R-universe search: needs:worrms

ropensci

taxize:Taxonomic Information from Around the Web

Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.

Maintained by Zachary Foster. Last updated 25 days ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper biodiversity darwincore data taxize

274 stars 13.63 score 1.6k scripts 23 dependents

pecanproject

PEcAn.assim.batch:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Istem Fer. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

216 stars 9.96 score 20 scripts 2 dependents

pecanproject

PEcAnRTM:PEcAn Functions Used for Radiative Transfer Modeling

Functions for performing forward runs and inversions of radiative transfer models (RTMs). Inversions can be performed using maximum likelihood, or more complex hierarchical Bayesian methods. Underlying numerical analyses are optimized for speed using Fortran code.

Maintained by Alexey Shiklomanov. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants fortran jags cpp

216 stars 9.70 score 132 scripts

grunwaldlab

metacoder:Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.

Maintained by Zachary Foster. Last updated 2 months ago.

community-diversity hierarchical metabarcoding pcr taxonomy trees cpp

140 stars 9.64 score 328 scripts

pecanproject

PEcAn.data.land:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Mike Dietze. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

216 stars 9.33 score 19 scripts 10 dependents

pecanproject

PEcAn.all:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by David LeBauer. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

216 stars 9.00 score 266 scripts

pecanproject

PEcAn.BIOCRO:PEcAn Package for Integration of the BioCro Model

This module provides functions to link BioCro to PEcAn.

Maintained by David LeBauer. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

216 stars 8.94 score 23 scripts

pecanproject

PEcAn.workflow:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. This package provides workhorse functions that can be used to run the major steps of a PEcAn analysis.

Maintained by David LeBauer. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

216 stars 8.83 score 15 scripts 4 dependents

pecanproject

PEcAn.ED2:PEcAn Package for Integration of ED2 Model

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. This package provides functions to link the Ecosystem Demography Model, version 2, to PEcAn.

Maintained by Mike Dietze. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

216 stars 8.74 score 145 scripts

ropensci

traits:Species Trait Data from Around the Web

Species trait data from many different sources, including sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant trait data from 'BETYdb', data from 'EOL' 'Traitbank', 'Birdlife' International, and more.

Maintained by David LeBauer. Last updated 2 months ago.

traits api web-services species taxonomy api-client

41 stars 8.65 score 82 scripts 11 dependents

pecanproject

PEcAn.SIPNET:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Mike Dietze. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

216 stars 8.36 score 61 scripts

pecanproject

PEcAn.LINKAGES:PEcAn Package for Integration of the LINKAGES Model

This module provides functions to link the (LINKAGES) to PEcAn.

Maintained by Ann Raiho. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

216 stars 8.35 score 59 scripts

pecanproject

PEcAnAssimSequential:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Mike Dietze. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

216 stars 8.12 score 35 scripts

pecanproject

PEcAn.LDNDC:PEcAn package for integration of the LDNDC model

This module provides functions to link the (LDNDC) to PEcAn.

Maintained by Henri Kajasilta. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

216 stars 7.58 score

ropensci

taxizedb:Tools for Working with 'Taxonomic' Databases

Tools for working with 'taxonomic' databases, including utilities for downloading databases, loading them into various 'SQL' databases, cleaning up files, and providing a 'SQL' connection that can be used to do 'SQL' queries directly or used in 'dplyr'.

Maintained by Tamás Stirling. Last updated 2 months ago.

itis taxize taxonomic-databases taxonomy

31 stars 5.86 score 86 scripts 1 dependents

europeanifcbgroup

iRfcb:Tools for Managing Imaging FlowCytobot (IFCB) Data

A comprehensive suite of tools for managing, processing, and analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports quality control, geospatial analysis, and preparation of IFCB data for publication in databases like <https://www.gbif.org>, <https://www.obis.org>, <https://emodnet.ec.europa.eu/en>, <https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package integrates with the MATLAB 'ifcb-analysis' tool, which is described in Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides features for working with raw, manually classified, and machine learning–classified image datasets. Key functionalities include image extraction, particle size distribution analysis, taxonomic data handling, and biomass concentration calculations, essential for plankton research.

Maintained by Anders Torstensson. Last updated 2 days ago.

data-export imaging-flow-cytometry imaging-flowcytobot oceanography plankton quality-control

1 stars 5.76 score

ropensci

phruta:Phylogenetic Reconstruction and Time-dating

The phruta R package is designed to simplify the basic phylogenetic pipeline. Specifically, all code is run within the same program and data from intermediate steps are saved in independent folders. Furthermore, all code is run within the same environment which increases the reproducibility of your analysis. phruta retrieves gene sequences, combines newly downloaded and local gene sequences, and performs sequence alignments.

Maintained by Cristian Roman Palacios. Last updated 9 months ago.

9 stars 4.75 score 14 scripts

ropensci

brranching:Fetch 'Phylogenies' from Many Sources

Includes methods for fetching 'phylogenies' from a variety of sources, including the 'Phylomatic' web service (<http://phylodiversity.net/phylomatic/>), and 'Phylocom' (<https://github.com/phylocom/phylocom/>).

Maintained by Luna L Sanchez Reyes. Last updated 2 years ago.

phylogeny tree phylomatic molecular plants phylogenies

19 stars 4.72 score 37 scripts 1 dependents

inbo

movepub:Prepare Movebank Data for Publication

Prepare animal tracking data from 'Movebank' (<https://movebank.org>) for publication in a research repository. With 'movepub' you can document data with metadata following the Data Package standard and transform these to Darwin Core and Ecological Metadata Language ('EML') for publication to the Global Biodiversity Information Facility ('GBIF') and the Ocean Biodiversity Information System ('OBIS').

Maintained by Peter Desmet. Last updated 17 days ago.

oscibio

3 stars 4.65 score 5 scripts

viralemergence

insectDisease:Ecological Database of the World's Insect Pathogens

David Onstad provided us with this insect disease database, sometimes referred to as the 'Ecological Database of the Worlds Insect Pathogens' or EDWIP. Files have been converted from 'SQL' to csv, and ported into 'R' for easy exploration and analysis. Thanks to the Macroecology of Infectious Disease Research Coordination Network (RCN) for funding and support. Data are also served online in a static format at <https://edwip.ecology.uga.edu/>.

Maintained by Tad Dallas. Last updated 2 months ago.

13 stars 4.41 score 2 scripts

ropensci

helminthR:Access London Natural History Museum Host-Helminth Record Database

Access to large host-parasite data is often hampered by the availability of data and difficulty in obtaining it in a programmatic way to encourage analyses. 'helminthR' provides a programmatic interface to the London Natural History Museum's host-parasite database, one of the largest host-parasite databases existing currently <https://www.nhm.ac.uk/research-curation/scientific-resources/taxonomy-systematics/host-parasites/>. The package allows the user to query by host species, parasite species, and geographic location.

Maintained by Tad Dallas. Last updated 2 years ago.

disease-networks helminth open-data parasites

7 stars 4.32 score 12 scripts

ropensci

rusda:Interface to USDA Databases

An interface to the web service methods provided by the United States Department of Agriculture (USDA). The Agricultural Research Service (ARS) provides a large set of databases. The current version of the package holds interfaces to the Systematic Mycology and Microbiology Laboratory (SMML), which consists of four databases: Fungus-Host Distributions, Specimens, Literature and the Nomenclature database. It provides functions for querying these databases. The main function is \code{associations}, which allows searching for fungus-host combinations.

Maintained by Franz-Sebastian Krah. Last updated 4 years ago.

14 stars 3.54 score 5 scripts

ropensci

ReLTER:An Interface for the eLTER Community

ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to: - retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function); - interact with the [ODSEurope](maps.opendatascience.eu) starting with the dataset shared by [DEIMS-SDR](https://deims.org/) (see e.g. [get_site_ODS](https://docs.ropensci.org/ReLTER/reference/get_site_ODS.html) function); - use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function); - improve the quality of the dataset (see e.g. get_id_worms). Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.

Maintained by Alessandro Oggioni. Last updated 1 years ago.

biodiversity-informatics data-science ecology elter research-infrastructure

12 stars 3.38 score 4 scripts

urodelan

LocaTT:Geographically-Conscious Taxonomic Assignment for Metabarcoding

A bioinformatics pipeline for performing taxonomic assignment of DNA metabarcoding sequence data while considering geographic location. A detailed tutorial is available at <https://urodelan.github.io/Local_Taxa_Tool_Tutorial/>. A manuscript describing these methods is in preparation.

Maintained by Kenen Goodwin. Last updated 1 years ago.

3.00 score

ropensci

onekp:Retrieve Data from the 1000 Plants Initiative (1KP)

The 1000 Plants Initiative (www.onekp.com) has sequenced the transcriptomes of over 1000 plant species. This package allows these sequences and metadata to be retrieved and filtered by code, species or recursively by clade. Scientific names and NCBI taxonomy IDs are both supported.

Maintained by Dhakal Rijan. Last updated 2 years ago.

13 stars 2.81 score 4 scripts

phylotastic

rphylotastic:An R Interface to 'Phylotastic' Web Services

This wraps the 'Phylotastic' services APIs described on Web Services at <www.phylotastic.org>. The main use case is to return a phylogenetic tree for a set of species, but the services also include ways to extract species names from web pages, perform taxonomic name resolution, retrieve a list of all descendant species of a taxon, find images of a species, and more.

Maintained by Brian OMeara. Last updated 2 years ago.

2.28 score 19 scripts

pieterprovoost

ghettoblaster:NCBI BLAST web client

NCBI BLAST web client.

Maintained by Pieter Provoost. Last updated 1 years ago.

1.70 score