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 1 years ago
multivariate-timeseriesstate-space-modelsstatisticstime-series
10.32 score 52 stars 3 dependents 592 scripts 658 downloadsbayesdfa - 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 4 months ago
cpp
8.37 score 28 stars 100 scripts 970 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 21 days ago
economicslocation-choice-modelnwfsc-fram
6.57 score 4 stars 12 scriptszoid - 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 10 months ago
mixture-modelsnwfsc-cbstancpp
6.49 score 8 stars 12 scripts 175 downloadsmaxnet - 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 2 years ago
5.60 score 7 dependents 171 scripts 2.2k downloadsphenomix - 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 10 months ago
cpp
4.83 score 5 stars 34 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
rCAX - Coordinated Assessments REST API R Client
This package is an R client for the StreamNet Coordinated Assessments HLI REST API.
Last updated 1 months ago
noaarest-apisalmon
4.48 score 5 stars 8 scriptskwdemog - Package for processing and exploring killer whale demographic data
Generates killer whale demographic data from rows (observations) and fits preliminary models.
Last updated 1 months ago
esakiller-whalemarine-mammalsnwfsc-cbsrkwstatus-review
4.47 score 2 stars 14 scriptstvvarss - 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 scriptsmarssTMB - 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 scriptsDM - 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.
Last updated 7 years ago
bayesianprotected-speciessalmonjagscpp
3.31 score 410 scriptsmvdlm - Multivariate Dynamic Linear Modelling With Stan
Fits multivariate dynamic linear models in a Bayesian framework using Stan.
Last updated 8 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 2 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 2 years ago
multivariate-timeseriestime-series
3.00 score 1 stars 9 downloadsvarlasso - 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 scriptsVRAPS - 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 1 years ago
cppnwfsc-cbnwfsc-cb-mathbioprotected-speciessalmoncpp
2.70 score
VRAP - VRAP for RER and Viability Computations
This is an optionally parallel R version of the VRAP program.
Last updated 3 months ago
protected-speciessalmon
1.70 scorezoidtmb - 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 1 years ago
nwfsc-cbcpp
1.70 score 1 stars