Showing 200 of total 207 results (show query)
fishr-core-team
FSAdata:Data to Support Fish Stock Assessment ('FSA') Package
The datasets to support the Fish Stock Assessment ('FSA') package.
Maintained by Derek Ogle. Last updated 2 years ago.
fishfisheriesfisheries-stock-assessmentfishr-websitestock-assessment
62.7 match 13 stars 5.67 score 285 scripts
sizespectrum
mizer:Dynamic Multi-Species Size Spectrum Modelling
A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.
Maintained by Gustav Delius. Last updated 2 months ago.
ecosystem-modelfish-population-dynamicsfisheriesfisheries-managementmarine-ecosystempopulation-dynamicssimulationsize-structurespecies-interactionstransport-equationcpp
32.3 match 39 stars 9.41 score 207 scripts
nschiett
fishualize:Color Palettes Based on Fish Species
Implementation of color palettes based on fish species.
Maintained by Nina M. D. Schiettekatte. Last updated 11 months ago.
29.3 match 155 stars 8.54 score 370 scripts
adeverse
ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Maintained by Aurélie Siberchicot. Last updated 8 days ago.
14.9 match 40 stars 15.10 score 2.2k scripts 257 dependents
pbs-assess
sdmTMB:Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Implements spatial and spatiotemporal GLMMs (Generalized Linear Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial Differential Equation) Gaussian Markov random field approximation to Gaussian random fields. One common application is for spatially explicit species distribution models (SDMs). See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.
Maintained by Sean C. Anderson. Last updated 2 days ago.
ecologyglmmspatial-analysisspecies-distribution-modellingtmbcpp
16.9 match 205 stars 11.04 score 848 scripts 1 dependents
tokami
TropFishR:Tropical Fisheries Analysis
A compilation of fish stock assessment methods for the analysis of length-frequency data in the context of data-poor fisheries. Includes methods and examples included in the FAO Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish stock assessment" (<http://www.fao.org/documents/card/en/c/9bb12a06-2f05-5dcb-a6ca-2d6dd3080f65/>), as well as other more recent methods.
Maintained by Tobias K. Mildenberger. Last updated 5 months ago.
assessmentfao-manualfishfish-stocks
23.4 match 25 stars 7.56 score 149 scriptsfishr-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
15.0 match 69 stars 11.16 score 1.7k scripts 6 dependents
gadget-framework
gadget3:Globally-Applicable Area Disaggregated General Ecosystem Toolbox V3
A framework to assist creation of marine ecosystem models, generating either 'R' or 'C++' code which can then be optimised using the 'TMB' package and standard 'R' tools. Principally designed to reproduce gadget2 models in 'TMB', but can be extended beyond gadget2's capabilities. Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) <doi:10.18637/jss.v070.i05> "TMB: Automatic Differentiation and Laplace Approximation.". Begley, J., & Howell, D. (2004) <https://core.ac.uk/download/pdf/225936648.pdf> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".
Maintained by Jamie Lentin. Last updated 2 days ago.
15.4 match 8 stars 8.66 score 170 scripts
poissonconsulting
fishbc:Fishes of British Columbia
Provides raw and curated data on the codes, classification and conservation status of freshwater fishes in British Columbia. Marine fishes will be added in a future release.
Maintained by Evan Amies-Galonski. Last updated 2 months ago.
26.4 match 5 stars 4.65 score 2 scripts
jonchang
fishtree:Interface to the Fish Tree of Life API
An interface to the Fish Tree of Life API to download taxonomies, phylogenies, fossil calibrations, and diversification rate information for ray-finned fishes.
Maintained by Jonathan Chang. Last updated 4 months ago.
18.4 match 11 stars 6.57 score 56 scripts 1 dependents
ropensci
rfishbase:R Interface to 'FishBase'
A programmatic interface to 'FishBase', re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to 'SeaLifeBase' data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'
Maintained by Carl Boettiger. Last updated 3 months ago.
11.5 match 116 stars 10.11 score 764 scripts 2 dependents
condwanaland
fishdata:A Small Collection of Fish Population Datasets
A collection of four datasets based around the population dynamics of migratory fish. Datasets contain both basic size information on a per fish basis, as well as otolith data that contains a per day record of fish growth history. All data in this package was collected by the author, from 2015-2016, in the Wellington region of New Zealand.
Maintained by Conor Neilson. Last updated 4 years ago.
25.8 match 1 stars 4.45 score 28 scriptsropensci
worrms:World Register of Marine Species (WoRMS) Client
Client for World Register of Marine Species (<https://www.marinespecies.org/>). Includes functions for each of the API methods, including searching for names by name, date and common names, searching using external identifiers, fetching synonyms, as well as fetching taxonomic children and taxonomic classification.
Maintained by Bart Vanhoorne.. Last updated 1 years ago.
biologysciencemarineapiwebapi-clientwormsspeciesapi-wrapperbiological-datafishjerico-relevantmarine-biologymarine-speciestaxizetaxonomy
11.0 match 27 stars 10.04 score 372 scripts 27 dependents
bmait101
hatchR:Predict Fish Hatch and Emergence Timing
Predict hatch and emergence timing for a wide range of wild fishes using the effective value framework (Sparks et al., (2019) <DOI:10.1139/cjfas-2017-0468>). 'hatchR' offers users access to established phenological models and the flexibility to incorporate custom parameterizations using external datasets.
Maintained by Bryan M. Maitland. Last updated 15 days ago.
18.2 match 1 stars 5.89 score
tidyverse
tidyr:Tidy Messy Data
Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).
Maintained by Hadley Wickham. Last updated 25 days ago.
4.5 match 1.4k stars 22.88 score 168k scripts 5.5k dependents
bbolker
emdbook:Support Functions and Data for "Ecological Models and Data"
Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).
Maintained by Ben Bolker. Last updated 9 months ago.
11.1 match 4 stars 8.04 score 656 scripts 21 dependents
gabrielnakamura
FishPhyloMaker:Phylogenies for a List of Finned-Ray Fishes
Provides an alternative to facilitate the construction of a phylogeny for fish species from a list of species or a community matrix using as a backbone the phylogenetic tree proposed by Rabosky et al. (2018) <doi:10.1038/s41586-018-0273-1>.
Maintained by Gabriel Nakamura. Last updated 1 years ago.
15.0 match 8 stars 5.49 score 13 scriptsfishr-core-team
RFishBC:Back-Calculation of Fish Length
Helps fisheries scientists collect measurements from calcified structures and back-calculate estimated lengths at previous ages using standard procedures and models. This is intended to replace much of the functionality provided by the now out-dated 'fishBC' software (<https://fisheries.org/bookstore/all-titles/software/70317/>).
Maintained by Derek H. Ogle. Last updated 1 years ago.
fishfisheriesfisheries-managementfisheries-stock-assessmentpopulation-dynamicsstock-assessment
19.2 match 13 stars 4.26 score 28 scripts
cran
NADA:Nondetects and Data Analysis for Environmental Data
Contains methods described by Dennis Helsel in his book "Nondetects And Data Analysis: Statistics for Censored Environmental Data".
Maintained by Lopaka Lee. Last updated 5 years ago.
18.0 match 2 stars 4.45 score 14 dependents
mlaib
FiSh:Fisher-Shannon Method
Proposes non-parametric estimates of the Fisher information measure and the Shannon entropy power. More theoretical and implementation details can be found in Guignard et al. <doi:10.3389/feart.2020.00255>. A 'python' version of this work is available on 'github' and 'PyPi' ('FiShPy').
Maintained by Mohamed Laib. Last updated 4 years ago.
56.9 match 1.30 scorepoissonconsulting
ypr:Yield Per Recruit
An implementation of equilibrium-based yield per recruit methods. Yield per recruit methods can used to estimate the optimal yield for a fish population as described by Walters and Martell (2004) <isbn:0-691-11544-3>. The yield can be based on the number of fish caught (or harvested) or biomass caught for all fish or just large (trophy) individuals.
Maintained by Joe Thorley. Last updated 2 months ago.
8.9 match 7 stars 7.84 score 55 scripts 1 dependents
biorgeo
bioregion:Comparison of Bioregionalisation Methods
The main purpose of this package is to propose a transparent methodological framework to compare bioregionalisation methods based on hierarchical and non-hierarchical clustering algorithms (Kreft & Jetz (2010) <doi:10.1111/j.1365-2699.2010.02375.x>) and network algorithms (Lenormand et al. (2019) <doi:10.1002/ece3.4718> and Leroy et al. (2019) <doi:10.1111/jbi.13674>).
Maintained by Maxime Lenormand. Last updated 22 days ago.
biogeographybioregionbioregionalizationcpp
10.7 match 7 stars 6.27 score 11 scripts
middleton-lab
abd:The Analysis of Biological Data
The abd package contains data sets and sample code for The Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009; Roberts & Company Publishers).
Maintained by Kevin M. Middleton. Last updated 11 months ago.
12.0 match 6 stars 5.53 score 182 scripts 1 dependents
justinmshea
wooldridge:115 Data Sets from "Introductory Econometrics: A Modern Approach, 7e" by Jeffrey M. Wooldridge
Students learning both econometrics and R may find the introduction to both challenging. The wooldridge data package aims to lighten the task by efficiently loading any data set found in the text with a single command. Data sets have been compressed to a fraction of their original size. Documentation files contain page numbers, the original source, time of publication, and notes from the author suggesting avenues for further analysis and research. If one needs an introduction to R model syntax, a vignette contains solutions to examples from chapters of the text. Data sets are from the 7th edition (Wooldridge 2020, ISBN-13 978-1-337-55886-0), and are backwards compatible with all previous versions of the text.
Maintained by Justin M. Shea. Last updated 4 months ago.
6.6 match 203 stars 9.38 score 1.4k scripts
shyentist
fishRman:The Fisheries Scientist's Toolbox
A bundle of analytics tools for fisheries scientists. A 'shiny' R App is included for a 'no-code' solution for retrieval, analysis, and visualization.
Maintained by Pasquale Buonomo. Last updated 1 years ago.
dashboardfisheriesfisheries-managementfisheries-researchfishing-effortglobal-fishing-watchglobalfishingwatchmarine-biologyopen-sourceshiny
16.0 match 14 stars 3.85 score 1 scripts
leiyang-fish
copyseparator:Assembling Long Gene Copies from Short Read Data
Assembles two or more gene copies from short-read Next-Generation Sequencing data. Works best when there are only two gene copies and read length >=250 base pairs. High and relatively even coverage are important.
Maintained by Lei Yang. Last updated 3 months ago.
15.0 match 4.00 score 2 scripts
flr
FLasher:Projection and Forecasting of Fish Populations, Stocks and Fleets
Projection of future population and fishery dynamics is carried out for a given set of management targets. A system of equations is solved, using Automatic Differentation (AD), for the levels of effort by fishery (fleet) that will result in the required abundances, catches or fishing mortalities.
Maintained by Iago Mosqueira. Last updated 21 days ago.
8.6 match 2 stars 6.86 score 254 scripts 6 dependents
lbbe-software
fitdistrplus:Help to Fit of a Parametric Distribution to Non-Censored or Censored Data
Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit estimation (MGE) and maximum spacing estimation (MSE) methods (available only for non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g. Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction to parametric estimation.
Maintained by Aurélie Siberchicot. Last updated 24 days ago.
3.5 match 54 stars 16.15 score 4.5k scripts 153 dependents
hojsgaard
doBy:Groupwise Statistics, LSmeans, Linear Estimates, Utilities
Utility package containing: 1) Facilities for working with grouped data: 'do' something to data stratified 'by' some variables. 2) LSmeans (least-squares means), general linear estimates. 3) Restrict functions to a smaller domain. 4) Miscellaneous other utilities.
Maintained by Søren Højsgaard. Last updated 1 days ago.
3.8 match 1 stars 14.99 score 3.2k scripts 948 dependents
otoliths
rfishdraw:Procedurally Generated Fish Drawings Via Javascript
Procedurally generated fish drawings via ggplot2 based on fishdraw JavaScript library <https://github.com/LingDong-/fishdraw>.
Maintained by Liuyong Ding. Last updated 1 years ago.
12.3 match 6 stars 4.48 score 3 scripts
mhpob
otndo:Understand your OTN data
This package provides functions to summarize the various type of OTN-style data.
Maintained by Michael OBrien. Last updated 21 days ago.
animal-trackingbiotelemetryfishfisheriesvisualization
11.0 match 4 stars 4.92 score 6 scripts 1 dependentspoissonconsulting
klexdatr:Kootenay Lake Exploitation Study Data
Six relational 'tibbles' from the Kootenay Lake Large Trout Exploitation study. The study which ran from 2008 to 2014 caught, tagged and released large Rainbow Trout and Bull Trout in Kootenay Lake by boat angling. The fish were tagged with internal acoustic tags and/or high reward external tags and subsequently detected by an acoustic receiver array as well as reported by anglers. The data are analysed by Thorley and Andrusak (1994) <doi:10.7717/peerj.2874> to estimate the natural and fishing mortality of both species.
Maintained by Joe Thorley. Last updated 2 months ago.
22.5 match 2.30 score 7 scripts
bioc
DECIPHER:Tools for curating, analyzing, and manipulating biological sequences
A toolset for deciphering and managing biological sequences.
Maintained by Erik Wright. Last updated 17 days ago.
clusteringgeneticssequencingdataimportvisualizationmicroarrayqualitycontrolqpcralignmentwholegenomemicrobiomeimmunooncologygenepredictionopenmp
4.7 match 10.55 score 1.1k scripts 14 dependents
hugomflavio
actel:Acoustic Telemetry Data Analysis
Designed for studies where animals tagged with acoustic tags are expected to move through receiver arrays. This package combines the advantages of automatic sorting and checking of animal movements with the possibility for user intervention on tags that deviate from expected behaviour. The three analysis functions (explore(), migration() and residency()) allow the users to analyse their data in a systematic way, making it easy to compare results from different studies. CJS calculations are based on Perry et al. (2012) <https://www.researchgate.net/publication/256443823_Using_mark-recapture_models_to_estimate_survival_from_telemetry_data>.
Maintained by Hugo Flávio. Last updated 1 months ago.
acoustic-telemetryfish-packagestelemetry-data
7.5 match 26 stars 6.46 score 16 scripts
jasono6359
flfishltm:A package for analyzing FL FWC Freshwater long-term monitoring (LTM) data
Provides functions for summarizing and analyzing FL FWC Freshwater Fish Long-term Monitoring Data.
Maintained by Jason OConnor. Last updated 9 months ago.
13.0 match 1 stars 3.70 scoreflr
FLCore:Core Package of FLR, Fisheries Modelling in R
Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.
Maintained by Iago Mosqueira. Last updated 8 days ago.
fisheriesflrfisheries-modelling
5.3 match 16 stars 8.78 score 956 scripts 23 dependents
inbo
etn:Access Data from the European Tracking Network
Package with functions to access and process data from the European Tracking Network hosted by VLIZ.
Maintained by Pieter Huybrechts. Last updated 2 months ago.
animal-movementanimal-trackingbiologgingdata-accessfishlifewatchoscibio
11.0 match 8 stars 4.15 score 14 scriptsmhpob
matos:Interface with the Mid-Atlantic Acoustic Telemetry Observing System (MATOS)
This package provides HTML-scaping functions to interact with the MATOS website (https://matos.asascience.com/), allowing aggregation of data and the downloading and posting of files.
Maintained by Michael OBrien. Last updated 3 months ago.
animal-trackingapiapi-wrapperbiotelemetryfishfisheriesfisheries-research
11.0 match 3 stars 4.13 score 9 scripts
tyee001
VGAMdata:Data Supporting the 'VGAM' Package
Mainly data sets to accompany the VGAM package and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7>. These are used to illustrate vector generalized linear and additive models (VGLMs/VGAMs), and associated models (Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models, and constrained and unconstrained ordination models in ecology). This package now contains some old VGAM family functions which have been replaced by newer ones (often because they are now special cases).
Maintained by Thomas Yee. Last updated 2 months ago.
15.3 match 1 stars 2.94 score 95 scripts 1 dependents
openintrostat
openintro:Datasets and Supplemental Functions from 'OpenIntro' Textbooks and Labs
Supplemental functions and data for 'OpenIntro' resources, which includes open-source textbooks and resources for introductory statistics (<https://www.openintro.org/>). The package contains datasets used in our open-source textbooks along with custom plotting functions for reproducing book figures. Note that many functions and examples include color transparency; some plotting elements may not show up properly (or at all) when run in some versions of Windows operating system.
Maintained by Mine Çetinkaya-Rundel. Last updated 3 months ago.
3.8 match 240 stars 11.39 score 6.0k scripts
r-forge
coin:Conditional Inference Procedures in a Permutation Test Framework
Conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems described in <doi:10.18637/jss.v028.i08>.
Maintained by Torsten Hothorn. Last updated 9 months ago.
3.5 match 11.70 score 1.6k scripts 73 dependents
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 2 months ago.
9.9 match 5 stars 4.12 score 136 scripts 1 dependentsadeverse
adespatial:Multivariate Multiscale Spatial Analysis
Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.
Maintained by Aurélie Siberchicot. Last updated 8 days ago.
3.6 match 36 stars 11.16 score 398 scripts 2 dependents
ocean-tracking-network
glatos:A package for the Great Lakes Acoustic Telemetry Observation System
Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
Maintained by Christopher Holbrook. Last updated 6 months ago.
6.2 match 10 stars 6.38 score 112 scripts
fukayak
occumb:Site Occupancy Modeling for Environmental DNA Metabarcoding
Fits multispecies site occupancy models to environmental DNA metabarcoding data collected using spatially-replicated survey design. Model fitting results can be used to evaluate and compare the effectiveness of species detection to find an efficient survey design. Reference: Fukaya et al. (2022) <doi:10.1111/2041-210X.13732>.
Maintained by Keiichi Fukaya. Last updated 2 months ago.
7.5 match 2 stars 5.30 score 10 scripts
valentint
rrcov:Scalable Robust Estimators with High Breakdown Point
Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point: principal component analysis (Filzmoser and Todorov (2013), <doi:10.1016/j.ins.2012.10.017>), linear and quadratic discriminant analysis (Todorov and Pires (2007)), multivariate tests (Todorov and Filzmoser (2010) <doi:10.1016/j.csda.2009.08.015>), outlier detection (Todorov et al. (2010) <doi:10.1007/s11634-010-0075-2>). See also Todorov and Filzmoser (2009) <urn:isbn:978-3838108148>, Todorov and Filzmoser (2010) <doi:10.18637/jss.v032.i03> and Boudt et al. (2019) <doi:10.1007/s11222-019-09869-x>.
Maintained by Valentin Todorov. Last updated 7 months ago.
3.8 match 2 stars 10.57 score 484 scripts 96 dependentsr-forge
mlogit:Multinomial Logit Models
Maximum Likelihood estimation of random utility discrete choice models, as described in Kenneth Train (2009) Discrete Choice Methods with Simulations <doi:10.1017/CBO9780511805271>.
Maintained by Yves Croissant. Last updated 5 years ago.
4.0 match 9.87 score 1.2k scripts 14 dependents
framverse
pssp:Package to interface with the WDFW Puget Sound sampling database
The pssp package serves as an interface between R and the Puget Sound sampling database. It"s goal is to ease the burden of retrieving and analyzing sport creel information in Puget Sound.
Maintained by Ty Garber. Last updated 4 months ago.
16.4 match 2.40 score
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 10 months ago.
11.2 match 2 stars 3.41 score 260 scriptsadeverse
adephylo:Exploratory Analyses for the Phylogenetic Comparative Method
Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. The package contains functions to represent comparative data, compute phylogenetic proximities, perform multivariate analysis with phylogenetic constraints and test for the presence of phylogenetic autocorrelation. The package is described in Jombart et al (2010) <doi:10.1093/bioinformatics/btq292>.
Maintained by Aurélie Siberchicot. Last updated 14 days ago.
3.6 match 9 stars 10.05 score 312 scripts 4 dependents
pln-team
PLNmodels:Poisson Lognormal Models
The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin, 2021 <doi:10.3389/fevo.2021.588292>) can be used for a variety of multivariate problems when count data are at play, including principal component analysis for count data, discriminant analysis, model-based clustering and network inference. Implements variational algorithms to fit such models accompanied with a set of functions for visualization and diagnostic.
Maintained by Julien Chiquet. Last updated 3 days ago.
count-datamultivariate-analysisnetwork-inferencepcapoisson-lognormal-modelopenblascpp
3.8 match 55 stars 9.54 score 226 scripts
alrobles
cofid:Copepod Fish Interaction Database
A curated list of copepod-fish ecological interaction records. It contains the taxonomy of the copepod and the fish and the publication from which the information was obtained. This database contains only marine and brackish water fish species. It excludes fish species that inhabit only freshwater.
Maintained by Angel Robles. Last updated 5 months ago.
10.5 match 3.40 score 3 scripts
wviechtb
metadat:Meta-Analysis Datasets
A collection of meta-analysis datasets for teaching purposes, illustrating/testing meta-analytic methods, and validating published analyses.
Maintained by Wolfgang Viechtbauer. Last updated 14 days ago.
3.4 match 30 stars 10.54 score 65 scripts 93 dependents
yufree
pmd:Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis
Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.
Maintained by Miao YU. Last updated 8 days ago.
mass-spectrometrymetabolomicsnon-target
5.2 match 10 stars 6.78 score 40 scripts
daijiang
megatrees:Subsets of randomly selected phylogenies from existing mega-phylogenies
There are an increasing number of mega-phylogenies available nowadays, with many of them being sets of thousands of posterior distribution phylogenies. For ecological studies, we may need to randomly select many such posterior phylogeneies to conduct analyses. This data package serves this purpose by providing a small number (100) of randomly selected posterior phylogenies (if available) so that we can readily use them for our downstream analyses without repeating the downloading and selecting processes.
Maintained by Daijiang Li. Last updated 3 months ago.
11.4 match 4 stars 3.08 score 2 scripts 1 dependents
mlcollyer
RRPP:Linear Model Evaluation with Randomized Residuals in a Permutation Procedure
Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Maintained by Michael Collyer. Last updated 1 months ago.
3.5 match 4 stars 9.89 score 173 scripts 7 dependentsices-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.
5.4 match 11 stars 6.24 score 131 scripts 2 dependents
vjontiveros
island:Stochastic Island Biogeography Theory Made Easy
Develops stochastic models based on the Theory of Island Biogeography (TIB) of MacArthur and Wilson (1967) <doi:10.1023/A:1016393430551> and extensions. It implements methods to estimate colonization and extinction rates (including environmental variables) given presence-absence data, simulates community assembly, and performs model selection.
Maintained by Vicente Jimenez. Last updated 1 years ago.
10.2 match 3.10 score 42 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
brandmaier
pdc:Permutation Distribution Clustering
Permutation Distribution Clustering is a clustering method for time series. Dissimilarity of time series is formalized as the divergence between their permutation distributions. The permutation distribution was proposed as measure of the complexity of a time series.
Maintained by Andreas M. Brandmaier. Last updated 2 years ago.
5.4 match 6 stars 5.61 score 25 scripts 9 dependents
ezwelty
linbin:Binning and Plotting of Linearly Referenced Data
Short for 'linear binning', the linbin package provides functions for manipulating, binning, and plotting linearly referenced data. Although developed for data collected on river networks, it can be used with any interval or point data referenced to a 1-dimensional coordinate system. Flexible bin generation and batch processing makes it easy to compute and visualize variables at multiple scales, useful for identifying patterns within and between variables and investigating the influence of scale of observation on data interpretation.
Maintained by Ethan Z. Welty. Last updated 2 years ago.
5.8 match 2 stars 5.18 score 25 scripts 1 dependents
rsetienne
DAISIE:Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Maintained by Rampal S. Etienne. Last updated 2 months ago.
3.5 match 9 stars 8.59 score 55 scripts 1 dependentsbioc
frenchFISH:Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections
FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.
Maintained by Adam Berman. Last updated 5 months ago.
softwarebiomedicalinformaticscellbiologygeneticshiddenmarkovmodelpreprocessing
7.3 match 4.00 score 3 scripts
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
flee598
nzffdr:Import, Clean and Update Data from the New Zealand Freshwater Fish Database
Access the New Zealand Freshwater Fish Database from R and a few functions to clean the data once in R.
Maintained by Finnbar Lee. Last updated 3 months ago.
8.7 match 2 stars 3.30 score 2 scripts
dsstoffer
astsa:Applied Statistical Time Series Analysis
Contains data sets and scripts for analyzing time series in both the frequency and time domains including state space modeling as well as supporting the texts Time Series Analysis and Its Applications: With R Examples (5th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2025, <https://link.springer.com/book/9783031705830>, and Time Series: A Data Analysis Approach Using R. Chapman-Hall, 2019, <DOI:10.1201/9780429273285>.
Maintained by David Stoffer. Last updated 2 months ago.
3.6 match 7 stars 7.86 score 2.2k scripts 8 dependents
ss3sim
ss3sim:Fisheries Stock Assessment Simulation Testing with Stock Synthesis
A framework for fisheries stock assessment simulation testing with Stock Synthesis (SS3) as described in Anderson et al. (2014) <doi:10.1371/journal.pone.0092725>.
Maintained by Kelli F. Johnson. Last updated 5 months ago.
fisheriessimulationstock-synthesis
3.2 match 39 stars 8.72 score 149 scripts
fishfollower
stockassessment:State-Space Assessment Model
Fitting SAM...
Maintained by Anders Nielsen. Last updated 25 days ago.
3.5 match 49 stars 7.76 score 324 scripts 2 dependents
mrheath
StrathE2E2:End-to-End Marine Food Web Model
A dynamic model of the big-picture, whole ecosystem effects of hydrodynamics, temperature, nutrients, and fishing on continental shelf marine food webs. The package is described in: Heath, M.R., Speirs, D.C., Thurlbeck, I. and Wilson, R.J. (2020) <doi:10.1111/2041-210X.13510> StrathE2E2: An R package for modelling the dynamics of marine food webs and fisheries. 8pp.
Maintained by Michael Heath. Last updated 4 years ago.
8.6 match 3.10 score 25 scripts
momx
Momocs:Morphometrics using R
The goal of 'Momocs' is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometrics analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.
Maintained by Vincent Bonhomme. Last updated 1 years ago.
3.5 match 51 stars 7.42 score 346 scripts
blue-matter
MSEtool:Management Strategy Evaluation Toolkit
Development, simulation testing, and implementation of management procedures for fisheries (see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Maintained by Adrian Hordyk. Last updated 3 days ago.
3.3 match 8 stars 7.71 score 163 scripts 3 dependents
cbmc-gcmp
dafishr:Download, Wrangle, and Analyse Vessel Monitoring System Data
Allows to download, clean and analyse raw Vessel Monitoring System, VMS, data from Mexican government. You can use the vms_download() function to download raw data, or you can use the sample_dataset provided within the package. You can follow the tutorial in the vignette available at <https://cbmc-gcmp.github.io/dafishr/index.html>.
Maintained by Fabio Favoretto. Last updated 9 months ago.
5.3 match 7 stars 4.85 score 5 scripts
guenardg
codep:Multiscale Codependence Analysis
Computation of Multiscale Codependence Analysis and spatial eigenvector maps.
Maintained by Guillaume Guenard. Last updated 12 months ago.
8.0 match 3.18 score 30 scripts
mstasinopoulos
gamlss.data:Data for Generalised Additive Models for Location Scale and Shape
Data used as examples in the current two books on Generalised Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>.
Maintained by Mikis Stasinopoulos. Last updated 1 years ago.
3.6 match 7.04 score 108 scripts 49 dependents
staffanbetner
rethinking:Statistical Rethinking book package
Utilities for fitting and comparing models
Maintained by Richard McElreath. Last updated 4 months ago.
4.5 match 5.42 score 4.4k scripts
kjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 12 months ago.
10.4 match 2.28 score 38 scriptsr-forge
Sleuth3:Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed)", Cengage Learning.
Maintained by Berwin A Turlach. Last updated 1 years ago.
3.8 match 6.29 score 522 scripts
schochastics
networkdata:Repository of Network Datasets
The package contains a large collection of network dataset with different context. This includes social networks, animal networks and movie networks. All datasets are in 'igraph' format.
Maintained by David Schoch. Last updated 1 years ago.
4.5 match 143 stars 5.01 score 143 scripts
isaacfab
rmetalog:The Metalog Distribution
Implementation of the metalog distribution in R. The metalog distribution is a modern, highly flexible, data-driven distribution. Metalogs are developed by Keelin (2016) <doi:10.1287/deca.2016.0338>. This package provides functions to build these distributions from raw data. Resulting metalog objects are then useful for exploratory and probabilistic analysis.
Maintained by Isaac Faber. Last updated 4 years ago.
3.6 match 34 stars 6.20 score 31 scripts
alecri
dosresmeta:Multivariate Dose-Response Meta-Analysis
Estimates dose-response relations from summarized dose-response data and to combines them according to principles of (multivariate) random-effects models.
Maintained by Alessio Crippa. Last updated 6 years ago.
3.4 match 11 stars 6.56 score 66 scripts
dwarton
ecostats:Code and Data Accompanying the Eco-Stats Text (Warton 2022)
Functions and data supporting the Eco-Stats text (Warton, 2022, Springer), and solutions to exercises. Functions include tools for using simulation envelopes in diagnostic plots, and a function for diagnostic plots of multivariate linear models. Datasets mentioned in the package are included here (where not available elsewhere) and there is a vignette for each chapter of the text with solutions to exercises.
Maintained by David Warton. Last updated 1 years ago.
3.3 match 8 stars 6.58 score 53 scriptscran
drc:Analysis of Dose-Response Curves
Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
Maintained by Christian Ritz. Last updated 9 years ago.
3.5 match 8 stars 6.25 score 28 dependentscran
flexclust:Flexible Cluster Algorithms
The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.
Maintained by Bettina Grün. Last updated 28 days ago.
3.8 match 3 stars 5.81 score 52 dependentsr-forge
Sleuth2:Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)", Duxbury.
Maintained by Berwin A Turlach. Last updated 1 years ago.
3.8 match 5.79 score 191 scripts
haddonm
MQMF:Modelling and Quantitative Methods in Fisheries
Complements the book "Using R for Modelling and Quantitative Methods in Fisheries" ISBN 9780367469894, published in 2021 by Chapman & Hall in their "Using R series". There are numerous functions and data-sets that are used in the book's many practical examples.
Maintained by Malcolm Haddon. Last updated 2 years ago.
ecologyfisherieshaddonquantitative-methodsuncertainty
5.1 match 11 stars 4.14 score 25 scripts
caetanods
ratematrix:Bayesian Estimation of the Evolutionary Rate Matrix
The Evolutionary Rate Matrix is a variance-covariance matrix which describes both the rates of trait evolution and the evolutionary correlation among multiple traits. This package has functions to estimate these parameters using Bayesian MCMC. It is possible to test if the pattern of evolutionary correlations among traits has changed between predictive regimes painted along the branches of the phylogenetic tree. Regimes can be created a priori or estimated as part of the MCMC under a joint estimation approach. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.
Maintained by Daniel Caetano. Last updated 2 years ago.
3.6 match 10 stars 5.91 score 18 scripts 1 dependents
mikkovihtakari
ggOceanMaps:Plot Data on Oceanographic Maps using 'ggplot2'
Allows plotting data on bathymetric maps using 'ggplot2'. Plotting oceanographic spatial data is made as simple as feasible, but also flexible for custom modifications. Data that contain geographic information from anywhere around the globe can be plotted on maps generated by the basemap() or qmap() functions using 'ggplot2' layers separated by the '+' operator. The package uses spatial shape- ('sf') and raster ('stars') files, geospatial packages for R to manipulate, and the 'ggplot2' package to plot these files. The package ships with low-resolution spatial data files and higher resolution files for detailed maps are stored in the 'ggOceanMapsLargeData' repository on GitHub and downloaded automatically when needed.
Maintained by Mikko Vihtakari. Last updated 5 months ago.
3.5 match 48 stars 5.97 score 193 scripts
natydasilva
PPforest:Projection Pursuit Classification Forest
Implements projection pursuit forest algorithm for supervised classification.
Maintained by Natalia da Silva. Last updated 9 months ago.
3.8 match 18 stars 5.53 score 19 scripts
statmanrobin
Lock5Data:Datasets for "Statistics: UnLocking the Power of Data"
Datasets for the third edition of "Statistics: Unlocking the Power of Data" by Lock^5 Includes version of datasets from earlier editions.
Maintained by Robin Lock. Last updated 4 years ago.
7.6 match 2.67 score 322 scripts
ejosymart
sizeMat:Estimate Size at Sexual Maturity
Estimate morphometric and gonadal size at sexual maturity for organisms, usually fish and invertebrates. It includes methods for classification based on relative growth (using principal components analysis, hierarchical clustering, discriminant analysis), logistic regression (Frequentist or Bayes), parameters estimation and some basic plots.
Maintained by Josymar Torrejon-Magallanes. Last updated 1 years ago.
allometric-variablesgonad-maturitymorphometric-maturity
4.3 match 4 stars 4.72 score 26 scriptsropensci
rredlist:'IUCN' Red List Client
'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.
Maintained by William Gearty. Last updated 2 months ago.
iucnbiodiversityapiweb-servicestraitshabitatspeciesconservationapi-wrapperiucn-red-listtaxize
1.8 match 53 stars 11.49 score 195 scripts 24 dependents
globalfishingwatch
gfwr:Access data from Global Fishing Watch APIs
This package connects to several Global Fishing Watch APIs to get vessel and events information in an R-friendly format.
Maintained by Andrea Sánchez-Tapia. Last updated 2 months ago.
api-wrapperglobalfishingwatchmapping
3.5 match 63 stars 5.79 score 66 scripts
polehalieutique
EcoTroph:An implementation of the EcoTroph Ecosystem modelling approach
An approach and software for modelling marine and freshwater ecosystems. It is articulated entirely around trophic levels. EcoTroph's key displays are bivariate plots, with trophic levels as the abscissa, and biomass flows or related quantities as ordinates. Thus, trophic ecosystem functioning can be modelled as a continuous flow of biomass surging up the food web, from lower to higher trophic levels, due to predation and ontogenic processes. Such an approach, wherein species as such disappear, may be viewed as the ultimate stage in the use of the trophic level metric for ecosystem modelling, providing a simplified but potentially useful caricature of ecosystem functioning and impacts of fishing. This version contains catch trophic spectrum analysis (CTSA) function and corrected versions of the mf.diagnosis and create.ETmain functions.
Maintained by Jerome Guitton. Last updated 2 years ago.
6.8 match 1 stars 2.93 score 17 scriptsstatmanrobin
Stat2Data:Datasets for Stat2
Datasets for the textbook Stat2: Modeling with Regression and ANOVA (second edition). The package also includes data for the first edition, Stat2: Building Models for a World of Data and a few functions for plotting diagnostics.
Maintained by Robin Lock. Last updated 6 years ago.
4.0 match 5 stars 4.94 score 544 scriptsices-tools-prod
icesVMS:Link to the ICES Vessel Monitoring System and Logbook Database Web Services
Links to the ICES Vessel Monitoring System (VMS) and logbook database web services <https://data.ices.dk/vms/webservices> to allow users to download summaries and data products.
Maintained by Colin Millar. Last updated 6 months ago.
7.3 match 2 stars 2.66 score 46 scripts
waldronlab
SingleCellMultiModal:Integrating Multi-modal Single Cell Experiment datasets
SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the 'citation' function and see <https://doi.org/10.1371/journal.pcbi.1011324>.
Maintained by Marcel Ramos. Last updated 4 months ago.
experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073
2.7 match 17 stars 7.29 score 60 scripts
thomasfillon
kernopt:Estimating Count Data Distributions with Discrete Optimal Symmetric Kernel
Implementation of Discrete Symmetric Optimal Kernel for estimating count data distributions, as described by T. Senga Kiessé and G. Durrieu (2024) <doi:10.1016/j.spl.2024.110078>.The nonparametric estimator using the discrete symmetric optimal kernel was illustrated on simulated data sets and a real-word data set included in the package, in comparison with two other discrete symmetric kernels.
Maintained by Thomas Fillon. Last updated 8 days ago.
3.8 match 5.18 scoreflr
FLash:Forecasting and Projection of Fish Stocks
Projecting the future dynamics of fish stocks is an essential part of fisheries science and management advice. The FLash package carries out forecasts of fish stocks (FLStock objects) according to a defined table of targets and limits (fwdControl) and applying and specified stock-recruitment relationship.
Maintained by Laurence T. Kell. Last updated 4 months ago.
3.9 match 4.92 score 186 scripts 1 dependents
arni-magnusson
scape:Statistical Catch-at-Age Plotting Environment
Import, plot, and diagnose results from statistical catch-at-age models, used in fisheries stock assessment.
Maintained by Arni Magnusson. Last updated 5 months ago.
3.3 match 5.72 score 35 scriptsarni-magnusson
fishgrowth:Fit Growth Curves to Fish Data
Fit growth models to otoliths and/or tagging data, using the 'RTMB' package and maximum likelihood. The otoliths (or similar measurements of age) provide direct observed coordinates of age and length. The tagging data provide information about the observed length at release and length at recapture at a later time, where the age at release is unknown and estimated as a vector of parameters. The growth models provided by this package can be fitted to otoliths only, tagging data only, or a combination of the two. Growth variability can be modelled as constant or increasing with length.
Maintained by Arni Magnusson. Last updated 1 months ago.
4.8 match 2 stars 3.95 score 5 scriptscran
optistock:Determine Optimum Stocking Times Used in Fishery Enhancements
A collection of functions that aid in calculating the optimum time to stock hatchery reared fish into a body of water given the growth, mortality and cost of raising a particular number of individuals to a certain length.
Maintained by Paul Frater. Last updated 2 years ago.
9.0 match 2.00 score
jonathansmart
BayesGrowth:Estimate Fish Growth Using MCMC Analysis
Estimate fish length-at-age models using MCMC analysis with 'rstan' models. This package allows a multimodel approach to growth fitting to be applied to length-at-age data and is supported by further analyses to determine model selection and result presentation. The core methods of this package are presented in Smart and Grammer (2021) "Modernising fish and shark growth curves with Bayesian length-at-age models". PLOS ONE 16(2): e0246734 <doi:10.1371/journal.pone.0246734>.
Maintained by Jonathan Smart. Last updated 1 years ago.
3.7 match 11 stars 4.74 score 8 scripts
jverzani
UsingR:Data Sets, Etc. for the Text "Using R for Introductory Statistics", Second Edition
A collection of data sets to accompany the textbook "Using R for Introductory Statistics," second edition.
Maintained by John Verzani. Last updated 3 years ago.
3.5 match 1 stars 4.97 score 1.4k scripts
cedricbriandgithub
stacomiR:Fish Migration Monitoring
Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Office for Biodiversity institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'.
Maintained by Cedric Briand. Last updated 1 years ago.
7.1 match 1 stars 2.43 score 27 scriptsdaijiang
neonDivData:Standardized NEON Organismal Data for Biodiversity Research
Cleaned, simplified, and standardized NEON organismal data for biodiversity research. The following taxonomic groups are included so far: algae, beetles, birds, fish, herptiles, macroinvertebrates, mosquitoes, plants, small_mammals, ticks, tick_pathogens, and zooplankton. NEON input data (<https://data.neonscience.org>) were processed and standardized using R package `ecocomDP` (<https://github.com/EDIorg/ecocomDP>).
Maintained by Daijiang Li. Last updated 11 months ago.
4.1 match 15 stars 4.18 score 17 scripts
hgerritsen
mapplots:Data Visualisation on Maps
Create simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data. The package was developed for displaying fisheries data but most functions can be used for more generic data visualisation.
Maintained by Hans Gerritsen. Last updated 2 years ago.
3.5 match 2 stars 4.90 score 442 scripts 3 dependents
hezibu
alien:Estimate Invasive and Alien Species (IAS) Introduction Rates
Easily estimate the introduction rates of alien species given first records data. It specializes in addressing the role of sampling on the pattern of discoveries, thus providing better estimates than using Generalized Linear Models which assume perfect immediate detection of newly introduced species.
Maintained by Yehezkel Buba. Last updated 9 months ago.
3.4 match 1 stars 5.08 score 10 scripts
rudeboybert
resampledata:Data Sets for Mathematical Statistics with Resampling in R
Package of data sets from "Mathematical Statistics with Resampling in R" (1st Ed. 2011, 2nd Ed. 2018) by Laura Chihara and Tim Hesterberg.
Maintained by Albert Y. Kim. Last updated 5 months ago.
3.3 match 15 stars 5.15 score 187 scriptsflr
FLFishery:Classes and Methods for Simpler Fleet/Fishery Modelling
A set of classes and methods for modelling of fleet dynamics. Fisheries are groups of vessels sharing an effort time series, with static or changing spatio-temporal patterns in selectivity.
Maintained by Iago Mosqueira. Last updated 4 months ago.
5.5 match 3.02 score 8 scripts 7 dependentsmhpob
simfish:simulate fish tracks & acoustic detections
facilitates simulation of fish tracks in featureless and semi-realistic environments (coastal oceans, fjords, and lakes). A user-defined raster defining the water body - land boundaries is used to constrain simulated tracks. Fish movements are simulated (currently) as either a correlated random walk or a biased & correlated random walk, with the bias toward a defined Centre-of-Attraction. A potential function is used to ensure the tracks avoid land. The package can also be used to simulate detections of acoustically-tagged fish by acoustic receivers at user-defined locations.
Maintained by Ian Jonsen. Last updated 1 years ago.
5.9 match 2.70 score 3 scriptscran
COUNT:Functions, Data and Code for Count Data
Functions, data and code for Hilbe, J.M. 2011. Negative Binomial Regression, 2nd Edition (Cambridge University Press) and Hilbe, J.M. 2014. Modeling Count Data (Cambridge University Press).
Maintained by Andrew Robinson. Last updated 8 years ago.
6.0 match 2.64 score 1 dependents
khliland
EMSC:Extended Multiplicative Signal Correction
Background correction of spectral like data. Handles variations in scaling, polynomial baselines, interferents, constituents and replicate variation. Parameters for corrections are stored for further analysis, and spectra are corrected accordingly.
Maintained by Kristian Hovde Liland. Last updated 1 years ago.
3.8 match 3 stars 4.18 score 9 scripts
noaa-nwfsc
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.
Maintained by Eric J. Ward. Last updated 11 days ago.
2.5 match 8 stars 6.19 score 12 scripts
iembry
ie2miscdata:Irucka Embry's Miscellaneous USGS Data Collection
A collection of Irucka Embry's miscellaneous USGS data sets (USGS Parameter codes with fixed values, USGS global time zone codes, and US Air Force Global Engineering Weather Data). Irucka created these data sets while a Cherokee Nation Technology Solutions (CNTS) United States Geological Survey (USGS) Contractor and/or USGS employee.
Maintained by Irucka Embry. Last updated 2 years ago.
3.8 match 4.00 score
tspaulding-esa
telemetR:Filter and Analyze Generalised Telemetry Data from Organisms
Analyze telemetry datasets generalized to allow any technology. The filtering steps check for false positives caused by reflected transmissions from surfaces and false pings from other noise generating equipment. The filters are based on JSATS filtering algorithms found in package 'filteRjsats' <https://CRAN.R-project.org/package=filteRjsats> but have been generalized to allow the user to define many of the filtering variables. Additionally, this package contains scripts used to help identify an optimal maximum blanking period as defined in Capello et al (2015) <doi:10.1371/journal.pone.0134002>. The functions were written according to their manuscript description, but have not been reviewed by the authors for accuracy. It is included here as is, without warranty.
Maintained by Taylor Spaulding. Last updated 1 years ago.
4.5 match 2 stars 3.30 score 3 scripts
vda1r22
bbnet:Create Simple Predictive Models on Bayesian Belief Networks
A system to build, visualise and evaluate Bayesian belief networks. The methods are described in Stafford et al. (2015) <doi:10.12688/f1000research.5981.1>.
Maintained by Victoria Dominguez Almela. Last updated 2 months ago.
3.4 match 4.30 score 9 scripts
eriqande
rubias:Bayesian Inference from the Conditional Genetic Stock Identification Model
Implements Bayesian inference for the conditional genetic stock identification model. It allows inference of mixed fisheries and also simulation of mixtures to predict accuracy. A full description of the underlying methods is available in a recently published article in the Canadian Journal of Fisheries and Aquatic Sciences: <doi:10.1139/cjfas-2018-0016>.
Maintained by Eric C. Anderson. Last updated 1 years ago.
2.5 match 3 stars 5.90 score 89 scriptspoissonconsulting
curtisquadata:Curtis and Qua Creeks Productivity Study Data
Fifteen relational tibbles from the Curtis and Qua Creeks Productivity study. The study which ran from 2015 to 2017 collected data on the water quality and temperature, periphyton, benthic invertebrates and fish populations of Curtis and Qua Creeks in the Salmo Watershed, British Columbia.
Maintained by Joe Thorley. Last updated 2 months ago.
6.5 match 2.18 score 2 scriptscran
cluster.datasets:Cluster Analysis Data Sets
A collection of data sets for teaching cluster analysis.
Maintained by Frederick Novomestky. Last updated 11 years ago.
6.9 match 2.00 score
prabhanjan-tattar
gpk:100 Data Sets for Statistics Education
Collection of datasets as prepared by Profs. A.P. Gore, S.A. Paranjape, and M.B. Kulkarni of Department of Statistics, Poona University, India. With their permission, first letter of their names forms the name of this package, the package has been built by me and made available for the benefit of R users. This collection requires a rich class of models and can be a very useful building block for a beginner.
Maintained by Prabhanjan Tattar. Last updated 12 years ago.
8.0 match 1.69 score 49 scripts
jlaake
marked:Mark-Recapture Analysis for Survival and Abundance Estimation
Functions for fitting various models to capture-recapture data including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and the multi-variate state model structure for survival estimation and POPAN structured Jolly-Seber models for abundance estimation. There are also Hidden Markov model (HMM) implementations of CJS and multistate models with and without state uncertainty and a simulation capability for HMM models.
Maintained by Jeff Laake. Last updated 1 years ago.
3.3 match 1 stars 4.09 score 85 scripts 1 dependents
ejikeugba
gofcat:Goodness-of-Fit Measures for Categorical Response Models
A post-estimation method for categorical response models (CRM). Inputs from objects of class serp(), clm(), polr(), multinom(), mlogit(), vglm() and glm() are currently supported. Available tests include the Hosmer-Lemeshow tests for the binary, multinomial and ordinal logistic regression; the Lipsitz and the Pulkstenis-Robinson tests for the ordinal models. The proportional odds, adjacent-category, and constrained continuation-ratio models are particularly supported at ordinal level. Tests for the proportional odds assumptions in ordinal models are also possible with the Brant and the Likelihood-Ratio tests. Moreover, several summary measures of predictive strength (Pseudo R-squared), and some useful error metrics, including, the brier score, misclassification rate and logloss are also available for the binary, multinomial and ordinal models. Ugba, E. R. and Gertheiss, J. (2018) <http://www.statmod.org/workshops_archive_proceedings_2018.html>.
Maintained by Ejike R. Ugba. Last updated 2 years ago.
brant-testbrier-scoreshosmer-lemeshow-testlikelihood-ratio-testlipsitz-testlog-loss-score-metriclogistic-regressionmisclassificationordinal-regressionproportional-odds-testpseudo-r2pulkstenis-robinson-test
4.0 match 2 stars 3.18 score 15 scriptseriqande
CKMRpop:Forward-in-Time Simulation and Tallying of Pairwise Relationships
Provides an R wrapper around the program 'spip' (<https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1471-8286.2005.00884.x>), a C program for the simulation of pedigrees within age-structured populations with user-specified life histories. Also includes a variety of functions to parse 'spip' output to compile information about related pairs amongst simulated, sampled individuals, to assess the feasibility and potential accuracy of close-kin mark-recapture (CKMR). Full documentation and vignettes are mirrored at <https://eriqande.github.io/CKMRpop/index.html> and can be read online there.
Maintained by Eric C. Anderson. Last updated 1 years ago.
2.3 match 4 stars 5.38 score 24 scripts
barnhilldave
TML:Tropical Geometry Tools for Machine Learning
Suite of tropical geometric tools for use in machine learning applications. These methods may be summarized in the following references: Yoshida, et al. (2022) <arxiv:2209.15045>, Barnhill et al. (2023) <arxiv:2303.02539>, Barnhill and Yoshida (2023) <doi:10.3390/math11153433>, Aliatimis et al. (2023) <arXiv:2306.08796>, Yoshida et al. (2022) <arXiv:2206.04206>, and Yoshida et al. (2019) <doi:10.1007/s11538-018-0493-4>.
Maintained by David Barnhill. Last updated 8 months ago.
3.5 match 3 stars 3.48 score 1 scriptscran
ecopower:Power Estimates and Equivalence Testing for Multivariate Data
Estimates power by simulation for multivariate abundance data to be used for sample size estimates. Multivariate equivalence testing by simulation from a Gaussian copula model. The package also provides functions for parameterising multivariate effect sizes and simulating multivariate abundance data jointly. The discrete Gaussian copula approach is described in Popovic et al. (2018) <doi:10.1016/j.jmva.2017.12.002>.
Maintained by Michelle Lim. Last updated 2 years ago.
4.5 match 2.70 scorebioc
FISHalyseR:FISHalyseR a package for automated FISH quantification
FISHalyseR provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis.
Maintained by Karesh Arunakirinathan. Last updated 5 months ago.
3.5 match 3.30 score 2 scripts
agroscope-ch
OpenFoodTox:EFSA OpenFoodTox Data Made Accessible as an R Package
Provides convenient access to data extracted from some of the spreadsheet files made available by the chemical hazards database of the European Food Safety Authority (EFSA), accessible via <https://www.efsa.europa.eu/en/data-report/chemical-hazards-database-openfoodtox>.
Maintained by Johannes Ranke. Last updated 8 months ago.
3.3 match 1 stars 3.48 score 2 scripts
timhesterberg
resampledata3:Data Sets for "Mathematical Statistics with Resampling and R" (3rd Ed)
Data sets for Chihara and Hesterberg (2022, ISBN: 978-1-119-87404-1) "Mathematical Statistics with Resampling in R" (3rd Ed).
Maintained by Tim Hesterberg. Last updated 3 years ago.
7.2 match 1.52 score 33 scriptsbioc
RNAsense:Analysis of Time-Resolved RNA-Seq Data
RNA-sense tool compares RNA-seq time curves in two experimental conditions, i.e. wild-type and mutant, and works in three steps. At Step 1, it builds expression profile for each transcript in one condition (i.e. wild-type) and tests if the transcript abundance grows or decays significantly. Dynamic transcripts are then sorted to non-overlapping groups (time profiles) by the time point of switch up or down. At Step 2, RNA-sense outputs the groups of differentially expressed transcripts, which are up- or downregulated in the mutant compared to the wild-type at each time point. At Step 3, Correlations (Fisher's exact test) between the outputs of Step 1 (switch up- and switch down- time profile groups) and the outputs of Step2 (differentially expressed transcript groups) are calculated. The results of the correlation analysis are printed as two-dimensional color plot, with time profiles and differential expression groups at y- and x-axis, respectively, and facilitates the biological interpretation of the data.
Maintained by Marcus Rosenblatt. Last updated 5 months ago.
rnaseqgeneexpressiondifferentialexpression
3.3 match 1 stars 3.30 score 2 scripts
juvlac
camerondata:Datasets from "Microeconometrics: Methods and Applications" by Cameron and Trivedi
Quick and easy access to datasets that let you replicate the empirical examples in Cameron and Trivedi (2005) "Microeconometrics: Methods and Applications" (ISBN: 9780521848053).The data are available as soon as you install and load the package (lazy-loading) as data frames. The documentation includes reference to chapter sections and page numbers where the datasets are used.
Maintained by Juliana Vega-Lacorte. Last updated 3 years ago.
4.0 match 2.70 score 1 scriptsblue-matter
SAMtool:Stock Assessment Methods Toolkit
Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Maintained by Quang Huynh. Last updated 1 months ago.
1.7 match 3 stars 6.39 score 36 scripts 1 dependents
sbashevkin
LTMRdata:Data for the IEP Long Term Monitoring Survey Review
Integration of the Fall Midwater Trawl, Bay Study, and Suisun Marsh Fish Study data for use in the IEP long-term monitoring survey review.
Maintained by Sam Bashevkin. Last updated 6 months ago.
2.5 match 5 stars 4.26 score 10 scriptscran
fishkirkko2015:Dataset of Measurements of Fish Species at Kirkkojarvi Lake, Finland
Dataset of 302 measurements of 11 fish species to accompany the manuscript "Length-weight relationships of six freshwater fish species from lake Kirkkojarvi, Finland".
Maintained by Jose Gama. Last updated 9 years ago.
10.6 match 1.00 score
peterkdunn
GLMsData:Generalized Linear Model Data Sets
Data sets from the book Generalized Linear Models with Examples in R by Dunn and Smyth.
Maintained by Peter K. Dunn. Last updated 3 years ago.
4.0 match 2.61 score 220 scripts
rdinnager
rbff:R Interface to Boundary First Flattening Software (BFF)
Flatten 3D meshes into arbitrary 2D shapes using boundary first flattening (<https://github.com/GeometryCollective/boundary-first-flattening>).
Maintained by Russell Dinnage. Last updated 3 years ago.
4.0 match 5 stars 2.40 score 6 scripts
pik-piam
mrfish:madrat data preparation for data connected to fish
Package contains routines to prepare data for validation exercises.
Maintained by Benjamin Leon Bodirsky. Last updated 1 years ago.
4.6 match 2.00 score 1 scripts
jsl5-code
mixexp:Design and Analysis of Mixture Experiments
Functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.
Maintained by John Lawson. Last updated 5 months ago.
3.3 match 1 stars 2.75 score 31 scripts 2 dependents
sborstein
dietr:Diet Estimated Trophic Levels
Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Borstein (2020) <doi:10.1007/s10750-020-04417-5>.
Maintained by Samuel R. Borstein. Last updated 2 months ago.
1.7 match 5 stars 5.41 score 13 scripts
cschwarz-stat-sfu-ca
BTSPAS:Bayesian Time-Stratified Population Analysis
Provides advanced Bayesian methods to estimate abundance and run-timing from temporally-stratified Petersen mark-recapture experiments. Methods include hierarchical modelling of the capture probabilities and spline smoothing of the daily run size. Theory described in Bonner and Schwarz (2011) <doi:10.1111/j.1541-0420.2011.01599.x>.
Maintained by Carl J Schwarz. Last updated 5 months ago.
1.6 match 1 stars 5.70 score 28 scripts 1 dependents
biointf
FBN:FISH Based Normalization and Copy Number Inference of SNP Microarray Data
Normalizes the data from a file containing the raw values of the SNP probes of microarray data by using the FISH probes and their corresponding copy number.
Maintained by Luca Agnelli. Last updated 2 years ago.
6.6 match 1.32 score 21 scripts
richardli
surveyPrev:Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas
Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.
Maintained by Qianyu Dong. Last updated 2 days ago.
1.5 match 1 stars 5.76 score 11 scripts
michaelspence
LeMaRns:Length-Based Multispecies Analysis by Numerical Simulation
Set up, run and explore the outputs of the Length-based Multi-species model (LeMans; Hall et al. 2006 <doi:10.1139/f06-039>), focused on the marine environment.
Maintained by Michael A. Spence. Last updated 5 years ago.
3.0 match 2.90 score 16 scriptsropensci
rtika:R Interface to 'Apache Tika'
Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
Maintained by Sasha Goodman. Last updated 2 years ago.
extract-metadataextract-textjavaparsepdf-filespeer-reviewedtesseracttika
1.3 match 55 stars 6.00 score 12 scriptsjlaake
RMark:R Code for Mark Analysis
An interface to the software package MARK that constructs input files for MARK and extracts the output. MARK was developed by Gary White and is freely available at <http://www.phidot.org/software/mark/downloads/> but is not open source.
Maintained by Jeff Laake. Last updated 3 years ago.
1.7 match 4.77 score 366 scripts 4 dependentscran
sensitivitymv:Sensitivity Analysis in Observational Studies
The package performs a sensitivity analysis in an observational study using an M-statistic, for instance, the mean. The main function in the package is senmv(), but amplify() and truncatedP() are also useful. The method is developed in Rosenbaum Biometrics, 2007, 63, 456-464, <doi:10.1111/j.1541-0420.2006.00717.x>.
Maintained by Paul R. Rosenbaum. Last updated 7 years ago.
3.8 match 2.08 score 4 dependents
torstax
amregtest:Runs Allelematch Regression Tests
Automates regression testing of package 'allelematch'. Over 2500 tests covers all functions in 'allelematch', reproduces the examples from the documentation and includes negative tests. The implementation is based on 'testthat'.
Maintained by Torvald Staxler. Last updated 12 months ago.
2.4 match 3.18 score 3 scripts
nicola-zaccarelli
RInSp:R Individual Specialization
Functions to calculate several ecological indices of individual and population niche width (Araujo's E, clustering and pairwise similarity among individuals, IS, Petraitis' W, and Roughgarden's WIC/TNW) to assess individual specialization based on data of resource use. Resource use can be quantified by counts of categories, measures of mass or length, or proportions. Monte Carlo resampling procedures are available for hypothesis testing against multinomial null models. Details are provided in Zaccarelli et al. (2013) <doi:10.1111/2041-210X.12079> and associated references.
Maintained by Dr. Nicola Zaccarelli. Last updated 3 years ago.
3.4 match 2.12 score 33 scripts
sprfmo
jjmR:Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model
Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model.
Maintained by Ricardo Oliveros-Ramos. Last updated 6 months ago.
1.9 match 2 stars 3.81 score 12 scripts 1 dependents
adrianhordyk
DLMtool:Data-Limited Methods Toolkit
A collection of data-limited management procedures that can be evaluated with management strategy evaluation with the 'MSEtool' package, or applied to fishery data to provide management recommendations.
Maintained by Adrian Hordyk. Last updated 3 years ago.
1.9 match 1 stars 3.67 score 229 scripts 1 dependents
ruben-hernan
CatDyn:Fishery Stock Assessment by Catch Dynamics Models
Based on fishery Catch Dynamics instead of fish Population Dynamics (hence CatDyn) and using high-frequency or medium-frequency catch in biomass or numbers, fishing nominal effort, and mean fish body weight by time step, from one or two fishing fleets, estimate stock abundance, natural mortality rate, and fishing operational parameters. It includes methods for data organization, plotting standard exploratory and analytical plots, predictions, for 100 types of models of increasing complexity, and 72 likelihood models for the data.
Maintained by Ruben H. Roa-Ureta. Last updated 6 years ago.
4.7 match 1 stars 1.45 score 28 scriptssprfmo
FLjjm:Running the JJM Stock Assessment Model Inside the MSE FLR System
Runs the JJM stock assessment model for Chilean Jack Mackerel inside the MSE system of FLR's mse package.
Maintained by Iago Mosqueira. Last updated 21 days ago.
1.8 match 3.74 score 3 scripts
nmartinkova
diemr:Diagnostic Index Expectation Maximisation in R
Likelihood-based genome polarisation finds which alleles of genomic markers belong to which side of the barrier. Co-estimates which individuals belong to either side of the barrier and barrier strength. Uses expectation maximisation in likelihood framework. The method is described in Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Maintained by Natalia Martinkova. Last updated 2 months ago.
2.0 match 3.26 score 1 scripts
kenkellner
IPMbook:Functions and Data for the Book 'Integrated Population Models'
Provides functions and data sets to accompany the book 'Integrated Population Models: Theory and Ecological Applications with R and JAGS' by Michael Schaub and Marc Kéry (ISBN: 9780128205648).
Maintained by Ken Kellner. Last updated 1 months ago.
1.5 match 1 stars 3.95 score 177 scripts
cseljatib
datana:Datasets and Functions to Accompany Analisis De Datos Con R
Datasets and functions to accompany the book 'Analisis de datos con el programa estadistico R: una introduccion aplicada' by Salas-Eljatib (2021, ISBN: 9789566086109). The package helps carry out data management, exploratory analyses, and model fitting.
Maintained by Christian Salas-Eljatib. Last updated 2 days ago.
4.0 match 1.48 score 1 scripts
jahmadkhan
DELTD:Kernel Density Estimation using Lifetime Distributions
A collection of asymmetrical kernels belong to lifetime distributions for kernel density estimation is presented. Mean Squared Errors (MSE) are calculated for estimated curves. For this purpose, R functions allow the distribution to be Gamma, Exponential or Weibull. For details see Chen (2000a,b), Jin and Kawczak (2003) and Salha et al. (2014) <doi:10.12988/pms.2014.4616>.
Maintained by Javaria Ahmad Khan. Last updated 3 years ago.
4.0 match 1.48 score 1 dependentscran
bayesmix:Bayesian Mixture Models with JAGS
Fits finite mixture models of univariate Gaussian distributions using JAGS within a Bayesian framework.
Maintained by Bettina Gruen. Last updated 2 years ago.
4.0 match 1.48 score 1 dependents
amoeba
upriver:An R package for in-river fish migration and timing calculation
An R package for in-river fish migration and timing calculation.
Maintained by Bryce Mecum. Last updated 8 years ago.
3.4 match 1.70 scorecran
EngrExpt:Data sets from "Introductory Statistics for Engineering Experimentation"
Datasets from Nelson, Coffin and Copeland "Introductory Statistics for Engineering Experimentation" (Elsevier, 2003) with sample code.
Maintained by Douglas Bates. Last updated 16 years ago.
5.6 match 1.00 score
mhpob
telemetar:Archetypes for Targets and Fish Telemetry
What the package does (one paragraph).
Maintained by Michael OBrien. Last updated 1 years ago.
3.1 match 1.70 score 3 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
1.8 match 5 stars 2.88 score 5 scripts
colinpmillar
rct3:Predict Fish Year-Class Strength from Survey Data
Predict fish year-class strength by calibration regression analysis of multiple recruitment index series.
Maintained by Colin Millar. Last updated 5 years ago.
5.1 match 1.00 score 1 scripts
markbravington
microscoping:Preliminary feasibility for CKMR
Rough-as-guts laugh-test design calculations for CKMR on fish
Maintained by Mark V. Bravington. Last updated 9 months ago.
2.3 match 2.18 score 1 dependents
nschuwirth
ecoval:Procedures for Ecological Assessment of Surface Waters
Functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions.
Maintained by Nele Schuwirth. Last updated 3 years ago.
3.7 match 1.34 score 22 scripts
hanzifei
gcKrig:Analysis of Geostatistical Count Data using Gaussian Copulas
Provides a variety of functions to analyze and model geostatistical count data with Gaussian copulas, including 1) data simulation and visualization; 2) correlation structure assessment (here also known as the Normal To Anything); 3) calculate multivariate normal rectangle probabilities; 4) likelihood inference and parallel prediction at predictive locations. Description of the method is available from: Han and DeOliveira (2018) <doi:10.18637/jss.v087.i13>.
Maintained by Zifei Han. Last updated 3 years ago.
3.6 match 1 stars 1.15 score 14 scripts
lisalibungan
shapeR:Collection and Analysis of Otolith Shape Data
Studies otolith shape variation among fish populations. Otoliths are calcified structures found in the inner ear of teleost fish and their shape has been known to vary among several fish populations and stocks, making them very useful in taxonomy, species identification and to study geographic variations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise, choose from conducting either a Fourier or wavelet transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.
Maintained by Lisa Anne Libungan. Last updated 7 years ago.
0.9 match 9 stars 4.45 score 21 scripts
hiweller
colordistance:Distance Metrics for Image Color Similarity
Loads and displays images, selectively masks specified background colors, bins pixels by color using either data-dependent or automatically generated color bins, quantitatively measures color similarity among images using one of several distance metrics for comparing pixel color clusters, and clusters images by object color similarity. Uses CIELAB, RGB, or HSV color spaces. Originally written for use with organism coloration (reef fish color diversity, butterfly mimicry, etc), but easily applicable for any image set.
Maintained by Hannah Weller. Last updated 1 years ago.
0.5 match 37 stars 7.93 score 76 scripts 2 dependents
jessica-arbour
LOST:Missing Morphometric Data Simulation and Estimation
Functions for simulating missing morphometric data randomly, with taxonomic bias and with anatomical bias. LOST also includes functions for estimating linear and geometric morphometric data.
Maintained by J. Arbour. Last updated 2 months ago.
1.7 match 2.30 score 4 scriptscran
submax:Effect Modification in Observational Studies Using the Submax Method
Effect modification occurs if a treatment effect is larger or more stable in certain subgroups defined by observed covariates. The submax or subgroup-maximum method of Lee et al. (2017) <arXiv:1702.00525> does an overall test and separate tests in subgroups, correcting for multiple testing using the joint distribution.
Maintained by Paul R. Rosenbaum. Last updated 7 years ago.
3.8 match 1.00 scorecran
sensitivitymw:Sensitivity Analysis for Observational Studies Using Weighted M-Statistics
Sensitivity analysis for tests, confidence intervals and estimates in matched observational studies with one or more controls using weighted or unweighted Huber-Maritz M-tests (including the permutational t-test). The method is from Rosenbaum (2014) Weighted M-statistics with superior design sensitivity in matched observational studies with multiple controls JASA, 109(507), 1145-1158 <doi:10.1080/01621459.2013.879261>.
Maintained by Paul R. Rosenbaum. Last updated 3 years ago.
3.8 match 1 stars 1.00 scorecran
KnowBR:Discriminating Well Surveyed Spatial Units from Exhaustive Biodiversity Databases
It uses species accumulation curves and diverse estimators to assess, at the same time, the levels of survey coverage in multiple geographic cells of a size defined by the user or polygons. It also enables the geographical depiction of observed species richness, survey effort and completeness values including a background with administrative areas.
Maintained by Castor Guisande Gonzalez. Last updated 1 years ago.
3.8 match 1.00 scorecran
SPEDInstabR:Estimation of the Relative Importance of Factors Affecting Species Distribution Based on Stability Concept
From output files obtained from the software 'ModestR', the relative contribution of factors to explain species distribution is depicted using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.
Maintained by Castor Guisande Gonzalez. Last updated 1 years ago.
3.8 match 1.00 score
lafaye
HellCor:The Hellinger Correlation
Empirical value of the Hellinger correlation, a measure of dependence between two continuous random variables. More details can be found in Geenens and Lafaye De Micheaux (2019) <arXiv:1810.10276v4>.
Maintained by Pierre Lafaye De Micheaux. Last updated 5 years ago.
3.3 match 1.00 score 3 scripts
atsa-es
atsar:Stan Routines For Univariate And Multivariate Time Series
Bundles univariate and multivariate STAN scripts for FISH 507 class.
Maintained by Eric J. Ward. Last updated 10 months ago.
0.6 match 48 stars 5.68 score 33 scripts
pbourkey
polyqtlR:QTL Analysis in Autopolyploid Bi-Parental F1 Populations
Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in autopolyploid bi-parental F1 populations. For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated. Significance thresholds, exploring QTL allele effects and visualising results are provided. For more background and to reference the package see <doi:10.1093/bioinformatics/btab574>.
Maintained by Peter Bourke. Last updated 1 years ago.
1.3 match 2.30 score 2 scripts
miguel-porto
SiMRiv:Simulating Multistate Movements in River/Heterogeneous Landscapes
Provides functions to generate and analyze spatially-explicit individual-based multistate movements in rivers, heterogeneous and homogeneous spaces. This is done by incorporating landscape bias on local behaviour, based on resistance rasters. Although originally conceived and designed to simulate trajectories of species constrained to linear habitats/dendritic ecological networks (e.g. river networks), the simulation algorithm is built to be highly flexible and can be applied to any (aquatic, semi-aquatic or terrestrial) organism, independently on the landscape in which it moves. Thus, the user will be able to use the package to simulate movements either in homogeneous landscapes, heterogeneous landscapes (e.g. semi-aquatic animal moving mainly along rivers but also using the matrix), or even in highly contrasted landscapes (e.g. fish in a river network). The algorithm and its input parameters are the same for all cases, so that results are comparable. Simulated trajectories can then be used as mechanistic null models (Potts & Lewis 2014, <DOI:10.1098/rspb.2014.0231>) to test a variety of 'Movement Ecology' hypotheses (Nathan et al. 2008, <DOI:10.1073/pnas.0800375105>), including landscape effects (e.g. resources, infrastructures) on animal movement and species site fidelity, or for predictive purposes (e.g. road mortality risk, dispersal/connectivity). The package should be relevant to explore a broad spectrum of ecological phenomena, such as those at the interface of animal behaviour, management, landscape and movement ecology, disease and invasive species spread, and population dynamics.
Maintained by Miguel Porto. Last updated 7 months ago.
animal-movementheterogeneous-landscapesmovement-ecologyriver-networkssimulation
0.5 match 15 stars 6.08 score 27 scripts 1 dependents
swarm-lab
swaRm:Processing Collective Movement Data
Function library for processing collective movement data (e.g. fish schools, ungulate herds, baboon troops) collected from GPS trackers or computer vision tracking software.
Maintained by Simon Garnier. Last updated 1 years ago.
animal-behavioranimal-behaviourcollective-behaviorcollective-behaviour
0.5 match 21 stars 5.50 score 8 scripts 1 dependentsswarm-lab
trackdf:Data Frame Class for Tracking Data
Data frame class for storing collective movement data (e.g. fish schools, ungulate herds, baboon troops) collected from GPS trackers or computer vision tracking software.
Maintained by Simon Garnier. Last updated 2 years ago.
animal-behavioranimal-behaviourgpsgps-data
0.5 match 4 stars 5.42 score 11 scripts 1 dependentsflr
FLFleet:Classes and Methods for Fleets and Metiers
This package contains classes and methods for modelling of fishing fleets and their activity on multiple fish stocks.
Maintained by Iago Mosqueira. Last updated 2 years ago.
0.9 match 1 stars 3.11 score 86 scripts 1 dependents
marinapapa
swaRmverse:Swarm Space Creation
Provides a pipeline for the comparative analysis of collective movement data (e.g. fish schools, bird flocks, baboon troops) by processing 2-dimensional positional data (x,y,t) from GPS trackers or computer vision tracking systems, discretizing events of collective motion, calculating a set of established metrics that characterize each event, and placing the events in a multi-dimensional swarm space constructed from these metrics. The swarm space concept, the metrics and data sets included are described in: Papadopoulou Marina, Furtbauer Ines, O'Bryan Lisa R., Garnier Simon, Georgopoulou Dimitra G., Bracken Anna M., Christensen Charlotte and King Andrew J. (2023) <doi:10.1098/rstb.2022.0068>.
Maintained by Marina Papadopoulou. Last updated 6 months ago.
0.5 match 2 stars 5.13 score 15 scriptsadrianhordyk
LBSPR:Length-Based Spawning Potential Ratio
Simulate expected equilibrium length composition, yield-per-recruit, and the spawning potential ratio (SPR) using the length-based SPR (LBSPR) model. Fit the LBSPR model to length data to estimate selectivity, relative apical fishing mortality, and the spawning potential ratio for data-limited fisheries. See Hordyk et al (2016) <doi:10.1139/cjfas-2015-0422> for more information about the LBSPR assessment method.
Maintained by Adrian Hordyk. Last updated 2 years ago.
0.5 match 7 stars 4.90 score 114 scripts
damianobaldan
RAC:R Package for Aqua Culture
Solves the individual bioenergetic balance for different aquaculture sea fish (Sea Bream and Sea Bass; Brigolin et al., 2014 <doi:10.3354/aei00093>) and shellfish (Mussel and Clam; Brigolin et al., 2009 <doi:10.1016/j.ecss.2009.01.029>; Solidoro et al., 2000 <doi:10.3354/meps199137>). Allows for spatialized model runs and population simulations.
Maintained by Baldan D.. Last updated 2 years ago.
0.5 match 4.54 scoreflr
FLXSA:eXtended Survivor Analysis for FLR
Calculates stock numbers and fishing mortality at age from commercial catch data and one or more indices of abundance suing the method in Darby and Flatman (1994) and Shepherd (1999).
Maintained by Iago Mosqueira. Last updated 4 months ago.
0.5 match 2 stars 4.36 score 95 scripts 1 dependentspoissonconsulting
shinyypr:Run ypr Shiny App
A user interface to the 'ypr' R package. 'Ypr' implements equilibrium-based yield per recruit methods for estimating the optimal yield for a fish population.
Maintained by Ayla Pearson. Last updated 2 months ago.
0.5 match 3 stars 4.26 score 3 scriptsejosymart
gnomonicM:Estimate Natural Mortality for Different Life Stages
Estimate natural mortality (M) throughout the life history for organisms, mainly fish and invertebrates, based on gnomonic interval approach proposed by Caddy (1996) <doi:10.1051/alr:1996023> and Martinez-Aguilar et al. (2005) <doi:10.1016/j.fishres.2004.04.008>. It includes estimation of duration of each gnomonic interval (life stage), the constant probability of death (G), and some basic plots.
Maintained by Josymar Torrejon-Magallanes. Last updated 4 years ago.
fisheriesgnomonicnatural-mortality
0.5 match 1 stars 3.70 score 2 scripts
mintoc
lhmixr:Fit Sex-Specific Life History Models with Missing Classifications
Fits sex-specific life-history models for fish and other taxa where some of the individuals have unknown sex.
Maintained by Coilin Minto. Last updated 8 years ago.
0.5 match 1 stars 2.70 score 9 scripts
kwb-r
kwb.misa:Functions to be Used in Project MiSa
Assessment of oxygen course in rivers. Assessment is aimed at reducing critical situations and fish deaths.
Maintained by Malte Zamzow. Last updated 3 years ago.
0.5 match 1 stars 2.70 score 2 scripts
willtirone
modelfactory:Combine Statistical Models into a Tibble for Comparison
Statisticians often want to compare the fit of different models on the same data set. However, this usually involves a lot of manual code to fish items out of summary() or plain model objects. 'modelfactory' offers the capability to pass multiple models in and get out metrics or coefficients for quick comparison with easy-to-remember syntax.
Maintained by Will Tirone. Last updated 1 years ago.
0.5 match 2.70 score 3 scriptscran
vcvComp:Comparison of Variance - Covariance Patterns
Comparison of variance - covariance patterns using relative principal component analysis (relative eigenanalysis), as described in Le Maitre and Mitteroecker (2019) <doi:10.1111/2041-210X.13253>. Also provides functions to compute group covariance matrices, distance matrices, and perform proportionality tests. A worked sample on the body shape of cichlid fishes is included, based on the dataset from Kerschbaumer et al. (2013) <doi:10.5061/dryad.fc02f>.
Maintained by Anne Le Maitre. Last updated 4 years ago.
0.5 match 2.48 score
fchianucci
hemispheR:Processing Hemispherical Canopy Images
Import and classify canopy fish-eye images, estimate angular gap fraction and derive canopy attributes like leaf area index and openness. Additional information is provided in the study by Chianucci F., Macek M. (2023) <doi:10.1016/j.agrformet.2023.109470>.
Maintained by Francesco Chianucci. Last updated 12 months ago.
0.5 match 3 stars 2.18 score 7 scriptscran
halk:Methods to Create Hierarchical Age Length Keys for Age Assignment
Provides methods for implementing hierarchical age length keys to estimate fish ages from lengths using data borrowing. Users can create hierarchical age length keys and use them to assign ages given length.
Maintained by Paul Frater. Last updated 1 years ago.
0.5 match 2.00 score