R Under development (unstable) (2024-09-30 r87204 ucrt) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(eDNAjoint)
>
> test_check("eDNAjoint")
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000449 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.49 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 100 [ 1%] (Warmup)
Chain 1: Iteration: 26 / 100 [ 26%] (Sampling)
Chain 1: Iteration: 100 / 100 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.084 seconds (Warm-up)
Chain 1: 5.707 seconds (Sampling)
Chain 1: 5.791 seconds (Total)
Chain 1:
Refer to the eDNAjoint guide for troubleshooting tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#troubleshooting-tips
SAMPLING FOR MODEL 'joint_binary_negbin' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000713 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.13 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 100 [ 1%] (Warmup)
Chain 1: Iteration: 26 / 100 [ 26%] (Sampling)
Chain 1: Iteration: 100 / 100 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.813 seconds (Warm-up)
Chain 1: 2.949 seconds (Sampling)
Chain 1: 3.762 seconds (Total)
Chain 1:
Refer to the eDNAjoint guide for visualization tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#visualization-tips
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000151 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.51 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 100 [ 1%] (Warmup)
Chain 1: Iteration: 26 / 100 [ 26%] (Sampling)
Chain 1: Iteration: 100 / 100 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.079 seconds (Warm-up)
Chain 1: 3.204 seconds (Sampling)
Chain 1: 3.283 seconds (Total)
Chain 1:
Refer to the eDNAjoint guide for troubleshooting tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#troubleshooting-tips
SAMPLING FOR MODEL 'joint_binary_negbin' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000854 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 8.54 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 100 [ 1%] (Warmup)
Chain 1: Iteration: 26 / 100 [ 26%] (Sampling)
Chain 1: Iteration: 100 / 100 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.137 seconds (Warm-up)
Chain 1: 2.805 seconds (Sampling)
Chain 1: 3.942 seconds (Total)
Chain 1:
Refer to the eDNAjoint guide for visualization tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#visualization-tips
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000796 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.96 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 1: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 1: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 1: Iteration: 2500 / 3000 [ 83%] (Sampling)
Chain 1: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 4.61 seconds (Warm-up)
Chain 1: 16.082 seconds (Sampling)
Chain 1: 20.692 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000749 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 7.49 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 2: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 2: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 2: Iteration: 2500 / 3000 [ 83%] (Sampling)
Chain 2: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 4.526 seconds (Warm-up)
Chain 2: 16.169 seconds (Sampling)
Chain 2: 20.695 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000892 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 8.92 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 3: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 3: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 3: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 5.038 seconds (Warm-up)
Chain 3: 15.61 seconds (Sampling)
Chain 3: 20.648 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000701 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 7.01 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 4: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 4: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 4: Iteration: 2500 / 3000 [ 83%] (Sampling)
Chain 4: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 4.296 seconds (Warm-up)
Chain 4: 15.85 seconds (Sampling)
Chain 4: 20.146 seconds (Total)
Chain 4:
Refer to the eDNAjoint guide for visualization tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#visualization-tips
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000685 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.85 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 1: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 1: Iteration: 501 / 3000 [ 16%] (Sampling)
Chain 1: Iteration: 1000 / 3000 [ 33%] (Sampling)
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Chain 1: Iteration: 2000 / 3000 [ 66%] (Sampling)
Chain 1: Iteration: 2500 / 3000 [ 83%] (Sampling)
Chain 1: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 4.783 seconds (Warm-up)
Chain 1: 16.232 seconds (Sampling)
Chain 1: 21.015 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000661 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 6.61 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 2: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 2: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 2: Iteration: 2000 / 3000 [ 66%] (Sampling)
Chain 2: Iteration: 2500 / 3000 [ 83%] (Sampling)
Chain 2: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 4.763 seconds (Warm-up)
Chain 2: 15.812 seconds (Sampling)
Chain 2: 20.575 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000742 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 7.42 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 3: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 3: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 3: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 4.702 seconds (Warm-up)
Chain 3: 15.966 seconds (Sampling)
Chain 3: 20.668 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.00064 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 6.4 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 4: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 4: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 4: Iteration: 2500 / 3000 [ 83%] (Sampling)
Chain 4: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 4.331 seconds (Warm-up)
Chain 4: 16.136 seconds (Sampling)
Chain 4: 20.467 seconds (Total)
Chain 4:
Refer to the eDNAjoint guide for visualization tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#visualization-tips
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000809 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 8.09 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 1: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 1: Iteration: 501 / 3000 [ 16%] (Sampling)
Chain 1: Iteration: 1000 / 3000 [ 33%] (Sampling)
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Chain 1: Iteration: 2500 / 3000 [ 83%] (Sampling)
Chain 1: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 5.681 seconds (Warm-up)
Chain 1: 27.628 seconds (Sampling)
Chain 1: 33.309 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000936 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 9.36 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 2: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 2: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 2: Iteration: 2500 / 3000 [ 83%] (Sampling)
Chain 2: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 5.724 seconds (Warm-up)
Chain 2: 16.623 seconds (Sampling)
Chain 2: 22.347 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000594 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 5.94 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 3: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 3: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 3: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 5.715 seconds (Warm-up)
Chain 3: 26.469 seconds (Sampling)
Chain 3: 32.184 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'joint_binary_cov_pois' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000727 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 7.27 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 4: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 4: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 4: Iteration: 2500 / 3000 [ 83%] (Sampling)
Chain 4: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 5.866 seconds (Warm-up)
Chain 4: 17.913 seconds (Sampling)
Chain 4: 23.779 seconds (Total)
Chain 4:
Refer to the eDNAjoint guide for visualization tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#visualization-tips
SAMPLING FOR MODEL 'joint_binary_negbin' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.002327 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 23.27 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 1: Iteration: 500 / 3000 [ 16%] (Warmup)
Chain 1: Iteration: 501 / 3000 [ 16%] (Sampling)
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Chain 1: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 16.179 seconds (Warm-up)
Chain 1: 49.527 seconds (Sampling)
Chain 1: 65.706 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'joint_binary_negbin' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.002379 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 23.79 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 2: Iteration: 500 / 3000 [ 16%] (Warmup)
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Chain 2: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 16.689 seconds (Warm-up)
Chain 2: 52.128 seconds (Sampling)
Chain 2: 68.817 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'joint_binary_negbin' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.001971 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 19.71 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 3: Iteration: 500 / 3000 [ 16%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 16.442 seconds (Warm-up)
Chain 3: 51.078 seconds (Sampling)
Chain 3: 67.52 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'joint_binary_negbin' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.002473 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 24.73 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: Iteration: 1 / 3000 [ 0%] (Warmup)
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Chain 4: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 15.278 seconds (Warm-up)
Chain 4: 49.616 seconds (Sampling)
Chain 4: 64.894 seconds (Total)
Chain 4:
Refer to the eDNAjoint guide for visualization tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#visualization-tips
SAMPLING FOR MODEL 'joint_binary_pois' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000616 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.16 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 1: Iteration: 500 / 3000 [ 16%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 4.625 seconds (Warm-up)
Chain 1: 15.17 seconds (Sampling)
Chain 1: 19.795 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'joint_binary_pois' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.00075 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 7.5 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 3000 [ 0%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 5.214 seconds (Warm-up)
Chain 2: 15.99 seconds (Sampling)
Chain 2: 21.204 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'joint_binary_pois' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000757 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 7.57 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: Iteration: 1 / 3000 [ 0%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 4.62 seconds (Warm-up)
Chain 3: 15.938 seconds (Sampling)
Chain 3: 20.558 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'joint_binary_pois' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.00089 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 8.9 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: Iteration: 1 / 3000 [ 0%] (Warmup)
Chain 4: Iteration: 500 / 3000 [ 16%] (Warmup)
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Chain 4: Iteration: 3000 / 3000 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 5.193 seconds (Warm-up)
Chain 4: 16.124 seconds (Sampling)
Chain 4: 21.317 seconds (Total)
Chain 4:
Refer to the eDNAjoint guide for visualization tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#visualization-tips
SAMPLING FOR MODEL 'joint_binary_catchability_negbin' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001874 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 18.74 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 100 [ 1%] (Warmup)
Chain 1: Iteration: 26 / 100 [ 26%] (Sampling)
Chain 1: Iteration: 100 / 100 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.986 seconds (Warm-up)
Chain 1: 2.152 seconds (Sampling)
Chain 1: 3.138 seconds (Total)
Chain 1:
Refer to the eDNAjoint guide for visualization tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#visualization-tips
SAMPLING FOR MODEL 'joint_binary_catchability_pois' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000632 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.32 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 100 [ 1%] (Warmup)
Chain 1: Iteration: 26 / 100 [ 26%] (Sampling)
Chain 1: Exception: model_joint_binary_catchability_pois_namespace::write_array: p11_dna[1] is -0.00256216, but must be greater than or equal to 0.000000 (in 'string', line 63, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_pois_namespace::write_array: p11_dna[1] is -0.00359261, but must be greater than or equal to 0.000000 (in 'string', line 63, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_pois_namespace::write_array: p11_dna[1] is -0.00445721, but must be greater than or equal to 0.000000 (in 'string', line 63, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_pois_namespace::write_array: p11_dna[1] is -0.0342411, but must be greater than or equal to 0.000000 (in 'string', line 63, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_pois_namespace::write_array: p11_dna[1] is -0.0162345, but must be greater than or equal to 0.000000 (in 'string', line 63, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_pois_namespace::write_array: p11_dna[1] is -0.0158599, but must be greater than or equal to 0.000000 (in 'string', line 63, column 2 to column 51)
Chain 1: Iteration: 100 / 100 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.823 seconds (Warm-up)
Chain 1: 2.487 seconds (Sampling)
Chain 1: 3.31 seconds (Total)
Chain 1:
Refer to the eDNAjoint guide for troubleshooting tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#troubleshooting-tips
[1] "Warning: There are 4 divergent transitions in your model fit. "
SAMPLING FOR MODEL 'joint_binary_catchability_gamma' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001165 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 11.65 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 100 [ 1%] (Warmup)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0233912, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.00767086, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Iteration: 26 / 100 [ 26%] (Sampling)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0303053, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0167087, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0111577, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[1] is -0.00125093, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.00163001, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0013677, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -5.25782e-05, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.014548, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0154663, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0714806, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.103427, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.077053, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0439451, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0548702, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0486027, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0322993, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.00551719, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0296548, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0270731, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0161959, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.00550149, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0510237, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.00450973, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Exception: model_joint_binary_catchability_gamma_namespace::write_array: p11_dna[2] is -0.0208466, but must be greater than or equal to 0.000000 (in 'string', line 69, column 2 to column 51)
Chain 1: Iteration: 100 / 100 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.585 seconds (Warm-up)
Chain 1: 5.057 seconds (Sampling)
Chain 1: 6.642 seconds (Total)
Chain 1:
Refer to the eDNAjoint guide for visualization tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#visualization-tips
SAMPLING FOR MODEL 'joint_binary_negbin' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.002546 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 25.46 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 100 [ 1%] (Warmup)
Chain 1: Iteration: 26 / 100 [ 26%] (Sampling)
Chain 1: Iteration: 100 / 100 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.986 seconds (Warm-up)
Chain 1: 4.852 seconds (Sampling)
Chain 1: 5.838 seconds (Total)
Chain 1:
Refer to the eDNAjoint guide for visualization tips: https://bookdown.org/abigailkeller/eDNAjoint_vignette/tips.html#visualization-tips