diff options
Diffstat (limited to 'tests/testthat')
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 | ||||
| -rw-r--r-- | tests/testthat/NAFTA_SOP_Appendix_B.txt | 18 | ||||
| -rw-r--r-- | tests/testthat/NAFTA_SOP_Appendix_D.txt | 18 | ||||
| -rw-r--r-- | tests/testthat/test_confidence.R | 4 | ||||
| -rw-r--r-- | tests/testthat/test_nlme.R | 6 |
5 files changed, 24 insertions, 24 deletions
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index 5d946ecd..f845cc1d 100644 --- a/tests/testthat/FOCUS_2006_D.csf +++ b/tests/testthat/FOCUS_2006_D.csf @@ -5,7 +5,7 @@ Description: MeasurementUnits: % AR TimeUnits: days Comments: Created using mkin::CAKE_export -Date: 2020-05-26 +Date: 2020-05-28 Optimiser: IRLS [Data] diff --git a/tests/testthat/NAFTA_SOP_Appendix_B.txt b/tests/testthat/NAFTA_SOP_Appendix_B.txt index 294ea09f..2a23f5da 100644 --- a/tests/testthat/NAFTA_SOP_Appendix_B.txt +++ b/tests/testthat/NAFTA_SOP_Appendix_B.txt @@ -7,17 +7,17 @@ Critical sum of squares for checking the SFO model: Parameters: $SFO - Estimate Pr(>t) Lower Upper -parent_0 51.243 2.12e-10 45.724 56.762 -k_parent_sink 0.253 2.95e-06 0.193 0.332 -sigma 3.529 1.28e-04 2.061 4.997 + Estimate Pr(>t) Lower Upper +parent_0 51.243 2.12e-10 45.724 56.762 +k_parent 0.253 2.95e-06 0.193 0.332 +sigma 3.529 1.28e-04 2.061 4.997 $IORE - Estimate Pr(>t) Lower Upper -parent_0 51.71053 2.60e-14 4.97e+01 53.68122 -k__iore_parent_sink 0.00135 5.21e-02 3.88e-04 0.00469 -N_parent 2.66147 3.67e-08 2.23e+00 3.08855 -sigma 1.25124 1.76e-04 7.24e-01 1.77811 + Estimate Pr(>t) Lower Upper +parent_0 51.71053 2.60e-14 4.97e+01 53.68122 +k__iore_parent 0.00135 5.21e-02 3.88e-04 0.00469 +N_parent 2.66147 3.67e-08 2.23e+00 3.08855 +sigma 1.25124 1.76e-04 7.24e-01 1.77811 $DFOP Estimate Pr(>t) Lower Upper diff --git a/tests/testthat/NAFTA_SOP_Appendix_D.txt b/tests/testthat/NAFTA_SOP_Appendix_D.txt index 375830b7..c0b7035c 100644 --- a/tests/testthat/NAFTA_SOP_Appendix_D.txt +++ b/tests/testthat/NAFTA_SOP_Appendix_D.txt @@ -7,17 +7,17 @@ Critical sum of squares for checking the SFO model: Parameters: $SFO - Estimate Pr(>t) Lower Upper -parent_0 83.7558 1.80e-14 77.18268 90.3288 -k_parent_sink 0.0017 7.43e-05 0.00112 0.0026 -sigma 8.7518 1.22e-05 5.64278 11.8608 + Estimate Pr(>t) Lower Upper +parent_0 83.7558 1.80e-14 77.18268 90.3288 +k_parent 0.0017 7.43e-05 0.00112 0.0026 +sigma 8.7518 1.22e-05 5.64278 11.8608 $IORE - Estimate Pr(>t) Lower Upper -parent_0 9.69e+01 NA 8.88e+01 1.05e+02 -k__iore_parent_sink 8.40e-14 NA 1.79e-18 3.94e-09 -N_parent 6.68e+00 NA 4.19e+00 9.17e+00 -sigma 5.85e+00 NA 3.76e+00 7.94e+00 + Estimate Pr(>t) Lower Upper +parent_0 9.69e+01 NA 8.88e+01 1.05e+02 +k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09 +N_parent 6.68e+00 NA 4.19e+00 9.17e+00 +sigma 5.85e+00 NA 3.76e+00 7.94e+00 $DFOP Estimate Pr(>t) Lower Upper diff --git a/tests/testthat/test_confidence.R b/tests/testthat/test_confidence.R index e85fdb7a..3fdd3f2c 100644 --- a/tests/testthat/test_confidence.R +++ b/tests/testthat/test_confidence.R @@ -67,9 +67,9 @@ test_that("Likelihood profile based confidence intervals work", { f <- fits[["SFO", "FOCUS_C"]] # negative log-likelihood for use with mle - f_nll <- function(parent_0, k_parent_sink, sigma) { + f_nll <- function(parent_0, k_parent, sigma) { - f$ll(c(parent_0 = as.numeric(parent_0), - k_parent_sink = as.numeric(k_parent_sink), + k_parent = as.numeric(k_parent), sigma = as.numeric(sigma))) } f_mle <- stats4::mle(f_nll, start = as.list(parms(f)), nobs = nrow(FOCUS_2006_C)) diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R index 31fb19de..5a8db142 100644 --- a/tests/testthat/test_nlme.R +++ b/tests/testthat/test_nlme.R @@ -51,10 +51,10 @@ test_that("nlme_function works correctly", { m_nlme_mmkin <- nlme(f) - m_nlme_raw_2 <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink), + m_nlme_raw_2 <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent), data = grouped_data, - fixed = parent_0 + log_k_parent_sink ~ 1, - random = pdDiag(parent_0 + log_k_parent_sink ~ 1), + fixed = parent_0 + log_k_parent ~ 1, + random = pdDiag(parent_0 + log_k_parent ~ 1), start = mean_degparms(f, random = TRUE)) expect_equal(m_nlme_raw_2$coefficients, m_nlme_mmkin$coefficients) |