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
MultiNMix_0.1.0.zip(r-4.7-any)MultiNMix_0.1.0.zip(r-4.6-any)MultiNMix_0.1.0.zip(r-4.5-any)
MultiNMix_0.1.0.tgz(r-4.6-any)MultiNMix_0.1.0.tgz(r-4.5-any)
MultiNMix_0.1.0.tar.gz(r-4.7-any)MultiNMix_0.1.0.tar.gz(r-4.6-any)
MultiNMix_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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:

2.70 score 1 stars 258 downloads 16 exports 58 dependencies

Last updated from:e71f2d5a4c. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	184
source / vignettes	OK	360
linux-release	NOTE	181
macos-release	NOTE	195
macos-oldrel	NOTE	179
windows-devel	NOTE	97
windows-release	NOTE	94
windows-oldrel	NOTE	120
wasm-release	OK	156

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 cpp11 desc distributional extraDistr farver generics ggplot2 glue gridExtra gtable igraph inline isoband labeling lattice lifecycle loo magrittr MASS Matrix matrixStats mvtnorm nimble numDeriv otel pillar pkgbuild pkgconfig posterior pracma processx ps QuickJSR R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel rlang rstan S7 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