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Type 'q()' to quit R. > library(testthat) > library(circacompare) > > test_check("circacompare") $fit Nonlinear regression model model: measure ~ k + (alpha) * cos((1/period) * time_r - (phi)) data: x k alpha phi 6.48863 0.06986 6.26774 residual sum-of-squares: 0.1968 Number of iterations to convergence: 8 Achieved convergence tolerance: 1.282e-08 $summary parameter value 1 rhythmic_p 0.13140351 2 mesor 6.48862989 3 amplitude 0.06985646 4 phase_radians 6.26774340 5 peak_time_hours 23.94101626 6 period 24.00000000 $fit Nonlinear regression model model: measure ~ k + (alpha) * cos((1/period) * time_r - (phi)) data: x k alpha phi 6.48863 0.06986 6.26774 residual sum-of-squares: 0.1968 Number of iterations to convergence: 8 Achieved convergence tolerance: 1.623e-07 $summary parameter value 1 rhythmic_p 0.13140361 2 mesor 6.48862989 3 amplitude 0.06985644 4 phase_radians 6.26774333 5 peak_time_hours 23.94101600 6 period 24.00000000 **Iteration 1 LME step: Loglik: -3640.757, nlminb iterations: 20 reStruct parameters: id 15.539 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 27696.9 fixed effects: 4.841362 9.993038 0.0007086164 8.690108e-05 iterations: 7 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 1560.172593 0.417756 0.000000 **Iteration 2 LME step: Loglik: -3466.19, nlminb iterations: 1 reStruct parameters: id 15.539 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 27696.7 fixed effects: 4.841948 9.992972 0.0006974086 -5.696158e-06 iterations: 2 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 1.607064e-02 3.886746e-13 0.000000e+00 **Iteration 3 LME step: Loglik: -3466.19, nlminb iterations: 1 reStruct parameters: id 15.53901 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 27696.7 fixed effects: 4.841948 9.992972 0.0006974086 -5.696158e-06 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.000000e+00 5.055495e-07 0.000000e+00 **Iteration 1 LME step: Loglik: -3509.379, nlminb iterations: 10 reStruct parameters: id 4.241865 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 27669.64 fixed effects: 4.840362 9.991897 0.002096356 13.99684 iterations: 7 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 664.1705461 0.1038672 0.0000000 **Iteration 2 LME step: Loglik: -3466.161, nlminb iterations: 4 reStruct parameters: id 3.432654 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 27667.8 fixed effects: 4.840362 9.991897 0.002096435 13.99684 iterations: 2 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 3.742804e-05 1.047930e-02 0.000000e+00 **Iteration 3 LME step: Loglik: -3466.161, nlminb iterations: 1 reStruct parameters: id 3.432652 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 27667.8 fixed effects: 4.840362 9.991897 0.002096435 13.99684 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.000000e+00 1.595971e-07 0.000000e+00 **Iteration 1 LME step: Loglik: -14555.4, nlminb iterations: 1 reStruct parameters: id 1.849877 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 119440.9 fixed effects: 4.871085 9.996911 6.282769 iterations: 7 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 6.33016e-01 1.07492e-08 0.00000e+00 **Iteration 2 LME step: Loglik: -14555.4, nlminb iterations: 1 reStruct parameters: id 1.849877 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 119440.9 fixed effects: 4.871085 9.997704 6.283142 iterations: 2 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 7.928814e-05 5.759595e-11 0.000000e+00 **Iteration 3 LME step: Loglik: -14555.4, nlminb iterations: 1 reStruct parameters: id 1.849877 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 119440.9 fixed effects: 4.871085 9.997704 6.283142 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0 0 0 **Iteration 1 LME step: Loglik: -14555.3, nlminb iterations: 5 reStruct parameters: id 1.846839 varStruct parameters: power -0.004554617 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 -9.997382 -3.14169 iterations: 5 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 3.626909488 0.001645515 1.000000000 **Iteration 2 LME step: Loglik: -14555.3, nlminb iterations: 1 reStruct parameters: id 1.846838 varStruct parameters: power -0.004554617 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 -9.997382 -3.14169 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0 0 0 **Iteration 1 LME step: Loglik: -14555.3, nlminb iterations: 5 reStruct parameters: id 1.846839 varStruct parameters: power -0.004554621 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 9.997689 -6.283279 iterations: 7 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.713215604 0.001645519 1.000000000 **Iteration 2 LME step: Loglik: -14555.3, nlminb iterations: 1 reStruct parameters: id 1.846838 varStruct parameters: power -0.004554621 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 9.997689 -6.283279 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0 0 0 **Iteration 1 LME step: Loglik: -14555.3, nlminb iterations: 5 reStruct parameters: id 1.846839 varStruct parameters: power -0.004554617 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 9.997592 -0.0001218675 iterations: 5 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 6.465756e+03 1.645511e-03 1.000000e+00 **Iteration 2 LME step: Loglik: -14555.3, nlminb iterations: 1 reStruct parameters: id 1.846838 varStruct parameters: power -0.004554617 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 9.997592 -0.0001218675 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.000000e+00 6.011479e-16 0.000000e+00 **Iteration 1 LME step: Loglik: -14555.3, nlminb iterations: 5 reStruct parameters: id 1.846839 varStruct parameters: power -0.004554616 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 9.997576 -0.0001508649 iterations: 4 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 1.723713e+03 1.645515e-03 1.000000e+00 **Iteration 2 LME step: Loglik: -14555.3, nlminb iterations: 1 reStruct parameters: id 1.846838 varStruct parameters: power -0.004554616 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 9.997576 -0.0001508649 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.000000e+00 8.416071e-16 0.000000e+00 **Iteration 1 LME step: Loglik: -14555.3, nlminb iterations: 5 reStruct parameters: id 1.846839 varStruct parameters: power -0.004554618 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 -9.997687 3.141499 iterations: 5 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 3.640205877 0.001645513 1.000000000 **Iteration 2 LME step: Loglik: -14555.3, nlminb iterations: 1 reStruct parameters: id 1.846838 varStruct parameters: power -0.004554618 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 -9.997687 3.141499 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0 0 0 **Iteration 1 LME step: Loglik: -14555.3, nlminb iterations: 5 reStruct parameters: id 1.846839 varStruct parameters: power -0.004554622 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 9.997639 -12.56646 iterations: 7 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.823382885 0.001645515 1.000000000 **Iteration 2 LME step: Loglik: -14555.3, nlminb iterations: 1 reStruct parameters: id 1.846838 varStruct parameters: power -0.004554622 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 9.997639 -12.56646 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.000000e+00 1.094593e-10 0.000000e+00 **Iteration 1 LME step: Loglik: -14555.3, nlminb iterations: 5 reStruct parameters: id 1.846839 varStruct parameters: power -0.004554614 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 9.997392 6.283087 iterations: 7 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 1.193914453 0.001645507 1.000000000 **Iteration 2 LME step: Loglik: -14555.3, nlminb iterations: 1 reStruct parameters: id 1.846838 varStruct parameters: power -0.004554614 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 118355.2 fixed effects: 4.871032 9.997392 6.283087 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.000000e+00 1.867631e-10 0.000000e+00 Error in stats::nls(formula = form, data = data, start = starting_params, : singular gradient Error in stats::nls(formula = form, data = data, start = starting_params, : step factor 0.000488281 reduced below 'minFactor' of 0.000976562 **Iteration 1 LME step: Loglik: -5362.31, nlminb iterations: 1 reStruct parameters: id 1.330561 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 2914.277 fixed effects: -0.00304645 10.00689 0.001165512 3.036079 iterations: 5 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 2.8415813 0.7183429 0.0000000 **Iteration 2 LME step: Loglik: -4181.778, nlminb iterations: 3 reStruct parameters: id 0.7491786 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 2914.277 fixed effects: -0.00304645 10.00689 0.001165512 3.036079 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0 0 0 **Iteration 1 LME step: Loglik: -5362.31, nlminb iterations: 1 reStruct parameters: id 1.330561 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 2914.277 fixed effects: -0.00304645 10.00689 0.001165512 3.036079 iterations: 5 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 2.8415813 0.7183429 0.0000000 **Iteration 2 LME step: Loglik: -4181.778, nlminb iterations: 3 reStruct parameters: id 0.7491786 varStruct parameters: power 0 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 2914.277 fixed effects: -0.00304645 10.00689 0.001165512 3.036079 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0 0 0 **Iteration 1 LME step: Loglik: -9253.195, nlminb iterations: 5 reStruct parameters: id 3.094586 varStruct parameters: power -0.002104767 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 2902.204 fixed effects: -0.003036708 10.00696 0.001187532 2.721892 iterations: 7 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 7.587492 17.938433 1.000000 **Iteration 2 LME step: Loglik: -4199.912, nlminb iterations: 7 reStruct parameters: id -0.2066936 varStruct parameters: power -0.0008369633 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 2909.464 fixed effects: -0.003042442 10.00692 0.001174232 2.721905 iterations: 2 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.011326745 0.006917199 1.514766617 **Iteration 3 LME step: Loglik: -4199.912, nlminb iterations: 8 reStruct parameters: id -0.2066936 varStruct parameters: power -0.0008368621 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 2909.465 fixed effects: -0.003042442 10.00692 0.001174232 2.721905 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.000000e+00 5.516596e-07 1.209345e-04 **Iteration 4 LME step: Loglik: -4199.912, nlminb iterations: 8 reStruct parameters: id -0.2066936 varStruct parameters: power -0.000836862 Beginning PNLS step: .. completed fit_nlme() step. PNLS step: RSS = 2909.465 fixed effects: -0.003042442 10.00692 0.001174232 2.721905 iterations: 1 Convergence crit. (must all become <= tolerance = 1e-05): fixed reStruct varStruct 0.000000e+00 1.493332e-10 3.273532e-08 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 5.81 0.43 6.23