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authorJohannes Ranke <jranke@uni-bremen.de>2019-10-31 01:55:01 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-10-31 01:59:05 +0100
commit7091d3738e7e55acb20edb88772b228f6f5b6c98 (patch)
treeb6e31700074605c702662e5238162c57de330453 /tests/testthat/setup_script.R
parent5e4ea59a41e00b05ea6664c08c7922e892e8ab77 (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.R38
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)

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