Data

Tools

Indexes

Applications

Experiments

Open Source Science

clumpedcalib

Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping

https://github.com/japhir/clumpedcalib

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.8%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping

Basic Info
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

clumpedcalib: Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping

Written by Ilja J. Kocken Feel free to use this stuff, as long as you adhere to the file:LICENSE.md

NOTE: This is just the method I use, I'm not publishing the actual calibration dataset that I'm using here!

  • Calculate bootstrapped York regression from clumped isotope calibration data. clumpedcalibboot().
  • Calculate bootstrapped sample means for the age, d13C, d18O, and D47. bootstrap_means().
  • Apply the bootstrapped calibration to calculate temperature and d18Osw. tempd18Oswcalc().
  • Summarize bootstrapped values and calculate 68 and 95% CIs. our_summary().
  • Also comes with the classic d18Occ calibrations. See temp_calc().
  • As well as the inverses, for when you have constraints on temperature and wish to calculate d18Osw. See d18Osw_calc().

How to calculate bootstrapped averages and apply a clumped-isotope specific temperature calibration.

To use this:

  1. Install this package clumpedcalib, see #installation.
  2. Update the input calibration data file:dat/example_calib.csv. Make sure the column names include X, D47, sd_X, sd_D47.
  3. Add your sample data at the replicate level.
  4. Check to see if you like the function that calculates d18Osw. Currently, it defaults to the Kim & O\'Neil 1997 calibration, as adjusted by Bemis et al., 1998.
  5. If you want to use the wrapper function: create your own definition of filter outliers so that it filters out bad measurements and NA\'s for your data.
  6. Use the wrapper function to do it all at once applycalibandd18Oboot(), or better yet:
  7. Walk through the example workflow step-by-step or apply the bulletpoint functions from above one-by-one.
  8. Have a look at the functions to better understand what's happening.

The bootstrapped calibration idea is based on a Matlab script written by Alvaro Fernandez.

installation

To install this development package:

{R} remotes::install_github("japhir/clumpedcalib")

Or you can look at all the functions and only copy what you like.

Owner

  • Name: Ilja Kocken
  • Login: japhir
  • Kind: user
  • Location: The Netherlands
  • Company: @UtrechtUniversity

PhD Candidate in Palaeoclimate | Data Steward for Earth Sciences

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  clumpedcalib: Calculate and apply clumped isotope calibrations using bootstrapping
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Ilja Japhir
    family-names: Kocken
    email: i.j.kocken@uu.nl
    affiliation: Utrecht University
    orcid: 'https://orcid.org/0000-0003-2196-8718'
identifiers:
  - type: doi
    value: 10.5281/zenodo.8148780
    description: Zenodo
repository-code: 'https://github.com/japhir/clumpedcalib'
repository: 'https://zenodo.org/record/8148780'
abstract: >-
  This document describes how to calculate bootstrapped averages and apply a clumped-isotope specific temperature calibration.
  - Calculate bootstrapped York regression from clumped isotope calibration data.
  - Calculate bootstrapped sample means for the age, d13C, d18O, and D47.
  - Apply the bootstrapped calibration to calculate temperature and d18Osw.
keywords:
  - clumped
  - isotope
  - clumped isotopes
  - bootstrapping
  - calibration
license: GPL-3.0-or-later

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • bfsl * imports
  • boot * imports
  • cli * imports
  • dplyr * imports
  • ggdist * imports
  • glue * imports
  • infer * imports
  • purrr * imports
  • readr * imports
  • stats * imports
  • tibble * imports
  • tidylog * imports
  • tidyr * imports
  • testthat >= 3.0.0 suggests