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-rw-r--r--man/create_deg_func.Rd11
-rw-r--r--test.log14
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/setup_script.R3
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_C.txt2
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt67
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_D_eigen.txt133
-rw-r--r--tests/testthat/test_mkinfit_errors.R2
-rw-r--r--tests/testthat/test_plots_summary_twa.R8
9 files changed, 128 insertions, 114 deletions
diff --git a/man/create_deg_func.Rd b/man/create_deg_func.Rd
index 2eefdb80..178661ff 100644
--- a/man/create_deg_func.Rd
+++ b/man/create_deg_func.Rd
@@ -22,5 +22,14 @@ Create degradation functions for known analytical solutions
SFO_SFO <- mkinmod(
parent = mkinsub("SFO", "m1"),
m1 = mkinsub("SFO"))
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+FOCUS_D <- subset(FOCUS_2006_D, value != 0) # to avoid warnings
+fit_1 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE)
+fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE)
+\dontrun{
+if (require(rbenchmark))
+ benchmark(
+ analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),
+ deSolve = mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),
+ replications = 1)
+}
}
diff --git a/test.log b/test.log
index 72ed4ee3..e5161e55 100644
--- a/test.log
+++ b/test.log
@@ -2,12 +2,12 @@ Loading mkin
Testing mkin
✔ | OK F W S | Context
✔ | 2 | Export dataset for reading into CAKE
-✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.7 s]
+✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.6 s]
✔ | 4 | Calculation of FOCUS chi2 error levels [2.2 s]
✔ | 7 | Fitting the SFORB model [11.7 s]
✔ | 5 | Calculation of Akaike weights
-✔ | 10 | Confidence intervals and p-values [9.3 s]
-✔ | 14 | Error model fitting [37.6 s]
+✔ | 10 | Confidence intervals and p-values [9.4 s]
+✔ | 14 | Error model fitting [37.4 s]
✔ | 6 | Test fitting the decline of metabolites from their maximum [0.8 s]
✔ | 1 | Fitting the logistic model [0.8 s]
✔ | 1 | Test dataset class mkinds used in gmkin
@@ -18,16 +18,16 @@ Testing mkin
✔ | 9 | Nonlinear mixed-effects models [12.0 s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
✔ | 3 | Summary
-✔ | 14 | Plotting [4.9 s]
+✔ | 14 | Plotting [5.1 s]
✔ | 4 | AIC calculation
✔ | 4 | Residuals extracted from mkinfit models
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
✔ | 1 | Summaries of old mkinfit objects
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s]
-✔ | 9 | Hypothesis tests [37.9 s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.3 s]
+✔ | 9 | Hypothesis tests [38.1 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 143.0 s
+Duration: 143.4 s
OK: 156
Failed: 0
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 7c29ab46..f27df430 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: 2020-05-07
+Date: 2020-05-08
Optimiser: IRLS
[Data]
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index e33f4af7..86d5089f 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -40,7 +40,8 @@ fits <- mmkin(models,
# One metabolite
SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
- m1 = list(type = "SFO"), quiet = TRUE)
+ m1 = list(type = "SFO"),
+ use_of_ff = "min", quiet = TRUE)
SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
m1 = list(type = "SFO"),
use_of_ff = "max", quiet = TRUE)
diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt
index 4f96c8d3..ab64a588 100644
--- a/tests/testthat/summary_DFOP_FOCUS_C.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_C.txt
@@ -47,7 +47,7 @@ g_ilr 1.2490 0.05811 1.0870 1.4100
sigma 0.6962 0.16410 0.2406 1.1520
Parameter correlation:
-NULL
+[1] "Correlation matrix is platform dependent, not tested"
Backtransformed parameters:
Confidence intervals for internally transformed parameters are asymmetric.
diff --git a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
index fe697794..9245c40b 100644
--- a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
@@ -4,8 +4,8 @@ Date of fit: Dummy date for testing
Date of summary: Dummy date for testing
Equations:
-d_parent/dt = - k_parent * parent
-d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
+d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
Model predictions using solution type deSolve
@@ -16,18 +16,18 @@ Error model: Constant variance
Error model algorithm: OLS
Starting values for parameters to be optimised:
- value type
-parent_0 100.7500 state
-k_parent 0.1000 deparm
-k_m1 0.1001 deparm
-f_parent_to_m1 0.5000 deparm
+ value type
+parent_0 100.7500 state
+k_parent_sink 0.1000 deparm
+k_parent_m1 0.1001 deparm
+k_m1_sink 0.1002 deparm
Starting values for the transformed parameters actually optimised:
- value lower upper
-parent_0 100.750000 -Inf Inf
-log_k_parent -2.302585 -Inf Inf
-log_k_m1 -2.301586 -Inf Inf
-f_parent_ilr_1 0.000000 -Inf Inf
+ value lower upper
+parent_0 100.750000 -Inf Inf
+log_k_parent_sink -2.302585 -Inf Inf
+log_k_parent_m1 -2.301586 -Inf Inf
+log_k_m1_sink -2.300587 -Inf Inf
Fixed parameter values:
value type
@@ -39,37 +39,38 @@ Results:
204.4486 212.6365 -97.22429
Optimised, transformed parameters with symmetric confidence intervals:
- Estimate Std. Error Lower Upper
-parent_0 99.60000 1.57000 96.40000 102.8000
-log_k_parent -2.31600 0.04087 -2.39900 -2.2330
-log_k_m1 -5.24800 0.13320 -5.51800 -4.9770
-f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694
-sigma 3.12600 0.35850 2.39600 3.8550
+ Estimate Std. Error Lower Upper
+parent_0 99.600 1.57000 96.400 102.800
+log_k_parent_sink -3.038 0.07626 -3.193 -2.883
+log_k_parent_m1 -2.980 0.04033 -3.062 -2.898
+log_k_m1_sink -5.248 0.13320 -5.518 -4.977
+sigma 3.126 0.35850 2.396 3.855
Parameter correlation:
-NULL
+[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 99.600000 63.430 2.298e-36 96.400000 1.028e+02
-k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01
-k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03
-f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01
-sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
+ Estimate t value Pr(>t) Lower Upper
+parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02
+k_parent_sink 0.047920 13.110 6.126e-15 0.041030 5.596e-02
+k_parent_m1 0.050780 24.800 3.269e-23 0.046780 5.512e-02
+k_m1_sink 0.005261 7.510 6.165e-09 0.004012 6.898e-03
+sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
FOCUS Chi2 error levels in percent:
err.min n.optim df
All data 6.398 4 15
-parent 6.459 2 7
-m1 4.690 2 8
+parent 6.827 3 6
+m1 4.490 1 9
Resulting formation fractions:
ff
-parent_m1 0.5145
parent_sink 0.4855
+parent_m1 0.5145
+m1_sink 1.0000
Estimated disappearance times:
DT50 DT90
@@ -82,10 +83,10 @@ Data:
0 parent 102.04 99.59848 2.442e+00
1 parent 93.50 90.23787 3.262e+00
1 parent 92.50 90.23787 2.262e+00
- 3 parent 63.23 74.07319 -1.084e+01
- 3 parent 68.99 74.07319 -5.083e+00
- 7 parent 52.32 49.91206 2.408e+00
- 7 parent 55.13 49.91206 5.218e+00
+ 3 parent 63.23 74.07320 -1.084e+01
+ 3 parent 68.99 74.07320 -5.083e+00
+ 7 parent 52.32 49.91207 2.408e+00
+ 7 parent 55.13 49.91207 5.218e+00
14 parent 27.27 25.01257 2.257e+00
14 parent 26.64 25.01257 1.627e+00
21 parent 11.50 12.53462 -1.035e+00
@@ -95,7 +96,7 @@ Data:
50 parent 0.69 0.71624 -2.624e-02
50 parent 0.63 0.71624 -8.624e-02
75 parent 0.05 0.06074 -1.074e-02
- 75 parent 0.06 0.06074 -7.381e-04
+ 75 parent 0.06 0.06074 -7.382e-04
1 m1 4.84 4.80296 3.704e-02
1 m1 5.64 4.80296 8.370e-01
3 m1 12.91 13.02400 -1.140e-01
diff --git a/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt b/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
index 6ddbc1ab..141f57a1 100644
--- a/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
@@ -4,8 +4,8 @@ Date of fit: Dummy date for testing
Date of summary: Dummy date for testing
Equations:
-d_parent/dt = - k_parent * parent
-d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
+d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
Model predictions using solution type eigen
@@ -16,18 +16,18 @@ Error model: Constant variance
Error model algorithm: OLS
Starting values for parameters to be optimised:
- value type
-parent_0 100.7500 state
-k_parent 0.1000 deparm
-k_m1 0.1001 deparm
-f_parent_to_m1 0.5000 deparm
+ value type
+parent_0 100.7500 state
+k_parent_sink 0.1000 deparm
+k_parent_m1 0.1001 deparm
+k_m1_sink 0.1002 deparm
Starting values for the transformed parameters actually optimised:
- value lower upper
-parent_0 100.750000 -Inf Inf
-log_k_parent -2.302585 -Inf Inf
-log_k_m1 -2.301586 -Inf Inf
-f_parent_ilr_1 0.000000 -Inf Inf
+ value lower upper
+parent_0 100.750000 -Inf Inf
+log_k_parent_sink -2.302585 -Inf Inf
+log_k_parent_m1 -2.301586 -Inf Inf
+log_k_m1_sink -2.300587 -Inf Inf
Fixed parameter values:
value type
@@ -39,37 +39,38 @@ Results:
204.4486 212.6365 -97.22429
Optimised, transformed parameters with symmetric confidence intervals:
- Estimate Std. Error Lower Upper
-parent_0 99.60000 1.57000 96.40000 102.8000
-log_k_parent -2.31600 0.04087 -2.39900 -2.2330
-log_k_m1 -5.24800 0.13320 -5.51800 -4.9770
-f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694
-sigma 3.12600 0.35850 2.39600 3.8550
+ Estimate Std. Error Lower Upper
+parent_0 99.600 1.57000 96.400 102.800
+log_k_parent_sink -3.038 0.07626 -3.193 -2.883
+log_k_parent_m1 -2.980 0.04033 -3.062 -2.898
+log_k_m1_sink -5.248 0.13320 -5.518 -4.977
+sigma 3.126 0.35850 2.396 3.855
Parameter correlation:
-NULL
+[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 99.600000 63.430 2.298e-36 96.400000 1.028e+02
-k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01
-k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03
-f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01
-sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
+ Estimate t value Pr(>t) Lower Upper
+parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02
+k_parent_sink 0.047920 13.110 6.126e-15 0.041030 5.596e-02
+k_parent_m1 0.050780 24.800 3.269e-23 0.046780 5.512e-02
+k_m1_sink 0.005261 7.510 6.165e-09 0.004012 6.898e-03
+sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
FOCUS Chi2 error levels in percent:
err.min n.optim df
All data 6.398 4 15
-parent 6.459 2 7
-m1 4.690 2 8
+parent 6.827 3 6
+m1 4.490 1 9
Resulting formation fractions:
ff
-parent_m1 0.5145
parent_sink 0.4855
+parent_m1 0.5145
+m1_sink 1.0000
Estimated disappearance times:
DT50 DT90
@@ -78,41 +79,41 @@ m1 131.761 437.70
Data:
time variable observed predicted residual
- 0 parent 99.46 99.59848 -1.385e-01
- 0 parent 102.04 99.59848 2.442e+00
- 1 parent 93.50 90.23787 3.262e+00
- 1 parent 92.50 90.23787 2.262e+00
- 3 parent 63.23 74.07320 -1.084e+01
- 3 parent 68.99 74.07320 -5.083e+00
- 7 parent 52.32 49.91207 2.408e+00
- 7 parent 55.13 49.91207 5.218e+00
- 14 parent 27.27 25.01257 2.257e+00
- 14 parent 26.64 25.01257 1.627e+00
- 21 parent 11.50 12.53462 -1.035e+00
- 21 parent 11.64 12.53462 -8.946e-01
- 35 parent 2.85 3.14787 -2.979e-01
- 35 parent 2.91 3.14787 -2.379e-01
- 50 parent 0.69 0.71624 -2.624e-02
- 50 parent 0.63 0.71624 -8.624e-02
- 75 parent 0.05 0.06074 -1.074e-02
- 75 parent 0.06 0.06074 -7.382e-04
- 1 m1 4.84 4.80296 3.704e-02
- 1 m1 5.64 4.80296 8.370e-01
- 3 m1 12.91 13.02400 -1.140e-01
- 3 m1 12.96 13.02400 -6.400e-02
- 7 m1 22.97 25.04476 -2.075e+00
- 7 m1 24.47 25.04476 -5.748e-01
- 14 m1 41.69 36.69002 5.000e+00
- 14 m1 33.21 36.69002 -3.480e+00
- 21 m1 44.37 41.65310 2.717e+00
- 21 m1 46.44 41.65310 4.787e+00
- 35 m1 41.22 43.31312 -2.093e+00
- 35 m1 37.95 43.31312 -5.363e+00
- 50 m1 41.19 41.21831 -2.831e-02
- 50 m1 40.01 41.21831 -1.208e+00
- 75 m1 40.09 36.44703 3.643e+00
- 75 m1 33.85 36.44703 -2.597e+00
- 100 m1 31.04 31.98163 -9.416e-01
- 100 m1 33.13 31.98163 1.148e+00
- 120 m1 25.15 28.78984 -3.640e+00
- 120 m1 33.31 28.78984 4.520e+00
+ 0 parent 99.46 99.59848 not tested
+ 0 parent 102.04 99.59848 not tested
+ 1 parent 93.50 90.23787 not tested
+ 1 parent 92.50 90.23787 not tested
+ 3 parent 63.23 74.07320 not tested
+ 3 parent 68.99 74.07320 not tested
+ 7 parent 52.32 49.91207 not tested
+ 7 parent 55.13 49.91207 not tested
+ 14 parent 27.27 25.01257 not tested
+ 14 parent 26.64 25.01257 not tested
+ 21 parent 11.50 12.53462 not tested
+ 21 parent 11.64 12.53462 not tested
+ 35 parent 2.85 3.14787 not tested
+ 35 parent 2.91 3.14787 not tested
+ 50 parent 0.69 0.71624 not tested
+ 50 parent 0.63 0.71624 not tested
+ 75 parent 0.05 0.06074 not tested
+ 75 parent 0.06 0.06074 not tested
+ 1 m1 4.84 4.80296 not tested
+ 1 m1 5.64 4.80296 not tested
+ 3 m1 12.91 13.02400 not tested
+ 3 m1 12.96 13.02400 not tested
+ 7 m1 22.97 25.04476 not tested
+ 7 m1 24.47 25.04476 not tested
+ 14 m1 41.69 36.69002 not tested
+ 14 m1 33.21 36.69002 not tested
+ 21 m1 44.37 41.65310 not tested
+ 21 m1 46.44 41.65310 not tested
+ 35 m1 41.22 43.31312 not tested
+ 35 m1 37.95 43.31312 not tested
+ 50 m1 41.19 41.21831 not tested
+ 50 m1 40.01 41.21831 not tested
+ 75 m1 40.09 36.44703 not tested
+ 75 m1 33.85 36.44703 not tested
+ 100 m1 31.04 31.98163 not tested
+ 100 m1 33.13 31.98163 not tested
+ 120 m1 25.15 28.78984 not tested
+ 120 m1 33.31 28.78984 not tested
diff --git a/tests/testthat/test_mkinfit_errors.R b/tests/testthat/test_mkinfit_errors.R
index 940e0b2e..c1e9da1d 100644
--- a/tests/testthat/test_mkinfit_errors.R
+++ b/tests/testthat/test_mkinfit_errors.R
@@ -25,7 +25,7 @@ test_that("mkinfit stops to prevent and/or explain user errors", {
parms.ini = c(f_parent_to_m1 = 1.1), quiet = TRUE),
"sum up to more than 1")
- expect_error(mkinfit(SFO_SFO.ff, FOCUS_2006_D, solution_type = "analytical"), "not implemented")
+ expect_error(mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "analytical"), "not implemented")
expect_error(mkinfit("FOMC", FOCUS_2006_A, solution_type = "eigen"), "coefficient matrix not present")
})
diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R
index 19ae8770..13d1dd0f 100644
--- a/tests/testthat/test_plots_summary_twa.R
+++ b/tests/testthat/test_plots_summary_twa.R
@@ -39,7 +39,7 @@ test_that("Summaries are reproducible", {
# The correlation matrix is quite platform dependent
# It differs between i386 and amd64 on Windows
# and between Travis and my own Linux system
- test_summary$Corr <- NULL
+ test_summary$Corr <- "Correlation matrix is platform dependent, not tested"
expect_known_output(print(test_summary), "summary_DFOP_FOCUS_C.txt")
test_summary_2 <- summary(f_sfo_sfo_eigen)
@@ -53,7 +53,9 @@ test_that("Summaries are reproducible", {
# It differs between i386 and amd64 on Windows
# and between Travis and my own Linux system
# Even more so when using the Eigen method
- test_summary_2$Corr <- NULL
+ test_summary_2$Corr <- "Correlation matrix is platform dependent, not tested"
+ # The residuals for this method are also platform sensitive
+ test_summary_2$data$residual <- "not tested"
expect_known_output(print(test_summary_2), "summary_DFOP_FOCUS_D_eigen.txt")
test_summary_3 <- summary(f_sfo_sfo_desolve)
@@ -66,7 +68,7 @@ test_that("Summaries are reproducible", {
# The correlation matrix is quite platform dependent
# It differs between i386 and amd64 on Windows
# and between Travis and my own Linux system
- test_summary_3$Corr <- NULL
+ test_summary_3$Corr <- "Correlation matrix is platform dependent, not tested"
expect_known_output(print(test_summary_3), "summary_DFOP_FOCUS_D_deSolve.txt")
})

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