Showing 107 of total 107 results (show query)
paulnorthrop
exdex:Estimation of the Extremal Index
Performs frequentist inference for the extremal index of a stationary time series. Two types of methodology are used. One type is based on a model that relates the distribution of block maxima to the marginal distribution of series and leads to the semiparametric maxima estimators described in Northrop (2015) <doi:10.1007/s10687-015-0221-5> and Berghaus and Bucher (2018) <doi:10.1214/17-AOS1621>. Sliding block maxima are used to increase precision of estimation. A graphical block size diagnostic is provided. The other type of methodology uses a model for the distribution of threshold inter-exceedance times (Ferro and Segers (2003) <doi:10.1111/1467-9868.00401>). Three versions of this type of approach are provided: the iterated weight least squares approach of Suveges (2007) <doi:10.1007/s10687-007-0034-2>, the K-gaps model of Suveges and Davison (2010) <doi:10.1214/09-AOAS292> and a similar approach of Holesovsky and Fusek (2020) <doi:10.1007/s10687-020-00374-3> that we refer to as D-gaps. For the K-gaps and D-gaps models this package allows missing values in the data, can accommodate independent subsets of data, such as monthly or seasonal time series from different years, and can incorporate information from right-censored inter-exceedance times. Graphical diagnostics for the threshold level and the respective tuning parameters K and D are provided.
Maintained by Paul J. Northrop. Last updated 11 months ago.
block-maximaextremal-indexextremeextreme-value-statisticsextremesinferencemaximasemiparametricsemiparametric-estimationsemiparametric-maxima-estimatorsthetathresholdvaluecpp
34.5 match 4.92 score 11 scripts 5 dependents
cran
evd:Functions for Extreme Value Distributions
Extends simulation, distribution, quantile and density functions to univariate and multivariate parametric extreme value distributions, and provides fitting functions which calculate maximum likelihood estimates for univariate and bivariate maxima models, and for univariate and bivariate threshold models.
Maintained by Alec Stephenson. Last updated 6 months ago.
16.9 match 2 stars 9.46 score 748 scripts 82 dependents
rcst
rim:Interface to 'Maxima', Enabling Symbolic Computation
An interface to the powerful and fairly complete computer algebra system 'Maxima'. It can be used to start and control 'Maxima' from within R by entering 'Maxima' commands. Results from 'Maxima' can be parsed and evaluated in R. It facilitates outputting results from 'Maxima' in 'LaTeX' and 'MathML'. 2D and 3D plots can be displayed directly. This package also registers a 'knitr'-engine enabling 'Maxima' code chunks to be written in 'RMarkdown' documents.
Maintained by Eric Stemmler. Last updated 5 months ago.
30.9 match 11 stars 4.34 score 10 scripts
borisberanger
ExtremalDep:Extremal Dependence Models
A set of procedures for parametric and non-parametric modelling of the dependence structure of multivariate extreme-values is provided. The statistical inference is performed with non-parametric estimators, likelihood-based estimators and Bayesian techniques. It adapts the methodologies of Beranger and Padoan (2015) <doi:10.48550/arXiv.1508.05561>, Marcon et al. (2016) <doi:10.1214/16-EJS1162>, Marcon et al. (2017) <doi:10.1002/sta4.145>, Marcon et al. (2017) <doi:10.1016/j.jspi.2016.10.004> and Beranger et al. (2021) <doi:10.1007/s10687-019-00364-0>. This package also allows for the modelling of spatial extremes using flexible max-stable processes. It provides simulation algorithms and fitting procedures relying on the Stephenson-Tawn likelihood as per Beranger at al. (2021) <doi:10.1007/s10687-020-00376-1>.
Maintained by Simone Padoan. Last updated 3 months ago.
32.0 match 3.30 score 1 scripts
aphalo
ggpmisc:Miscellaneous Extensions to 'ggplot2'
Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Statistics: locate and tag peaks and valleys; label plot with the equation of a fitted polynomial or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' and 'broom.mixed' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.
Maintained by Pedro J. Aphalo. Last updated 4 months ago.
data-analysisdatavizggplot2-annotationsggplot2-statsstatistics
3.5 match 105 stars 13.32 score 4.4k scripts 14 dependents
bioc
MassSpecWavelet:Peak Detection for Mass Spectrometry data using wavelet-based algorithms
Peak Detection in Mass Spectrometry data is one of the important preprocessing steps. The performance of peak detection affects subsequent processes, including protein identification, profile alignment and biomarker identification. Using Continuous Wavelet Transform (CWT), this package provides a reliable algorithm for peak detection that does not require any type of smoothing or previous baseline correction method, providing more consistent results for different spectra. See <doi:10.1093/bioinformatics/btl355} for further details.
Maintained by Sergio Oller Moreno. Last updated 3 months ago.
immunooncologymassspectrometryproteomicspeakdetection
4.8 match 9 stars 9.38 score 37 scripts 17 dependentsbioc
matter:Out-of-core statistical computing and signal processing
Toolbox for larger-than-memory scientific computing and visualization, providing efficient out-of-core data structures using files or shared memory, for dense and sparse vectors, matrices, and arrays, with applications to nonuniformly sampled signals and images.
Maintained by Kylie A. Bemis. Last updated 3 months ago.
infrastructuredatarepresentationdataimportdimensionreductionpreprocessingcpp
4.1 match 57 stars 9.52 score 64 scripts 2 dependents
r-forge
SpatialExtremes:Modelling Spatial Extremes
Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction. Other approaches (although not completely in agreement with the extreme value theory) are available such as the use of (spatial) copula and Bayesian hierarchical models assuming the so-called conditional assumptions. The latter approaches is handled through an (efficient) Gibbs sampler. Some key references: Davison et al. (2012) <doi:10.1214/11-STS376>, Padoan et al. (2010) <doi:10.1198/jasa.2009.tm08577>, Dombry et al. (2013) <doi:10.1093/biomet/ass067>.
Maintained by Mathieu Ribatet. Last updated 11 months ago.
7.1 match 5.36 score 189 scripts 2 dependents
astamm
roahd:Robust Analysis of High Dimensional Data
A collection of methods for the robust analysis of univariate and multivariate functional data, possibly in high-dimensional cases, and hence with attention to computational efficiency and simplicity of use. See the R Journal publication of Ieva et al. (2019) <doi:10.32614/RJ-2019-032> for an in-depth presentation of the 'roahd' package. See Aleman-Gomez et al. (2021) <arXiv:2103.08874> for details about the concept of depthgram.
Maintained by Aymeric Stamm. Last updated 3 years ago.
5.2 match 2 stars 6.29 score 164 scripts 2 dependentsbioc
BiocGenerics:S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Maintained by Hervé Pagès. Last updated 1 months ago.
infrastructurebioconductor-packagecore-package
2.3 match 12 stars 14.22 score 612 scripts 2.2k dependents
mikeblazanin
gcplyr:Wrangle and Analyze Growth Curve Data
Easy wrangling and model-free analysis of microbial growth curve data, as commonly output by plate readers. Tools for reshaping common plate reader outputs into 'tidy' formats and merging them with design information, making data easy to work with using 'gcplyr' and other packages. Also streamlines common growth curve processing steps, like smoothing and calculating derivatives, and facilitates model-free characterization and analysis of growth data. See methods at <https://mikeblazanin.github.io/gcplyr/>.
Maintained by Mike Blazanin. Last updated 2 months ago.
4.0 match 30 stars 7.90 score 75 scripts
henrikbengtsson
matrixStats:Functions that Apply to Rows and Columns of Matrices (and to Vectors)
High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Maintained by Henrik Bengtsson. Last updated 2 months ago.
1.7 match 208 stars 18.09 score 20k scripts 2.3k dependents
sebkrantz
collapse:Advanced and Fast Data Transformation
A C/C++ based package for advanced data transformation and statistical computing in R that is extremely fast, class-agnostic, robust and programmer friendly. Core functionality includes a rich set of S3 generic grouped and weighted statistical functions for vectors, matrices and data frames, which provide efficient low-level vectorizations, OpenMP multithreading, and skip missing values by default. These are integrated with fast grouping and ordering algorithms (also callable from C), and efficient data manipulation functions. The package also provides a flexible and rigorous approach to time series and panel data in R. It further includes fast functions for common statistical procedures, detailed (grouped, weighted) summary statistics, powerful tools to work with nested data, fast data object conversions, functions for memory efficient R programming, and helpers to effectively deal with variable labels, attributes, and missing data. It is well integrated with base R classes, 'dplyr'/'tibble', 'data.table', 'sf', 'units', 'plm' (panel-series and data frames), and 'xts'/'zoo'.
Maintained by Sebastian Krantz. Last updated 5 days ago.
data-aggregationdata-analysisdata-manipulationdata-processingdata-sciencedata-transformationeconometricshigh-performancepanel-datascientific-computingstatisticstime-seriesweightedweightscppopenmp
1.7 match 672 stars 16.63 score 708 scripts 97 dependents
lbelzile
mev:Modelling of Extreme Values
Various tools for the analysis of univariate, multivariate and functional extremes. Exact simulation from max-stable processes [Dombry, Engelke and Oesting (2016) <doi:10.1093/biomet/asw008>, R-Pareto processes for various parametric models, including Brown-Resnick (Wadsworth and Tawn, 2014, <doi:10.1093/biomet/ast042>) and Extremal Student (Thibaud and Opitz, 2015, <doi:10.1093/biomet/asv045>). Threshold selection methods, including Wadsworth (2016) <doi:10.1080/00401706.2014.998345>, and Northrop and Coleman (2014) <doi:10.1007/s10687-014-0183-z>. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes, e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>.
Maintained by Leo Belzile. Last updated 5 months ago.
extreme-value-statisticslikelihood-functionsmax-stablesimulationthreshold-selectionopenblascppopenmp
3.4 match 13 stars 8.23 score 94 scripts 4 dependents
cshs-hydrology
CSHShydRology:Canadian Hydrological Analyses
A collection of user submitted functions to aid in the analysis of hydrological data.
Maintained by Kevin Shook. Last updated 3 years ago.
5.3 match 4 stars 5.26 score 23 scripts
rpolars
polars:Lightning-Fast 'DataFrame' Library
Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.
Maintained by Soren Welling. Last updated 3 days ago.
2.0 match 499 stars 12.01 score 1.0k scripts 2 dependentsbioc
MsCoreUtils:Core Utils for Mass Spectrometry Data
MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.
Maintained by RforMassSpectrometry Package Maintainer. Last updated 4 days ago.
infrastructureproteomicsmassspectrometrymetabolomicsbioconductormass-spectrometryutils
2.3 match 16 stars 10.52 score 41 scripts 71 dependentsaphalo
photobiology:Photobiological Calculations
Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Maintained by Pedro J. Aphalo. Last updated 2 days ago.
lightphotobiologyquantificationr4photobiology-suiteradiationspectrasun-position
2.5 match 4 stars 9.35 score 604 scripts 12 dependentsr-forge
Rmpfr:Interface R to MPFR - Multiple Precision Floating-Point Reliable
Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, the package interfaces to the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Maintained by Martin Maechler. Last updated 4 months ago.
2.0 match 11.30 score 316 scripts 141 dependents
brry
extremeStat:Extreme Value Statistics and Quantile Estimation
Fit, plot and compare several (extreme value) distribution functions. Compute (truncated) distribution quantile estimates and plot return periods on a linear scale. On the fitting method, see Asquith (2011): Distributional Analysis with L-moment Statistics [...] ISBN 1463508417.
Maintained by Berry Boessenkool. Last updated 1 years ago.
3.8 match 14 stars 5.88 score 36 scripts 1 dependents
jfrench
smerc:Statistical Methods for Regional Counts
Implements statistical methods for analyzing the counts of areal data, with a focus on the detection of spatial clusters and clustering. The package has a heavy emphasis on spatial scan methods, which were first introduced by Kulldorff and Nagarwalla (1995) <doi:10.1002/sim.4780140809> and Kulldorff (1997) <doi:10.1080/03610929708831995>.
Maintained by Joshua French. Last updated 5 months ago.
3.5 match 3 stars 6.11 score 45 scripts 3 dependentsbioc
sparseMatrixStats:Summary Statistics for Rows and Columns of Sparse Matrices
High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.
Maintained by Constantin Ahlmann-Eltze. Last updated 5 months ago.
infrastructuresoftwaredatarepresentationcpp
1.7 match 54 stars 11.98 score 174 scripts 126 dependentscran
astrochron:A Computational Tool for Astrochronology
Routines for astrochronologic testing, astronomical time scale construction, and time series analysis <doi:10.1016/j.earscirev.2018.11.015>. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Maintained by Stephen Meyers. Last updated 6 months ago.
5.3 match 5 stars 3.85 score 141 scriptsbioc
DelayedMatrixStats:Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.
Maintained by Peter Hickey. Last updated 2 months ago.
infrastructuredatarepresentationsoftware
1.7 match 16 stars 11.86 score 211 scripts 112 dependentsbioc
MatrixGenerics:S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.
Maintained by Peter Hickey. Last updated 2 months ago.
infrastructuresoftwarebioconductor-packagecore-package
1.7 match 12 stars 11.64 score 129 scripts 1.3k dependents
dgkf
parttime:Partial Datetime Handling
Datetimes and timestamps are invariably an imprecise notation, with any partial representation implying some amount of uncertainty. To handle this, 'parttime' provides classes for embedding partial missingness as a central part of its datetime classes. This central feature allows for more ergonomic use of datetimes for challenging datetime computation, including calculations of overlapping date ranges, imputations, and more thoughtful handling of ambiguity that arises from uncertain time zones. This package was developed first and foremost with pharmaceutical applications in mind, but aims to be agnostic to application to accommodate general use cases just as conveniently.
Maintained by Doug Kelkhoff. Last updated 1 years ago.
4.5 match 17 stars 3.93 score 3 scriptsr-forge
Rwave:Time-Frequency analysis of 1-D signals
Rwave is a library of R functions which provide an environment for the Time-Frequency analysis of 1-D signals (and especially for the wavelet and Gabor transforms of noisy signals). It was originally written for Splus by Rene Carmona, Bruno Torresani, and Wen L. Hwang, first at the University of California at Irvine and then at Princeton University. Credit should also be given to Andrea Wang whose functions on the dyadic wavelet transform are included. Rwave is based on the book: "Practical Time-Frequency Analysis: Gabor and Wavelet Transforms with an Implementation in S", by Rene Carmona, Wen L. Hwang and Bruno Torresani, Academic Press, 1998. This package is no longer actively maintained. A C++ rewrite of core functionality is in progress. If you'd like to participate, please contact Christian Gunning.
Maintained by Brandon Whitcher. Last updated 13 years ago.
3.6 match 4.82 score 88 scripts 5 dependents
tpetzoldt
FAdist:Distributions that are Sometimes Used in Hydrology
Probability distributions that are sometimes useful in hydrology.
Maintained by Thomas Petzoldt. Last updated 3 years ago.
3.8 match 4 stars 4.49 score 51 scripts 1 dependents
cbielow
PTXQC:Quality Report Generation for MaxQuant and mzTab Results
Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.
Maintained by Chris Bielow. Last updated 1 years ago.
drag-and-drophacktoberfestheatmapmatch-between-runsmaxquantmetricmztabopenmsproteomicsquality-controlquality-metricsreport
1.8 match 42 stars 9.35 score 105 scripts 1 dependentsbioc
csaw:ChIP-Seq Analysis with Windows
Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
Maintained by Aaron Lun. Last updated 2 months ago.
multiplecomparisonchipseqnormalizationsequencingcoveragegeneticsannotationdifferentialpeakcallingcurlbzip2xz-utilszlibcpp
2.0 match 8.32 score 498 scripts 7 dependents
kwb-r
kwb.utils:General Utility Functions Developed at KWB
This package contains some small helper functions that aim at improving the quality of code developed at Kompetenzzentrum Wasser gGmbH (KWB).
Maintained by Hauke Sonnenberg. Last updated 12 months ago.
2.3 match 8 stars 7.33 score 12 scripts 78 dependents
manueleleonelli
extrememix:Bayesian Estimation of Extreme Value Mixture Models
Fits extreme value mixture models, which are models for tails not requiring selection of a threshold, for continuous data. It includes functions for model comparison, estimation of quantity of interest in extreme value analysis and plotting. Reference: CN Behrens, HF Lopes, D Gamerman (2004) <doi:10.1191/1471082X04st075oa>. FF do Nascimento, D. Gamerman, HF Lopes <doi:10.1007/s11222-011-9270-z>.
Maintained by Manuele Leonelli. Last updated 5 months ago.
3.6 match 2 stars 4.48 score 4 scripts
moviedo5
fda.usc:Functional Data Analysis and Utilities for Statistical Computing
Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.
Maintained by Manuel Oviedo de la Fuente. Last updated 4 months ago.
functional-data-analysisfortran
1.6 match 12 stars 9.72 score 560 scripts 22 dependents
antoinelucas64
gmp:Multiple Precision Arithmetic
Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the C library GMP (GNU Multiple Precision Arithmetic).
Maintained by Antoine Lucas. Last updated 7 months ago.
2.0 match 7.69 score 530 scripts 317 dependents
tomasfryda
h2o:R Interface for the 'H2O' Scalable Machine Learning Platform
R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
Maintained by Tomas Fryda. Last updated 1 years ago.
1.9 match 3 stars 8.20 score 7.8k scripts 11 dependents
asgr
imager:Image Processing Library Based on 'CImg'
Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.
Maintained by Aaron Robotham. Last updated 26 days ago.
1.1 match 17 stars 13.62 score 2.4k scripts 45 dependents
clementcalenge
adehabitatHR:Home Range Estimation
A collection of tools for the estimation of animals home range.
Maintained by Clement Calenge. Last updated 6 months ago.
1.8 match 6 stars 8.73 score 752 scripts 9 dependents
shabbychef
madness:Automatic Differentiation of Multivariate Operations
An object that supports automatic differentiation of matrix- and multidimensional-valued functions with respect to multidimensional independent variables. Automatic differentiation is via 'forward accumulation'.
Maintained by Steven E. Pav. Last updated 4 years ago.
2.3 match 31 stars 6.59 score 28 scripts 3 dependents
spkaluzny
splus2R:Supplemental S-PLUS Functionality in R
Currently there are many functions in S-PLUS that are missing in R. To facilitate the conversion of S-PLUS packages to R packages, this package provides some missing S-PLUS functionality in R.
Maintained by Stephen Kaluzny. Last updated 1 years ago.
2.3 match 1 stars 6.56 score 82 scripts 30 dependents
cecilemercadier
satdad:Sensitivity Analysis Tools for Dependence and Asymptotic Dependence
Tools for analyzing tail dependence in any sample or in particular theoretical models. The package uses only theoretical and non parametric methods, without inference. The primary goals of the package are to provide: (a)symmetric multivariate extreme value models in any dimension; theoretical and empirical indices to order tail dependence; theoretical and empirical graphical methods to visualize tail dependence.
Maintained by Cécile Mercadier. Last updated 2 years ago.
6.6 match 2.00 score 2 scriptscran
mc2d:Tools for Two-Dimensional Monte-Carlo Simulations
A complete framework to build and study Two-Dimensional Monte-Carlo simulations, aka Second-Order Monte-Carlo simulations. Also includes various distributions (pert, triangular, Bernoulli, empirical discrete and continuous).
Maintained by Regis Pouillot. Last updated 9 months ago.
2.0 match 1 stars 6.28 score 16 dependents
robinhankin
spray:Sparse Arrays and Multivariate Polynomials
Sparse arrays interpreted as multivariate polynomials. Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/ARXIV.2210.03856>). To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2210.10848>.
Maintained by Robin K. S. Hankin. Last updated 2 months ago.
1.9 match 2 stars 6.62 score 35 scripts 4 dependents
s-fleck
dint:A Toolkit for Year-Quarter, Year-Month and Year-Isoweek Dates
S3 classes and methods to create and work with year-quarter, year-month and year-isoweek vectors. Basic arithmetic operations (such as adding and subtracting) are supported, as well as formatting and converting to and from standard R date types.
Maintained by Stefan Fleck. Last updated 4 months ago.
datedatesmonthperiodquarterweek
2.0 match 14 stars 6.11 score 58 scripts 1 dependents
rje42
rje:Miscellaneous Useful Functions for Statistics
A series of functions in some way considered useful to the author. These include methods for subsetting tables and generating indices for arrays, conditioning and intervening in probability distributions, generating combinations, fast transformations, and more...
Maintained by Robin Evans. Last updated 12 months ago.
1.9 match 6.50 score 173 scripts 10 dependents
mottensmann
GCalignR:Simple Peak Alignment for Gas-Chromatography Data
Aligns peak based on peak retention times and matches homologous peaks across samples. The underlying alignment procedure comprises three sequential steps. (1) Full alignment of samples by linear transformation of retention times to maximise similarity among homologous peaks (2) Partial alignment of peaks within a user-defined retention time window to cluster homologous peaks (3) Merging rows that are likely representing homologous substances (i.e. no sample shows peaks in both rows and the rows have similar retention time means). The algorithm is described in detail in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.
Maintained by Meinolf Ottensmann. Last updated 6 months ago.
1.8 match 5 stars 6.39 score 41 scripts
uchidamizuki
dibble:Dimensional Data Frames
Provides a 'dibble' that implements data cubes (derived from 'dimensional tibble'), and allows broadcasting by dimensional names.
Maintained by Mizuki Uchida. Last updated 28 days ago.
multidimensional-arraystidy-data
2.3 match 14 stars 5.05 score 8 scripts
nicwir
QurvE:Robust and User-Friendly Analysis of Growth and Fluorescence Curves
High-throughput analysis of growth curves and fluorescence data using three methods: linear regression, growth model fitting, and smooth spline fit. Analysis of dose-response relationships via smoothing splines or dose-response models. Complete data analysis workflows can be executed in a single step via user-friendly wrapper functions. The results of these workflows are summarized in detailed reports as well as intuitively navigable 'R' data containers. A 'shiny' application provides access to all features without requiring any programming knowledge. The package is described in further detail in Wirth et al. (2023) <doi:10.1038/s41596-023-00850-7>.
Maintained by Nicolas T. Wirth. Last updated 1 years ago.
1.8 match 25 stars 6.00 score 7 scripts
magnuskristoffersen
detzrcr:Compare Detrital Zircon Suites
Compare detrital zircon suites by uploading univariate, U-Pb age, or bivariate, U-Pb age and Lu-Hf data, in a 'shiny'-based user-interface. Outputs publication quality figures using 'ggplot2', and tables of statistics currently in use in the detrital zircon geochronology community.
Maintained by Magnus Kristoffersen. Last updated 2 years ago.
2.3 match 9 stars 4.65 score 1 scripts
jmmonnet
lidaRtRee:Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Provides functions for forest objects detection, structure metrics computation, model calibration and mapping with airborne laser scanning: co-registration of field plots (Monnet and Mermin (2014) <doi:10.3390/f5092307>); tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation with the area-based approach: model calibration with ground reference, and maps export (Aussenac et al. (2023) <doi:10.12688/openreseurope.15373.2>); extraction of both physical (gaps, edges, trees) and statistical features useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>) and forest maturity mapping (Fuhr et al. (2022) <doi:10.1002/rse2.274>).
Maintained by Jean-Matthieu Monnet. Last updated 2 months ago.
4.7 match 3 stars 2.18 score
looping027
far:Modelization for Functional AutoRegressive Processes
Modelizations and previsions functions for Functional AutoRegressive processes using nonparametric methods: functional kernel, estimation of the covariance operator in a subspace, ...
Maintained by Julien Damon. Last updated 6 months ago.
2.0 match 4 stars 5.06 score 64 scripts 3 dependentsbioc
ASSET:An R package for subset-based association analysis of heterogeneous traits and subtypes
An R package for subset-based analysis of heterogeneous traits and disease subtypes. The package allows the user to search through all possible subsets of z-scores to identify the subset of traits giving the best meta-analyzed z-score. Further, it returns a p-value adjusting for the multiple-testing involved in the search. It also allows for searching for the best combination of disease subtypes associated with each variant.
Maintained by Samsiddhi Bhattacharjee. Last updated 5 months ago.
statisticalmethodsnpgenomewideassociationmultiplecomparison
1.8 match 5.71 score 85 scripts 1 dependentsrobinhankin
frab:How to Add Two R Tables
Methods to "add" two R tables; also an alternative interpretation of named vectors as generalized R tables, so that c(a=1,b=2,c=3) + c(b=3,a=-1) will return c(b=5,c=3). Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/arXiv.2210.03856>). Extraction and replacement methods are provided. The underlying mathematical structure is the Free Abelian group, hence the name. To cite in publications please use Hankin (2023) <doi:10.48550/arXiv.2307.13184>.
Maintained by Robin K. S. Hankin. Last updated 3 months ago.
1.9 match 1 stars 5.26 score 1 dependents
bayesiandemography
rvec:Vector Representing a Random Variable
Random vectors, called rvecs. An rvec holds multiple draws, but tries to behave like a standard R vector, including working well in data frames. Rvecs are useful for working with output from a simulation or a Bayesian analysis.
Maintained by John Bryant. Last updated 6 months ago.
1.8 match 2 stars 5.46 score 24 scripts 2 dependents
joeroe
era:Year-Based Time Scales
Provides a consistent representation of year-based time scales as a numeric vector with an associated 'era'. There are built-in era definitions for many year numbering systems used in contemporary and historic calendars (e.g. Common Era, Islamic 'Hijri' years); year-based time scales used in archaeology, astronomy, geology, and other palaeosciences (e.g. Before Present, SI-prefixed 'annus'); and support for arbitrary user-defined eras. Years can converted from any one era to another using a generalised transformation function. Methods are also provided for robust casting and coercion between years and other numeric types, type-stable arithmetic with years, and pretty-printing in tables.
Maintained by Joe Roe. Last updated 4 months ago.
archaeologygeologypaleoclimatepaleontologyvctrs
2.0 match 15 stars 4.88 score 4 scripts
paciorek
climextRemes:Tools for Analyzing Climate Extremes
Functions for fitting GEV and POT (via point process fitting) models for extremes in climate data, providing return values, return probabilities, and return periods for stationary and nonstationary models. Also provides differences in return values and differences in log return probabilities for contrasts of covariate values. Functions for estimating risk ratios for event attribution analyses, including uncertainty. Under the hood, many of the functions use functions from 'extRemes', including for fitting the statistical models. Details are given in Paciorek, Stone, and Wehner (2018) <doi:10.1016/j.wace.2018.01.002>.
Maintained by Christopher Paciorek. Last updated 1 years ago.
3.3 match 2.85 score 14 scriptsbioc
ptairMS:Pre-processing PTR-TOF-MS Data
This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a singl<e ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation and feature annotation. Applications to exhaled air and cell culture in headspace are described in the vignettes and examples. This package was used for data analysis of Gassin Delyle study on adults undergoing invasive mechanical ventilation in the intensive care unit due to severe COVID-19 or non-COVID-19 acute respiratory distress syndrome (ARDS), and permit to identfy four potentiel biomarquers of the infection.
Maintained by camille Roquencourt. Last updated 5 months ago.
softwaremassspectrometrypreprocessingmetabolomicspeakdetectionalignmentcpp
1.8 match 7 stars 5.15 score 3 scripts
yannabraham
hilbertSimilarity:Hilbert Similarity Index for High Dimensional Data
Quantifying similarity between high-dimensional single cell samples is challenging, and usually requires some simplifying hypothesis to be made. By transforming the high dimensional space into a high dimensional grid, the number of cells in each sub-space of the grid is characteristic of a given sample. Using a Hilbert curve each sample can be visualized as a simple density plot, and the distance between samples can be calculated from the distribution of cells using the Jensen-Shannon distance. Bins that correspond to significant differences between samples can identified using a simple bootstrap procedure.
Maintained by Yann Abraham. Last updated 5 years ago.
1.9 match 5 stars 4.74 score 11 scripts
shichenxie
xefun:X-Engineering or Supporting Functions
Miscellaneous functions used for x-engineering (feature engineering) or for supporting in other packages maintained by 'Shichen Xie'.
Maintained by Shichen Xie. Last updated 1 months ago.
2.3 match 2 stars 3.87 score 2 dependents
henningte
ir:Functions to Handle and Preprocess Infrared Spectra
Functions to import and handle infrared spectra (import from '.csv' and Thermo Galactic's '.spc', baseline correction, binning, clipping, interpolating, smoothing, averaging, adding, subtracting, dividing, multiplying, plotting).
Maintained by Henning Teickner. Last updated 3 years ago.
chemometricsinfraredinfrared-spectrair-packagemid-infrared-spectraspectroscopy
1.6 match 6 stars 5.32 score 35 scripts
jonathanlees
RSEIS:Seismic Time Series Analysis Tools
Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Maintained by Jonathan M. Lees. Last updated 6 months ago.
2.0 match 3 stars 4.27 score 262 scripts 4 dependents
irsn
Renext:Renewal Method for Extreme Values Extrapolation
Peaks Over Threshold (POT) or 'methode du renouvellement'. The distribution for the excesses can be chosen, and heterogeneous data (including historical data or block data) can be used in a Maximum-Likelihood framework.
Maintained by Yann Richet. Last updated 1 years ago.
1.6 match 4.99 score 82 scripts 4 dependents
ghtaranto
scapesClassification:User-Defined Classification of Raster Surfaces
Series of algorithms to translate users' mental models of seascapes, landscapes and, more generally, of geographic features into computer representations (classifications). Spaces and geographic objects are classified with user-defined rules taking into account spatial data as well as spatial relationships among different classes and objects.
Maintained by Gerald H. Taranto. Last updated 3 years ago.
classification-algorithmobject-detectionrasterspatial
1.9 match 1 stars 4.22 score 33 scripts
tgouhier
synchrony:Methods for Computing Spatial, Temporal, and Spatiotemporal Statistics
Methods for computing spatial, temporal, and spatiotemporal statistics as described in Gouhier and Guichard (2014) [https://doi.org/10.1111/2041-210X.12188]. These methods include empirical univariate, bivariate and multivariate variograms; fitting variogram models; phase locking and synchrony analysis; generating autocorrelated and cross-correlated matrices.
Maintained by Tarik C. Gouhier. Last updated 5 years ago.
1.6 match 10 stars 4.84 score 46 scripts
pcruniversum
MBmca:Nucleic Acid Melting Curve Analysis
Lightweight utilities for nucleic acid melting curve analysis are important in life sciences and diagnostics. This software can be used for the analysis and presentation of melting curve data from microbead-based assays (surface melting curve analysis) and reactions in solution (e.g., quantitative PCR (qPCR), real-time isothermal Amplification). Further information are described in detail in two publications in The R Journal [ <https://journal.r-project.org/archive/2013-2/roediger-bohm-schimke.pdf>; <https://journal.r-project.org/archive/2015-1/RJ-2015-1.pdf>].
Maintained by Stefan Roediger. Last updated 4 years ago.
1.7 match 4 stars 4.53 score 17 scriptsbioc
HilbertVis:Hilbert curve visualization
Functions to visualize long vectors of integer data by means of Hilbert curves
Maintained by Simon Anders. Last updated 5 months ago.
1.7 match 4.40 score 14 scripts 1 dependentscran
extRemes:Extreme Value Analysis
General functions for performing extreme value analysis. In particular, allows for inclusion of covariates into the parameters of the extreme-value distributions, as well as estimation through MLE, L-moments, generalized (penalized) MLE (GMLE), as well as Bayes. Inference methods include parametric normal approximation, profile-likelihood, Bayes, and bootstrapping. Some bivariate functionality and dependence checking (e.g., auto-tail dependence function plot, extremal index estimation) is also included. For a tutorial, see Gilleland and Katz (2016) <doi: 10.18637/jss.v072.i08> and for bootstrapping, please see Gilleland (2020) <doi: 10.1175/JTECH-D-20-0070.1>.
Maintained by Eric Gilleland. Last updated 4 months ago.
2.0 match 2 stars 3.75 score 5 dependents
coatless-rpkg
jjb:Balamuta Miscellaneous
Set of common functions used for manipulating colors, detecting and interacting with 'RStudio', modeling, formatting, determining users' operating system, feature scaling, and more!
Maintained by James Balamuta. Last updated 1 years ago.
1.9 match 2 stars 3.97 score 31 scripts 1 dependentscran
RSDA:R to Symbolic Data Analysis
Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Maintained by Oldemar Rodriguez. Last updated 1 years ago.
2.3 match 1 stars 3.26 score 3 dependents
conradwasko
hydroEvents:Extract Event Statistics in Hydrologic Time Series
Events from individual hydrologic time series are extracted, and events from multiple time series can be matched to each other. Tang, W. & Carey, S. K. (2017) <doi:10.1002/hyp.11185>. Kaur, S., Horne, A., Stewardson, M.J., Nathan, R., Costa, A.M., Szemis, J.M., & Webb, J.A. (2017) <doi:10.1080/24705357.2016.1276418>. Ladson, A., Brown, R., Neal, B., & Nathan, R. J. (2013) <doi:10.7158/W12-028.2013.17.1>.
Maintained by Conrad Wasko. Last updated 1 months ago.
1.8 match 6 stars 4.03 score 36 scriptscran
MCMC4Extremes:Posterior Distribution of Extreme Value Models in R
Provides some function to perform posterior estimation for some distribution, with emphasis to extreme value distributions. It contains some extreme datasets, and functions that perform the runs of posterior points of the GPD and GEV distribution. The package calculate some important extreme measures like return level for each t periods of time, and some plots as the predictive distribution, and return level plots.
Maintained by Fernando Ferraz do Nascimento. Last updated 9 years ago.
6.9 match 1.00 score
ilapros
winfapReader:Interact with Peak Flow Data in the United Kingdom
Obtain information on peak flow data from the National River Flow Archive (NRFA) in the United Kingdom, either from the Peak Flow Dataset files <https://nrfa.ceh.ac.uk/peak-flow-dataset> once these have been downloaded to the user's computer or using the NRFA's API. These files are in a format suitable for direct use in the 'WINFAP' software, hence the name of the package.
Maintained by Ilaria Prosdocimi. Last updated 9 months ago.
1.7 match 2 stars 4.00 score 5 scripts
shotaochi
scorepeak:Peak Functions for Peak Detection in Univariate Time Series
Provides peak functions, which enable us to detect peaks in time series. The methods implemented in this package are based on Girish Keshav Palshikar (2009) <https://www.researchgate.net/publication/228853276_Simple_Algorithms_for_Peak_Detection_in_Time-Series>.
Maintained by Shota Ochi. Last updated 4 years ago.
1.7 match 1 stars 3.70 score 6 scripts
seil85
spectral:Common Methods of Spectral Data Analysis
On discrete data spectral analysis is performed by Fourier and Hilbert transforms as well as with model based analysis called Lomb-Scargle method. Fragmented and irregularly spaced data can be processed in almost all methods. Both, FFT as well as LOMB methods take multivariate data and return standardized PSD. For didactic reasons an analytical approach for deconvolution of noise spectra and sampling function is provided. A user friendly interface helps to interpret the results.
Maintained by Martin Seilmayer. Last updated 4 years ago.
2.3 match 2.81 score 36 scripts 1 dependentscran
crone:Structural Crystallography in 1d
Functions to carry out the most important crystallographic calculations for crystal structures made of 1d Gaussian-shaped atoms, especially useful for methods development. Main reference: E. Smith, G. Evans, J. Foadi (2017) <doi:10.1088/1361-6404/aa8188>.
Maintained by James Foadi. Last updated 6 years ago.
1.8 match 3.40 score
noramvillanueva
seq2R:Simple Method to Detect Compositional Changes in Genomic Sequences
This software is useful for loading '.fasta' or '.gbk' files, and for retrieving sequences from 'GenBank' dataset <https://www.ncbi.nlm.nih.gov/genbank/>. This package allows to detect differences or asymmetries based on nucleotide composition by using local linear kernel smoothers. Also, it is possible to draw inference about critical points (i. e. maximum or minimum points) related with the derivative curves. Additionally, bootstrap methods have been used for estimating confidence intervals and speed computational techniques (binning techniques) have been implemented in 'seq2R'.
Maintained by Nora M. Villanueva. Last updated 4 months ago.
bootstrapchange-pointsdna-sequencesgenome-analysismachine-learningnonparametric-statisticsregressionfortran
1.9 match 3.00 score 10 scriptscran
flood:Statistical Methods for the (Regional) Analysis of Flood Frequency
Includes several statistical methods for the estimation of parameters and high quantiles of river flow distributions. The focus is on regional estimation based on homogeneity assumptions and computed from multivariate observations (multiple measurement stations). For details see Kinsvater et al. (2017) <arXiv:1701.06455>.
Maintained by Friederike Deiters. Last updated 8 years ago.
5.4 match 1.00 score
harrysouthworth
texmex:Statistical Modelling of Extreme Values
Statistical extreme value modelling of threshold excesses, maxima and multivariate extremes. Univariate models for threshold excesses and maxima are the Generalised Pareto, and Generalised Extreme Value model respectively. These models may be fitted by using maximum (optionally penalised-)likelihood, or Bayesian estimation, and both classes of models may be fitted with covariates in any/all model parameters. Model diagnostics support the fitting process. Graphical output for visualising fitted models and return level estimates is provided. For serially dependent sequences, the intervals declustering algorithm of Ferro and Segers (2003) <doi:10.1111/1467-9868.00401> is provided, with diagnostic support to aid selection of threshold and declustering horizon. Multivariate modelling is performed via the conditional approach of Heffernan and Tawn (2004) <doi:10.1111/j.1467-9868.2004.02050.x>, with graphical tools for threshold selection and to diagnose estimation convergence.
Maintained by Harry Southworth. Last updated 1 years ago.
0.8 match 7 stars 6.92 score 66 scripts 1 dependentscran
IDF:Estimation and Plotting of IDF Curves
Intensity-duration-frequency (IDF) curves are a widely used analysis-tool in hydrology to assess extreme values of precipitation [e.g. Mailhot et al., 2007, <doi:10.1016/j.jhydrol.2007.09.019>]. The package 'IDF' provides functions to estimate IDF parameters for given precipitation time series on the basis of a duration-dependent generalized extreme value distribution [Koutsoyiannis et al., 1998, <doi:10.1016/S0022-1694(98)00097-3>].
Maintained by Felix S. Fauer. Last updated 3 years ago.
1.8 match 2.30 scorecran
dSTEM:Multiple Testing of Local Extrema for Detection of Change Points
Simultaneously detect the number and locations of change points in piecewise linear models under stationary Gaussian noise allowing autocorrelated random noise. The core idea is to transform the problem of detecting change points into the detection of local extrema (local maxima and local minima)through kernel smoothing and differentiation of the data sequence, see Cheng et al. (2020) <doi:10.1214/20-EJS1751>. A low-computational and fast algorithm call 'dSTEM' is introduced to detect change points based on the 'STEM' algorithm in D. Cheng and A. Schwartzman (2017) <doi:10.1214/16-AOS1458>.
Maintained by Zhibing He. Last updated 2 years ago.
3.9 match 1.00 scorer-forge
fExtremes:Rmetrics - Modelling Extreme Events in Finance
Provides functions for analysing and modelling extreme events in financial time Series. The topics include: (i) data pre-processing, (ii) explorative data analysis, (iii) peak over threshold modelling, (iv) block maxima modelling, (v) estimation of VaR and CVaR, and (vi) the computation of the extreme index.
Maintained by Paul J. Northrop. Last updated 3 months ago.
0.5 match 1 stars 7.30 score 118 scripts 4 dependents
tidyfun
tf:S3 Classes and Methods for Tidy Functional Data
Defines S3 vector data types for vectors of functional data (grid-based, spline-based or functional principal components-based) with all arithmetic and summary methods, derivation, integration and smoothing, plotting, data import and export, and data wrangling, such as re-evaluating, subsetting, sub-assigning, zooming into sub-domains, or extracting functional features like minima/maxima and their locations. The implementation allows including such vectors in data frames for joint analysis of functional and scalar variables.
Maintained by Fabian Scheipl. Last updated 4 days ago.
0.5 match 7 stars 6.14 score 13 scripts 2 dependents
bpfaff
evir:Extreme Values in R
Functions for extreme value theory, which may be divided into the following groups; exploratory data analysis, block maxima, peaks over thresholds (univariate and bivariate), point processes, gev/gpd distributions.
Maintained by Bernhard Pfaff. Last updated 8 years ago.
0.5 match 2 stars 5.89 score 211 scripts 6 dependentscran
mSTEM:Multiple Testing of Local Extrema for Detection of Change Points
A new approach to detect change points based on smoothing and multiple testing, which is for long data sequence modeled as piecewise constant functions plus stationary Gaussian noise, see Dan Cheng and Armin Schwartzman (2015) <arXiv:1504.06384>.
Maintained by Zhibing He. Last updated 5 years ago.
1.8 match 1.70 score
e-gregory
RMallow:Fit Multi-Modal Mallows' Models to Ranking Data
An EM algorithm to fit Mallows' Models to full or partial rankings, with or without ties. Based on Adkins and Flinger (1998) <doi:10.1080/03610929808832223>.
Maintained by Erik Gregory. Last updated 5 years ago.
1.6 match 1.95 score 10 scripts 3 dependentscran
thermocouple:Temperature Measurement with Thermocouples, RTD and IC Sensors
Temperature measurement data, equations and methods for thermocouples, wire RTD, thermistors, IC thermometers, bimetallic strips and the ITS-90.
Maintained by Jose Gama. Last updated 10 years ago.
1.7 match 1.68 score 48 scriptscran
maxstablePCA:Apply a PCA Like Procedure Suited for Multivariate Extreme Value Distributions
Dimension reduction for multivariate data of extreme events with a PCA like procedure as described in Reinbott, Janßen, (2024), <doi:10.48550/arXiv.2408.10650>. Tools for necessary transformations of the data are provided.
Maintained by Felix Reinbott. Last updated 6 months ago.
1.7 match 1.70 score
ericgilleland
ismev:An Introduction to Statistical Modeling of Extreme Values
Functions to support the computations carried out in `An Introduction to Statistical Modeling of Extreme Values' by Stuart Coles. The functions may be divided into the following groups; maxima/minima, order statistics, peaks over thresholds and point processes.
Maintained by Eric Gilleland. Last updated 7 years ago.
0.5 match 1 stars 5.19 score 326 scripts 13 dependents
patrickroocks
rPref:Database Preferences and Skyline Computation
Routines to select and visualize the maxima for a given strict partial order. This especially includes the computation of the Pareto frontier, also known as (Top-k) Skyline operator (see Börzsönyi, et al. (2001) <doi:10.1109/ICDE.2001.914855>), and some generalizations known as database preferences (see Kießling (2002) <doi:10.1016/B978-155860869-6/50035-4>).
Maintained by Patrick Roocks. Last updated 2 years ago.
0.5 match 2 stars 5.14 score 115 scripts 4 dependents
biointf
FBN:FISH Based Normalization and Copy Number Inference of SNP Microarray Data
Normalizes the data from a file containing the raw values of the SNP probes of microarray data by using the FISH probes and their corresponding copy number.
Maintained by Luca Agnelli. Last updated 2 years ago.
1.8 match 1.32 score 21 scripts
cran
IDPmisc:'Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)'
Different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.
Maintained by Christoph Hofer. Last updated 1 years ago.
0.5 match 1 stars 3.64 score 22 dependents
skranz
skUtils:Helper functions for repgames and dyngames
Helper functions needed by my package repgames and dyngames
Maintained by Sebastian Kranz. Last updated 4 years ago.
1.8 match 1.00 score
veronicanava
RamanMP:Analysis and Identification of Raman Spectra of Microplastics
Pre-processing and polymer identification of Raman spectra of plastics. Pre-processing includes normalisation functions, peak identification based on local maxima, smoothing process and removal of spectral region of no interest. Polymer identification can be performed using Pearson correlation coefficient or Euclidean distance (Renner et al. (2019), <doi:10.1016/j.trac.2018.12.004>), and the comparison can be done with a user-defined database or with the database already implemented in the package, which currently includes 356 spectra, with several spectra of plastic colorants.
Maintained by Veronica Nava. Last updated 3 years ago.
0.5 match 6 stars 3.48 score 1 scripts
frankpapenmeier
segmag:Determine Event Boundaries in Event Segmentation Experiments
Contains functions that help to determine event boundaries in event segmentation experiments by bootstrapping a critical segmentation magnitude under the null hypothesis that all key presses were randomly distributed across the experiment. Segmentation magnitude is defined as the sum of Gaussians centered at the times of the segmentation key presses performed by the participants. Within a participant, the maximum of the overlaid Gaussians is used to prevent an excessive influence of a single participant on the overall outcome (e.g. if a participant is pressing the key multiple times in succession). Further functions are included, such as plotting the results.
Maintained by Frank Papenmeier. Last updated 9 years ago.
1.8 match 1.00 score 4 scriptscran
SQMtools:Analyze Results Generated by the 'SqueezeMeta' Pipeline
'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.
Maintained by Fernando Puente-Sánchez. Last updated 1 years ago.
1.7 match 1 stars 1.00 score
jeromepcollet
ModEstM:Mode Estimation, Even in the Multimodal Case
Function ModEstM() is the only one of this package, it estimates the modes of an empirical univariate distribution. It relies on the stats::density() function, even for input control. Due to very good performance of the density estimation, computation time is not an issue. The multiple modes are handled using dplyr::group_by(). For conditions and rates of convergences, see Eddy (1980) <doi:10.1214/aos/1176345080>.
Maintained by Jerome Collet. Last updated 3 years ago.
1.6 match 1.00 score
rvaradhan
features:Feature Extraction for Discretely-Sampled Functional Data
Discretely-sampled function is first smoothed. Features of the smoothed function are then extracted. Some of the key features include mean value, first and second derivatives, critical points (i.e. local maxima and minima), curvature of cunction at critical points, wiggliness of the function, noise in data, and outliers in data.
Maintained by Ravi Varadhan. Last updated 9 years ago.
0.5 match 2.53 score 112 scriptscran
ampd:An Algorithm for Automatic Peak Detection in Noisy Periodic and Quasi-Periodic Signals
A method for automatic detection of peaks in noisy periodic and quasi-periodic signals. This method, called automatic multiscale-based peak detection (AMPD), is based on the calculation and analysis of the local maxima scalogram, a matrix comprising the scale-dependent occurrences of local maxima. For further information see <doi:10.3390/a5040588>.
Maintained by Oliver Sieber. Last updated 8 years ago.
0.8 match 1.00 score
pengjunucas
tgcd:Thermoluminescence Glow Curve Deconvolution
Deconvolving thermoluminescence glow curves according to various kinetic models (first-order, second-order, general-order, and mixed-order) using a modified Levenberg-Marquardt algorithm (More, 1978) <DOI:10.1007/BFb0067700>. It provides the possibility of setting constraints or fixing any of parameters. It offers an interactive way to initialize parameters by clicking with a mouse on a plot at positions where peak maxima should be located. The optimal estimate is obtained by "trial-and-error". It also provides routines for simulating first-order, second-order, and general-order glow peaks.
Maintained by Jun Peng. Last updated 2 years ago.
0.5 match 1.00 score 6 scripts
mathiasambuehl
cnaOpt:Optimizing Consistency and Coverage in Configurational Causal Modeling
This is an add-on to the 'cna' package <https://CRAN.R-project.org/package=cna> comprising various functions for optimizing consistency and coverage scores of models of configurational comparative methods as Coincidence Analysis (CNA) and Qualitative Comparative Analysis (QCA). The function conCovOpt() calculates con-cov optima, selectMax() selects con-cov maxima among the con-cov optima, DNFbuild() can be used to build models actually reaching those optima, and findOutcomes() identifies those factor values in analyzed data that can be modeled as outcomes. For a theoretical introduction to these functions see Baumgartner and Ambuehl (2021) <doi:10.1177/0049124121995554>.
Maintained by Mathias Ambuehl. Last updated 3 years ago.
0.5 match 1.00 score 4 scripts