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| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-10-31 01:55:01 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-10-31 01:59:05 +0100 |
| commit | 7091d3738e7e55acb20edb88772b228f6f5b6c98 (patch) | |
| tree | b6e31700074605c702662e5238162c57de330453 /tests/testthat/setup_script.R | |
| parent | 5e4ea59a41e00b05ea6664c08c7922e892e8ab77 (diff) | |
Add likelihood ratio test and other methods, fixes
The likelihood ratio test method is lrtest, in addition,
methods for update and residuals were added.
Diffstat (limited to 'tests/testthat/setup_script.R')
| -rw-r--r-- | tests/testthat/setup_script.R | 38 |
1 files changed, 34 insertions, 4 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index cfa978fc..fc972a3d 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -14,6 +14,27 @@ 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 +# We set up some models and fits with nls for comparisons +SFO_trans <- function(t, parent_0, log_k_parent_sink) { + parent_0 * exp(- exp(log_k_parent_sink) * t) +} +SFO_notrans <- function(t, parent_0, k_parent_sink) { + parent_0 * exp(- k_parent_sink * t) +} +f_1_nls_trans <- nls(value ~ SFO_trans(time, parent_0, log_k_parent_sink), + data = FOCUS_2006_A, + start = list(parent_0 = 100, log_k_parent_sink = log(0.1))) +f_1_nls_notrans <- nls(value ~ SFO_notrans(time, parent_0, k_parent_sink), + data = FOCUS_2006_A, + start = list(parent_0 = 100, k_parent_sink = 0.1)) + +f_1_mkin_trans <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE) +f_1_mkin_notrans <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE, + transform_rates = FALSE) + +f_2_mkin <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE) +f_2_nls <- nls(value ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = FOCUS_2006_C) + # mmkin object of parent fits for tests models <- c("SFO", "FOMC", "DFOP", "HS") fits <- mmkin(models, @@ -54,8 +75,8 @@ m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), 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, +fit_nw_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE) +fit_nw_1_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 @@ -69,5 +90,14 @@ fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE 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) +# Experimental data for UBA +dfop_sfo_sfo <- mkinmod( + parent = mkinsub("DFOP", to = "A1"), + A1 = mkinsub("SFO", to = "A2"), + A2 = mkinsub("SFO"), + use_of_ff = "max" +) + +f_soil_1_tc <- mkinfit(dfop_sfo_sfo, + experimental_data_for_UBA_2019[[1]]$data, + error_model = "tc", quiet = TRUE) |