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-rw-r--r--R/summary.saem.mmkin.R4
-rw-r--r--tests/testthat/print_saem_biphasic_s.txt37
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_C.txt125
-rw-r--r--tests/testthat/summary_saem_biphasic_s.txt77
-rw-r--r--tests/testthat/test_f_time_norm.R6
-rw-r--r--tests/testthat/test_saem.R16
6 files changed, 196 insertions, 69 deletions
diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R
index 27c2ce6c..3f50c42d 100644
--- a/R/summary.saem.mmkin.R
+++ b/R/summary.saem.mmkin.R
@@ -207,11 +207,11 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
tc = "Two-component variance function"), "\n")
cat("\nMean of starting values for individual parameters:\n")
- print(x$mean_dp_start)
+ print(x$mean_dp_start, digits = digits)
cat("\nFixed degradation parameter values:\n")
if(length(x$fixed$value) == 0) cat("None\n")
- else print(x$fixed)
+ else print(x$fixed, digits = digits)
cat("\nResults:\n\n")
cat("Likelihood computed by importance sampling\n")
diff --git a/tests/testthat/print_saem_biphasic_s.txt b/tests/testthat/print_saem_biphasic_s.txt
new file mode 100644
index 00000000..4d20117e
--- /dev/null
+++ b/tests/testthat/print_saem_biphasic_s.txt
@@ -0,0 +1,37 @@
+Kinetic nonlinear mixed-effects model fit by SAEM
+Structural model:
+d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+ time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
+ * parent
+d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
+ * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
+ exp(-k2 * time))) * parent - k_m1 * m1
+
+Data:
+509 observations of 2 variable(s) grouped in 15 datasets
+
+Likelihood computed by importance sampling
+ AIC BIC logLik
+ 2692 2702 -1333
+
+Fitted parameters:
+ estimate lower upper
+parent_0 1.002e+02 99.302986 1.011e+02
+k_m1 2.182e-03 0.001576 2.788e-03
+f_parent_to_m1 4.883e-01 0.447687 5.289e-01
+k1 4.014e-02 0.023941 5.634e-02
+k2 1.517e-02 0.008507 2.184e-02
+g 5.007e-01 0.380534 6.208e-01
+Var.parent_0 1.511e+00 -0.551247 3.574e+00
+Var.k_m1 1.912e-02 -0.151313 1.896e-01
+Var.f_parent_to_m1 8.082e-02 0.018430 1.432e-01
+Var.k1 5.037e-01 0.095343 9.121e-01
+Var.k2 6.129e-01 0.124868 1.101e+00
+Var.g 7.107e-02 -0.244901 3.870e-01
+a.1 2.749e+00 2.568674 2.929e+00
+SD.parent_0 1.229e+00 0.390443 2.068e+00
+SD.k_m1 1.383e-01 -0.477984 7.545e-01
+SD.f_parent_to_m1 2.843e-01 0.174562 3.940e-01
+SD.k1 7.097e-01 0.422037 9.974e-01
+SD.k2 7.829e-01 0.471184 1.095e+00
+SD.g 2.666e-01 -0.326044 8.592e-01
diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt
index 2b0210c0..da3276e1 100644
--- a/tests/testthat/summary_DFOP_FOCUS_C.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_C.txt
@@ -1,82 +1,77 @@
-mkin version used for fitting: Dummy 0.0 for testing
-R version used for fitting: Dummy R version for testing
-Date of fit: Dummy date for testing
-Date of summary: Dummy date for testing
+saemix version used for fitting: 3.1.9000
+mkin version used for pre-fitting: 0.9.50.4
+R version used for fitting: 4.0.3
+Date of fit: Wed Dec 9 08:16:28 2020
+Date of summary: Wed Dec 9 08:23:19 2020
Equations:
d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
* parent
+d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
+ * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
+ exp(-k2 * time))) * parent - k_m1 * m1
-Model predictions using solution type analytical
-
-Fitted using test 0 model solutions performed in test time 0 s
+Data:
+509 observations of 2 variable(s) grouped in 15 datasets
-Error model: Constant variance
+Model predictions using solution type analytical
-Error model algorithm: OLS
+Fitted in 10.222 s using 300, 100 iterations
-Starting values for parameters to be optimised:
- value type
-parent_0 85.10 state
-k1 0.10 deparm
-k2 0.01 deparm
-g 0.50 deparm
+Variance model: Constant variance
-Starting values for the transformed parameters actually optimised:
- value lower upper
-parent_0 85.100000 -Inf Inf
-log_k1 -2.302585 -Inf Inf
-log_k2 -4.605170 -Inf Inf
-g_qlogis 0.000000 -Inf Inf
+Mean of starting values for individual parameters:
+ parent_0 k_m1 f_parent_to_m1 k1 k2
+ 1.007005e+02 1.837381e-03 4.803953e-01 4.534096e-02 1.918378e-02
+ g
+ 5.068235e-01
-Fixed parameter values:
+Fixed degradation parameter values:
None
Results:
- AIC BIC logLik
- 29.02372 30.00984 -9.511861
-
-Optimised, transformed parameters with symmetric confidence intervals:
- Estimate Std. Error Lower Upper
-parent_0 85.0000 0.66620 83.1500 86.8500
-log_k1 -0.7775 0.03380 -0.8713 -0.6836
-log_k2 -4.0260 0.13100 -4.3890 -3.6620
-g_qlogis 1.7660 0.08218 1.5380 1.9940
-sigma 0.6962 0.16410 0.2406 1.1520
-
-Parameter correlation:
-[1] "Correlation matrix is platform dependent, not tested"
-
-Backtransformed parameters:
-Confidence intervals for internally transformed parameters are asymmetric.
-t-test (unrealistically) based on the assumption of normal distribution
-for estimators of untransformed parameters.
- Estimate t value Pr(>t) Lower Upper
-parent_0 85.00000 127.600 1.131e-08 83.15000 86.85000
-k1 0.45960 29.580 3.887e-06 0.41840 0.50480
-k2 0.01785 7.636 7.901e-04 0.01241 0.02568
-g 0.85390 83.310 6.221e-08 0.82310 0.88020
-sigma 0.69620 4.243 6.618e-03 0.24060 1.15200
-
-FOCUS Chi2 error levels in percent:
- err.min n.optim df
-All data 2.661 4 5
-parent 2.661 4 5
+Likelihood computed by importance sampling
+ AIC BIC logLik
+ 2692 2702 -1333
+
+Optimised parameters:
+ est. lower upper
+parent_0 1.002e+02 99.302986 1.011e+02
+k_m1 2.182e-03 0.001576 2.788e-03
+f_parent_to_m1 4.883e-01 0.447687 5.289e-01
+k1 4.014e-02 0.023941 5.634e-02
+k2 1.517e-02 0.008507 2.184e-02
+g 5.007e-01 0.380534 6.208e-01
+
+Correlation:
+ prnt_0 k_m1 f_p__1 k1 k2
+k_m1 -0.152
+f_parent_to_m1 -0.138 0.396
+k1 0.085 -0.036 -0.026
+k2 0.005 0.067 0.018 -0.043
+g -0.075 -0.113 -0.029 -0.248 -0.263
+
+Random effects:
+ est. lower upper
+SD.parent_0 1.2293 0.3904 2.0682
+SD.k_m1 0.1383 -0.4780 0.7545
+SD.f_parent_to_m1 0.2843 0.1746 0.3940
+SD.k1 0.7097 0.4220 0.9974
+SD.k2 0.7829 0.4712 1.0946
+SD.g 0.2666 -0.3260 0.8592
+
+Variance model:
+ est. lower upper
+a.1 2.749 2.569 2.929
+
+Resulting formation fractions:
+ ff
+parent_m1 0.4883
+parent_sink 0.5117
Estimated disappearance times:
- DT50 DT90 DT50back DT50_k1 DT50_k2
-parent 1.887 21.25 6.397 1.508 38.83
-
-Data:
- time variable observed predicted residual
- 0 parent 85.1 85.003 0.09726
- 1 parent 57.9 58.039 -0.13912
- 3 parent 29.9 30.054 -0.15351
- 7 parent 14.6 13.866 0.73388
- 14 parent 9.7 9.787 -0.08657
- 28 parent 6.6 7.532 -0.93205
- 63 parent 4.0 4.033 -0.03269
- 91 parent 3.9 2.447 1.45348
- 119 parent 0.6 1.484 -0.88424
+ DT50 DT90 DT50back DT50_k1 DT50_k2
+parent 27.07 110.1 33.14 17.27 45.68
+m1 317.69 1055.4 NA NA NA
diff --git a/tests/testthat/summary_saem_biphasic_s.txt b/tests/testthat/summary_saem_biphasic_s.txt
new file mode 100644
index 00000000..b5777ce1
--- /dev/null
+++ b/tests/testthat/summary_saem_biphasic_s.txt
@@ -0,0 +1,77 @@
+saemix version used for fitting: Dummy 0.0 for testing
+mkin version used for pre-fitting: Dummy 0.0 for testing
+R version used for fitting: Dummy R version for testing
+Date of fit: Dummy date for testing
+Date of summary: Dummy date for testing
+
+Equations:
+d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+ time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
+ * parent
+d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
+ * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
+ exp(-k2 * time))) * parent - k_m1 * m1
+
+Data:
+509 observations of 2 variable(s) grouped in 15 datasets
+
+Model predictions using solution type analytical
+
+Fitted in test time 0 s using 300, 100 iterations
+
+Variance model: Constant variance
+
+Mean of starting values for individual parameters:
+ parent_0 k_m1 f_parent_to_m1 k1 k2
+ 1.0e+02 1.8e-03 4.8e-01 4.5e-02 1.9e-02
+ g
+ 5.1e-01
+
+Fixed degradation parameter values:
+None
+
+Results:
+
+Likelihood computed by importance sampling
+ AIC BIC logLik
+ 2692 2702 -1333
+
+Optimised parameters:
+ est. lower upper
+parent_0 1.0e+02 99.3030 1.0e+02
+k_m1 2.2e-03 0.0016 2.8e-03
+f_parent_to_m1 4.9e-01 0.4477 5.3e-01
+k1 4.0e-02 0.0239 5.6e-02
+k2 1.5e-02 0.0085 2.2e-02
+g 5.0e-01 0.3805 6.2e-01
+
+Correlation:
+ prnt_0 k_m1 f_p__1 k1 k2
+k_m1 -0.152
+f_parent_to_m1 -0.138 0.396
+k1 0.085 -0.036 -0.026
+k2 0.005 0.067 0.018 -0.043
+g -0.075 -0.113 -0.029 -0.248 -0.263
+
+Random effects:
+ est. lower upper
+SD.parent_0 1.23 0.39 2.07
+SD.k_m1 0.14 -0.48 0.75
+SD.f_parent_to_m1 0.28 0.17 0.39
+SD.k1 0.71 0.42 1.00
+SD.k2 0.78 0.47 1.09
+SD.g 0.27 -0.33 0.86
+
+Variance model:
+ est. lower upper
+a.1 2.7 2.6 2.9
+
+Resulting formation fractions:
+ ff
+parent_m1 0.49
+parent_sink 0.51
+
+Estimated disappearance times:
+ DT50 DT90 DT50back DT50_k1 DT50_k2
+parent 27 110 33 17 46
+m1 318 1055 NA NA NA
diff --git a/tests/testthat/test_f_time_norm.R b/tests/testthat/test_f_time_norm.R
new file mode 100644
index 00000000..790cce8b
--- /dev/null
+++ b/tests/testthat/test_f_time_norm.R
@@ -0,0 +1,6 @@
+context("Time step normalisation")
+
+test_that("Simple temperature and moisture normalisation works", {
+ expect_equal(round(f_time_norm_focus(25, 20, 25), 2), 1.37)
+})
+
diff --git a/tests/testthat/test_saem.R b/tests/testthat/test_saem.R
index 0b6d4531..d41efbfa 100644
--- a/tests/testthat/test_saem.R
+++ b/tests/testthat/test_saem.R
@@ -102,15 +102,27 @@ test_that("Parent only models can be fitted with saemix", {
test_that("Simple models with metabolite can be fitted with saemix", {
+ expect_known_output(print(saem_biphasic_s), "print_saem_biphasic_s.txt")
+
+ test_summary <- summary(saem_biphasic_s)
+ test_summary$saemixversion <- "Dummy 0.0 for testing"
+ test_summary$mkinversion <- "Dummy 0.0 for testing"
+ test_summary$Rversion <- "Dummy R version for testing"
+ test_summary$date.fit <- "Dummy date for testing"
+ test_summary$date.summary <- "Dummy date for testing"
+ test_summary$time <- c(elapsed = "test time 0")
+
+ expect_known_output(print(test_summary, digits = 2), "summary_saem_biphasic_s.txt")
+
dfop_sfo_pop <- as.numeric(dfop_sfo_pop)
ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back
expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop))
expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop))
- # The following does not work, the k1 and k2 are not fitted well
+ # The following does not work, as k1 and k2 are not fitted well
ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$confint_back
# expect_true(all(ci_dfop_sfo_s_m[, "lower"] < dfop_sfo_pop))
- #expect_true(all(ci_dfop_sfo_s_m[, "upper"] > dfop_sfo_pop))
+ # expect_true(all(ci_dfop_sfo_s_m[, "upper"] > dfop_sfo_pop))
# Somehow this does not work at the moment. But it took forever (~ 10 min) anyways...
#saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE)

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