StratPal
Stratigraphic Paleobiology Modeling Pipelines
Description
The fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382). This package allowing to simulate biological processes in the time domain (e.g., trait evolution, fossil abundance, phylogenetic trees), and examine how their expression in the rock record (stratigraphic domain) is influenced based on age-depth models, ecological niche models, and taphonomic effects. Functions simulating common processes used in modeling trait evolution, biostratigraphy or event type data such as first/last occurrences are provided and can be used standalone or as part of a pipeline. The package comes with example data sets and tutorials in several vignettes, which can be used as a template to set up one's own simulation.
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|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
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| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
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Check details (1 non-OK)
tests
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # 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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(StratPal)
>
> test_check("StratPal")
Saving _problems/test_apply_taphonomy-50.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_apply_taphonomy.R:50:3'): warning is thrown with fossil age uncertainty ──
Expected `apply_taphonomy(f, pres_potential, ctc)` to throw a warning.
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
Error:
! Test failures.
Execution halted
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 6, 2026
tests
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Wh
...[truncated]...
ure ('test_apply_taphonomy.R:50:3'): warning is thrown with fossil age uncertainty ──
Expected `apply_taphonomy(f, pres_potential, ctc)` to throw a warning.
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
Error:
! Test failures.
Execution halted
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 3, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 2, 2026
tests
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Wh
...[truncated]...
ure ('test_apply_taphonomy.R:50:3'): warning is thrown with fossil age uncertainty ──
Expected `apply_taphonomy(f, pres_potential, ctc)` to throw a warning.
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
Error:
! Test failures.
Execution halted
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 28, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 27, 2026
tests
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Wh
...[truncated]...
════════════
── Failure ('test_apply_niche.R:39:3'): warning is thrown for age uncertainty ──
Expected `apply_niche(f, niche_def, gc)` to throw a warning.
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
Error:
! Test failures.
Execution halted