Showing 200 of total 311 results (show query)

fishr-core-team

FSA:Simple Fisheries Stock Assessment Methods

A variety of simple fish stock assessment methods.

Maintained by Derek H. Ogle. Last updated 2 months ago.

fishfisheriesfisheries-managementfisheries-stock-assessmentpopulation-dynamicsstock-assessment

24.5 match 68 stars 11.08 score 1.7k scripts 6 dependents

ices-tools-prod

icesSAG:Stock Assessment Graphs Database Web Services

R interface to access the web services of the ICES Stock Assessment Graphs database <https://sg.ices.dk>.

Maintained by Colin Millar. Last updated 5 months ago.

17.7 match 11 stars 6.24 score 131 scripts 2 dependents

framverse

framrosetta:FRAM LUTs and mappings

Look-up tables and convenience functions for working with FRAM tables.

Maintained by Ty Garber. Last updated 2 months ago.

24.1 match 1 stars 3.95 score 3 scripts 1 dependents

framverse

framrsquared:FRAM Database Interface

A convenient tool for interfacing with FRAM access databases in R environments.

Maintained by Ty Garber. Last updated 2 months ago.

16.4 match 6 stars 5.06 score 9 scripts

felixfan

FinCal:Time Value of Money, Time Series Analysis and Computational Finance

Package for time value of money calculation, time series analysis and computational finance.

Maintained by Felix Yanhui Fan. Last updated 8 years ago.

9.8 match 23 stars 6.02 score 203 scripts 1 dependents

bioc

igvR:igvR: integrative genomics viewer

Access to igv.js, the Integrative Genomics Viewer running in a web browser.

Maintained by Arkadiusz Gladki. Last updated 5 months ago.

visualizationthirdpartyclientgenomebrowsers

7.1 match 43 stars 8.31 score 118 scripts

flr

FLSAM:An Implementation of the State-Space Assessment Model for FLR

This package provides an FLR wrapper to the SAM state-space assessment model.

Maintained by N.T. Hintzen. Last updated 3 months ago.

12.2 match 4 stars 4.51 score 406 scripts

rtsay1

MTS:All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models

Multivariate Time Series (MTS) is a general package for analyzing multivariate linear time series and estimating multivariate volatility models. It also handles factor models, constrained factor models, asymptotic principal component analysis commonly used in finance and econometrics, and principal volatility component analysis. (a) For the multivariate linear time series analysis, the package performs model specification, estimation, model checking, and prediction for many widely used models, including vector AR models, vector MA models, vector ARMA models, seasonal vector ARMA models, VAR models with exogenous variables, multivariate regression models with time series errors, augmented VAR models, and Error-correction VAR models for co-integrated time series. For model specification, the package performs structural specification to overcome the difficulties of identifiability of VARMA models. The methods used for structural specification include Kronecker indices and Scalar Component Models. (b) For multivariate volatility modeling, the MTS package handles several commonly used models, including multivariate exponentially weighted moving-average volatility, Cholesky decomposition volatility models, dynamic conditional correlation (DCC) models, copula-based volatility models, and low-dimensional BEKK models. The package also considers multiple tests for conditional heteroscedasticity, including rank-based statistics. (c) Finally, the MTS package also performs forecasting using diffusion index , transfer function analysis, Bayesian estimation of VAR models, and multivariate time series analysis with missing values.Users can also use the package to simulate VARMA models, to compute impulse response functions of a fitted VARMA model, and to calculate theoretical cross-covariance matrices of a given VARMA model.

Maintained by Ruey S. Tsay. Last updated 3 years ago.

cpp

8.4 match 6 stars 6.52 score 272 scripts 6 dependents

ices-tools-prod

icesFO:Functions to support the creation of ICES Fisheries Overviews

Functions to support the creation of ICES Fisheries Overviews.

Maintained by Adriana Villamor. Last updated 9 months ago.

15.1 match 2 stars 3.41 score 260 scripts

ataher76

aLBI:Estimating Length-Based Indicators for Fish Stock

Provides tools for estimating length-based indicators from length frequency data to assess fish stock status and manage fisheries sustainably. Implements methods from Cope and Punt (2009) <doi:10.1577/C08-025.1> for data-limited stock assessment and Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> for detecting overfishing using simple indicators. Key functions include: FrequencyTable(): Calculate the frequency table from the collected and also the extract the length frequency data from the frequency table with the upper length_range. A numeric value specifying the bin width for class intervals. If not provided, the bin width is automatically calculated using Sturges (1926) <doi:10.1080/01621459.1926.10502161> formula. CalPar(): Calculates various lengths used in fish stock assessment as biological length indicators such as asymptotic length (Linf), maximum length (Lmax), length at sexual maturity (Lm), and optimal length (Lopt). FishPar(): Calculates length-based indicators (LBIs) proposed by Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> such as the percentage of mature fish (Pmat), percentage of optimal length fish (Popt), percentage of mega spawners (Pmega), and the sum of these as Pobj. This function also estimates confidence intervals for different lengths, visualizes length frequency distributions, and provides data frames containing calculated values. FishSS(): Makes decisions based on input from Cope and Punt (2009) <doi:10.1577/C08-025.1> and parameters calculated by FishPar() (e.g., Pobj, Pmat, Popt, LM_ratio) to determine stock status as target spawning biomass (TSB40) and limit spawning biomass (LSB25). These tools support fisheries management decisions by providing robust, data-driven insights.

Maintained by Ataher Ali. Last updated 4 months ago.

11.0 match 1 stars 4.60 score 7 scripts

calbertsen

multiStockassessment:Fitting Multiple State-Space Assessment Models

Fitting multiple SAM models.

Maintained by Christoffer Moesgaard Albertsen. Last updated 3 months ago.

fisheriesfisheries-stock-assessmentstock-assessmentstockassessmentcpp

16.2 match 5 stars 2.88 score 5 scripts

gnelson12

fishmethods:Fishery Science Methods and Models

Functions for applying a wide range of fisheries stock assessment methods.

Maintained by Gary A. Nelson. Last updated 1 months ago.

10.9 match 5 stars 4.12 score 136 scripts 1 dependents

flr

FLSRTMB:FLSR in TMB

Estimates FLR spawner recruitment relationships in TMB

Maintained by Henning Winker. Last updated 15 days ago.

stock-recruitfisheriesflrtmbadcpp

11.0 match 3.67 score 26 scripts 1 dependents

hdvinod

generalCorr:Generalized Correlations, Causal Paths and Portfolio Selection

Function gmcmtx0() computes a more reliable (general) correlation matrix. Since causal paths from data are important for all sciences, the package provides many sophisticated functions. causeSummBlk() and causeSum2Blk() give easy-to-interpret causal paths. Let Z denote control variables and compare two flipped kernel regressions: X=f(Y, Z)+e1 and Y=g(X, Z)+e2. Our criterion Cr1 says that if |e1*Y|>|e2*X| then variation in X is more "exogenous or independent" than in Y, and the causal path is X to Y. Criterion Cr2 requires |e2|<|e1|. These inequalities between many absolute values are quantified by four orders of stochastic dominance. Our third criterion Cr3, for the causal path X to Y, requires new generalized partial correlations to satisfy |r*(x|y,z)|< |r*(y|x,z)|. The function parcorVec() reports generalized partials between the first variable and all others. The package provides several R functions including get0outliers() for outlier detection, bigfp() for numerical integration by the trapezoidal rule, stochdom2() for stochastic dominance, pillar3D() for 3D charts, canonRho() for generalized canonical correlations, depMeas() measures nonlinear dependence, and causeSummary(mtx) reports summary of causal paths among matrix columns. Portfolio selection: decileVote(), momentVote(), dif4mtx(), exactSdMtx() can rank several stocks. Functions whose names begin with 'boot' provide bootstrap statistical inference, including a new bootGcRsq() test for "Granger-causality" allowing nonlinear relations. A new tool for evaluation of out-of-sample portfolio performance is outOFsamp(). Panel data implementation is now included. See eight vignettes of the package for theory, examples, and usage tips. See Vinod (2019) \doi{10.1080/03610918.2015.1122048}.

Maintained by H. D. Vinod. Last updated 1 years ago.

8.8 match 2 stars 4.48 score 63 scripts 1 dependents

ices-tools-prod

icesSD:Stock Database Web Services

R interface to access the web services of the ICES Stock Database <https://sd.ices.dk>.

Maintained by Colin Millar. Last updated 5 months ago.

11.4 match 1 stars 3.16 score 29 scripts

flr

FLRef:Reference point computation for advice rules

Blah

Maintained by Henning Winker. Last updated 8 days ago.

10.2 match 3 stars 3.45 score 11 scripts

alanarnholt

BSDA:Basic Statistics and Data Analysis

Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.

Maintained by Alan T. Arnholt. Last updated 2 years ago.

3.4 match 7 stars 9.11 score 1.3k scripts 6 dependents

joshuaulrich

quantmod:Quantitative Financial Modelling Framework

Specify, build, trade, and analyse quantitative financial trading strategies.

Maintained by Joshua M. Ulrich. Last updated 15 days ago.

algorithmic-tradingchartingdata-importfinancetime-series

1.9 match 839 stars 16.17 score 8.1k scripts 343 dependents

doserjef

rFIA:Estimation of Forest Variables using the FIA Database

The goal of 'rFIA' is to increase the accessibility and use of the United States Forest Services (USFS) Forest Inventory and Analysis (FIA) Database by providing a user-friendly, open source toolkit to easily query and analyze FIA Data. Designed to accommodate a wide range of potential user objectives, 'rFIA' simplifies the estimation of forest variables from the FIA Database and allows all R users (experts and newcomers alike) to unlock the flexibility inherent to the Enhanced FIA design. Specifically, 'rFIA' improves accessibility to the spatial-temporal estimation capacity of the FIA Database by producing space-time indexed summaries of forest variables within user-defined population boundaries. Direct integration with other popular R packages (e.g., 'dplyr', 'tidyr', and 'sf') facilitates efficient space-time query and data summary, and supports common data representations and API design. The package implements design-based estimation procedures outlined by Bechtold & Patterson (2005) <doi:10.2737/SRS-GTR-80>, and has been validated against estimates and sampling errors produced by FIA 'EVALIDator'. Current development is focused on the implementation of spatially-enabled model-assisted and model-based estimators to improve population, change, and ratio estimates.

Maintained by Jeffrey Doser. Last updated 9 days ago.

compute-estimatesfiafia-databasefia-datamartforest-inventoryforest-variablesinventoriesspace-timespatial

5.1 match 49 stars 5.93 score

fishfollower

stockassessment:State-Space Assessment Model

Fitting SAM...

Maintained by Anders Nielsen. Last updated 14 days ago.

stockassessmentcpp

3.8 match 49 stars 7.76 score 324 scripts 2 dependents

sbgraves237

Ecdat:Data Sets for Econometrics

Data sets for econometrics, including political science.

Maintained by Spencer Graves. Last updated 4 months ago.

4.0 match 2 stars 7.25 score 740 scripts 3 dependents

lcrawlab

mvMAPIT:Multivariate Genome Wide Marginal Epistasis Test

Epistasis, commonly defined as the interaction between genetic loci, is known to play an important role in the phenotypic variation of complex traits. As a result, many statistical methods have been developed to identify genetic variants that are involved in epistasis, and nearly all of these approaches carry out this task by focusing on analyzing one trait at a time. Previous studies have shown that jointly modeling multiple phenotypes can often dramatically increase statistical power for association mapping. In this package, we present the 'multivariate MArginal ePIstasis Test' ('mvMAPIT') – a multi-outcome generalization of a recently proposed epistatic detection method which seeks to detect marginal epistasis or the combined pairwise interaction effects between a given variant and all other variants. By searching for marginal epistatic effects, one can identify genetic variants that are involved in epistasis without the need to identify the exact partners with which the variants interact – thus, potentially alleviating much of the statistical and computational burden associated with conventional explicit search based methods. Our proposed 'mvMAPIT' builds upon this strategy by taking advantage of correlation structure between traits to improve the identification of variants involved in epistasis. We formulate 'mvMAPIT' as a multivariate linear mixed model and develop a multi-trait variance component estimation algorithm for efficient parameter inference and P-value computation. Together with reasonable model approximations, our proposed approach is scalable to moderately sized genome-wide association studies. Crawford et al. (2017) <doi:10.1371/journal.pgen.1006869>. Stamp et al. (2023) <doi:10.1093/g3journal/jkad118>.

Maintained by Julian Stamp. Last updated 5 months ago.

cppepistasisepistasis-analysisgwasgwas-toolslinear-mixed-modelsmapitmvmapitvariance-componentsopenblascppopenmp

4.0 match 11 stars 6.90 score 17 scripts 1 dependents

wch

gcookbook:Data for "R Graphics Cookbook"

Data sets used in the book "R Graphics Cookbook" by Winston Chang, published by O'Reilly Media.

Maintained by Winston Chang. Last updated 6 years ago.

4.0 match 10 stars 6.77 score 1.3k scripts 1 dependents

steve-the-bayesian

bsts:Bayesian Structural Time Series

Time series regression using dynamic linear models fit using MCMC. See Scott and Varian (2014) <DOI:10.1504/IJMMNO.2014.059942>, among many other sources.

Maintained by Steven L. Scott. Last updated 1 years ago.

cpp

4.0 match 33 stars 6.54 score 338 scripts 3 dependents

pik-piam

mredgebuildings:Prepare data to be used by the EDGE-Buildings model

Prepare data to be used by the EDGE-Buildings model.

Maintained by Robin Hasse. Last updated 3 days ago.

7.0 match 3.72 score

flr

AAP:Aarts and Poos Stock Assessment Model that Estimates Bycatch

FLR version of Aarts and Poos stock assessment model.

Maintained by Iago Mosqueira. Last updated 1 years ago.

7.9 match 2.70 score 5 scripts

tobiaskley

quantspec:Quantile-Based Spectral Analysis of Time Series

Methods to determine, smooth and plot quantile periodograms for univariate and multivariate time series.

Maintained by Tobias Kley. Last updated 9 years ago.

cpp

3.3 match 10 stars 5.84 score 46 scripts 1 dependents

dvmlls

bdscale:Remove Weekends and Holidays from ggplot2 Axes

Provides a continuous date scale, omitting weekends and holidays.

Maintained by Dave Mills. Last updated 9 years ago.

3.3 match 10 stars 5.10 score 25 scripts

braverock

FinancialInstrument:Financial Instrument Model Infrastructure for R

Infrastructure for defining meta-data and relationships for financial instruments.

Maintained by Ross Bennett. Last updated 7 years ago.

3.3 match 19 stars 4.99 score 102 scripts

bpfaff

urca:Unit Root and Cointegration Tests for Time Series Data

Unit root and cointegration tests encountered in applied econometric analysis are implemented.

Maintained by Bernhard Pfaff. Last updated 10 months ago.

fortran

1.8 match 6 stars 8.91 score 1.4k scripts 269 dependents

joshuaulrich

IBrokers:R API to Interactive Brokers Trader Workstation

Provides native R access to Interactive Brokers Trader Workstation API.

Maintained by Joshua M. Ulrich. Last updated 6 months ago.

2.0 match 69 stars 7.59 score 93 scripts

pik-piam

remind2:The REMIND R package (2nd generation)

Contains the REMIND-specific routines for data and model output manipulation.

Maintained by Renato Rodrigues. Last updated 7 days ago.

1.7 match 8.88 score 161 scripts 5 dependents

pik-piam

mrindustry:input data generation for the REMIND industry module

The mrindustry packages contains data preprocessing for the REMIND model.

Maintained by Falk Benke. Last updated 4 days ago.

2.7 match 5.41 score 2 dependents

milosvil

belex:Download Historical Data from the Belgrade Stock Exchange

Tools for downloading historical financial data from the www.belex.rs.

Maintained by Milos Vilotic. Last updated 6 years ago.

4.7 match 2.70 score 4 scripts