kableExtra - Construct Complex Table with 'kable' and Pipe Syntax

Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.

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15.01 score 181 dependents 80k scripts 220k downloads

leaflet.extras - Extra Functionality for 'leaflet' Package

The 'leaflet' JavaScript library provides many plugins some of which are available in the core 'leaflet' package, but there are many more. It is not possible to support them all in the core 'leaflet' package. This package serves as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet' plugins.

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data-visualizationgeospatialleaflet

11.16 score 223 stars 9 dependents 3.5k scripts 8.6k downloads

git2rdata - Store and Retrieve Data.frames in a Git Repository

The git2rdata package is an R package for writing and reading dataframes as plain text files. A metadata file stores important information. 1) Storing metadata allows to maintain the classes of variables. By default, git2rdata optimizes the data for file storage. The optimization is most effective on data containing factors. The optimization makes the data less human readable. The user can turn this off when they prefer a human readable format over smaller files. Details on the implementation are available in vignette("plain_text", package = "git2rdata"). 2) Storing metadata also allows smaller row based diffs between two consecutive commits. This is a useful feature when storing data as plain text files under version control. Details on this part of the implementation are available in vignette("version_control", package = "git2rdata"). Although we envisioned git2rdata with a git workflow in mind, you can use it in combination with other version control systems like subversion or mercurial. 3) git2rdata is a useful tool in a reproducible and traceable workflow. vignette("workflow", package = "git2rdata") gives a toy example. 4) vignette("efficiency", package = "git2rdata") provides some insight into the efficiency of file storage, git repository size and speed for writing and reading.

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reproducible-researchversion-control

10.29 score 104 stars 4 dependents 244 scripts 851 downloads

frictionless - Read and Write Frictionless Data Packages

Read and write Frictionless Data Packages. A 'Data Package' (<https://specs.frictionlessdata.io/data-package/>) is a simple container format and standard to describe and package a collection of (tabular) data. It is typically used to publish FAIR (<https://www.go-fair.org/fair-principles/>) and open datasets.

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frictionlessdataoscibio

9.96 score 36 stars 6 dependents 101 scripts 837 downloads

qgisprocess - Use 'QGIS' Processing Algorithms

Provides seamless access to the 'QGIS' (<https://qgis.org>) processing toolbox using the standalone 'qgis_process' command-line utility. Both native and third-party (plugin) processing providers are supported. Beside referring data sources from file, also common objects from 'sf', 'terra' and 'stars' are supported. The native processing algorithms are documented by QGIS.org (2024) <https://docs.qgis.org/latest/en/docs/user_manual/processing_algs/>.

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9.59 score 221 stars 280 scripts 1.2k downloads

zen4R - Interface to 'Zenodo' REST API

Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, including management of depositions, attribution of DOIs by 'Zenodo' and upload and download of files.

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apidatacitedepositionsdepositsdoifairzenodo

9.54 score 57 stars 3 dependents 130 scripts 1.1k downloads

codemetar - Generate 'CodeMeta' Metadata for R Packages

The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.

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metadatacodemetaropenscicitationcreditlinked-datajson-ldpeer-reviewed

9.05 score 67 stars 6 dependents 49 scripts 767 downloads

checklist - A Thorough and Strict Set of Checks for R Packages and Source Code

An opinionated set of rules for R packages and R source code projects.

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checklistcontinuous-integrationcontinuous-testingquality-assurance

7.77 score 21 stars 3 dependents 26 scripts

etn - Access Data from the European Tracking Network

Access data from the European Tracking Network ('ETN', <https://www.lifewatch.be/etn/>). With etn you can query metadata (animals, tags, deployments, receivers, projects) and data (acoustic detections, sensor data) from the 'ETN' database and use these in your analyses. Data access requires user credentials and is subject to a data policy.

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animal-movementanimal-trackingbiologgingdata-accessfishlifewatchoscibio

6.54 score 12 stars 22 scripts

n2khab - Providing Preprocessed Reference Data for Flemish Natura 2000 Habitat Analyses

The n2khab package is an R package with preprocessing functions and standard reference data, useful for analyses regarding Flemish Natura 2000 habitats and regionally important biotopes (RIBs).

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habitatnatura2000preprocessing-functionsreproducibility

6.44 score 2 stars 1 dependents 185 scripts

inborutils - Collection of Useful R Utilities

While working on research projects, typical small functionalities are useful across these projects. Instead of copy-pasting these functions in all individual project repositories/folders, this package collects these functions for reuse by ourself and - if useful - others as well.

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6.30 score 10 stars 111 scripts

trias - Process Data for the Project Tracking Invasive Alien Species (TrIAS)

R package to provide functionality to facilitate the data processing for the project Tracking Invasive Alien Species (TrIAS <https://trias-project.be>).

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invasive-speciesoscibio

6.11 score 4 stars 45 scripts

inbodb - Connect to and Retrieve Data from Databases on the INBO Server

A bundle of functions to connect to and retrieve data from databases on the INBO server, with dedicated functions to query some of these databases.

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database

6.01 score 1 dependents 121 scripts

camtraptor - Read, Explore and Visualize Camera Trap Data Packages

Read, explore and visualize Camera Trap Data Packages (Camtrap DP). 'Camtrap DP' (<https://camtrap-dp.tdwg.org>) is a community developed data exchange format for this type of data. With camtraptor you can read and filter data, create overviews of observed species, relative abundance or effort, and plot these data on a map.

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camera-trapsoscibio

5.97 score 15 stars 22 scripts

camtrapdp - Read and Manipulate Camera Trap Data Packages

Read and manipulate Camera Trap Data Packages ('Camtrap DP'). 'Camtrap DP' (<https://camtrap-dp.tdwg.org>) is a data exchange format for camera trap data. With 'camtrapdp' you can read, filter and transform data (including to Darwin Core) before further analysis in e.g. 'camtraptor' or 'camtrapR'.

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camtrap-dposcibio

5.85 score 15 stars 19 scripts 544 downloads

effectclass - Classification and Visualisation of Effects

Classify effects by comparing the confidence intervals with thresholds.

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effect-sizefan-chart

5.66 score 5 stars 2 dependents 51 scripts

INBOtheme - Themes for ggplot2

Several themes for the ggplot2 package. Among others themes complying with the style guide for the Research Institute for Nature and Forest (INBO) and Elsevier journals.

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ggplot2ggplot2-themes

5.46 score 4 stars 482 scripts

wateRinfo - Download Time Series Data from Waterinfo.be

wateRinfo facilitates access to waterinfo.be (<https://www.waterinfo.be>), a website managed by the Flanders Environment Agency (VMM) and Flanders Hydraulics Research. The website provides access to real-time water and weather related environmental variables for Flanders (Belgium), such as rainfall, air pressure, discharge, and water level. The package provides functions to search for stations and variables, and download time series.

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apiclimatelifewatchopen-scienceoscibioropensciwaterweather

5.46 score 14 stars 34 scripts

INBOmd - Markdown Templates for INBO

Several templates to generate reports, presentations and posters.

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bookdownrmarkdownxelatex

5.00 score 12 stars 28 scripts

movepub - Prepare Movebank Data for Publication

Prepare animal tracking data from 'Movebank' (<https://www.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').

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biologgingoscibio

4.88 score 5 stars 6 scripts

watina - Querying and Processing Data from the INBO Watina Data Warehouse

The R-package watina contains functions to query and process data from the Watina database at the Research Institute for Nature and Forest (INBO). This database primarily provides groundwater level and chemical data, mainly from natural areas in Flanders (Belgium).

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groundwaterpreprocessing-functionsreproducibility

4.48 score 2 stars 19 scripts

inbospatial - A Collection of Useful R Functions for Spatial Data

Useful R functions developed at the Research Institute for Nature and Forest (INBO) for dealing with spatial raster or vector data.

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4.40 score 6 stars 14 scripts

LSVI - Rekenmodule Lokale Staat Van Instandhouding van habitattypen

Het package LSVI bundelt een aantal functies in verband met het ophalen van informatie over en het berekenen van de Lokale Staat Van Instandhouding (LSVI) van habitattypes.

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4.16 score 1 stars 29 scripts

protocolhelper - Helper Functions to Manage Protocols

Helper functions to manage INBO protocols.

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4.08 score 5 stars 80 scripts

citeme - Manage Person and Organisation Information

Manage person and organisation information with validation and formatting capabilities. Provides R6 classes for managing organisations and their members, with support for multiple languages, ORCID identifiers, ROR identifiers, licensing requirements, publisher information, and integration with citation management systems.

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quarto

3.65 score 2 scripts

mnedesigndata - Design data of the Monitoring Programme for the Natural Environment (MNE)

mnedesigndata is an R package to distribute and document R data objects that reflect the current implementation design of the Monitoring Programme for the Natural Environment (MNE). Aspects are covered such as the scheme's spatial sampling frames, the spatiotemporal samples and the designed revisit patterns of the most important field activities. The objects originate particularly from the REP workflow (revisitplan) and scripts tied to it.

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2.30 score 1 scripts

inlatools - Diagnostic Tools for INLA Models

Several functions which can be useful to choose sensible priors and diagnose the fitted model.

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bayesian-statisticsgplv3inlamixed-modelsmodel-checkingmodel-validation

4.73 score 4 stars 89 scripts

forrescalc - Calculation of Aggregated Values on Dendrometry, Regeneration and Vegetation of Forests, Starting from Individual Tree Measures from Fieldmap

A collection of functions to load and aggregate measurements related to dendrometry, rejuvenation and vegetation, and to access plot level results from Flemish forest reserves in data package forresdat.

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3.78 score 120 scripts

multimput - Using Multiple Imputation to Address Missing Data

Accompanying package for the paper: Working with population totals in the presence of missing data comparing imputation methods in terms of bias and precision. Published in 2017 in the Journal of Ornithology volume 158 page 603–615 (<doi:10.1007/s10336-016-1404-9>).

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imputationimputation-model

3.32 score 1 stars 1 dependents 14 scripts

n2kanalysis - Generic Functions to Analyse Data from the 'Natura 2000' Monitoring

All generic functions and classes for the analysis for the 'Natura 2000' monitoring. The classes contain all required data and definitions to fit the model without the need to access other sources. Potentially they might need access to one or more parent objects. An aggregation object might for example need the result of an imputation object. The actual definition of the analysis, using these generic function and classes, is defined in dedictated analysis R packages for every monitoring scheme. For example 'abvanalysis' and 'watervogelanalysis'.

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analysismonitoringnatura2000

3.18 score 1 stars 7 scripts

dhcurve - Automated Modelling of Diameter Height Curves for Trees

Model diameter height curves for individual tree species and forests.

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analysisforestry

3.00 score 8 scripts

grtsdb - Create a Sampling Frame Using GRTS

Create an SQLite database containing the sampling framework for different levels of resolution. Take a sample from this framework.

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grtssamplingsampling-methodssqlite

2.81 score 1 stars 13 scripts

flandersqmd - Auxiliary Function for the Flandersqmd Quarto Extensions

Prepare new documents using the Flandersqmd extensions.

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corporate-identityquarto

2.30 score 1 stars 5 scripts

n2khelper - Auxiliary Functions for the Analysis and Reporting of the Natura 2000 Monitoring

Auxiliary functions for analysing Natura 2000 monitoring data.

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natura2000

2.18 score 1 dependents 1 scripts

designpower - Design Power Analysis Tools

Tools for iterative power analysis and design optimization using simulation and adaptive sampling strategies.

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2.00 score 2 scripts

n2khabmon - Prepare and Manage N2KHAB Monitoring Schemes

n2khabmon is an R package with utilities to prepare and manage Flemish monitoring schemes regarding Natura 2000 habitats and regionally important biotopes (RIBs).

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1.70 score 9 scripts

territoria - Clustering Observations from Breeding Birds into Territoria

Clusters individual observations based on breeding indication and distance between observations.

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birdbreedingclusterhome-rangeterritory

1.70 score 4 scripts

ladybird - Analysis of Ladybird Occurrence Data

Analysis of ladybird occurrence data from Belgium, the Netherlands and the UK since 1990.

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1.70 score 3 scripts

n2kupdate - Auxiliary Functions to Update the n2kresult Database

The functions are useful to store the results from https:// github.com/inbo/n2kanalysis into a PostgreSQL database created with https:// github.com/inbo/n2kresult.

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etlnatura2000

1.70 score 1 scripts

lipsum - Generate dummy text

Functions that generate dummy text. This is useful when developping a corporate identity for documents.

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lipsumtypography

1.51 score 32 scripts