Showing 8 of total 8 results (show query)
epiforecasts
scoringutils:Utilities for Scoring and Assessing Predictions
Facilitate the evaluation of forecasts in a convenient framework based on data.table. It allows user to to check their forecasts and diagnose issues, to visualise forecasts and missing data, to transform data before scoring, to handle missing forecasts, to aggregate scores, and to visualise the results of the evaluation. The package mostly focuses on the evaluation of probabilistic forecasts and allows evaluating several different forecast types and input formats. Find more information about the package in the Vignettes as well as in the accompanying paper, <doi:10.48550/arXiv.2205.07090>.
Maintained by Nikos Bosse. Last updated 28 days ago.
forecast-evaluationforecasting
52 stars 11.37 score 326 scripts 7 dependents
mlverse
luz:Higher Level 'API' for 'torch'
A high level interface for 'torch' providing utilities to reduce the the amount of code needed for common tasks, abstract away torch details and make the same code work on both the 'CPU' and 'GPU'. It's flexible enough to support expressing a large range of models. It's heavily inspired by 'fastai' by Howard et al. (2020) <arXiv:2002.04688>, 'Keras' by Chollet et al. (2015) and 'PyTorch Lightning' by Falcon et al. (2019) <doi:10.5281/zenodo.3828935>.
Maintained by Daniel Falbel. Last updated 7 months ago.
89 stars 9.86 score 318 scripts 4 dependents
jedick
chem16S:Chemical Metrics for Microbial Communities
Combines taxonomic classifications of high-throughput 16S rRNA gene sequences with reference proteomes of archaeal and bacterial taxa to generate amino acid compositions of community reference proteomes. Calculates chemical metrics including carbon oxidation state ('Zc'), stoichiometric oxidation and hydration state ('nO2' and 'nH2O'), H/C, N/C, O/C, and S/C ratios, grand average of hydropathicity ('GRAVY'), isoelectric point ('pI'), protein length, and average molecular weight of amino acid residues. Uses precomputed reference proteomes for archaea and bacteria derived from the Genome Taxonomy Database ('GTDB'). Also includes reference proteomes derived from the NCBI Reference Sequence ('RefSeq') database and manual mapping from the 'RDP Classifier' training set to 'RefSeq' taxonomy as described by Dick and Tan (2023) <doi:10.1007/s00248-022-01988-9>. Processes taxonomic classifications in 'RDP Classifier' format or OTU tables in 'phyloseq-class' objects from the Bioconductor package 'phyloseq'.
Maintained by Jeffrey Dick. Last updated 10 days ago.
16s-rrnacarbon-oxidation-statechemical-metricsgenomic-adaptationmicrobial-communities
4 stars 5.89 score 8 scripts
cadam00
priorCON:Graph Community Detection Methods into Systematic Conservation Planning
An innovative tool-set that incorporates graph community detection methods into systematic conservation planning. It is designed to enhance spatial prioritization by focusing on the protection of areas with high ecological connectivity. Unlike traditional approaches that prioritize individual planning units, 'priorCON' focuses on clusters of features that exhibit strong ecological linkages. The 'priorCON' package is built upon the 'prioritizr' package <doi:10.32614/CRAN.package.prioritizr>, using commercial and open-source exact algorithm solvers that ensure optimal solutions to prioritization problems.
Maintained by Christos Adam. Last updated 2 months ago.
biodiversitycommunity-detectionconservationconservation-planninggraph-theoryprioritization
3 stars 5.37 score 13 scripts
pascalcrepey
HospitalNetwork:Building Networks of Hospitals Through Patients Transfers
Set of tools to help interested researchers to build hospital networks from data on hospitalized patients transferred between hospitals. Methods provided have been used in Donker T, Wallinga J, Grundmann H. (2010) <doi:10.1371/journal.pcbi.1000715>, and Nekkab N, Crépey P, Astagneau P, Opatowski L, Temime L. (2020) <doi:10.1038/s41598-020-71212-6>.
Maintained by Pascal Crépey. Last updated 3 months ago.
hospital-networkspatient-databasepatients-transfers
7 stars 5.10 score 12 scripts
schlosslab
clustur:Clustering
A tool that implements the clustering algorithms from 'mothur' (Schloss PD et al. (2009) <doi:10.1128/AEM.01541-09>). 'clustur' make use of the cluster() and make.shared() command from 'mothur'. Our cluster() function has five different algorithms implemented: 'OptiClust', 'furthest', 'nearest', 'average', and 'weighted'. 'OptiClust' is an optimized clustering method for Operational Taxonomic Units, and you can learn more here, (Westcott SL, Schloss PD (2017) <doi:10.1128/mspheredirect.00073-17>). The make.shared() command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.
Maintained by Patrick Schloss. Last updated 4 months ago.
1 stars 4.85 score 7 scripts
hjeglinton
riskscores:Optimized Integer Risk Score Models
Implements an optimized approach to learning risk score models, where sparsity and integer constraints are integrated into the model-fitting process.
Maintained by Hannah Eglinton. Last updated 5 months ago.
1 stars 4.85 score 7 scripts
certe-medical-epidemiology
certestats:A Certe R Package for Statistical Modelling
A Certe R Package for early-warning, applying statistical modelling (such as creating machine learning models), QC rules and distribution analysis. This package is part of the 'certedata' universe.
Maintained by Matthijs S. Berends. Last updated 5 months ago.
3.02 score 1 scripts 1 dependents