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rcs

Regional curve standardization developed for Tree Nob geoduck

https://github.com/daveedge1/rcs

Science Score: 44.0%

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    Found CITATION.cff file
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    Low similarity (13.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Regional curve standardization developed for Tree Nob geoduck

Basic Info
  • Host: GitHub
  • Owner: DaveEdge1
  • Language: R
  • Default Branch: main
  • Size: 1 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created 11 months ago · Last pushed 8 months ago
Metadata Files
Readme Citation

README.md

RCS

This code was developed to perform regional curve standardization on geoduck (Panopea generosa)

Features

  • Build a custom regional curve based on the rwl and po (pith offset) files
  • RCS detrending

Requirements

R, the language, is availalble from CRAN. R Studio is an IDE that will work using R and make your workflow much easier.

R

https://cran.r-project.org

R Studio

https://www.rstudio.com

Installation

Create a new project in R Studio and start with a fresh workspace:

Workspace

Install remotes in the console window:

install.packages("remotes")

Use remotes to install the RCS package from github:

remotes::install_github("DaveEdge1/RCS")

Load the RCS package:

library(RCS)

And that's it! You have successfully installed RCS and are ready to start working.

Core functions

robustRC()

Purpose: Created a regional curve by 1) estimating the average ontogenetic growth and 2) fitting a curve to the average values. Curve fitting is by dplR methods or a custom age-varying spline method, tvSpline().

Parameters:

rwlFile

ring width file as created by read.rwl in dplR

poFile

two-column file created by dplR

truncRC

limit curve calculation to regions of a designated minimum sample depth

tvSpline

TRUE/FALSE, use an age-varying spline (recommended fit method, dMethod must be set to NULL)

tvRange

min and max spline lengths in nyrs (if using tvSpline), eg. c(3,80)

tvStiff

set the age at which the spline length will max out (if using tvSpline)

Returns:

RC

regional curve by age

rcInfo

additional details from RC creation

AgeAligned

the growth increment series aligned by ontogenetic age

plot

visualization of RC creation

newRCS()

Purpose: Detrend the growth increment series using the custom RC created from robustRC

Parameters:

rwlFile

ring width file as created by read.rwl in dplR

poFile

two-column file created by dplR

truncRC

limit curve calculation to regions of a designated minimum sample depth

ratios

T/F, detrend by division

rcIn

custom regional curve, the RC output from robustRC()

ageMin

minimum ontogentic age of samples for inclusion in chronology

ageMax

maximum ontogentic age of samples for inclusion in chronology

If you use this code, please cite the original publication using the GitHub "cite this repository" feature in the right-hand margin.

Owner

  • Name: Dave Edge
  • Login: DaveEdge1
  • Kind: user
  • Company: Northern Arizona University

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this dataset or code, please cite the following article:"
authors:
  - family-names: Edge
    given-names: David C
  - family-names: Reynolds
    given-names: David J
  - family-names: Wanamaker
    given-names: Alan D
  - family-names: Griffin
    given-names: Daniel
  - family-names: Bureau
    given-names: Dominique
  - family-names: Outridge
    given-names: Christine
  - family-names: Stevick
    given-names: Bethany C
  - family-names: Weng
    given-names: Richard
  - family-names: Black
    given-names: Bryan A
title: >
  A multicentennial proxy record of Northeast Pacific sea surface
  temperatures from the annual growth increments of Panopea generosa
version: 1.0.0
date-released: 2021-09-01
doi: 10.1029/2021PA004291
type: peer_reviewed_article
journal: Paleoceanography and Paleoclimatology
volume: 36
issue: 9
pages: e2021PA004291
publisher: Wiley Online Library

GitHub Events

Total
  • Push event: 9
  • Create event: 2
Last Year
  • Push event: 9
  • Create event: 2

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 9
  • Total Committers: 1
  • Avg Commits per committer: 9.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 9
  • Committers: 1
  • Avg Commits per committer: 9.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Dave Edge 1****1 9

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Last synced: 9 months ago

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Past Year
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Dependencies

DESCRIPTION cran
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