Nothing
###############################################################################
test_that("get parameter using survival analysis", {
datafile <- system.file("extdata", "survival_aml.csv", package = "packDAMipd")
data_for_survival <- read.csv(datafile)
surv_results <- use_survival_analysis("status", datafile,
"x", info_get_method = "parametric",
info_distribution
= "weibull", covariates = NA, "time"
)
expect_equal(surv_results$model_coeff[1], 0.00554, tol = 1e-5)
data_for_survival <- na.omit(data_for_survival)
surv_results <- use_survival_analysis("status", data_for_survival,
"x",
info_get_method = "parametric", info_distribution
= "weibull", covariates = NA, "time"
)
expect_equal(surv_results$model_coeff[1], 0.00554, tol = 1e-5)
surv_results <- use_survival_analysis("status", data_for_survival,
"x",
info_get_method = "km",
info_distribution = "weibull",
covariates = NA, "time"
)
expect_equal(surv_results$fit$n, c(11, 12))
surv_results <- use_survival_analysis("status", data_for_survival,
"x",
info_get_method = "fh",
info_distribution
= "weibull", covariates = NA, "time"
)
expect_equal(surv_results$fit$n, c(11, 12))
surv_results <- use_survival_analysis("status", data_for_survival,
"x",
info_get_method = "fh2",
info_distribution = "weibull",
covariates = NA, "time"
)
expect_equal(surv_results$fit$n, c(11, 12))
surv_results <- use_survival_analysis("status", data_for_survival,
"x",
info_get_method = "coxph",
info_distribution = "weibull",
covariates = NA, "time"
)
expect_equal(unname(surv_results$fit$coefficients), 0.9155, tol = 1e-4)
# columns cant be found
expect_error(use_survival_analysis("status", data_for_survival,
"sex",
info_get_method = "parametric",
info_distribution = "weibull",
covariates = NA, "time"
))
# Error - parameter to be estimated is not found
expect_error(use_survival_analysis(NULL, data_for_survival,
"x",
info_get_method = "parametric",
info_distribution = "weibull",
covariates = NA, "time"
))
# Error - dataset is not found
expect_error(use_survival_analysis("status", NULL, "x",
info_get_method = "parametric",
info_distribution = "weibull",
covariates = NA, "time"))
# Error - independent variable is not found
expect_error(use_survival_analysis("status", data_for_survival,
NA,
info_get_method = "parametric",
info_distribution = "weibull",
covariates = NA, "time"
))
# Error - method is missing
expect_error(use_survival_analysis("status", data_for_survival, "x", NA,
info_distribution = "weibull",
covariates = NA,
"time"
))
})
###############################################################################
test_that("get parameter using parametric regression survival analysis", {
datafile <- system.file("extdata", "survival_lung.csv",
package = "packDAMipd")
data_for_survival <- read.csv(datafile)
surv_estimated <- use_parametric_survival("status", data_for_survival, "sex",
info_distribution = "weibull",
covariates = c("ph.ecog"), "time")
expect_equal(surv_estimated$model_coeff[1], 0.00035, tol = 1e-4)
surv_estimated <- use_parametric_survival("status", datafile, "sex",
info_distribution = "weibull",
covariates = c("ph.ecog"), "time")
expect_equal(surv_estimated$model_coeff[1], 0.00035, tol = 1e-4)
# error - param to be estimated not valid
expect_error(use_parametric_survival(NA, data_for_survival, "sex",
info_distribution = "weibull", covariates = NA,
"time"
))
#error - no dataset
expect_error(use_parametric_survival("status", NULL, "sex",
info_distribution = "weibull", covariates = NA,
"time"
))
# error - no independent variable
expect_error(use_parametric_survival("status", data_for_survival, NA,
info_distribution = "weibull", covariates = NA,
"time"
))
# Error - no information on distribution
expect_error(use_parametric_survival("status", data_for_survival,
"sex",
NA,
covariates = NA, "time"
))
# Error - no information on the time variable
expect_error(use_parametric_survival("status", data_for_survival, "sex",
info_distribution = "weibull", covariates = NA, NA
))
# Error - no cluster variable in dataset
expect_error(use_parametric_survival("status", data_for_survival, "sex",
info_distribution = "weibull",
covariates = NA, "time",
cluster_var = "open"
))
# Error - no cluster variable in dataset
expect_error(use_parametric_survival("status", data_for_survival, "sex",
info_distribution = "weibull",
covariates = "ph.ecog", "time",
cluster_var = "open"
))
data_for_survival <- data_for_survival[!is.na(data_for_survival$meal.cal), ]
surv_estimated <- use_parametric_survival("status", data_for_survival, "sex",
info_distribution = "weibull",
covariates = c("ph.ecog"), "time",
cluster_var = "meal.cal"
)
expect_equal(surv_estimated$model_coeff[1], 0.00035, tol = 1e-4)
surv_estimated <- use_parametric_survival("status", data_for_survival, "sex",
info_distribution = "weibull",
covariates = NA, "time",
cluster_var = "meal.cal"
)
expect_equal(surv_estimated$model_coeff[1], 0.000816, tol = 1e-4)
})
###############################################################################
test_that("get parameter using kaplan meier survival analysis", {
datafile <- system.file("extdata", "survival_lung.csv",
package = "packDAMipd")
data_for_survival <- read.csv(datafile)
surv_estimated_aml <- use_km_survival("status", data_for_survival, "sex",
covariates = c("ph.ecog"), "time")
expect_equal(surv_estimated_aml$fit$n, c(36, 27, 71, 42, 29, 21, 1))
surv_estimated_aml <- use_km_survival("status", datafile, "sex",
covariates = c("ph.ecog"), "time")
expect_equal(surv_estimated_aml$fit$n, c(36, 27, 71, 42, 29, 21, 1))
datafile <- system.file("extdata", "survival_aml.csv",
package = "packDAMipd")
data_for_survival <- read.csv(datafile)
surv_estimated_aml <- use_km_survival("status", data_for_survival, "x",
covariates = NA, "time")
expect_equal(surv_estimated_aml$fit$n, c(11, 12))
surv_estimated_aml <- use_km_survival("status", datafile, "x",
covariates = NA, "time")
expect_equal(surv_estimated_aml$fit$n, c(11, 12))
# Error - parameter to be estimated is not found
expect_error(use_km_survival(NA, data_for_survival, "x",
covariates = NA, "time"))
# Error - dataset not provided
expect_error(use_km_survival("status", NULL, "x", covariates = NA, "time"))
# Error - independent variable not given
expect_error(use_km_survival("status", data_for_survival, NA,
covariates = NA, "time"))
# Error - time variable not given
expect_error(use_km_survival("status", data_for_survival, "x",
covariates = NA, NA))
})
###############################################################################
test_that("get parameter using FH survival analysis", {
datafile <- system.file("extdata", "survival_lung.csv",
package = "packDAMipd")
data_for_survival <- read.csv(datafile)
surv_estimated_aml <- use_fh_survival("status", data_for_survival, "sex",
covariates = c("ph.ecog"), "time")
expect_equal(surv_estimated_aml$fit$n, c(36, 27, 71, 42, 29, 21, 1))
surv_estimated_aml <- use_fh_survival("status", datafile, "sex",
covariates = c("ph.ecog"), "time")
expect_equal(surv_estimated_aml$fit$n, c(36, 27, 71, 42, 29, 21, 1))
data_for_survival <- survival::aml
data_for_survival <- na.omit(data_for_survival)
surv_estimated_aml <- use_fh_survival("status", data_for_survival, "x",
covariates = NA, "time")
# Error - parameter to be estimated is not found
expect_error(use_fh_survival(NA, data_for_survival, "x", covariates = NA,
"time"))
# Error - dataset not provided
expect_error(use_fh_survival("status", NULL, "x", covariates = NA, "time"))
# Error - independent variable not given
expect_error(use_fh_survival("status", data_for_survival, NA,
covariates = NA, "time"))
# Error - time variable not given
expect_error(use_fh_survival("status", data_for_survival, "x",
covariates = NA, NA))
})
###############################################################################
test_that("get parameter using FH2 survival analysis", {
datafile <- system.file("extdata", "survival_lung.csv",
package = "packDAMipd")
data_for_survival <- read.csv(datafile)
surv_estimated_aml <- use_fh2_survival("status", data_for_survival, "sex",
covariates = c("ph.ecog"), "time")
expect_equal(surv_estimated_aml$fit$n, c(36, 27, 71, 42, 29, 21, 1))
surv_estimated_aml <- use_fh2_survival("status", datafile, "sex",
covariates = c("ph.ecog"), "time")
expect_equal(surv_estimated_aml$fit$n, c(36, 27, 71, 42, 29, 21, 1))
data_for_survival <- survival::aml
data_for_survival <- na.omit(data_for_survival)
surv_estimated_aml <- use_fh2_survival("status", data_for_survival, "x",
covariates = NA, "time")
# Error - parameter to be estimated is not found
expect_error(use_fh2_survival(NA, data_for_survival, "x",
covariates = NA, "time"))
# Error - dataset not provided
expect_error(use_fh2_survival("status", NULL, "x", covariates = NA, "time"))
# Error - independent variable not given
expect_error(use_fh2_survival("status", data_for_survival, NA,
covariates = NA, "time"))
# Error - time variable not given
expect_error(use_fh2_survival("status", data_for_survival, "x",
covariates = NA, NA))
})
###############################################################################
test_that("get parameter using cox ph survival analysis", {
datafile <- system.file("extdata", "survival_lung.csv",
package = "packDAMipd")
data_for_survival <- read.csv(datafile)
myvars <- c("status", "time", "sex", "ph.ecog")
data_for_survival <- data_for_survival[myvars]
data_for_survival <- na.omit(data_for_survival)
surv_estimated_aml <- use_coxph_survival("status", data_for_survival, "sex",
covariates = c("ph.ecog"), "time")
expect_equal(surv_estimated_aml$fit$n, c(227))
surv_estimated <- use_coxph_survival("status", data_for_survival, "sex",
covariates = c("ph.ecog"), "time"
)
# Error - parameter to be estimated is not found
expect_error(use_coxph_survival(NA, data_for_survival, "sex",
covariates = NA, "time"))
# Error - dataset not provided
expect_error(use_coxph_survival("status", NULL, "sex", covariates = NA,
"time"))
# Error - independent variable not given
expect_error(use_coxph_survival("status", data_for_survival, NA,
covariates = NA, "time"))
# Error - time variable not given
expect_error(use_coxph_survival("status", data_for_survival, "sex",
covariates = NA, NA))
})
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