Showing 42 of total 42 results (show query)
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
139.2 match 6 stars 5.32 score 35 scripts
gbm-developers
gbm:Generalized Boosted Regression Models
An implementation of extensions to Freund and Schapire's AdaBoost algorithm and Friedman's gradient boosting machine. Includes regression methods for least squares, absolute loss, t-distribution loss, quantile regression, logistic, multinomial logistic, Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and Learning to Rank measures (LambdaMart). Originally developed by Greg Ridgeway. Newer version available at github.com/gbm-developers/gbm3.
Maintained by Greg Ridgeway. Last updated 9 months ago.
10.0 match 52 stars 13.85 score 6.8k scripts 91 dependents
richardli
surveyPrev:Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas
Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.
Maintained by Qianyu Dong. Last updated 2 hours ago.
22.8 match 1 stars 5.76 score 11 scripts
aphalo
photobiologyWavebands:Waveband Definitions for UV, VIS, and IR Radiation
Constructors of waveband objects for commonly used biological spectral weighting functions (BSWFs) and for different wavebands describing named ranges of wavelengths in the ultraviolet (UV), visible (VIS) and infrared (IR) regions of the electromagnetic spectrum. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Maintained by Pedro J. Aphalo. Last updated 8 months ago.
8.4 match 1 stars 6.53 score 378 scripts 3 dependents
bryanhanson
ChemoSpec:Exploratory Chemometrics for Spectroscopy
A collection of functions for top-down exploratory data analysis of spectral data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed for structured experiments, such as metabolomics investigations, where the samples fall into treatment and control groups. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and to help you get usable results quickly. A vignette covering typical operations is available.
Maintained by Bryan A. Hanson. Last updated 1 years ago.
infrarednmrramanspectroscopyultravioletvisiblexrf
5.4 match 59 stars 7.77 score 45 scripts 1 dependents
mrc-ide
odin:ODE Generation and Integration
Generate systems of ordinary differential equations (ODE) and integrate them, using a domain specific language (DSL). The DSL uses R's syntax, but compiles to C in order to efficiently solve the system. A solver is not provided, but instead interfaces to the packages 'deSolve' and 'dde' are generated. With these, while solving the differential equations, no allocations are done and the calculations remain entirely in compiled code. Alternatively, a model can be transpiled to R for use in contexts where a C compiler is not present. After compilation, models can be inspected to return information about parameters and outputs, or intermediate values after calculations. 'odin' is not targeted at any particular domain and is suitable for any system that can be expressed primarily as mathematical expressions. Additional support is provided for working with delays (delay differential equations, DDE), using interpolated functions during interpolation, and for integrating quantities that represent arrays.
Maintained by Rich FitzJohn. Last updated 9 months ago.
3.8 match 106 stars 9.74 score 290 scripts 3 dependents
pommedeterresautee
unine:Unine Light Stemmer
Implementation of "light" stemmers for French, German, Italian, Spanish, Portuguese, Finnish, Swedish. They are based on the same work as the "light" stemmers found in 'SolR' <https://lucene.apache.org/solr/> or 'ElasticSearch' <https://www.elastic.co/fr/products/elasticsearch>. A "light" stemmer consists in removing inflections only for noun and adjectives. Indexing verbs for these languages is not of primary importance compared to nouns and adjectives. The stemming procedure for French is described in (Savoy, 1999) <doi:10.1002/(SICI)1097-4571(1999)50:10%3C944::AID-ASI9%3E3.3.CO;2-H>.
Maintained by Michaël Benesty. Last updated 6 years ago.
finishfrenchgermaninformation-retrievaliritaliannlpportuguesespanishstemmerswedishcpp
11.0 match 4 stars 3.30 score 1 scripts
risktoollib
RTL:Risk Tool Library - Trading, Risk, Analytics for Commodities
A toolkit for Commodities 'analytics', risk management and trading professionals. Includes functions for API calls to <https://commodities.morningstar.com/#/>, <https://developer.genscape.com/>, and <https://www.bankofcanada.ca/valet/docs>.
Maintained by Philippe Cote. Last updated 21 days ago.
analyticsapicommoditiescommodities-apifinancegenscapemorningstarpythonrisk-managementcpp
4.0 match 30 stars 7.51 score 198 scripts
igraph
igraph:Network Analysis and Visualization
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Maintained by Kirill Müller. Last updated 17 hours ago.
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphfortranlibxml2glpkopenblascpp
1.3 match 583 stars 21.10 score 31k scripts 1.9k dependents
wincowgerdev
OpenSpecy:Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples (Cowger et al. 2021, <doi:10.1021/acs.analchem.1c00123>). With read_any(), Open Specy provides a single function for reading individual, batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies processing spectra, including smoothing, baseline correction, range restriction and flattening, intensity conversions, wavenumber alignment, and min-max normalization. Spectra can be identified in batch using an onboard reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available via run_app() or online at <https://openanalysis.org/openspecy/>.
Maintained by Win Cowger. Last updated 20 days ago.
3.3 match 29 stars 7.58 score 22 scripts
assaforon
cir:Centered Isotonic Regression and Dose-Response Utilities
Isotonic regression (IR) and its improvement: centered isotonic regression (CIR). CIR is recommended in particular with small samples. Also, interval estimates for both, and additional utilities such as plotting dose-response data. For dev version and change history, see GitHub assaforon/cir.
Maintained by Assaf P. Oron. Last updated 2 months ago.
5.5 match 4.45 score 19 scripts 1 dependents
svmiller
stevemisc:Steve's Miscellaneous Functions
These are miscellaneous functions that I find useful for my research and teaching. The contents include themes for plots, functions for simulating quantities of interest from regression models, functions for simulating various forms of fake data for instructional/research purposes, and many more. All told, the functions provided here are broadly useful for data organization, data presentation, data recoding, and data simulation.
Maintained by Steve Miller. Last updated 8 days ago.
dplyrmixed-effects-modelsmultivariate-normal-distributiontidyverse
3.3 match 10 stars 6.85 score 392 scripts 2 dependents
ahgroup
DSAIRM:Dynamical Systems Approach to Immune Response Modeling
Simulation models (apps) of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.
Maintained by Andreas Handel. Last updated 8 months ago.
3.6 match 34 stars 6.19 score 23 scripts
r-lum
Luminescence:Comprehensive Luminescence Dating Data Analysis
A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Maintained by Sebastian Kreutzer. Last updated 1 hours ago.
bayesian-statisticsdata-sciencegeochronologyluminescenceluminescence-datingopen-scienceoslplottingradiofluorescencetlxsygcpp
1.8 match 15 stars 10.74 score 178 scripts 8 dependents
nrcan
PlotFTIR:Plot FTIR Spectra
The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions. L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
Maintained by Philip Bulsink. Last updated 1 months ago.
3.7 match 4.98 score 5 scripts
ktabelow
qMRI:Methods for Quantitative Magnetic Resonance Imaging ('qMRI')
Implementation of methods for estimation of quantitative maps from Multi-Parameter Mapping (MPM) acquisitions (Weiskopf et al. (2013) <doi:10.3389/fnins.2013.00095>) and analysis of Inversion Recovery MRI data. Usage of the package is described in Polzehl and Tabelow (2023), "Magnetic Resonance Brain Imaging", 2nd Edition, Chapter 6 and 7, Springer, Use R! Series. <doi:10.1007/978-3-031-38949-8>. J. Polzehl and K. Tabelow (2023), "Magnetic Resonance Brain Imaging - Modeling and Data Analysis Using R: Code and Data." <doi:10.20347/WIAS.DATA.6> provides extensive example code and data.
Maintained by Karsten Tabelow. Last updated 13 days ago.
3.5 match 4.81 score 36 scripts
spatpomp-org
spatPomp:Inference for Spatiotemporal Partially Observed Markov Processes
Inference on panel data using spatiotemporal partially-observed Markov process (SpatPOMP) models. The 'spatPomp' package extends 'pomp' to include algorithms taking advantage of the spatial structure in order to assist with handling high dimensional processes. See Asfaw et al. (2024) <doi:10.48550/arXiv.2101.01157> for further description of the package.
Maintained by Edward Ionides. Last updated 4 months ago.
1.7 match 2 stars 7.38 score 93 scripts
bioc
SpliceWiz:interactive analysis and visualization of alternative splicing in R
The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.
Maintained by Alex Chit Hei Wong. Last updated 7 days ago.
softwaretranscriptomicsrnaseqalternativesplicingcoveragedifferentialsplicingdifferentialexpressionguisequencingcppopenmp
1.8 match 16 stars 6.41 score 8 scriptsmrc-ide
malariasimulation:An individual based model for malaria
Specifies the latest and greatest malaria model.
Maintained by Giovanni Charles. Last updated 30 days ago.
1.3 match 17 stars 8.19 score 146 scripts
yanrong-stacy-song
creditr:Credit Default Swaps
Price credit default swaps using 'C' code from the International Swaps and Derivatives Association CDS Standard Model. See <https://www.cdsmodel.com/cdsmodel/documentation.html> for more information about the model and <https://www.cdsmodel.com/cdsmodel/cds-disclaimer.html> for license details for the 'C' code.
Maintained by Yanrong Song. Last updated 23 days ago.
2.0 match 4.98 score 32 scriptsbioc
srnadiff:Finding differentially expressed unannotated genomic regions from RNA-seq data
srnadiff is a package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation. To do so, the package implements the identify-then-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.
Maintained by Zytnicki Matthias. Last updated 2 months ago.
immunooncologygeneexpressioncoveragesmallrnaepigeneticsstatisticalmethodpreprocessingdifferentialexpressioncpp
2.5 match 3.70 score 3 scripts
andrewzm
EFDR:Wavelet-Based Enhanced FDR for Detecting Signals from Complete or Incomplete Spatially Aggregated Data
Enhanced False Discovery Rate (EFDR) is a tool to detect anomalies in an image. The image is first transformed into the wavelet domain in order to decorrelate any noise components, following which the coefficients at each resolution are standardised. Statistical tests (in a multiple hypothesis testing setting) are then carried out to find the anomalies. The power of EFDR exceeds that of standard FDR, which would carry out tests on every wavelet coefficient: EFDR choose which wavelets to test based on a criterion described in Shen et al. (2002). The package also provides elementary tools to interpolate spatially irregular data onto a grid of the required size. The work is based on Shen, X., Huang, H.-C., and Cressie, N. 'Nonparametric hypothesis testing for a spatial signal.' Journal of the American Statistical Association 97.460 (2002): 1122-1140.
Maintained by Andrew Zammit-Mangion. Last updated 2 years ago.
1.9 match 5 stars 4.74 score 22 scripts
teazrq
orthoDr:Semi-Parametric Dimension Reduction Models Using Orthogonality Constrained Optimization
Utilize an orthogonality constrained optimization algorithm of Wen & Yin (2013) <DOI:10.1007/s10107-012-0584-1> to solve a variety of dimension reduction problems in the semiparametric framework, such as Ma & Zhu (2012) <DOI:10.1080/01621459.2011.646925>, Ma & Zhu (2013) <DOI:10.1214/12-AOS1072>, Sun, Zhu, Wang & Zeng (2019) <arXiv:1704.05046> and Zhou, Zhu & Zeng (2021) <arXiv:1802.06156>. It also serves as a general purpose optimization solver for problems with orthogonality constraints. Parallel computing for approximating the gradient is enabled through 'OpenMP'.
Maintained by Ruoqing Zhu. Last updated 3 years ago.
1.7 match 8 stars 4.53 score 14 scripts 2 dependents
jalilian
jalcal:Conversion Between Jalali (Persian or Solar Hijri) and Gregorian Calendar Dates
Jalali, also known as Persian, Solar Hijri and Hijri Shamsi calendar is the official calendar of Iran and Afghanistan. It begins on Nowruz, the March equinox, as determined by astronomical calculation and has years of 365 or 366 days. Adapting the algorithms in <https://jdf.scr.ir/>, this package provides tools for converting the Jalali and Gregorian dates.
Maintained by Abdollah Jalilian. Last updated 1 months ago.
2.1 match 4 stars 3.30 score 2 scripts
r-hyperspec
hyperSpec:Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Comfortable ways to work with hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.
Maintained by Claudia Beleites. Last updated 10 months ago.
data-wranglinghyperspectralimaginginfrarednmrramanspectroscopyuv-visxrf
0.5 match 16 stars 8.13 score 233 scripts 2 dependents
aahani-r
FAO56:Evapotranspiration Based on FAO Penman-Monteith Equation
Calculation of Evapotranspiration by FAO Penman-Monteith equation based on Allen, R. G., Pereira, L. S., Raes, D., Smith, M. (1998, ISBN:92-5-104219-5) "Crop evapotranspiration - Guidelines for computing crop water requirements - FAO Irrigation and drainage paper 56".
Maintained by Ali Ahani. Last updated 1 years ago.
2.4 match 1.70 score 2 scripts
lsubioscomputing
titeIR:Isotonic Designs for Phase 1 Trials with Late-Onset Toxicities
Functions to design phase 1 trials using an isotonic regression based design incorporating time-to-event information. Simulation and design functions are available, which incorporate information about followup and DLTs, and apply isotonic regression to devise estimates of DLT probability.
Maintained by Lee McDaniel. Last updated 6 years ago.
3.7 match 1.00 score 2 scripts
cran
noisemodel:Noise Models for Classification Datasets
Implementation of models for the controlled introduction of errors in classification datasets. This package contains the noise models described in Saez (2022) <doi:10.3390/math10203736> that allow corrupting class labels, attributes and both simultaneously.
Maintained by José A. Sáez. Last updated 2 years ago.
1.8 match 2.00 scorecran
centiserve:Find Graph Centrality Indices
Calculates centrality indices additional to the 'igraph' package centrality functions.
Maintained by Mahdi Jalili. Last updated 8 years ago.
1.7 match 1 stars 2.08 score 1 dependents
prabinameher
corrDNA:Finding Associations in Position-Wise Aligned DNA Sequence Dataset
Can be useful for finding associations among different positions in a position-wise aligned sequence dataset. The approach adopted for finding associations among positions is based on the latent multivariate normal distribution.
Maintained by Prabina Kumar Meher. Last updated 7 years ago.
3.5 match 1.00 score 8 scriptsbryanhanson
readJDX:Import Data in the JCAMP-DX Format
Import data written in the JCAMP-DX format. This is an instrument-independent format used in the field of spectroscopy. Examples include IR, NMR, and Raman spectroscopy. See the vignette for background and supported formats. The official JCAMP-DX site is <http://www.jcamp-dx.org/>.
Maintained by Bryan A. Hanson. Last updated 1 years ago.
0.5 match 8 stars 6.48 score 7 scripts 5 dependents
larsot23
Benchmarking:Benchmark and Frontier Analysis Using DEA and SFA
Methods for frontier analysis, Data Envelopment Analysis (DEA), under different technology assumptions (fdh, vrs, drs, crs, irs, add/frh, and fdh+), and using different efficiency measures (input based, output based, hyperbolic graph, additive, super, and directional efficiency). Peers and slacks are available, partial price information can be included, and optimal cost, revenue and profit can be calculated. Evaluation of mergers is also supported. Methods for graphing the technology sets are also included. There is also support for comparative methods based on Stochastic Frontier Analyses (SFA) and for convex nonparametric least squares of convex functions (STONED). In general, the methods can be used to solve not only standard models, but also many other model variants. It complements the book, Bogetoft and Otto, Benchmarking with DEA, SFA, and R, Springer-Verlag, 2011, but can of course also be used as a stand-alone package.
Maintained by Lars Otto. Last updated 29 days ago.
0.5 match 7 stars 6.17 score 192 scripts 7 dependents
objornstad
epimdr2:Functions and Data for "Epidemics: Models and Data in R (2nd Edition)"
Functions, data sets and shiny apps for "Epidemics: Models and Data in R (2nd edition)" by Ottar N. Bjornstad (ISBN: 978-3-031-12055-8) <https://link.springer.com/book/9783031120558>. The package contains functions to study the S(E)IR model, spatial and age-structured SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the Coursera Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.
Maintained by Ottar N. Bjornstad. Last updated 2 years ago.
0.5 match 19 stars 3.98 scorecran
cliot:Clinical Indices and Outcomes Tools
Collection of indices and tools relating to cardiovascular, nephrology, and hepatic research that aid epidemiological chort or retrospective chart review with big data. All indices and tools take commonly used lab values and patient demographics and measurements to compute various risk and predictive values for survival. References to original literature and validation contained in each function documentation.
Maintained by Neel Agarwal. Last updated 1 years ago.
1.7 match 1.00 scorecran
deident:Persistent Data Anonymization Pipeline
A framework for the replicable removal of personally identifiable data (PID) in data sets. The package implements a suite of methods to suit different data types based on the suggestions of Garfinkel (2015) <doi:10.6028/NIST.IR.8053> and the ICO "Guidelines on Anonymization" (2012) <https://ico.org.uk/media/1061/anonymisation-code.pdf>.
Maintained by Robert Cook. Last updated 4 months ago.
0.5 match 3.16 score 16 scripts
atanubhattacharjee
ILRCM:Convert Irregular Longitudinal Data to Regular Intervals and Perform Clustering
Convert irregularly spaced longitudinal data into regular intervals for further analysis, and perform clustering using advanced machine learning techniques. The package is designed for handling complex longitudinal datasets, optimizing them for research in healthcare, demography, and other fields requiring temporal data modeling.
Maintained by Atanu Bhattacharjee. Last updated 4 months ago.
1.6 match 1.00 score
davidnsousa
qsort:Scoring Q-Sort Data
Computes scores from Q-sort data, using criteria sorts and derived scales from subsets of items. The 'qsort' package includes descriptions and scoring procedures for four different Q-sets commonly used in developmental psychology research: Attachment Q-set (version 3.0) (Waters, 1995, <doi:10.1111/j.1540-5834.1995.tb00214.x>); California Child Q-set (Block and Block, 1969, <doi:10.1037/0012-1649.21.3.508>); Maternal Behaviour Q-set (version 3.1) (Pederson et al., 1999, <https://ir.lib.uwo.ca/cgi/viewcontent.cgi?article=1000&context=psychologypub>); Preschool Q-set (Baumrind, 1968 revised by Wanda Bronson, <doi:10.1111/j.1540-5834.1995.tb00214.x>).
Maintained by David N Sousa. Last updated 6 years ago.
0.5 match 2.70 score 8 scriptsobjornstad
epimdr:Functions and Data for "Epidemics: Models and Data in R"
Functions, data sets and shiny apps for "Epidemics: Models and Data in R" by Ottar N. Bjornstad (ISBN 978-3-319-97487-3) <https://www.springer.com/gp/book/9783319974866>. The package contains functions to study the S(E)IR model, spatial and age-structured SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the coursera Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.
Maintained by Ottar N. Bjornstad. Last updated 5 years ago.
0.5 match 1.65 score 45 scripts