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Merged

NiklasHohmann merged 6 commits into dev from main

May 21, 2025

CITATION.cff

            
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    @@ -15,7 +15,7 @@ authors:
  
        affiliation: Utrecht University

    identifiers:

      - type: doi

        value: 10.5281/zenodo.15279284

        value: 10.5281/zenodo.15479049

        description: Archived version on Zenodo

    repository-code: 'https://github.com/MindTheGap-ERC/admtools'

    url: 'https://mindthegap-erc.github.io/admtools/'

    @@ -28,5 +28,5 @@ keywords:
  
      - Stratigraphy

      - Sedimentology

    license: GPL-3.0

    version: 0.5.0

    date-released: '2025-04-24'

    version: 0.6.0

    date-released: '2025-05-20'

DESCRIPTION

            
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    @@ -1,6 +1,6 @@
  
    Package: admtools

    Title: Estimate and Manipulate Age-Depth Models

    Version: 0.5.0.9000

    Version: 0.6.0.9000

    Authors@R: 

        person("Niklas", "Hohmann", , "N.H.Hohmann@uu.nl", role = c("aut", "cre"),

               comment = c(ORCID = "0000-0003-1559-1838"))

    @@ -14,7 +14,7 @@ Encoding: UTF-8
  
    Roxygen: list(markdown = TRUE)

    RoxygenNote: 7.3.2

    Depends: 

        R (>= 2.10),

        R (>= 4.2),

    Imports:

        ape

    LazyData: true

NAMESPACE

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@@ Expand Up / @@ -68,6 +68,9 @@ S3method(plot,timelist) @@
     S3method(print,adm)
     S3method(print,multiadm)
     S3method(print,sac)
+    S3method(rev_dir,default)
+    S3method(rev_dir,fossils)
+    S3method(rev_dir,taxonomy)
     S3method(sed_rate_l,adm)
     S3method(sed_rate_l,multiadm)
     S3method(sed_rate_t,adm)
@@ Expand Down Expand Up / @@ -148,6 +151,7 @@ export(plot_erosive_intervals) @@
     export(plot_sed_rate_l)
     export(plot_sed_rate_t)
     export(quantile_adm)
+    export(rev_dir)
     export(sac_to_adm)
     export(sed_rate_from_matrix)
     export(sed_rate_gen_from_bounds)
@@ Expand Down @@

NEWS.md

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@@ -1,5 +1,11 @@
     # admtools (development version)
+    # admtools 0.6.0
+    * transformation between age and time for integration with `FossilSim`
+    * vignette for connection between `admtools` and `FossilSim`
     # admtools 0.5.0
     * new helper functions for estimation of age-depth models
@@ Expand Down @@

R/rev_dir.R

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+    rev_dir = function(x, ref){
+      #' @export
+      #'
+      #' @title reverse direction of time/depth axis
+      #'
+      #' @param x object to transform - typically a `fossil` or `taxonomy` object
+      #' @param ref reference point used for reversal
+      #'
+      #' @description
+        #' The `FossilSim` package simulates fossils, trees, and taxonomies using age
+        #' meaning 0 represents the present and larger numbers indicate older ages
+        #' To interact with `admtools`, the direction of time must be reversed
+        #' effectively replaces the time component `t` of an object by `ref - t`
+        #'
+      #' @examples
+        #' \dontrun{
+        #'   # for usage example, see
+        #'   vignette("FossilSim_integration")
+        #' }
+        #'
+        #'
+      UseMethod("rev_dir")
+    }
+    rev_dir.default = function(x, ref){
+      #' @export
+      .NotYetImplemented()
+    }
+    rev_dir.fossils = function(x, ref){
+      #' @export
+      #'
+      hmin = ref - x$hmin
+      hmax = ref - x$hmax
+      x$hmin = hmin
+      x$hmax = hmax
+      return(x)
+    }
+    rev_dir.taxonomy = function(x, ref){
+      #' @export
+      start1 = ref - x$start
+      end1 = ref - x$end
+      x$start = start1
+      x$end = end1
+      return(x)
+    }

README.md

            
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    @@ -6,7 +6,7 @@ R package to estimate age-depth models from stratigraphic and sedimentological d
  
      [![R-CMD-check](https://github.com/MindTheGap-ERC/admtools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/MindTheGap-ERC/admtools/actions/workflows/R-CMD-check.yaml)

    [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu)

      [![](https://www.r-pkg.org/badges/version/admtools?color=pink)](https://cran.r-project.org/package=admtools)

    [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13888709.svg)](https://doi.org/10.5281/zenodo.13888709)

    [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15479049.svg)](https://doi.org/10.5281/zenodo.15479049)

      <!-- badges: end -->

    ## Authors

    @@ -85,7 +85,7 @@ For contribution guidelines see the CONTRIBUTING.md file
  
    To cite the package, use

    * Hohmann, N. (2025). admtools (v0.5.0). Zenodo. https://doi.org/10.5281/zenodo.15279284

    * Hohmann, N. (2025). admtools (v0.6.0). Zenodo. https://doi.org/10.5281/zenodo.15479049

    or run

inst/CITATION

            
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    @@ -3,8 +3,8 @@ bibentry(
  
      title    = "admtools: R package for estimating age-depth models and transform data",

      author   = "Niklas Hohmann",

      year     = "2024",

      doi      ="10.5281/zenodo.15279284",

      doi      ="10.5281/zenodo.15479049",

      publisher = "Zenodo",

      version = "v0.5.0",

      url = "https://doi.org/10.5281/zenodo.15279284"

      version = "v0.6.0",

      url = "https://doi.org/10.5281/zenodo.15479049"

    )

man/rev_dir.Rd

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

tests/testthat/test_rev_dir.R

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@@ -0,0 +1,9 @@
+    test_that("double transformation returns original object",{
+      t = ape::rbdtree(birth = 3, death = 1, Tmax = 2)
+      # simulate taxonomy along the tree
+      s = FossilSim::sim.taxonomy(tree = t)
+      # simulate fossils based on taxonomy
+      f = FossilSim::sim.fossils.poisson(rate = 4, taxonomy = s)
+      expect_identical(f, f |> rev_dir( ref = 0) |> rev_dir( ref = 0))
+      expect_identical(s, s |> rev_dir( ref = 0) |> rev_dir( ref = 0))
+    })

vignettes/FossilSim_integration.Rmd

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@@ Expand Up @@
     ## Integration with the `FossilSim` package
-    `admtools` can transform phylogenetic trees coded as `phylo` objects as well as `fossils` and `taxonomy` objects as defined by the `FossilSim` package. This allows to transform phylogenetic trees with their associated taxonomic information and fossil locations between the time and the stratigraphic domain. We give an example of this workflow
+    `admtools` can transform phylogenetic trees coded as `phylo` objects as well as `fossils` and `taxonomy` objects as defined by the `FossilSim` package. This allows to transform phylogenetic trees with their associated taxonomic information and fossil locations between the time and the stratigraphic domain.
+    In contrast to `admtools`, `FossilSim` uses age (time before the present) instead of time. To successfully transform data generated by `FossilSim`, this must be reversed using `rev_dir`.
+    We give an example of this workflow
     ```{r}
     set.seed(42)
@@ Expand All / @@ -41,12 +45,25 @@ f = FossilSim::sim.fossils.poisson(rate = 4, taxonomy = s) @@
     FossilSim:::plot.fossils(f, tree = t, taxonomy = s, show.taxonomy = TRUE)
     ## transform everything into the strat domain
-    t_strat = time_to_strat(t, my_adm)
-    s_strat = time_to_strat(s, my_adm, destructive = FALSE)
-    f_strat = time_to_strat(f, my_adm, destructive = FALSE)
+    t_strat = time_to_strat(t, my_adm) # no transformation of time to age required
+    s_strat = s |>  # taxonomy object in the time domain
+      rev_dir(ref = max_time(my_adm)) |> # convert age to time
+      time_to_strat( my_adm, destructive = FALSE) |> # transform using age-depth model
+      rev_dir(ref = max_height(my_adm)) # transform back into age
+    f_strat =  f |> # same here
+      rev_dir(ref = max_time(my_adm)) |>
+      time_to_strat( my_adm, destructive = TRUE)|> # destroy fossils coinciding with gaps
+      rev_dir(ref = max_height(my_adm))
     FossilSim:::plot.fossils(f_strat, tree = t_strat, taxonomy = s_strat, show.taxonomy = TRUE)
     ```
+    Important point are
+    -   `rev_dir` must be applied directly after data was generated and and directly before the data is further processed using `FossilSim`. As a principle, use `rev_dir` before data from FossilSim enters the `admtools` and `StratPal` ecosystem, and as it leaves the ecosystem.
+    -   By default, `FossilSim` plots have axis labels "Time before present", although the trees after the transformation can be trees in the stratigraphic domain. Because of this fixed reference point used, 0 in the above plot represents the uppermost height of the section, the axis units are lengths and not times, and the "Age" is stratigraphic position below the top of the section.
     ## Integration with `paleotree`
     To combine the `admtools` package with the `paleotree` package, please convert the `paleotree` format into the `FossilSim` format as described in the `paleotree` vignette of the `FossilSim` vignette:
@@ Expand All @@
     ## References
-    *  Barido-Sottani J, Pett W, O'Reilly JE, Warnock RCM. Fossilsim: An r package for simulating fossil occurrence data under mechanistic models of preservation and recovery. Methods Ecol Evol. 2019; 10: 835–840. <https://doi.org/10.1111/2041-210X.13170>
-    *  Bapst, D.W. (2012), paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology and Evolution, 3: 803-807. <https://doi.org/10.1111/j.2041-210X.2012.00223.x>
-    *  Warnock R, Barido-Sottani J, Pett W, Joseph O, Stolz U (2024). _FossilSim: Simulation and Plots for Fossil and Taxonomy Data_. R package version 2.4.1,
-      <https://CRAN.R-project.org/package=FossilSim>
+    -   Barido-Sottani J, Pett W, O'Reilly JE, Warnock RCM. Fossilsim: An r package for simulating fossil occurrence data under mechanistic models of preservation and recovery. Methods Ecol Evol. 2019; 10: 835--840. <https://doi.org/10.1111/2041-210X.13170>
+    -   Bapst, D.W. (2012), paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology and Evolution, 3: 803-807. <https://doi.org/10.1111/j.2041-210X.2012.00223.x>
+    -   Warnock R, Barido-Sottani J, Pett W, Joseph O, Stolz U (2024). *FossilSim: Simulation and Plots for Fossil and Taxonomy Data*. R package version 2.4.1, <https://CRAN.R-project.org/package=FossilSim>

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