Roxygenize, adapt tests

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")
 })