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Code for "Identification of the Mode of Evolution in Incomplete Carbonate Successions"

License: Apache License 2.0

R 100.00%

aic biological-simulations biology earth-science evolution fossils geoscience geosciences sedimentology stratigraphy

carbonatestratpalevo's Introduction

CarboStratPalEvo

Supplementary code for "Identification of the mode of evolution in incomplete carbonate successions", DOI: 10.1101/2023.12.18.572098.

Authors

Niklas Hohmann
Utrecht University
email: n.h.hohmann [at] uu.nl
Web page: www.uu.nl/staff/NHohmann
ORCID: 0000-0003-1559-1838

Jan Roel Koelewijn
Utrecht University
ORCID: 0000-0002-4668-3797

Emilia Jarochowska
Utrecht University
email: e.b.jarochowska [at] uu.nl
Web page: www.uu.nl/staff/EBJarochowska
ORCID: 0000-0001-8937-9405

Software requirements

R and the Rstudio IDE.
Matlab is necessary tu fully reproduce the study from scratch. However, all data generated by Matlab can also be downloaded from a repository when only the part simulating and testing the mode of evolution is reproduced, which can be done fully in R Software.

Usage

Open the Rproject file "CarbonateStratPalEvo.Rproj" in Rstudio. This will bootstrap the renv package if it is not installed yet. Next, run

renv::restore()

This will install all required packages and their dependencies needed in the project. Last, download all required data from OSF by running the following in R:

source("code/utils.R")
get_data_from_osf(link = "https://osf.io/zbpwa/")

See REPRODUCEME file for more info on running code and examining data.

Repository Structure

.gitignore : Untracked files
.Rprofile : R project settings
CarbonateStratPalEvo.Rproj : Rstudio project file
LICENSE : Apache 2.0 license text
README.md : Readme file
renv.lock : lock file from renv
REPRODUCEME.md : Instructions for repetition of the study
code : Folder with main code
make_plots.R : generate plots
- parameters_for_tests.R : define test & simulation settings
- process_adm_from_matlab.R : extreact adm from Matlab data & determine hiatuses & completeness
- simulate_and_test_modes_of_evolution.R : perform simulations & tests
- utils : utility functions to simulate trait evolution in time & strat domain, determine sample ages, completeness , etc.
- visualize_data : Visualize downloadable data
data : Folder for data. After downloading data, it contains the following files:
- matlab_outputs : Folder with raw data generated by CarboCATLite in Matlab
  - scenarioA_glob_matlab_outputs.mat : raw data of scenario A
  - scenarioB_glob_matlab_outputs.mat : raw data of scenario B
  - scenarioA_and_B_matlab_to_R.m : function to extract ADMs from CarboCATLite outputs
  - get_adm_from_carbocat_outputs.m : ADMs from CarboCATLite for import in R
  - codebook.md : Describes contents of .mat files in this folder
  - figs : folder with figures from CarboCAT Lite
- R_outputs : Folder with data generated by R
  - ageDepthModelsScenariosAandB.Rdata : ADMs, completeness, & hiatus durations from scenario A and B
  - parameters_for_tests.Rdata : test & simulation settings
  - results_modes_of_evolution.Rdata : test and simulation results
  - codebook.md : Describes contents of .Rdata files in this folder
figs : Folder with figures
- R : figures generated by /code/make_plots.R
renv : Folder generated by renv package

Copyright

Citation

To cite this repository, please use

Hohmann, N., Koelewijn, J. R., Burgess, P., & Jarochowska, E. (2023). Supplementary code for "Identification of the Mode of Evolution in Incomplete Carbonate Successions" (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.10390267

License

The code is licensed under the Apache 2.0 License, see LICENSE file for full license text.

This data is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original authors and the source, provide a link to the Creative Commons license, and indicate if changes were made. If your intended use exceeds the permitted use, you will need to obtain permission directly from the authors. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Funding information

Funded by the European Union (ERC, MindTheGap, StG project no 101041077). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.

carbonatestratpalevo's People

Contributors

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carbonatestratpalevo's Issues

Add labels (2 km, 4 km etc) in the code generating Fig. 5

Adjust Figures

Name figures according to their name in the manuscript _raw (e.g. Fig1_raw.pdf, FigS2_raw.pdf)
Redo Figs. 4-7. Specifically 6 & 7 based on new data
Adjust figure size to Journal requirements (https://bmcecolevol.biomedcentral.com/submission-guidelines/preparing-your-manuscript#preparing+figures)
Reduce temporal resolution for plots of trait evo in time domain, (maybe 200 sampling points, distributed over the 2 / 2.56 Myr)
Check if for stasis, figures become more clear with only one lineage. If yes, plot only one lineage for stasis
Make axis labels smaller & titles larger
Rearrange order of subfigures in Fig. 5 & similar figures (ADM & time domain 1st row, dist. from shore in 2nd & 3rd row) - Maybe there is a better/more aesthetic arrangement?
Automate labeling of subfigures (A, B, C, ...)

Make plot of strat completeness & hiatus duration

Make a fists sketch of the figure with stratigraphic completeness and hiatus duration vs. basin position.
Make one plot for each scenario, name it scenarioX_strat_info.pdf
The plot should contain:

x axis: ranging from 0.1 to 15, distance from shore [km]
left y axis: stratigraphic completeness as percent
right y axis: hiatus duration in myr. Start with plotting median, max, and 1st and 3rd quartile of the hiatus distribution. Use a log scale if if necessary

Make figure of time elapsed between successive samples

Make a figure with 2 rows (one for each scenario) and 5 rows (one for each distance from shore)
Each subfigure is a histogram of the time elapsed between successive samples taken in the stratigraphic domain. The y axis is number (dimensionless), the x axis is time difference (myr). Make sure the x axis limits are the same for each subplot and start at 0

Figure of spatial variability in preservation

Make figure displaying spatial variability in preservation. Use strong Brownian drift in scenario A

Data extraction for figures

Implement functions get_AIC_scenario, get_AIC_time, and get_AIC_no_of_sampl_loc in code/make_plots.R

Make figure comparing preservation under comparable completenesses

Figure should compare preservation of strong Brownian drift 2 km offshore in scenario A (left) vs 6 km offshore in scenario B (right). Both locations have comparable completeness, but scenario A has longer gaps

Beautify figure completeness_and_hiat_duration_raw.pdf

Reduce whitespace at the bottom
x axis labels consistent "Distance from shore [km]"
left y axis labels "Stratigraphic completeness [%]"
right y axis labels "Hiatus duration [Myr]"
Change header to "scenario X"
Make letter same size as header
cut off x axis at 13 km
Add legend to top left corner, listing
- Completeness
- maximum hiatus dur.
- 1st quartile hiatus dur.
- Median hiatus dur.
- 3rd quartile hiatus dur.

Add AIC treshold to figures

Add dashed line to figures 4,5,and 6 at AIC = 0.9 to indicate good model fit

Write author contribution statement

Start sketching the author contribution statement in the manuscript. Have a look at https://www.elsevier.com/authors/policies-and-guidelines/credit-author-statement and the guidelines by the journal: https://www.biomedcentral.com/getpublished/editorial-policies#authorship

Deposit raw data on OSF

When ms is in final stage

Deposit large data files on osf, specifically .mat, .Rdata files
Add code to automate data download

Minor Adjustments Figures

Make capitalization consistent (Trait value -> Trait Value, Time domain -> Time Domain etc.)
Make axis labels consistent (e.g. in fig. 4 parts are "Stratigraphic Height [m]", others just "Height [m]")
Reduce font size of titles to avoid cut-off of titles (e.g. fig. 4 bottom right)
Shift letters indicating sub-plots a bit to the right to reduce ambiguity
fig 6 & related figures:
- move km from ticks labels to axis labels
- reduce line width on box plots
- make y axis consistent from 0 to 1
- move legend out of plot windows on the right
- adjust capitalization of titles

Redo figures 1 & 2 based on captions in manuscript. Raw figures are on GH under figs/matlab

Beautify figure equal_completeness_comparison.pdf

x axis lablel "Stratigraphic height [m]"
y axis label "Trait value"
reduce whitespace at bottom
Letter same size as title
correct whitespace in title