R-universe search: exports:metrics

Showing 18 of total 18 results (show query)

tidymodels

yardstick:Tidy Characterizations of Model Performance

Tidy tools for quantifying how well model fits to a data set such as confusion matrices, class probability curve summaries, and regression metrics (e.g., RMSE).

Maintained by Emil Hvitfeldt. Last updated 18 days ago.

387 stars 15.47 score 2.2k scripts 60 dependents

flr

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 10 days ago.

fisheries flr fisheries-modelling

16 stars 8.78 score 956 scripts 23 dependents

myles-lewis

nestedcv:Nested Cross-Validation with 'glmnet' and 'caret'

Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package <doi:10.1093/bioadv/vbad048>. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.

Maintained by Myles Lewis. Last updated 10 days ago.

12 stars 7.90 score 46 scripts

bioc

beadarray:Quality assessment and low-level analysis for Illumina BeadArray data

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

Maintained by Mark Dunning. Last updated 5 months ago.

microarray onechannel qualitycontrol preprocessing

7.88 score 70 scripts 4 dependents

bioc

wateRmelon:Illumina DNA methylation array normalization and metrics

15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.

Maintained by Leo C Schalkwyk. Last updated 4 months ago.

dnamethylation microarray twochannel preprocessing qualitycontrol

7.75 score 247 scripts 2 dependents

apariciojohan

flexFitR:Flexible Non-Linear Least Square Model Fitting

Provides tools for flexible non-linear least squares model fitting using general-purpose optimization techniques. The package supports a variety of optimization algorithms, including those provided by the 'optimx' package, making it suitable for handling complex non-linear models. Features include parallel processing support via the 'future' and 'foreach' packages, comprehensive model diagnostics, and visualization capabilities. Implements methods described in Nash and Varadhan (2011, <doi:10.18637/jss.v043.i09>).

Maintained by Johan Aparicio. Last updated 4 days ago.

nls optimization

2 stars 7.12 score 77 scripts

flr

mse:Tools for Running Management Strategy Evaluations using FLR

A set of functions and methods to enable the development and running of Management Strategy Evaluation (MSE) analyses, using the FLR packages and classes and the a4a methods and algorithms.

Maintained by Iago Mosqueira. Last updated 1 months ago.

simulation mse fisheries flr a4a

4 stars 6.99 score 137 scripts 3 dependents

bioc

musicatk:Mutational Signature Comprehensive Analysis Toolkit

Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.

Maintained by Joshua D. Campbell. Last updated 5 months ago.

software biologicalquestion somaticmutation variantannotation

13 stars 6.97 score 20 scripts

fabrice-rossi

mixvlmc:Variable Length Markov Chains with Covariates

Estimates Variable Length Markov Chains (VLMC) models and VLMC with covariates models from discrete sequences. Supports model selection via information criteria and simulation of new sequences from an estimated model. See Bühlmann, P. and Wyner, A. J. (1999) <doi:10.1214/aos/1018031204> for VLMC and Zanin Zambom, A., Kim, S. and Lopes Garcia, N. (2022) <doi:10.1111/jtsa.12615> for VLMC with covariates.

Maintained by Fabrice Rossi. Last updated 11 months ago.

machine-learning markov-chain markov-model statistics time-series cpp

2 stars 6.23 score 20 scripts

jburkhardt

RAdwords:Loading Google Adwords Data into R

Aims at loading Google Adwords data into R. Adwords is an online advertising service that enables advertisers to display advertising copy to web users (see <https://developers.google.com/adwords/> for more information). Therefore the package implements three main features. First, the package provides an authentication process for R with the Google Adwords API (see <https://developers.google.com/adwords/api/> for more information) via OAUTH2. Second, the package offers an interface to apply the Adwords query language in R and query the Adwords API with ad-hoc reports. Third, the received data are transformed into suitable data formats for further data processing and data analysis.

Maintained by Johannes Burkhardt. Last updated 3 years ago.

99 stars 5.91 score 41 scripts

robinhankin

knotR:Knot Diagrams using Bezier Curves

Makes visually pleasing diagrams of knot projections using optimized Bezier curves.

Maintained by Robin K. S. Hankin. Last updated 1 years ago.

6 stars 5.69 score 164 scripts

banboo-data

r4googleads:'Google Ads API' Interface

Interface for the 'Google Ads API'. 'Google Ads' is an online advertising service that enables advertisers to display advertising to web users (see <https://developers.google.com/google-ads/> for more information).

Maintained by Johannes Burkhardt. Last updated 3 years ago.

google-ads-api marketing-analytics marketing-automation

4 stars 4.78 score 6 scripts

paulocortez4

rminer:Data Mining Classification and Regression Methods

Facilitates the use of data mining algorithms in classification and regression (including time series forecasting) tasks by presenting a short and coherent set of functions. Versions: 1.4.8 improved help, several warning and error code fixes (more stable version, all examples run correctly); 1.4.7 improved Importance function and examples, minor error fixes; 1.4.6 / 1.4.5 / 1.4.4 new automated machine learning (AutoML) and ensembles, via improved fit(), mining() and mparheuristic() functions, and new categorical preprocessing, via improved delevels() function; 1.4.3 new metrics (e.g., macro precision, explained variance), new "lssvm" model and improved mparheuristic() function; 1.4.2 new "NMAE" metric, "xgboost" and "cv.glmnet" models (16 classification and 18 regression models); 1.4.1 new tutorial and more robust version; 1.4 - new classification and regression models, with a total of 14 classification and 15 regression methods, including: Decision Trees, Neural Networks, Support Vector Machines, Random Forests, Bagging and Boosting; 1.3 and 1.3.1 - new classification and regression metrics; 1.2 - new input importance methods via improved Importance() function; 1.0 - first version.

Maintained by Paulo Cortez. Last updated 5 months ago.

3 stars 4.52 score 536 scripts

foucher-y

survivalSL:Super Learner for Survival Prediction from Censored Data

Several functions and S3 methods to construct a super learner in the presence of censored times-to-event and to evaluate its prognostic capacities.

Maintained by Yohann Foucher. Last updated 2 months ago.

2 stars 3.70 score

cran

PlayerRatings:Dynamic Updating Methods for Player Ratings Estimation

Implements schemes for estimating player or team skill based on dynamic updating. Implemented methods include Elo, Glicko, Glicko-2 and Stephenson. Contains pdf documentation of a reproducible analysis using approximately two million chess matches. Also contains an Elo based method for multi-player games where the result is a placing or a score. This includes zero-sum games such as poker and mahjong.

Maintained by Alec Stephenson. Last updated 5 years ago.

9 stars 3.43 score

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.

statistics

3.02 score 1 scripts 1 dependents

jcaledo

EnvNJ:Whole Genome Phylogenies Using Sequence Environments

Contains utilities for the analysis of protein sequences in a phylogenetic context. Allows the generation of phylogenetic trees base on protein sequences in an alignment-independent way. Two different methods have been implemented. One approach is based on the frequency analysis of n-grams, previously described in Stuart et al. (2002) <doi:10.1093/bioinformatics/18.1.100>. The other approach is based on the species-specific neighborhood preference around amino acids. Features include the conversion of a protein set into a vector reflecting these neighborhood preferences, pairwise distances (dissimilarity) between these vectors, and the generation of trees based on these distance matrices.

Maintained by Juan Carlos Aledo. Last updated 4 years ago.

1.04 score 11 scripts

merlot1998

OenoKPM:Modeling the Kinetics of Carbon Dioxide Production in Alcoholic Fermentation

Developed to help researchers who need to model the kinetics of carbon dioxide (CO2) production in alcoholic fermentation of wines, beers and other fermented products. The following models are available for modeling the carbon dioxide production curve as a function of time: 5PL, Gompertz and 4PL. This package has different functions, which applied can: perform the modeling of the data obtained in the fermentation and return the coefficients, analyze the model fit and return different statistical metrics, and calculate the kinetic parameters: Maximum production of carbon dioxide; Maximum rate of production of carbon dioxide; Moment in which maximum fermentation rate occurs; Duration of the latency phase for carbon dioxide production; Carbon dioxide produced until maximum fermentation rate occurs. In addition, a function that generates graphs with the observed and predicted data from the models, isolated and combined, is available. Gava, A., Borsato, D., & Ficagna, E. (2020)."Effect of mixture of fining agents on the fermentation kinetics of base wine for sparkling wine production: Use of methodology for modeling". <doi:10.1016/j.lwt.2020.109660>.

Maintained by Angelo Gava. Last updated 12 months ago.

1.00 score