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/>.

Last updated 9 months ago

multivariate-timeseriesstate-space-modelsstatisticstime-series

10.61 score 52 stars 3 packages 580 scripts 941 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.

Last updated 1 months ago

cpp

8.57 score 28 stars 104 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.

Last updated 13 days ago

economicslocation-choice-modelnwfsc-fram

6.62 score 4 stars 12 scripts

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.

Last updated 7 months ago

mixture-modelsnwfsc-cbstancpp

6.58 score 8 stars 12 scripts 151 downloads

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.

Last updated 1 years ago

5.63 score 6 packages 156 scripts 3.0k downloads

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).

Last updated 7 months ago

cpp

5.01 score 5 stars 34 scripts

rCAX - Coordinated Assessments REST API R Client

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

Last updated 12 months ago

noaarest-apisalmon

4.78 score 5 stars 8 scripts

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.

Last updated 3 years ago

dataprotected-speciessalmon

4.64 score 2 stars 20 scripts

kwdemog - Package for processing and exploring killer whale demographic data

Generates killer whale demographic data from rows (observations) and fits preliminary models.

Last updated 1 days ago

esakiller-whalemarine-mammalsnwfsc-cbsrkwstatus-review

4.47 score 2 stars 14 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.

Last updated 3 years ago

bayesianmultivariate-timeseriesstate-spacetime-seriescpp

4.04 score 10 stars 11 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.

Last updated 2 years ago

marssmultivariate-timeseriesstate-space-modeltime-seriestmb

3.68 score 1 stars 19 scripts

satf - Stock Assessment Tables and Figures

Creates exploratory and finished tables and figures for stock assessment documents from U.S. stock assessment model outputs. This packages addresses parts of the stock assessment workflow that interprets outputs of stock assessment models as well as allows the analyst to create report ready tables and figures, reducing the need to create their own and format then when adding into a report. This package is intended to be used in conjuction with `asar`, a partially automated template for writing various stock assessment reports. Throughout development, we will be creating a set of standardized figures and tables for a stock assessment report, developing functions to produce a variety of diagonostic plots, and other helpful materials. The advantage of using this package over others is that it applies to a range of stock assessment model outputs and standardizes them.

Last updated 5 hours ago

3.65 score 2 stars 2 scripts

mvdlm - Multivariate Dynamic Linear Modelling With Stan

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

Last updated 6 months ago

bayesiandlmstantime-seriescpp

3.18 score 1 stars 3 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().

Last updated 1 years ago

marssnoaaprotected-speciessalmontime-series

3.18 score 1 stars

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.

Last updated 1 years ago

multivariate-timeseriestime-series

3.00 score 1 stars 11 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).

Last updated 2 years ago

bayesianmultivariate-timeseriestime-seriescpp

3.00 score 2 stars 2 scripts

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 10 months ago

nwfsc-cbcpp

2.18 score 1 stars

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 3 years ago

2.00 score 5 scripts

VRAP - VRAP for RER and Viability Computations

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

Last updated 4 days ago

protected-speciessalmon

1.70 score