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MARSS - Multivariate Autoregressive State-Space Modeling

The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models, including partially deterministic models. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Fitting available via Expectation-Maximization (EM), BFGS (using optim), and 'TMB' (using the 'marssTMB' companion package). Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, model selection criteria including bootstrap AICb, confidences intervals via the Hessian approximation or bootstrapping, and all conditional residual types. See the user guide for examples of dynamic factor analysis, dynamic linear models, outlier and shock detection, and multivariate AR-p models. Online workshops (lectures, eBook, and computer labs) at <https://atsa-es.github.io/>.

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multivariate-timeseriesstate-space-modelsstatisticstime-series

10.83 score 54 stars 3 dependents 1.2k scripts 1.5k downloads

bayesdfa - Bayesian Dynamic Factor Analysis (DFA) with 'Stan'

Implements Bayesian dynamic factor analysis with 'Stan'. Dynamic factor analysis is a dimension reduction tool for multivariate time series. 'bayesdfa' extends conventional dynamic factor models in several ways. First, extreme events may be estimated in the latent trend by modeling process error with a student-t distribution. Second, alternative constraints (including proportions are allowed). Third, the estimated dynamic factors can be analyzed with hidden Markov models to evaluate support for latent regimes.

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cpp

7.94 score 29 stars 103 scripts 1.0k downloads

FishSET - Spatial Economics Toolbox for Fisheries

The Spatial Economics Toolbox for Fisheries (FishSET) is a set of tools for organizing data; developing, improving and disseminating modeling best practices.

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economicslocation-choice-modelnwfsc-framcpp

6.37 score 9 stars 12 scripts

maxnet - Fitting 'Maxent' Species Distribution Models with 'glmnet'

Procedures to fit species distributions models from occurrence records and environmental variables, using 'glmnet' for model fitting. Model structure is the same as for the 'Maxent' Java package, version 3.4.0, with the same feature types and regularization options. See the 'Maxent' website <http://biodiversityinformatics.amnh.org/open_source/maxent> for more details.

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6.37 score 9 dependents 263 scripts 6.6k downloads

zoid - Bayesian Zero-and-One Inflated Dirichlet Regression Modelling

Fits Dirichlet regression and zero-and-one inflated Dirichlet regression with Bayesian methods implemented in Stan. These models are sometimes referred to as trinomial mixture models; covariates and overdispersion can optionally be included.

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mixture-modelsnwfsc-cbstancpp

6.00 score 9 stars 14 scripts 171 downloads

VRData - NWFSC PNW Salmonid Viability Reports Data Package

This R package has the spawner and fraction wild data used to make the common metrics tables and figures used in the PNW Salmonid Viability Reports.

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dataprotected-speciessalmon

4.82 score 3 stars 20 scripts

phenomix - Fit Density Curves to Peak Timing Data that Varies over Time

The 'phenomix' package fits time-varying density curves to run timing type data commonly encountered in fisheries and ecology. Example applications include to peak run timing curves collected for juvenile or adult Pacific salmon, though could also be applied to other kinds of data such as hydrographs, plant phenology (flowering, leaf out).

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4.61 score 6 stars 34 scripts

tvvarss - Time Varying Vector Autoregressive State Space Models

The tvvarss package uses Stan (mc-stan.org) to fit multi-site multivariate autoregressive (aka vector autoregressive) state space models with a time varying interaction matrix.

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bayesianmultivariate-timeseriesstate-spacetime-seriescpp

4.26 score 12 stars 15 scripts

marssTMB - Fast fitting of MARSS models with TMB

Companion to the MARSS package. Fast fitting of MARSS models with TMB. See the MARSS documentation. All the model syntax and features are the same as for the MARSS package.

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marssmultivariate-timeseriesstate-space-modeltime-seriestmb

3.98 score 1 stars 38 scripts

NWCTrends - Standardized Trend Metrics for Salmonid Populations

This is runs the standardized trends metrics used in the 2016 and 2020 5-year NWFSC Viability Reports for listed PNW salmonids. To run, type library(NWCTrends) and then NWCTrends_report().

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marssnoaaprotected-speciessalmontime-series

3.48 score 2 stars 7 scripts

DM - Dynamic Model

This package uses comma-delimited data exported from the A&P Excel files to estimate the SR parameters for a user-specified SR function.

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bayesianprotected-speciessalmonjagscpp

3.39 score 487 scripts

MAR1 - Multivariate Autoregressive Modeling for Analysis of Community Time-Series Data

The MAR1 package provides basic tools for preparing ecological community time-series data for MAR modeling, building MAR-1 models via model selection and bootstrapping, and visualizing and exporting model results. It is intended to make MAR analysis sensu Ives et al. (2003) Analysis of community stability and ecological interactions from time-series data) a more accessible tool for anyone studying community dynamics. The user need not necessarily be familiar with time-series modeling or command-based statistics programs such as R.

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multivariate-timeseriestime-series

3.00 score 1 stars 2 downloads

varlasso - Vector Autoregressive State Space Models With Shrinkage

The varlasso package uses Stan (mc-stan.org) to fit VAR state space models with optional shrinkage priors on B matrix elements (autoregression coefficients).

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bayesianmultivariate-timeseriestime-seriescpp

3.00 score 2 stars 2 scripts

rCAX - Coordinated Assessments REST API R Client

This package is an R client for the StreamNet Coordinated Assessments HLI REST API.

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noaarest-apisalmon

2.98 score 5 stars 19 scripts

mvdlm - Multivariate Dynamic Linear Modelling With Stan

Fits multivariate dynamic linear models in a Bayesian framework using Stan.

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bayesiandlmstantime-seriescpp

2.70 score 1 stars 3 scripts

VRAPS - VRAP 2nd edition with C++ for RER and Viability Computations

This is a rewrite of the R version of the VRAP program. The original VRAP R package was a one-to-one translation from the original Visual Basic code. VRAPCpp is the same equations, but completely re-written by Martin Liermann to be more efficient. VRAPCpp does not have all the functionality of VRAP. Many of the rav options in VRAP were not used and are removed. There is a shiny that emulates the VRAP 1.0 shiny app.

Last updated

cppnwfsc-cbnwfsc-cb-mathbioprotected-speciessalmoncpp

2.70 score

shellfishrisks - Package for running agent based model exploring genetic risks of aquaculture production

This package runs an agent based model in Python, exploring the genetic risks of aquaculture production on wild populations.

Last updated

2.00 score 5 scripts

VRAP - VRAP for RER and Viability Computations

This is an optionally parallel R version of the VRAP program.

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protected-speciessalmon

1.70 score

zoidtmb - Zero-and-One Inflated Dirichlet Regression Modelling in TMB

Fits Dirichlet regression and zero-and-one inflated Dirichlet regression with Bayesian methods implemented in Stan. These models are sometimes referred to as trinomial mixture models; covariates and overdispersion can optionally be included.

Last updated

nwfsc-cbcpp

1.70 score 1 stars