "surv_curv"=FALSE, "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
})
test_that( "Coxph plot no type", {
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(0,1,0,0,0,1,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "martingale"=FALSE, "surv_curv"=FALSE, "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
})
test_that( "Coxph plot strata col not in data", {
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(0,1,0,0,0,1,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv", "run" ), "martingale"=FALSE, "surv_curv"=FALSE, "strat_haz"=TRUE, "strat_col"="e", "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
})
test_that( "Coxph plot strata col not given", {
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(0,1,0,0,0,1,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv", "run" ), "martingale"=FALSE, "surv_curv"=FALSE, "strat_haz"=TRUE, "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
})
test_that( "Coxph plot martingale dose col not in data", {
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(0,1,0,0,0,1,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv", "run" ), "martingale"=TRUE, "surv_curv"=FALSE, "strat_haz"=FALSE, "smooth_haz"=FALSE, "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
})
test_that( "Coxph plot martingale dose col not given", {
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(0,1,0,0,0,1,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv", "run" ), "martingale"=TRUE, "surv_curv"=FALSE, "strat_haz"=FALSE, "smooth_haz"=FALSE, "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
})
test_that( "Coxph plot Survival ID col not in data", {
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(0,1,0,0,0,1,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv", "run" ), "martingale"=FALSE, "surv_curv"=FALSE, "strat_haz"=FALSE, "smooth_haz"=FALSE, "studyid"="f", 'verbose'=4, "km"=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
})
test_that( "Coxph plot Survival ID col not given", {
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(0,1,0,0,0,1,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv", "run" ), "martingale"=FALSE, "surv_curv"=FALSE, "strat_haz"=FALSE, "smooth_haz"=FALSE, 'verbose'=4, "km"=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
})

test_that( "Coxph risk too few unique values", {
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(1,0,1,0,1,0,0)
    d <- c(3,3,3,3,3,3,3)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "RISK",paste(tempfile(), "run",sep="" )), "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
})

test_that( "Coxph plot no error", {
    tfile <- file(paste(tempfile(), ".txt",sep="" ),open = "wt")
    sink(file=tfile)
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(1,0,1,0,1,0,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv",paste(tempfile(), "run",sep="" )), "surv_curv"=TRUE, "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_no_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
    sink(NULL)
    close(tfile)
})
test_that( "Coxph plot stratafied no error", {
    tfile <- file(paste(tempfile(), ".txt",sep="" ),open = "wt")
    sink(file=tfile)
    a <- c(0,0,0,0,0,0,1)
	b <- c(2,3,4,2,3,2,4)
	c <- c(1,0,1,0,1,1,0)
	d <- c(3,4,5,6,7,8,9)
	e <- c(1,1,0,0,1,0,1)
	df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d, "e"=e)
	time1 <- "a"
	time2 <- "b"
	event <- "c"
	names <- c( "d" )
	term_n <- c(0)
	tform <- c( "loglin" )
	keep_constant <- c(0)
	a_n <- c(-0.1)
	modelform <- "M"
	fir <- 0
	der_iden <- 0
	control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
	plot_options <- list( "type"=c( "surv",paste(tempfile(), "run",sep="" )), "surv_curv"=TRUE, "strat_haz"=TRUE, "strat_col"="e", "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_no_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
    sink(NULL)
    close(tfile)
})

test_that( "Coxph risk no error", {
    tfile <- file(paste(tempfile(), ".txt",sep="" ),open = "wt")
    sink(file=tfile)
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(1,0,1,0,1,0,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "RISK",paste(tempfile(), "run",sep="" )), "studyid"="a", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_no_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
    sink(NULL)
    close(tfile)
})

test_that( "Coxph schoenfeld no error", {
    tfile <- file(paste(tempfile(), ".txt",sep="" ),open = "wt")
    sink(file=tfile)
    fname <- 'MULTI_COV.csv'
    colTypes <- c( "double", "double", "integer", "integer", "integer" )
    df <- fread(fname,nThread=min(c(detectCores(),2)),data.table=TRUE,header=TRUE,colClasses=colTypes,verbose=FALSE,fill=TRUE)
    time1 <- "t0"
    time2 <- "t1"
    event <- "lung"
    names <- c( "a", "b" )
    term_n <- c(0,1)
    tform <- c( "loglin", "loglin" )
    keep_constant <- c(0,0)
    a_n <- c(0.01,-15)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "SCHOENFELD",paste(tempfile(), "run",sep="" )), "studyid"="t0", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_no_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
    sink(NULL)
    close(tfile)
})
test_that( "Coxph martingale no error", {
    tfile <- file(paste(tempfile(), ".txt",sep="" ),open = "wt")
    sink(file=tfile)
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(0,1,0,0,0,1,0)
    d <- c(3,4,5,6,7,8,9)
    e <- c(1,1,2,2,3,3,3)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d, "e"=e)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv",paste(tempfile(), "run",sep="" )), "martingale"=TRUE, "cov_cols"="d", "surv_curv"=FALSE, "strat_haz"=FALSE, "smooth_haz"=FALSE, "studyid"="e", 'verbose'=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_no_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
    sink(NULL)
    close(tfile)
})
test_that( "Coxph km no error", {
    tfile <- file(paste(tempfile(), ".txt",sep="" ),open = "wt")
    sink(file=tfile)
    a <- c(0,1,2,3,4,5,6)
    b <- c(1,2,3,4,5,6,7)
    c <- c(1,0,1,0,1,0,0)
    d <- c(3,4,5,6,7,8,9)
    df <- data.table( "a"=a, "b"=b, "c"=c, "d"=d)
    time1 <- "a"
    time2 <- "b"
    event <- "c"
    names <- c( "d" )
    term_n <- c(0)
    tform <- c( "loglin" )
    keep_constant <- c(0)
    a_n <- c(-0.1)
    modelform <- "M"
    fir <- 0
    der_iden <- 0
    control <- list( "ncores"=2, 'lr' = 0.75, 'maxiter' = -1, 'halfmax' = 5, 'epsilon' = 1e-9,  'deriv_epsilon' = 1e-9, 'abs_max'=1.0, 'change_all'=TRUE, 'dose_abs_max'=100.0, 'verbose'=4, 'ties'='breslow', 'double_step'=1)
    plot_options <- list( "type"=c( "surv",paste(tempfile(), "run",sep="" )), "surv_curv"=TRUE, "studyid"="a", 'verbose'=4, "km"=TRUE)
    if (system.file(package='ggplot2' )!="" ){
        expect_no_error(RunCoxPlots(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, fir, control, plot_options))
    }
    sink(NULL)
    close(tfile)
})