Package: jtdm 0.1-3

jtdm: Joint Modelling of Functional Traits

Fitting and analyzing a Joint Trait Distribution Model. The Joint Trait Distribution Model is implemented in the Bayesian framework using conjugate priors and posteriors, thus guaranteeing fast inference. In particular the package computes joint probabilities and multivariate confidence intervals, and enables the investigation of how they depend on the environment through partial response curves. The method implemented by the package is described in Poggiato et al. (2023) <doi:10.1111/geb.13706>.

Authors:Giovanni Poggiato [aut, cre, cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
jtdm/json (API)

# Install 'jtdm' in R:

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

Bug tracker:https://github.com/giopogg/jtdm/issues

Pkgdown/docs site:https://giopogg.github.io

Datasets:

X - Site x environmental covariates dataset
Y - Site x CWM traits dataset

On CRAN:

4.65 score 9 stars 8 scripts 267 downloads 9 exports 35 dependencies

Last updated from:1c04e3da1d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	170
source / vignettes	OK	310
linux-release-x86_64	OK	166
macos-release-arm64	OK	130
macos-oldrel-arm64	OK	145
windows-devel	OK	117
windows-release	OK	102
windows-oldrel	OK	112
wasm-release	OK	123

Exports:ellipse_plot get_sigma getB joint_trait_prob joint_trait_prob_gradient jtdm_fit jtdm_predict jtdmCV partial_response

Dependencies:base64enc cli cpp11 farver ggforce ggplot2 glue gridExtra gtable isoband jsonlite labeling lifecycle magrittr MASS mniw mvtnorm plyr polyclip R6 RColorBrewer Rcpp RcppEigen reshape2 rlang S7 scales stringi stringr systemfonts tidyselect tweenr vctrs viridisLite withr

ORCHAMP_dataset

Rendered fromORCHAMP_dataset.Rmdusingknitr::rmarkdown

Last update: 2023-01-23
Started: 2023-01-18

Help page	Topics
Partial response curve of the pairwise most suitable community-level strategy and of the pairwise envelop of possible community-level strategy	ellipse_plot
Get the inferred residual covariance matrix	get_sigma
Get the inferred regression coefficients	getB
Global	global
Computes joint probabilities.	joint_trait_prob
Computes partial response curves of joint probabilities	joint_trait_prob_gradient
Fitting joint trait distribution models	jtdm_fit
Predict method for joint trait distribution model	jtdm_predict
K-fold cross validation predictions and goodness of fit metrics	jtdmCV
Computes and plots the trait-environment relationship of a given CWM trait and a given environmental variable	partial_response
Plots the parameters of a fitted jtdm	plot.jtdm_fit
Prints the summary of a fitted jtdm	summary.jtdm_fit
Site x environmental covariates dataset	X
Site x CWM traits dataset	Y

Package: jtdm 0.1-3

jtdm: Joint Modelling of Functional Traits

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