Package: bayclumpr 0.1.2

Cristian Roman Palacios

bayclumpr: Bayesian Analysis of Clumped Isotope Datasets

Simulating synthetic clumped isotope dataset, fitting linear regression models under Bayesian and non-Bayesian frameworks, and generating temperature reconstructions for the same two approaches.

Authors:Cristian Roman Palacios [aut, cre], Hannah M. Carroll [aut], Aradhna Tripati [aut]

bayclumpr_0.1.2.tar.gz
bayclumpr_0.1.2.zip(r-4.7-any)bayclumpr_0.1.2.zip(r-4.6-any)bayclumpr_0.1.2.zip(r-4.5-any)
bayclumpr_0.1.2.tgz(r-4.6-any)bayclumpr_0.1.2.tgz(r-4.5-any)
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bayclumpr_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
bayclumpr/json (API)

# Install 'bayclumpr' in R:

install.packages('bayclumpr', repos = c('https://tripati-lab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tripati-lab/bayclumpr/issues

Pkgdown/docs site:https://tripati-lab.github.io

On CRAN:

4.00 score 2 stars 10 scripts 328 downloads 13 exports 51 dependencies

Last updated from:904de1c46d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	180
source / vignettes	OK	223
linux-release	OK	163
macos-release	OK	153
macos-oldrel	OK	200
windows-devel	OK	133
windows-release	OK	133
windows-oldrel	OK	117
wasm-release	OK	154

Exports:cal.bayesian cal.ci cal.dataset cal.deming cal.ion.bayesian cal.ols cal.prior cal.wols cal.york rec.bayesian rec.clumped rec.ion.bayesian rec.prior

Dependencies:abind backports BH boot callr checkmate cli cpp11 deming desc distributional farver generics ggplot2 glue gridExtra gtable inline isoband IsoplotR labeling lifecycle loo magrittr MASS matrixStats numDeriv otel pillar pkgbuild pkgconfig posterior processx ps QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel rlang rstan S7 scales StanHeaders tensorA tibble utf8 vctrs viridisLite withr

bayclumpr

Performing calibrations using bayclumpr | Reconstructing temperatures in bayclumpr | Including a co-variate (with sample-specific errors in the covariate) | Including a co-variate (without error in the covariate) | Outlook

Rendered frombayclumpr.Rmdusingknitr::rmarkdown

Last update: 2025-10-01
Started: 2022-10-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bayesian regressions to calibrate the clumped isotopes paleothermometer using 'stan'.	cal.bayesian
This function is used to generate CI estimates at given intervals. It is currently used for plotting in BayClump.	cal.ci
Generate a synthetic dataset for clumped isotopes calibrations	cal.dataset
Fit Deming regression models on a given calibration dataset	cal.deming
Bayesian regressions to calibrate the clumped isotopes paleothermometer using 'stan'.	cal.ion.bayesian
Fit OLS regression models on a given calibration dataset	cal.ols
Generate a dataset reflecting the priors used to run the analyses	cal.prior
Fit weighted OLS regression models on a given calibration dataset	cal.wols
Fit York regression models on a given calibration dataset	cal.york
This function generate temperature predictions (in 10^6/T2) based on a calibration dataset and target D47. Note that this approach additionally accounts for measured error in the target D47. This approach is congruent with the one used in McClelland et al. (2022).	rec.bayesian
This function performs temp reconstruction (10^6/T^2 with T in K) for multiple replicates of the same target.	rec.clumped
This function generates temperature predictions (in 10^6/T2) based on a calibration dataset and target D47. It includes measured error in the target D47 and ion as an additional predictor.	rec.ion.bayesian
Generate a dataset reflecting the priors used to run the analyses	rec.prior