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fitdistrplus - Help to Fit of a Parametric Distribution to Non-Censored or Censored Data

Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit estimation (MGE) and maximum spacing estimation (MSE) methods (available only for non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g. Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction to parametric estimation.

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16.24 score 61 stars 215 dependents 4.7k scripts 67k downloads

ade4 - Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.

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openblascpp

14.77 score 45 stars 290 dependents 2.7k scripts 61k downloads

adespatial - Multivariate Multiscale Spatial Analysis

Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

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openblas

11.09 score 41 stars 2 dependents 620 scripts 10.0k downloads

adegraphics - An S4 Lattice-Based Package for the Representation of Multivariate Data

Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.

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9.93 score 9 stars 6 dependents 433 scripts 6.0k downloads

adephylo - Exploratory Analyses for the Phylogenetic Comparative Method

Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. The package contains functions to represent comparative data, compute phylogenetic proximities, perform multivariate analysis with phylogenetic constraints and test for the presence of phylogenetic autocorrelation. The package is described in Jombart et al (2010) <doi:10.1093/bioinformatics/btq292>.

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9.82 score 10 stars 4 dependents 539 scripts 10k downloads

nlstools - Tools for Nonlinear Regression Analysis

Several tools for assessing the quality of fit of a gaussian nonlinear model are provided.

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9.15 score 7 stars 8 dependents 720 scripts 2.3k downloads

kissDE - Retrieves Condition-Specific Variants in RNA-Seq Data

Retrieves condition-specific variants in RNA-seq data (SNVs, alternative-splicings, indels). It has been developed as a post-treatment of 'KisSplice' but can also be used with user's own data.

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alternativesplicingdifferentialsplicingexperimentaldesigngenomicvariationrnaseqtranscriptomicsquarto

6.38 score 3 stars 7 scripts 360 downloads

DRomics - Dose Response for Omics

Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Delignette-Muller et al (2023) <DOI:10.24072/pcjournal.325> and Larras et al (2018) <DOI:10.1021/acs.est.8b04752>.

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6.04 score 8 stars 17 scripts 399 downloads

phylter - Detect and Remove Outliers in Phylogenomics Datasets

Analyzis and filtering of phylogenomics datasets. It takes an input either a collection of gene trees (then transformed to matrices) or directly a collection of gene matrices and performs an iterative process to identify what species in what genes are outliers, and whose elimination significantly improves the concordance between the input matrices. The methods builds upon the Distatis approach (Abdi et al. (2005) <doi:10.1101/2021.09.08.459421>), a generalization of classical multidimensional scaling to multiple distance matrices.

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phylogenetic-treesphylogeneticsphylogenomicscpp

5.76 score 19 stars 8 scripts 222 downloads

MareyMap - Estimation of Meiotic Recombination Rates Using Marey Maps

Local recombination rates are graphically estimated across a genome using Marey maps.

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5.52 score 2 stars 33 scripts 223 downloads

nlsMicrobio - Nonlinear Regression in Predictive Microbiology

Data sets and nonlinear regression models dedicated to predictive microbiology.

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5.44 score 2 stars 1 dependents 46 scripts 276 downloads

aods3 - Analysis of Overdispersed Data using S3 Methods

Provides functions to analyse overdispersed counts or proportions. These functions should be considered as complements to more sophisticated methods such as generalized estimating equations (GEE) or generalized linear mixed effect models (GLMM). aods3 is an S3 re-implementation of the deprecated S4 package aod.

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5.33 score 1 dependents 52 scripts 3.9k downloads

LifemapR - Data Visualisation on 'Lifemap' Tree

Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap <https://lifemap.cnrs.fr/>. It takes as input a dataframe with at least a "taxid" column containing NCBI format TaxIds and allows to draw multiple layers with different visualisation tools.

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5.20 score 8 stars 180 downloads

ade4TkGUI - 'ade4' Tcl/Tk Graphical User Interface

A Tcl/Tk GUI for some basic functions in the 'ade4' package.

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4.57 score 2 stars 9 scripts 3.7k downloads

Mondrian - A Simple Graphical Representation of the Relative Occurrence and Co-Occurrence of Events

The unique function of this package allows representing in a single graph the relative occurrence and co-occurrence of events measured in a sample. As examples, the package was applied to describe the occurrence and co-occurrence of different species of bacterial or viral symbionts infecting arthropods at the individual level. The graphics allows determining the prevalence of each symbiont and the patterns of multiple infections (i.e. how different symbionts share or not the same individual hosts). We named the package after the famous painter as the graphical output recalls Mondrian’s paintings.

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4.18 score 3 stars 8 scripts 656 downloads

Interatrix - Compute Chi-Square Measures with Corrections

Chi-square tests are computed with corrections.

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quarto

3.70 score 9 scripts 194 downloads

LDcorSV - Linkage Disequilibrium Corrected by the Structure and the Relatedness

Four measures of linkage disequilibrium are provided: the usual r^2 measure, the r^2_S measure (r^2 corrected by the structure sample), the r^2_V (r^2 corrected by the relatedness of genotyped individuals), the r^2_VS measure (r^2 corrected by both the relatedness of genotyped individuals and the structure of the sample).

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2.88 score 15 scripts 194 downloads

OnAge - Test of Between-Group Differences in the Onset of Senescence

Implementation of a likelihood ratio test of differential onset of senescence between two groups. Given two groups with measures of age and of an individual trait likely to be subjected to senescence (e.g. body mass), 'OnAge' provides an asymptotic p-value for the null hypothesis that senescence starts at the same age in both groups. The package implements the procedure used in Douhard et al. (2017) <doi:10.1111/oik.04421>.

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2.70 score 5 scripts 498 downloads

ssd4mosaic - Web Application for the SSD Module of the MOSAIC Platform

Web application using 'shiny' for the SSD (Species Sensitivity Distribution) module of the MOSAIC (MOdeling and StAtistical tools for ecotoxICology) platform. It estimates the Hazardous Concentration for x% of the species (HCx) from toxicity values that can be censored and provides various plotting options for a better understanding of the results. See our companion paper Kon Kam King et al. (2014) <doi:10.48550/arXiv.1311.5772>.

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2.30 score 484 downloads

CINID - Curculionidae INstar IDentification

Method for identifying the instar of Curculionid larvae from the observed distribution of the headcapsule size of mature larvae.

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1.70 score 3 scripts 212 downloads