Package: bayclumpr 0.1.1

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]

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

On CRAN:

4.04 score 1 stars 11 scripts 260 downloads 11 exports 55 dependencies

Last updated 5 months agofrom:db19e2abc6. Checks:9 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 13 2025
R-4.5-win	OK	Mar 13 2025
R-4.5-mac	OK	Mar 13 2025
R-4.5-linux	OK	Mar 13 2025
R-4.4-win	OK	Mar 13 2025
R-4.4-mac	OK	Mar 13 2025
R-4.4-linux	OK	Mar 13 2025
R-4.3-win	OK	Mar 13 2025
R-4.3-mac	OK	Mar 13 2025

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

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

bayclumpr

Rendered frombayclumpr.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2023-03-10
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
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
Generate a dataset reflecting the priors used to run the analyses	rec.prior