Package: MultiNMix 0.1.0

MultiNMix: Multi-Species N-Mixture (MNM) Models with 'nimble'

Simulating data and fitting multi-species N-mixture models using 'nimble'. Includes features for handling zero-inflation and temporal correlation, Bayesian inference, model diagnostics, parameter estimation, and predictive checks. Designed for ecological studies with zero-altered or time-series data. Mimnagh, N., Parnell, A., Prado, E., & Moral, R. A. (2022) <doi:10.1007/s10651-022-00542-7>. Royle, J. A. (2004) <doi:10.1111/j.0006-341X.2004.00142.x>.

Authors:Niamh Mimnagh [aut, cre], Rafael de Andrade Moral [aut]

MultiNMix_0.1.0.tar.gz
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MultiNMix.pdf |MultiNMix.html✨
MultiNMix/json (API)

# Install 'MultiNMix' in R:

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

Bug tracker:https://github.com/niamhmimnagh/multinmix/issues

Datasets:

birds - Birds Dataset - Subset of the North American Breeding Bird Survey Dataset
birds_ZI - Zero-Inflated Birds Dataset - Subset of the North American Breeding Bird Survey Dataset

On CRAN:

3.18 score 1 stars 16 exports 60 dependencies

Last updated 21 days agofrom:e71f2d5a4c. Checks:1 OK, 8 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 20 2025
R-4.5-win	NOTE	Mar 20 2025
R-4.5-mac	NOTE	Mar 20 2025
R-4.5-linux	NOTE	Mar 20 2025
R-4.4-win	NOTE	Mar 20 2025
R-4.4-mac	NOTE	Mar 20 2025
R-4.4-linux	NOTE	Mar 20 2025
R-4.3-win	NOTE	Mar 20 2025
R-4.3-mac	NOTE	Mar 20 2025

Exports:AIC BIC check_convergence density logLik MNM MNM_AR MNM_control MNM_fit MNM_Hurdle MNM_Hurdle_AR predictY simulateData tracePlot validate_all_priors validate_prior

Dependencies:abind backports BH callr checkmate cli clusterGeneration coda colorspace cpp11 desc distributional extraDistr fansi farver generics ggplot2 glue gridExtra gtable igraph inline isoband labeling lattice lifecycle loo magrittr MASS Matrix matrixStats mgcv munsell mvtnorm nimble nlme numDeriv pillar pkgbuild pkgconfig posterior pracma processx ps QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel rlang rstan scales StanHeaders tensorA tibble utf8 vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
AIC Method for "MNM" Class	AIC,MNM-method
BIC Method for "MNM" Class	BIC,MNM-method
Birds Dataset - Subset of the North American Breeding Bird Survey Dataset	birds
Zero-Inflated Birds Dataset - Subset of the North American Breeding Bird Survey Dataset	birds_ZI
Convergence Check Generic Function	check_convergence
Convergence Check for "MNM" Class	check_convergence,MNM-method
Density Plot Method for "MNM" Class	density,MNM-method
List of Valid Nimble Distributions and Their Arguments	distribution_args
Log-Likelihood Method for "MNM" Class	logLik,MNM-method
Fit a Multi-Species N-Mixture Model (MNM) using Nimble	MNM
Fit a Multi-Species N-Mixture Model with AR-1 Using Nimble	MNM_AR
Generate Nimble Code for Multi-Species N-Mixture (MNM) Models	MNM_control
Fit a Multi-Species N-Mixture (MNM) Model in Nimble	MNM_fit
Fit a Multi-Species N-Mixture Model with Hurdle Component using Nimble	MNM_Hurdle
Fit a multi-species N-mixture (MNM) Hurdle-AR model using Nimble	MNM_Hurdle_AR
Multi-Species N-Mixture (MNM) Model Class	MNM-class
Predict Fitted Values for "MNM" Class	predictY predictY,MNM-method
Simulate Data for Multi-Species N-Mixture Models	simulateData
Trace Plot Generic and Method for "MNM" Class	tracePlot tracePlot,MNM-method
Validate User-Specified Priors for Nimble Models	validate_all_priors
Validate User-Specified Prior for a Single Prior	validate_prior