From d0517ca51ae9837bbf58ab2502820cbcab9c6400 Mon Sep 17 00:00:00 2001 From: ericward-noaa Date: Tue, 11 Jun 2024 13:42:38 -0700 Subject: [PATCH] update codecov for NFT --- .Rbuildignore | 1 + .github/workflows/pkgdown.yaml | 5 + .github/workflows/test-coverage.yaml | 61 +++++++ DESCRIPTION | 3 +- README.md | 4 + codecov.yml | 14 ++ docs/articles/a01_overview.html | 2 +- docs/articles/a02_fitting_models.html | 2 +- docs/articles/a03_expanding_estimates.html | 2 +- docs/articles/a04_diagnosing_problems.html | 2 +- docs/index.html | 1 + docs/pkgdown.yml | 2 +- docs/reference/fit_bycatch.html | 198 ++++++++++----------- docs/reference/get_expanded.html | 22 +-- docs/reference/get_fitted.html | 14 +- docs/reference/get_total.html | 20 +-- docs/reference/plot_expanded.html | 30 ++-- docs/reference/plot_fitted.html | 120 ++++++------- src/bycatch.so | Bin 2842640 -> 2842640 bytes 19 files changed, 295 insertions(+), 208 deletions(-) create mode 100644 .github/workflows/test-coverage.yaml create mode 100644 codecov.yml diff --git a/.Rbuildignore b/.Rbuildignore index 2fe604a..9e3b899 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -6,3 +6,4 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^codecov\.yml$ diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 854000b..8d83155 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -46,3 +46,8 @@ jobs: git config --local user.email "actions@github.com" git config --local user.name "GitHub Actions" Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' + + - name: Upload coverage reports to Codecov + uses: codecov/codecov-action@v4.0.1 + with: + token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 0000000..fefc52e --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,61 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: test-coverage + +permissions: read-all + +jobs: + test-coverage: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Test coverage + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + covr::to_cobertura(cov) + shell: Rscript {0} + + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/DESCRIPTION b/DESCRIPTION index b6c352b..bf508ea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -30,7 +30,7 @@ LinkingTo: BH (>= 1.66.0), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: - testthat, + testthat (>= 3.0.0), parallel, knitr, rmarkdown, @@ -43,3 +43,4 @@ VignetteBuilder: knitr Roxygen: list(markdown = TRUE) SystemRequirements: GNU make Biarch: true +Config/testthat/edition: 3 diff --git a/README.md b/README.md index c85bc6a..a4b8030 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,10 @@ [![R-CMD-check](https://github.com/ericward-noaa/bycatch/workflows/R-CMD-check/badge.svg)](https://github.com/ericward-noaa/bycatch/actions) + + [![Codecov test coverage](https://codecov.io/gh/ericward-noaa/bycatch/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ericward-noaa/bycatch?branch=master) + + # bycatch This is a repository for applications of Bayesian bycatch models, using Stan for estimation. These models fit Bayesian GLMs (with or without time varying parameters, and with or without covariates) to estimate bycatch rates. The package includes functions to estimate fleet-level estimates. The primary applications of these models (linked to below) are protected species bycatch (e.g. ESA listed birds, marine mammals) in the west coast groundfish fisheries off the west coast of the USA. Data compilation and analysis is done at the Northwest Fisheries Science Center (NWFSC) in Seattle. The pkgdown version of this site can be found here: [https://ericward-noaa.github.io/bycatch/](https://ericward-noaa.github.io/bycatch/) diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..04c5585 --- /dev/null +++ b/codecov.yml @@ -0,0 +1,14 @@ +comment: false + +coverage: + status: + project: + default: + target: auto + threshold: 1% + informational: true + patch: + default: + target: auto + threshold: 1% + informational: true diff --git a/docs/articles/a01_overview.html b/docs/articles/a01_overview.html index 5328a0c..922dd3d 100644 --- a/docs/articles/a01_overview.html +++ b/docs/articles/a01_overview.html @@ -88,7 +88,7 @@

Overview of bycatch package

Eric J. Ward, Jason E. Jannot

-

2024-05-03

+

2024-06-11

Source: vignettes/a01_overview.Rmd diff --git a/docs/articles/a02_fitting_models.html b/docs/articles/a02_fitting_models.html index e3b7aeb..2560e00 100644 --- a/docs/articles/a02_fitting_models.html +++ b/docs/articles/a02_fitting_models.html @@ -88,7 +88,7 @@

Fitting models with the bycatch package

Eric J. Ward, Jason E. Jannot

-

2024-05-03

+

2024-06-11

Source: vignettes/a02_fitting_models.Rmd diff --git a/docs/articles/a03_expanding_estimates.html b/docs/articles/a03_expanding_estimates.html index 8bbec2e..96785c9 100644 --- a/docs/articles/a03_expanding_estimates.html +++ b/docs/articles/a03_expanding_estimates.html @@ -88,7 +88,7 @@

Expanding bycatch estimates

Eric J. Ward, Jason E. Jannot

-

2024-05-03

+

2024-06-11

Source: vignettes/a03_expanding_estimates.Rmd diff --git a/docs/articles/a04_diagnosing_problems.html b/docs/articles/a04_diagnosing_problems.html index 7bbc569..6fabac2 100644 --- a/docs/articles/a04_diagnosing_problems.html +++ b/docs/articles/a04_diagnosing_problems.html @@ -88,7 +88,7 @@

Diagnosing errors

Eric J. Ward, Jason E. Jannot

-

2024-05-03

+

2024-06-11

Source: vignettes/a04_diagnosing_problems.Rmd diff --git a/docs/index.html b/docs/index.html index 0131f5a..4c745df 100644 --- a/docs/index.html +++ b/docs/index.html @@ -85,6 +85,7 @@

R-CMD-check

+

Codecov test coverage

bycatch

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index bdfe745..2c73249 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,5 +6,5 @@ articles: a02_fitting_models: a02_fitting_models.html a03_expanding_estimates: a03_expanding_estimates.html a04_diagnosing_problems: a04_diagnosing_problems.html -last_built: 2024-05-03T21:01Z +last_built: 2024-06-11T20:31Z diff --git a/docs/reference/fit_bycatch.html b/docs/reference/fit_bycatch.html index 1dc7a8f..371ec00 100644 --- a/docs/reference/fit_bycatch.html +++ b/docs/reference/fit_bycatch.html @@ -189,8 +189,8 @@

Examples

#> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 8e-06 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 2: Gradient evaluation took 7e-06 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -214,8 +214,8 @@

Examples

#> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 8e-06 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 3: Gradient evaluation took 9e-06 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -232,9 +232,9 @@

Examples

#> Chain 3: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 3: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.013 seconds (Warm-up) -#> Chain 3: 0.009 seconds (Sampling) -#> Chain 3: 0.022 seconds (Total) +#> Chain 3: Elapsed Time: 0.014 seconds (Warm-up) +#> Chain 3: 0.011 seconds (Sampling) +#> Chain 3: 0.025 seconds (Total) #> Chain 3: loo::loo(fit$fitted_model)$estimates #> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details. @@ -269,8 +269,8 @@

Examples

#> Chain 1: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 1: #> Chain 1: Elapsed Time: 0.012 seconds (Warm-up) -#> Chain 1: 0.013 seconds (Sampling) -#> Chain 1: 0.025 seconds (Total) +#> Chain 1: 0.014 seconds (Sampling) +#> Chain 1: 0.026 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). @@ -294,8 +294,8 @@

Examples

#> Chain 2: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 2: #> Chain 2: Elapsed Time: 0.013 seconds (Warm-up) -#> Chain 2: 0.012 seconds (Sampling) -#> Chain 2: 0.025 seconds (Total) +#> Chain 2: 0.014 seconds (Sampling) +#> Chain 2: 0.027 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). @@ -319,8 +319,8 @@

Examples

#> Chain 3: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 3: #> Chain 3: Elapsed Time: 0.013 seconds (Warm-up) -#> Chain 3: 0.013 seconds (Sampling) -#> Chain 3: 0.026 seconds (Total) +#> Chain 3: 0.014 seconds (Sampling) +#> Chain 3: 0.027 seconds (Total) #> Chain 3: plot_fitted(fit, xlab = "Year", ylab = "Fleet-level bycatch", @@ -338,8 +338,8 @@

Examples

#> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.6e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.16 seconds. +#> Chain 1: Gradient evaluation took 1.7e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -356,15 +356,15 @@

Examples

#> Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.119 seconds (Warm-up) -#> Chain 1: 0.113 seconds (Sampling) -#> Chain 1: 0.232 seconds (Total) +#> Chain 1: Elapsed Time: 0.13 seconds (Warm-up) +#> Chain 1: 0.116 seconds (Sampling) +#> Chain 1: 0.246 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 1.2e-05 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. +#> Chain 2: Gradient evaluation took 1.3e-05 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -381,15 +381,15 @@

Examples

#> Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 2: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.088 seconds (Warm-up) -#> Chain 2: 0.075 seconds (Sampling) -#> Chain 2: 0.163 seconds (Total) +#> Chain 2: Elapsed Time: 0.09 seconds (Warm-up) +#> Chain 2: 0.083 seconds (Sampling) +#> Chain 2: 0.173 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 1.1e-05 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 3: Gradient evaluation took 1e-05 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -406,15 +406,15 @@

Examples

#> Chain 3: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 3: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.164 seconds (Warm-up) -#> Chain 3: 0.082 seconds (Sampling) -#> Chain 3: 0.246 seconds (Total) +#> Chain 3: Elapsed Time: 0.122 seconds (Warm-up) +#> Chain 3: 0.087 seconds (Sampling) +#> Chain 3: 0.209 seconds (Total) #> Chain 3: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 4). #> Chain 4: -#> Chain 4: Gradient evaluation took 1.1e-05 seconds -#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 4: Gradient evaluation took 1.7e-05 seconds +#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds. #> Chain 4: Adjust your expectations accordingly! #> Chain 4: #> Chain 4: @@ -431,9 +431,9 @@

Examples

#> Chain 4: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 4: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 4: -#> Chain 4: Elapsed Time: 0.099 seconds (Warm-up) -#> Chain 4: 0.106 seconds (Sampling) -#> Chain 4: 0.205 seconds (Total) +#> Chain 4: Elapsed Time: 0.103 seconds (Warm-up) +#> Chain 4: 0.109 seconds (Sampling) +#> Chain 4: 0.212 seconds (Total) #> Chain 4: # fit a time varying model @@ -444,8 +444,8 @@

Examples

#> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 3e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.3 seconds. +#> Chain 1: Gradient evaluation took 3.1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -462,15 +462,15 @@

Examples

#> Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 1: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.141 seconds (Warm-up) -#> Chain 1: 0.12 seconds (Sampling) -#> Chain 1: 0.261 seconds (Total) +#> Chain 1: Elapsed Time: 0.155 seconds (Warm-up) +#> Chain 1: 0.13 seconds (Sampling) +#> Chain 1: 0.285 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 1e-05 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 2: Gradient evaluation took 1.2e-05 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -487,15 +487,15 @@

Examples

#> Chain 2: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 2: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.191 seconds (Warm-up) -#> Chain 2: 0.105 seconds (Sampling) -#> Chain 2: 0.296 seconds (Total) +#> Chain 2: Elapsed Time: 0.186 seconds (Warm-up) +#> Chain 2: 0.114 seconds (Sampling) +#> Chain 2: 0.3 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 1.3e-05 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds. +#> Chain 3: Gradient evaluation took 1.9e-05 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -512,9 +512,9 @@

Examples

#> Chain 3: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 3: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.183 seconds (Warm-up) -#> Chain 3: 0.162 seconds (Sampling) -#> Chain 3: 0.345 seconds (Total) +#> Chain 3: Elapsed Time: 0.199 seconds (Warm-up) +#> Chain 3: 0.185 seconds (Sampling) +#> Chain 3: 0.384 seconds (Total) #> Chain 3: #> Warning: There were 2 divergent transitions after warmup. See #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup @@ -538,8 +538,8 @@

Examples

#> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.4e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.14 seconds. +#> Chain 1: Gradient evaluation took 1.3e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -556,15 +556,15 @@

Examples

#> Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.118 seconds (Warm-up) -#> Chain 1: 0.139 seconds (Sampling) -#> Chain 1: 0.257 seconds (Total) +#> Chain 1: Elapsed Time: 0.12 seconds (Warm-up) +#> Chain 1: 0.14 seconds (Sampling) +#> Chain 1: 0.26 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 1.3e-05 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds. +#> Chain 2: Gradient evaluation took 1.4e-05 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.14 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -581,15 +581,15 @@

Examples

#> Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 2: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.123 seconds (Warm-up) -#> Chain 2: 0.121 seconds (Sampling) -#> Chain 2: 0.244 seconds (Total) +#> Chain 2: Elapsed Time: 0.124 seconds (Warm-up) +#> Chain 2: 0.127 seconds (Sampling) +#> Chain 2: 0.251 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 1.2e-05 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. +#> Chain 3: Gradient evaluation took 1.9e-05 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -606,9 +606,9 @@

Examples

#> Chain 3: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 3: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.1 seconds (Warm-up) -#> Chain 3: 0.108 seconds (Sampling) -#> Chain 3: 0.208 seconds (Total) +#> Chain 3: Elapsed Time: 0.103 seconds (Warm-up) +#> Chain 3: 0.113 seconds (Sampling) +#> Chain 3: 0.216 seconds (Total) #> Chain 3: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 4). @@ -631,9 +631,9 @@

Examples

#> Chain 4: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 4: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 4: -#> Chain 4: Elapsed Time: 0.12 seconds (Warm-up) -#> Chain 4: 0.133 seconds (Sampling) -#> Chain 4: 0.253 seconds (Total) +#> Chain 4: Elapsed Time: 0.124 seconds (Warm-up) +#> Chain 4: 0.14 seconds (Sampling) +#> Chain 4: 0.264 seconds (Total) #> Chain 4: # fit a model with a lognormal distribution @@ -666,15 +666,15 @@

Examples

#> Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.067 seconds (Warm-up) -#> Chain 1: 0.056 seconds (Sampling) -#> Chain 1: 0.123 seconds (Total) +#> Chain 1: Elapsed Time: 0.07 seconds (Warm-up) +#> Chain 1: 0.057 seconds (Sampling) +#> Chain 1: 0.127 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 1e-05 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 2: Gradient evaluation took 1.2e-05 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -691,15 +691,15 @@

Examples

#> Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 2: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.072 seconds (Warm-up) -#> Chain 2: 0.072 seconds (Sampling) -#> Chain 2: 0.144 seconds (Total) +#> Chain 2: Elapsed Time: 0.073 seconds (Warm-up) +#> Chain 2: 0.073 seconds (Sampling) +#> Chain 2: 0.146 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 1e-05 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 3: Gradient evaluation took 9e-06 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -717,14 +717,14 @@

Examples

#> Chain 3: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 3: #> Chain 3: Elapsed Time: 0.074 seconds (Warm-up) -#> Chain 3: 0.052 seconds (Sampling) -#> Chain 3: 0.126 seconds (Total) +#> Chain 3: 0.054 seconds (Sampling) +#> Chain 3: 0.128 seconds (Total) #> Chain 3: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 4). #> Chain 4: -#> Chain 4: Gradient evaluation took 1e-05 seconds -#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 4: Gradient evaluation took 1.6e-05 seconds +#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.16 seconds. #> Chain 4: Adjust your expectations accordingly! #> Chain 4: #> Chain 4: @@ -741,9 +741,9 @@

Examples

#> Chain 4: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 4: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 4: -#> Chain 4: Elapsed Time: 0.073 seconds (Warm-up) -#> Chain 4: 0.064 seconds (Sampling) -#> Chain 4: 0.137 seconds (Total) +#> Chain 4: Elapsed Time: 0.075 seconds (Warm-up) +#> Chain 4: 0.067 seconds (Sampling) +#> Chain 4: 0.142 seconds (Total) #> Chain 4: # add zeros and fit a delta-gamma distribution @@ -777,15 +777,15 @@

Examples

#> Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.123 seconds (Warm-up) -#> Chain 1: 0.107 seconds (Sampling) -#> Chain 1: 0.23 seconds (Total) +#> Chain 1: Elapsed Time: 0.132 seconds (Warm-up) +#> Chain 1: 0.113 seconds (Sampling) +#> Chain 1: 0.245 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 1.4e-05 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.14 seconds. +#> Chain 2: Gradient evaluation took 1.8e-05 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -802,15 +802,15 @@

Examples

#> Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 2: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.159 seconds (Warm-up) -#> Chain 2: 0.145 seconds (Sampling) -#> Chain 2: 0.304 seconds (Total) +#> Chain 2: Elapsed Time: 0.168 seconds (Warm-up) +#> Chain 2: 0.152 seconds (Sampling) +#> Chain 2: 0.32 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 1.4e-05 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.14 seconds. +#> Chain 3: Gradient evaluation took 1.3e-05 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -827,9 +827,9 @@

Examples

#> Chain 3: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 3: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.143 seconds (Warm-up) -#> Chain 3: 0.122 seconds (Sampling) -#> Chain 3: 0.265 seconds (Total) +#> Chain 3: Elapsed Time: 0.153 seconds (Warm-up) +#> Chain 3: 0.129 seconds (Sampling) +#> Chain 3: 0.282 seconds (Total) #> Chain 3: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 4). @@ -852,9 +852,9 @@

Examples

#> Chain 4: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 4: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 4: -#> Chain 4: Elapsed Time: 0.164 seconds (Warm-up) -#> Chain 4: 0.142 seconds (Sampling) -#> Chain 4: 0.306 seconds (Total) +#> Chain 4: Elapsed Time: 0.172 seconds (Warm-up) +#> Chain 4: 0.133 seconds (Sampling) +#> Chain 4: 0.305 seconds (Total) #> Chain 4: # }
diff --git a/docs/reference/get_expanded.html b/docs/reference/get_expanded.html index 5c1406a..a9203e2 100644 --- a/docs/reference/get_expanded.html +++ b/docs/reference/get_expanded.html @@ -104,8 +104,8 @@

Examples

#> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 9e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. +#> Chain 1: Gradient evaluation took 1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -122,9 +122,9 @@

Examples

#> Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 1: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.015 seconds (Warm-up) +#> Chain 1: Elapsed Time: 0.016 seconds (Warm-up) #> Chain 1: 0.014 seconds (Sampling) -#> Chain 1: 0.029 seconds (Total) +#> Chain 1: 0.03 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). @@ -147,15 +147,15 @@

Examples

#> Chain 2: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 2: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.016 seconds (Warm-up) +#> Chain 2: Elapsed Time: 0.018 seconds (Warm-up) #> Chain 2: 0.013 seconds (Sampling) -#> Chain 2: 0.029 seconds (Total) +#> Chain 2: 0.031 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 8e-06 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 3: Gradient evaluation took 7e-06 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -172,9 +172,9 @@

Examples

#> Chain 3: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 3: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.015 seconds (Warm-up) -#> Chain 3: 0.014 seconds (Sampling) -#> Chain 3: 0.029 seconds (Total) +#> Chain 3: Elapsed Time: 0.023 seconds (Warm-up) +#> Chain 3: 0.015 seconds (Sampling) +#> Chain 3: 0.038 seconds (Total) #> Chain 3: expanded <- get_expanded(fit) # } diff --git a/docs/reference/get_fitted.html b/docs/reference/get_fitted.html index 2a4b080..fa89135 100644 --- a/docs/reference/get_fitted.html +++ b/docs/reference/get_fitted.html @@ -124,15 +124,15 @@

Examples

#> Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 1: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.014 seconds (Warm-up) -#> Chain 1: 0.012 seconds (Sampling) -#> Chain 1: 0.026 seconds (Total) +#> Chain 1: Elapsed Time: 0.016 seconds (Warm-up) +#> Chain 1: 0.016 seconds (Sampling) +#> Chain 1: 0.032 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 8e-06 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 2: Gradient evaluation took 7e-06 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -149,9 +149,9 @@

Examples

#> Chain 2: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 2: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.012 seconds (Warm-up) +#> Chain 2: Elapsed Time: 0.013 seconds (Warm-up) #> Chain 2: 0.013 seconds (Sampling) -#> Chain 2: 0.025 seconds (Total) +#> Chain 2: 0.026 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). diff --git a/docs/reference/get_total.html b/docs/reference/get_total.html index 46b125f..babb0e3 100644 --- a/docs/reference/get_total.html +++ b/docs/reference/get_total.html @@ -123,14 +123,14 @@

Examples

#> Chain 1: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 1: #> Chain 1: Elapsed Time: 0.014 seconds (Warm-up) -#> Chain 1: 0.011 seconds (Sampling) -#> Chain 1: 0.025 seconds (Total) +#> Chain 1: 0.013 seconds (Sampling) +#> Chain 1: 0.027 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 8e-06 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 2: Gradient evaluation took 7e-06 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -147,15 +147,15 @@

Examples

#> Chain 2: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 2: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.014 seconds (Warm-up) +#> Chain 2: Elapsed Time: 0.015 seconds (Warm-up) #> Chain 2: 0.013 seconds (Sampling) -#> Chain 2: 0.027 seconds (Total) +#> Chain 2: 0.028 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 7e-06 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 3: Gradient evaluation took 8e-06 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -173,8 +173,8 @@

Examples

#> Chain 3: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 3: #> Chain 3: Elapsed Time: 0.014 seconds (Warm-up) -#> Chain 3: 0.012 seconds (Sampling) -#> Chain 3: 0.026 seconds (Total) +#> Chain 3: 0.014 seconds (Sampling) +#> Chain 3: 0.028 seconds (Total) #> Chain 3: expanded <- get_total(fit) # } diff --git a/docs/reference/plot_expanded.html b/docs/reference/plot_expanded.html index dcc4ebf..8bc03f2 100644 --- a/docs/reference/plot_expanded.html +++ b/docs/reference/plot_expanded.html @@ -126,8 +126,8 @@

Examples

#> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 9e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -144,15 +144,15 @@

Examples

#> Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 1: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.014 seconds (Warm-up) -#> Chain 1: 0.012 seconds (Sampling) -#> Chain 1: 0.026 seconds (Total) +#> Chain 1: Elapsed Time: 0.015 seconds (Warm-up) +#> Chain 1: 0.013 seconds (Sampling) +#> Chain 1: 0.028 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 8e-06 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 2: Gradient evaluation took 7e-06 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -169,15 +169,15 @@

Examples

#> Chain 2: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 2: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.013 seconds (Warm-up) -#> Chain 2: 0.011 seconds (Sampling) -#> Chain 2: 0.024 seconds (Total) +#> Chain 2: Elapsed Time: 0.014 seconds (Warm-up) +#> Chain 2: 0.012 seconds (Sampling) +#> Chain 2: 0.026 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 8e-06 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 3: Gradient evaluation took 9e-06 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -194,9 +194,9 @@

Examples

#> Chain 3: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 3: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.015 seconds (Warm-up) -#> Chain 3: 0.01 seconds (Sampling) -#> Chain 3: 0.025 seconds (Total) +#> Chain 3: Elapsed Time: 0.014 seconds (Warm-up) +#> Chain 3: 0.012 seconds (Sampling) +#> Chain 3: 0.026 seconds (Total) #> Chain 3: plot_expanded( fitted_model = fit, diff --git a/docs/reference/plot_fitted.html b/docs/reference/plot_fitted.html index 6d463c2..fdf6280 100644 --- a/docs/reference/plot_fitted.html +++ b/docs/reference/plot_fitted.html @@ -142,15 +142,15 @@

Examples

#> Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 1: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.013 seconds (Warm-up) -#> Chain 1: 0.012 seconds (Sampling) -#> Chain 1: 0.025 seconds (Total) +#> Chain 1: Elapsed Time: 0.014 seconds (Warm-up) +#> Chain 1: 0.015 seconds (Sampling) +#> Chain 1: 0.029 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 8e-06 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 2: Gradient evaluation took 7e-06 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -167,15 +167,15 @@

Examples

#> Chain 2: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 2: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.013 seconds (Warm-up) -#> Chain 2: 0.012 seconds (Sampling) -#> Chain 2: 0.025 seconds (Total) +#> Chain 2: Elapsed Time: 0.014 seconds (Warm-up) +#> Chain 2: 0.013 seconds (Sampling) +#> Chain 2: 0.027 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 7e-06 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 3: Gradient evaluation took 8e-06 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -192,8 +192,8 @@

Examples

#> Chain 3: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 3: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.014 seconds (Warm-up) -#> Chain 3: 0.013 seconds (Sampling) +#> Chain 3: Elapsed Time: 0.013 seconds (Warm-up) +#> Chain 3: 0.014 seconds (Sampling) #> Chain 3: 0.027 seconds (Total) #> Chain 3: plot_fitted(fit, @@ -212,8 +212,8 @@

Examples

#> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. +#> Chain 1: Gradient evaluation took 1.3e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -230,9 +230,9 @@

Examples

#> Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.115 seconds (Warm-up) -#> Chain 1: 0.087 seconds (Sampling) -#> Chain 1: 0.202 seconds (Total) +#> Chain 1: Elapsed Time: 0.154 seconds (Warm-up) +#> Chain 1: 0.09 seconds (Sampling) +#> Chain 1: 0.244 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). @@ -255,15 +255,15 @@

Examples

#> Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 2: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.116 seconds (Warm-up) -#> Chain 2: 0.08 seconds (Sampling) -#> Chain 2: 0.196 seconds (Total) +#> Chain 2: Elapsed Time: 0.112 seconds (Warm-up) +#> Chain 2: 0.083 seconds (Sampling) +#> Chain 2: 0.195 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 1.2e-05 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. +#> Chain 3: Gradient evaluation took 1e-05 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -280,15 +280,15 @@

Examples

#> Chain 3: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 3: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.114 seconds (Warm-up) +#> Chain 3: Elapsed Time: 0.11 seconds (Warm-up) #> Chain 3: 0.094 seconds (Sampling) -#> Chain 3: 0.208 seconds (Total) +#> Chain 3: 0.204 seconds (Total) #> Chain 3: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 4). #> Chain 4: -#> Chain 4: Gradient evaluation took 1.1e-05 seconds -#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 4: Gradient evaluation took 1.3e-05 seconds +#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds. #> Chain 4: Adjust your expectations accordingly! #> Chain 4: #> Chain 4: @@ -305,9 +305,9 @@

Examples

#> Chain 4: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 4: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 4: -#> Chain 4: Elapsed Time: 0.1 seconds (Warm-up) -#> Chain 4: 0.09 seconds (Sampling) -#> Chain 4: 0.19 seconds (Total) +#> Chain 4: Elapsed Time: 0.138 seconds (Warm-up) +#> Chain 4: 0.091 seconds (Sampling) +#> Chain 4: 0.229 seconds (Total) #> Chain 4: #> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. #> Running the chains for more iterations may help. See @@ -339,15 +339,15 @@

Examples

#> Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 1: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.172 seconds (Warm-up) -#> Chain 1: 0.147 seconds (Sampling) -#> Chain 1: 0.319 seconds (Total) +#> Chain 1: Elapsed Time: 0.187 seconds (Warm-up) +#> Chain 1: 0.166 seconds (Sampling) +#> Chain 1: 0.353 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 1.1e-05 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 2: Gradient evaluation took 1e-05 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -364,15 +364,15 @@

Examples

#> Chain 2: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 2: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.296 seconds (Warm-up) -#> Chain 2: 0.238 seconds (Sampling) -#> Chain 2: 0.534 seconds (Total) +#> Chain 2: Elapsed Time: 0.319 seconds (Warm-up) +#> Chain 2: 0.257 seconds (Sampling) +#> Chain 2: 0.576 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). #> Chain 3: -#> Chain 3: Gradient evaluation took 1.8e-05 seconds -#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds. +#> Chain 3: Gradient evaluation took 1.2e-05 seconds +#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. #> Chain 3: Adjust your expectations accordingly! #> Chain 3: #> Chain 3: @@ -389,9 +389,9 @@

Examples

#> Chain 3: Iteration: 900 / 1000 [ 90%] (Sampling) #> Chain 3: Iteration: 1000 / 1000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.203 seconds (Warm-up) -#> Chain 3: 0.175 seconds (Sampling) -#> Chain 3: 0.378 seconds (Total) +#> Chain 3: Elapsed Time: 0.21 seconds (Warm-up) +#> Chain 3: 0.182 seconds (Sampling) +#> Chain 3: 0.392 seconds (Total) #> Chain 3: #> Warning: There were 4 divergent transitions after warmup. See #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup @@ -420,8 +420,8 @@

Examples

#> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. +#> Chain 1: Gradient evaluation took 1.3e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -438,15 +438,15 @@

Examples

#> Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.087 seconds (Warm-up) -#> Chain 1: 0.084 seconds (Sampling) -#> Chain 1: 0.171 seconds (Total) +#> Chain 1: Elapsed Time: 0.09 seconds (Warm-up) +#> Chain 1: 0.085 seconds (Sampling) +#> Chain 1: 0.175 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 1.2e-05 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. +#> Chain 2: Gradient evaluation took 1e-05 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -463,9 +463,9 @@

Examples

#> Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 2: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.128 seconds (Warm-up) -#> Chain 2: 0.106 seconds (Sampling) -#> Chain 2: 0.234 seconds (Total) +#> Chain 2: Elapsed Time: 0.132 seconds (Warm-up) +#> Chain 2: 0.116 seconds (Sampling) +#> Chain 2: 0.248 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 3). @@ -488,15 +488,15 @@

Examples

#> Chain 3: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 3: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 3: -#> Chain 3: Elapsed Time: 0.094 seconds (Warm-up) -#> Chain 3: 0.077 seconds (Sampling) -#> Chain 3: 0.171 seconds (Total) +#> Chain 3: Elapsed Time: 0.095 seconds (Warm-up) +#> Chain 3: 0.081 seconds (Sampling) +#> Chain 3: 0.176 seconds (Total) #> Chain 3: #> #> SAMPLING FOR MODEL 'bycatch' NOW (CHAIN 4). #> Chain 4: -#> Chain 4: Gradient evaluation took 1.1e-05 seconds -#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 4: Gradient evaluation took 1e-05 seconds +#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 4: Adjust your expectations accordingly! #> Chain 4: #> Chain 4: @@ -513,9 +513,9 @@

Examples

#> Chain 4: Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 4: Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 4: -#> Chain 4: Elapsed Time: 0.102 seconds (Warm-up) -#> Chain 4: 0.084 seconds (Sampling) -#> Chain 4: 0.186 seconds (Total) +#> Chain 4: Elapsed Time: 0.104 seconds (Warm-up) +#> Chain 4: 0.089 seconds (Sampling) +#> Chain 4: 0.193 seconds (Total) #> Chain 4: # }
diff --git a/src/bycatch.so b/src/bycatch.so index 3802c3de8e73b060fdc78f528b1ee78932475258..ade4702c74960a2be637396fe4279f1043e51669 100755 GIT binary patch delta 143 zcmWN=ISztQ07cQ@7v~8_5d97~TdD<(2@UJAxQQ(ru`{7EaUU$gE%;7yvhT~u^npVO zLm8I}Rch2}(45oQdhdx TNH@CGo$mFZM?K|5dcFmJvClL6 delta 143 zcmWN=w++HT0ESVS!{i)o3`Y(J^$p<0b5VQ}t*4-)Lvn@09^Qfp_@DIh?<>glPCx}i zm5>^B8Z>FqrbCw=eFh8}F=oP)8FM0H79=cLy=|15r}IUU+D~YH&Oge`>RLCt)t&D3 RphrFFSug7JT9nz%$A7^jG)Vve