Roxygenize, adapt tests

1 files changed, 34 insertions, 33 deletions

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