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pierreroudier

spectacles:Storing, Manipulating and Analysis Spectroscopy and Associated Data

Stores and eases the manipulation of spectra and associated data, with dedicated classes for spatial and soil-related data.

Maintained by Pierre Roudier. Last updated 2 years ago.

11 stars 6.17 score 45 scripts 1 dependents

gorelab

waves:Vis-NIR Spectral Analysis Wrapper

Originally designed application in the context of resource-limited plant research and breeding programs, 'waves' provides an open-source solution to spectral data processing and model development by bringing useful packages together into a streamlined pipeline. This package is wrapper for functions related to the analysis of point visible and near-infrared reflectance measurements. It includes visualization, filtering, aggregation, preprocessing, cross-validation set formation, model training, and prediction functions to enable open-source association of spectral and reference data. This package is documented in a peer-reviewed manuscript in the Plant Phenome Journal <doi:10.1002/ppj2.20012>. Specialized cross-validation schemes are described in detail in Jarquín et al. (2017) <doi:10.3835/plantgenome2016.12.0130>. Example data is from Ikeogu et al. (2017) <doi:10.1371/journal.pone.0188918>.

Maintained by Jenna Hershberger. Last updated 12 months ago.

6 stars 5.98 score 53 scripts

gokmenzararsiz

dtComb:Statistical Combination of Diagnostic Tests

A system for combining two diagnostic tests using various approaches that include statistical and machine-learning-based methodologies. These approaches are divided into four groups: linear combination methods, non-linear combination methods, mathematical operators, and machine learning algorithms. See the <https://biotools.erciyes.edu.tr/dtComb/> website for more information, documentation, and examples.

Maintained by Gokmen Zararsiz. Last updated 3 days ago.

4.85 score 7 scripts

bioc

granulator:Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data

granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.

Maintained by Sabina Pfister. Last updated 5 months ago.

rnaseqgeneexpressiondifferentialexpressiontranscriptomicssinglecellstatisticalmethodregression

3 stars 4.48 score 7 scripts

rostats

RSurveillance:Design and Analysis of Disease Surveillance Activities

A range of functions for the design and analysis of disease surveillance activities. These functions were originally developed for animal health surveillance activities but can be equally applied to aquatic animal, wildlife, plant and human health surveillance activities. Utilities are included for sample size calculation and analysis of representative surveys for disease freedom, risk-based studies for disease freedom and for prevalence estimation. This package is based on Cameron A., Conraths F., Frohlich A., Schauer B., Schulz K., Sergeant E., Sonnenburg J., Staubach C. (2015). R package of functions for risk-based surveillance. Deliverable 6.24, WP 6 - Decision making tools for implementing risk-based surveillance, Grant Number no. 310806, RISKSUR (<https://www.fp7-risksur.eu/sites/default/files/documents/Deliverables/RISKSUR_%28310806%29_D6.24.pdf>). Many of the 'RSurveillance' functions are incorporated into the 'epitools' website: Sergeant, ESG, 2019. Epitools epidemiological calculators. Ausvet Pty Ltd. Available at: <http://epitools.ausvet.com.au>.

Maintained by Rohan Sadler. Last updated 5 years ago.

3.98 score 64 scripts

ejikeugba

gofcat:Goodness-of-Fit Measures for Categorical Response Models

A post-estimation method for categorical response models (CRM). Inputs from objects of class serp(), clm(), polr(), multinom(), mlogit(), vglm() and glm() are currently supported. Available tests include the Hosmer-Lemeshow tests for the binary, multinomial and ordinal logistic regression; the Lipsitz and the Pulkstenis-Robinson tests for the ordinal models. The proportional odds, adjacent-category, and constrained continuation-ratio models are particularly supported at ordinal level. Tests for the proportional odds assumptions in ordinal models are also possible with the Brant and the Likelihood-Ratio tests. Moreover, several summary measures of predictive strength (Pseudo R-squared), and some useful error metrics, including, the brier score, misclassification rate and logloss are also available for the binary, multinomial and ordinal models. Ugba, E. R. and Gertheiss, J. (2018) <http://www.statmod.org/workshops_archive_proceedings_2018.html>.

Maintained by Ejike R. Ugba. Last updated 2 years ago.

brant-testbrier-scoreshosmer-lemeshow-testlikelihood-ratio-testlipsitz-testlog-loss-score-metriclogistic-regressionmisclassificationordinal-regressionproportional-odds-testpseudo-r2pulkstenis-robinson-test

2 stars 3.18 score 15 scripts

loremerdrignac

EpiStats:Tools for Epidemiologists

Provides set of functions aimed at epidemiologists. The package includes commands for measures of association and impact for case control studies and cohort studies. It may be particularly useful for outbreak investigations including univariable analysis and stratified analysis. The functions for cohort studies include the CS(), CSTable() and CSInter() commands. The functions for case control studies include the CC(), CCTable() and CCInter() commands. References - Cornfield, J. 1956. A statistical problem arising from retrospective studies. In Vol. 4 of Proceedings of the Third Berkeley Symposium, ed. J. Neyman, 135-148. Berkeley, CA - University of California Press. Woolf, B. 1955. On estimating the relation between blood group disease. Annals of Human Genetics 19 251-253. Reprinted in Evolution of Epidemiologic Ideas Annotated Readings on Concepts and Methods, ed. S. Greenland, pp. 108-110. Newton Lower Falls, MA Epidemiology Resources. Gilles Desve & Peter Makary, 2007. 'CSTABLE Stata module to calculate summary table for cohort study' Statistical Software Components S456879, Boston College Department of Economics. Gilles Desve & Peter Makary, 2007. 'CCTABLE Stata module to calculate summary table for case-control study' Statistical Software Components S456878, Boston College Department of Economics.

Maintained by Lore Merdrignac. Last updated 1 years ago.

2.91 score 82 scripts

cran

PSS.Health:Power and Sample Size for Health Researchers via Shiny

Power and Sample Size for Health Researchers is a Shiny application that brings together a series of functions related to sample size and power calculations for common analysis in the healthcare field. There are functionalities to calculate the power, sample size to estimate or test hypotheses for means and proportions (including test for correlated groups, equivalence, non-inferiority and superiority), association, correlations coefficients, regression coefficients (linear, logistic, gamma, and Cox), linear mixed model, Cronbach's alpha, interobserver agreement, intraclass correlation coefficients, limit of agreement on Bland-Altman plots, area under the curve, sensitivity and specificity incorporating the prevalence of disease. You can also use the online version at <https://hcpa-unidade-bioestatistica.shinyapps.io/PSS_Health/>.

Maintained by Rogério Boff Borges. Last updated 3 months ago.

2.00 score

danny-ldc

RcmdrPlugin.EBM:Rcmdr Evidence Based Medicine Plug-in Package

Rcmdr plug-in GUI extension for Evidence Based Medicine medical indicators calculations (Sensitivity, specificity, absolute risk reduction, relative risk, ...).

Maintained by Daniel-Corneliu Leucuta. Last updated 10 years ago.

1.00 score 1 scripts

cran

Dtableone:Tabular Comparison of Paired Diagnostic Tests

Offers statistical methods to compare diagnostic performance between two binary diagnostic tests on the same subject in clinical studies. Includes functions for generating formatted tables to display diagnostic outcomes, facilitating a clear and comprehensive comparison directly through the R console. Inspired by and extending the functionalities of the 'DTComPair', 'tableone', and 'gtsummary' packages.

Maintained by Youngmi Park. Last updated 1 years ago.

1.00 score

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