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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)
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