Improve tests, remove geometric_mean

1 files changed, 125 insertions, 0 deletions

diff --git a/tests/testthat/summary_DFOP_FOCUS_D.txt b/tests/testthat/summary_DFOP_FOCUS_D.txt
new file mode 100644
index 00000000..8abc15e7
--- /dev/null
+++ b/tests/testthat/summary_DFOP_FOCUS_D.txt
@@ -0,0 +1,125 @@
+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 
+
+Equations:
+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 
+
+Fitted using test 0 model solutions performed in test time 0 s
+
+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
+
+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
+
+Fixed parameter values:
+     value  type
+m1_0     0 state
+
+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
+
+Parameter correlation:
+                  parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+parent_0             1e+00             6e-01          -6e-02        -2e-01
+log_k_parent_sink    6e-01             1e+00          -9e-02        -6e-01
+log_k_parent_m1     -6e-02            -9e-02           1e+00         5e-01
+log_k_m1_sink       -2e-01            -6e-01           5e-01         1e+00
+sigma                1e-09            -9e-10           2e-08        -1e-10
+                   sigma
+parent_0           1e-09
+log_k_parent_sink -9e-10
+log_k_parent_m1    2e-08
+log_k_m1_sink     -1e-10
+sigma              1e+00
+
+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
+
+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
+
+Resulting formation fractions:
+                ff
+parent_sink 0.4855
+parent_m1   0.5145
+m1_sink     1.0000
+
+Estimated disappearance times:
+          DT50   DT90
+parent   7.023  23.33
+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