path: root/tests/testthat/setup_script.R

require(mkin)
require(testthat)

# Per default (on my box where I set NOT_CRAN) use all cores minus one
if (identical(Sys.getenv("NOT_CRAN"), "true")) {
  n_cores <- parallel::detectCores() - 1
} else {
  n_cores <- 1
}

# We are only allowed one core on travis, but they also set NOT_CRAN=true
if (Sys.getenv("TRAVIS") != "") n_cores = 1

# On Windows we would need to make a cluster first
if (Sys.info()["sysname"] == "Windows") n_cores = 1

# mmkin object of parent fits for tests
models <- c("SFO", "FOMC", "DFOP", "HS")
fits <- mmkin(models,
  list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
  quiet = TRUE, cores = n_cores)

# One metabolite
SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
                   m1 = list(type = "SFO"), quiet = TRUE)
SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
                      m1 = list(type = "SFO"),
                      use_of_ff = "max", quiet = TRUE)

f_sfo_sfo_desolve <- mkinfit(SFO_SFO,
  subset(FOCUS_2006_D, value != 0),
  solution_type = "deSolve", quiet = TRUE)
f_sfo_sfo_eigen <- mkinfit(SFO_SFO,
  subset(FOCUS_2006_D, value != 0),
  solution_type = "eigen", quiet = TRUE)

f_sfo_sfo.ff <- mkinfit(SFO_SFO.ff,
  subset(FOCUS_2006_D, value != 0),
  quiet = TRUE)

# Two metabolites
SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data

DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data

m_synth_SFO_lin <- mkinmod(
  parent = mkinsub("SFO", "M1"),
  M1 = mkinsub("SFO", "M2"),
  M2 = mkinsub("SFO"),
  use_of_ff = "max", quiet = TRUE)

m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
  M1 = mkinsub("SFO"),
  M2 = mkinsub("SFO"),
  use_of_ff = "max", quiet = TRUE)

f_SFO_lin_mkin_OLS <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE)
f_SFO_lin_mkin_ML <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE,
  error_model = "const", error_model_algorithm = "direct")

# We know direct optimization is OK and direct needs 4 sec versus 5.5 for threestep and 6 for IRLS
fit_obs_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "obs", quiet = TRUE,
  error_model_algorithm = "direct")
# We know threestep is OK, and threestep (and IRLS) need 4.8 se versus 5.6 for direct
fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE,
  error_model_algorithm = "threestep")

# We know direct optimization is OK and direct needs 8 sec versus 11 sec for threestep
f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc",
  error_model_algorithm = "direct", quiet = TRUE)

f_tc_2_ntf <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc",
  transform_fractions = FALSE, error_model_algorithm = "direct", quiet = TRUE)