pavo - Perceptual Analysis, Visualization and Organization of Spectral Colour Data
A cohesive framework for the spectral and spatial analysis of colour described in Maia, Eliason, Bitton, Doucet & Shawkey (2013) <doi:10.1111/2041-210X.12069> and Maia, Gruson, Endler & White (2019) <doi:10.1111/2041-210X.13174>.
Last updated 1 months ago
9.58 score 70 stars 1 dependents 145 scripts 921 downloads
linelist - Tagging and Validating Epidemiological Data
Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.
Last updated 1 days ago
datadata-structuresepidemiologyepiverseoutbreakssdg-3structured-data
9.10 score 8 stars 3 dependents 66 scripts 660 downloadslinelist - Tagging and Validating Epidemiological Data
Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.
Last updated 1 days ago
datadata-structuresepidemiologyepiverseoutbreakssdg-3structured-data
9.10 score 8 stars 3 dependents 66 scripts 660 downloads
fundiversity - Easy Computation of Functional Diversity Indices
Computes six functional diversity indices. These are namely, Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic), Functional Richness intersections (FRic_intersect), Functional Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008 <doi:10.1890/07-1206.1>). Provides efficient, modular, and parallel functions to compute functional diversity indices (Grenié & Gruson 2023 <doi:10.1111/ecog.06585>).
Last updated 5 months ago
biodiversitybiodiversity-indicatorsbiodiversity-informaticsfunctional-diversityfunctional-ecologyfunctional-traitfunctional-traitstraittrait-basedtraits
7.43 score 32 stars 37 scripts 419 downloads
lightr - Read Spectrometric Data and Metadata
Parse various reflectance/transmittance/absorbance spectra file formats to extract spectral data and metadata, as described in Gruson, White & Maia (2019) <doi:10.21105/joss.01857>. Among other formats, it can import files from 'Avantes' <https://www.avantes.com/>, 'CRAIC' <https://www.microspectra.com/>, and 'OceanOptics'/'OceanInsight' <https://www.oceanoptics.com/> brands.
Last updated 10 days ago
file-importreproducibilityreproducible-researchreproducible-sciencespectral-dataspectroscopy
7.09 score 13 stars 2 dependents 13 scripts 712 downloads
lightr - Read Spectrometric Data and Metadata
Parse various reflectance/transmittance/absorbance spectra file formats to extract spectral data and metadata, as described in Gruson, White & Maia (2019) <doi:10.21105/joss.01857>. Among other formats, it can import files from 'Avantes' <https://www.avantes.com/>, 'CRAIC' <https://www.microspectra.com/>, and 'OceanOptics'/'OceanInsight' <https://www.oceanoptics.com/> brands.
Last updated 10 days ago
file-importreproducibilityreproducible-researchreproducible-sciencespectral-dataspectroscopy
7.09 score 13 stars 2 dependents 13 scripts 712 downloadscransays - Creates an Overview of CRAN Incoming Submissions
It scrapes the CRAN incoming FTP folder to find where each submission is.
Last updated 4 months ago
6.55 score 80 stars
contactdata - Social Contact Matrices for 177 Countries
Data package for the supplementary data in Prem et al. (2017) <doi:10.1371/journal.pcbi.1005697> and Prem et al. <doi:10.1371/journal.pcbi.1009098>. Provides easy access to contact data for 177 countries, for use in epidemiological, demographic or social sciences research.
Last updated 6 days ago
demographicsepidemiologysocial-sciences
5.65 score 9 stars 11 scripts 318 downloadsxlcutter - Parse Batches of 'xlsx' Files Based on a Template
Parse entire folders of non-rectangular 'xlsx' files into a single rectangular and tidy 'data.frame' based on a custom template file defining the column names of the output.
Last updated 10 months ago
data-extractionexcelnon-rectangular-datatidy-data
4.85 score 7 stars 3 scripts 149 downloadsmcmcensemble - Ensemble Sampler for Affine-Invariant MCMC
Provides ensemble samplers for affine-invariant Monte Carlo Markov Chain, which allow a faster convergence for badly scaled estimation problems. Two samplers are proposed: the 'differential.evolution' sampler from ter Braak and Vrugt (2008) <doi:10.1007/s11222-008-9104-9> and the 'stretch' sampler from Goodman and Weare (2010) <doi:10.2140/camcos.2010.5.65>.
Last updated 9 months ago
mcmcmcmc-sampler
4.60 score 2 stars 8 scripts 245 downloadstracetheme - A 'ggplot2' Theme and Scale Using 'Epiverse-TRACE' Visual Style
A 'ggplot2' theme and scale using 'Epiverse-TRACE' visual style, colour scheme, and visualisation guidelines.
Last updated 8 months ago
4.32 score 1 stars 5 scripts
asymptor - Estimate Asymptomatic Cases via Capture/Recapture Methods
Estimate the lower and upper bound of asymptomatic cases in an epidemic using the capture/recapture methods from Böhning et al. (2020) <doi:10.1016/j.ijid.2020.06.009> and Rocchetti et al. (2020) <doi:10.1101/2020.07.14.20153445>. Note there is currently some discussion about the validity of the methods implemented in this package. You should read carefully the original articles, alongside this answer from Li et al. (2022) <doi:10.48550/arXiv.2209.11334> before using this package in your project.
Last updated 2 years ago
epidemiology
4.18 score 3 stars 8 scripts 288 downloadssimpleMH - Simple Metropolis-Hastings MCMC Algorithm
A very bare-bones interface to use the Metropolis-Hastings Monte Carlo Markov Chain algorithm. It is suitable for teaching and testing purposes.
Last updated 10 months ago
3.70 score 4 scripts 152 downloads