Another overhaul of analytical solutions

Still in preparation for analytical solutions of coupled models

7 files changed, 90 insertions, 73 deletions

diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index fa96de74..7c29ab46 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: 2020-05-06
+Date: 2020-05-07
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/SFO_SFO_printed.txt b/tests/testthat/SFO_SFO_printed.txt
index d0402fc0..a3a04be2 100644
--- a/tests/testthat/SFO_SFO_printed.txt
+++ b/tests/testthat/SFO_SFO_printed.txt
@@ -1,5 +1,5 @@
 <mkinmod> model generated with
-Use of formation fractions $use_of_ff: min 
+Use of formation fractions $use_of_ff: max 
 Specification $spec:
 $parent
 $type: SFO; $to: m1; $sink: TRUE
@@ -7,5 +7,5 @@ $m1
 $type: SFO; $sink: TRUE
 Coefficient matrix $coefmat available
 Differential equations:
-d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+d_parent/dt = - k_parent * parent
+d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt
index 14e00f62..4f96c8d3 100644
--- a/tests/testthat/summary_DFOP_FOCUS_C.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_C.txt
@@ -33,6 +33,11 @@ g_ilr     0.000000  -Inf   Inf
 Fixed 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
diff --git a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
index 66ab9348..fe697794 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_sink * parent - k_parent_m1 * parent
-d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+d_parent/dt = - k_parent * parent
+d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
 
 Model predictions using solution type deSolve 
 
@@ -16,30 +16,35 @@ Error model: Constant variance
 Error model algorithm: OLS 
 
 Starting values for parameters to be optimised:
-                 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
+                  value   type
+parent_0       100.7500  state
+k_parent         0.1000 deparm
+k_m1             0.1001 deparm
+f_parent_to_m1   0.5000 deparm
 
 Starting values for the transformed parameters actually optimised:
-                       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
+                    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
 
 Fixed parameter values:
      value  type
 m1_0     0 state
 
+Results:
+
+       AIC      BIC    logLik
+  204.4486 212.6365 -97.22429
+
 Optimised, transformed parameters with symmetric confidence intervals:
-                  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
+               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
 
 Parameter correlation:
 NULL
@@ -48,24 +53,23 @@ 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_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
+                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
 
 FOCUS Chi2 error levels in percent:
          err.min n.optim df
 All data   6.398       4 15
-parent     6.827       3  6
-m1         4.490       1  9
+parent     6.459       2  7
+m1         4.690       2  8
 
 Resulting formation fractions:
                 ff
-parent_sink 0.4855
 parent_m1   0.5145
-m1_sink     1.0000
+parent_sink 0.4855
 
 Estimated disappearance times:
           DT50   DT90
@@ -78,10 +82,10 @@ 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  74.07320 -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
+    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
    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
@@ -91,7 +95,7 @@ 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 -7.382e-04
+   75   parent     0.06   0.06074 -7.381e-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 1626c5da..6ddbc1ab 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_sink * parent - k_parent_m1 * parent
-d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+d_parent/dt = - k_parent * parent
+d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
 
 Model predictions using solution type eigen 
 
@@ -16,30 +16,35 @@ Error model: Constant variance
 Error model algorithm: OLS 
 
 Starting values for parameters to be optimised:
-                 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
+                  value   type
+parent_0       100.7500  state
+k_parent         0.1000 deparm
+k_m1             0.1001 deparm
+f_parent_to_m1   0.5000 deparm
 
 Starting values for the transformed parameters actually optimised:
-                       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
+                    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
 
 Fixed parameter values:
      value  type
 m1_0     0 state
 
+Results:
+
+       AIC      BIC    logLik
+  204.4486 212.6365 -97.22429
+
 Optimised, transformed parameters with symmetric confidence intervals:
-                  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
+               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
 
 Parameter correlation:
 NULL
@@ -48,24 +53,23 @@ 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_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
+                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
 
 FOCUS Chi2 error levels in percent:
          err.min n.optim df
 All data   6.398       4 15
-parent     6.827       3  6
-m1         4.490       1  9
+parent     6.459       2  7
+m1         4.690       2  8
 
 Resulting formation fractions:
                 ff
-parent_sink 0.4855
 parent_m1   0.5145
-m1_sink     1.0000
+parent_sink 0.4855
 
 Estimated disappearance times:
           DT50   DT90
diff --git a/tests/testthat/test_SFORB.R b/tests/testthat/test_SFORB.R
index ad9881a8..4fb736ec 100644
--- a/tests/testthat/test_SFORB.R
+++ b/tests/testthat/test_SFORB.R
@@ -15,16 +15,20 @@ test_that("Fitting the SFORB model is equivalent to fitting DFOP", {
     use_of_ff = "max", quiet = TRUE)
   SFORB_SFO <- mkinmod(parent = mkinsub("SFORB", "M1"),
     M1 = mkinsub("SFO"),
+    use_of_ff = "min", quiet = TRUE)
+  SFORB_SFO_ff <- mkinmod(parent = mkinsub("SFORB", "M1"),
+    M1 = mkinsub("SFO"),
     use_of_ff = "max", quiet = TRUE)
 
-  SFORB_SFO$coefmat
-
   f_dfop_sfo <- mkinfit(DFOP_SFO, DFOP_par_c, quiet = TRUE)
   f_sforb_sfo <- mkinfit(SFORB_SFO, DFOP_par_c, quiet = TRUE)
+  f_sforb_sfo_ff <- mkinfit(SFORB_SFO_ff, DFOP_par_c, quiet = TRUE)
   f_sforb_sfo_eigen <- mkinfit(SFORB_SFO, DFOP_par_c, solution_type = "eigen", quiet = TRUE)
 
   expect_equivalent(endpoints(f_sforb_sfo)$distimes, endpoints(f_dfop_sfo)$distimes,
     tolerance = 1e-6)
+  expect_equivalent(endpoints(f_sforb_sfo_ff)$distimes, endpoints(f_dfop_sfo)$distimes,
+    tolerance = 1e-6)
   expect_equivalent(endpoints(f_sforb_sfo_eigen)$distimes, endpoints(f_dfop_sfo)$distimes,
     tolerance = 1e-6)
 })
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
index e5e19c60..31fb19de 100644
--- a/tests/testthat/test_nlme.R
+++ b/tests/testthat/test_nlme.R
@@ -2,20 +2,21 @@ context("Nonlinear mixed-effects models")
 
 library(nlme)
 
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+
 test_that("nlme_function works correctly", {
 
-  sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
   m_SFO <- mkinmod(parent = mkinsub("SFO"))
   d_SFO_1 <- mkinpredict(m_SFO,
-    c(k_parent_sink = 0.1),
+    c(k_parent = 0.1),
     c(parent = 98), sampling_times)
   d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
   d_SFO_2 <- mkinpredict(m_SFO,
-    c(k_parent_sink = 0.05),
+    c(k_parent = 0.05),
     c(parent = 102), sampling_times)
   d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
   d_SFO_3 <- mkinpredict(m_SFO,
-    c(k_parent_sink = 0.02),
+    c(k_parent = 0.02),
     c(parent = 103), sampling_times)
   d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
 
@@ -33,7 +34,6 @@ test_that("nlme_function works correctly", {
   # The following assignment was introduced for nlme as evaluated by testthat
   # to find the function
   assign("nlme_f", nlme_f, pos = globalenv())
-  assign("sampling_times", sampling_times, pos = globalenv())
 
   m_nlme_raw <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
     data = grouped_data,
@@ -101,7 +101,7 @@ test_that("nlme_function works correctly in other cases", {
   SFO <- mkinmod(parent = mkinsub("SFO"))
   pred_sfo <- function(k) {
     mkinpredict(SFO,
-      c(k_parent_sink = k),
+      c(k_parent = k),
       c(parent = 100),
       sampling_times)
   }