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r-paintmap
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public |
Plots matrices of colours as grids of coloured squares - aka heatmaps, guaranteeing legible row and column names, without transformation of values, without re-ordering rows or columns, and without dendrograms.
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2023-06-16 |
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r-pagi
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public |
The package can identify the dysregulated KEGG pathways based on global influence from the internal effect of pathways and crosstalk between pathways. (1) The PAGI package can prioritize the pathways associated with two biological states by statistical significance or FDR. (2) The PAGI package can evaluated the global influence factor (GIF) score in the global gene-gene network constructed based on the relationships of genes extracted from each pathway in KEGG database and the overlapped genes between pathways.
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2023-06-16 |
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r-orthopanels
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public |
Implements the orthogonal reparameterization approach recommended by Lancaster (2002) to estimate dynamic panel models with fixed effects (and optionally: panel specific intercepts). The approach uses a likelihood-based estimator and produces estimates that are asymptotically unbiased as N goes to infinity, with a T as low as 2.
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2023-06-16 |
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r-orsifronts
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public |
A data set package with the "Orsi" fronts as a 'SpatialLinesDataFrame' object. The Orsi et al. (1995) fronts are published at the Southern Ocean Atlas Database Page, please see package CITATION for details.
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2023-06-16 |
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r-ores
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public |
A connector to ORES (<http://ores.wmflabs.org/>), an AI project to provide edit scoring for content on Wikipedia and other Wikimedia projects. This lets a researcher identify if edits are likely to be reverted, damaging, or made in good faith.
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2023-06-16 |
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r-optr
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public |
Solves linear systems of form Ax=b via Gauss elimination, LU decomposition, Gauss-Seidel, Conjugate Gradient Method (CGM) and Cholesky methods.
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2023-06-16 |
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r-obs.agree
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public |
The package includes two functions for measuring agreement. Raw Agreement Indices (RAI) to categorical data and Information-Based Measure of Disagreement (IBMD) to continuous data. It can be used for multiple raters and multiple readings cases.
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2023-06-16 |
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r-nws
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public |
Provides coordination and parallel execution facilities, as well as limited cross-language data exchange, using the netWorkSpaces server developed by REvolution Computing
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2023-06-16 |
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r-pepsavims
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public |
An implementation of the data processing and data analysis portion of a pipeline named the PepSAVI-MS which is currently under development by the Hicks laboratory at the University of North Carolina. The statistical analysis package presented herein provides a collection of software tools used to facilitate the prioritization of putative bioactive peptides from a complex biological matrix. Tools are provided to deconvolute mass spectrometry features into a single representation for each peptide charge state, filter compounds to include only those possibly contributing to the observed bioactivity, and prioritize these remaining compounds for those most likely contributing to each bioactivity data set.
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2023-06-16 |
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r-pcamixdata
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public |
Implements principal component analysis, orthogonal rotation and multiple factor analysis for a mixture of quantitative and qualitative variables.
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2023-06-16 |
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r-paswr
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public |
Data and functions for the book PROBABILITY and STATISTICS WITH R.
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2023-06-16 |
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r-pas
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public |
An R package for polygenic trait analysis.
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2023-06-16 |
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r-partiallyoverlapping
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public |
Tests for a comparison of two partially overlapping samples. A comparison of means using the partially overlapping samples t-test: See Derrick, Russ, Toher and White (2017), Test statistics for the comparison of means for two samples which include both paired observations and independent observations, Journal of Modern Applied Statistical Methods, 16(1). A comparison of proportions using the partially overlapping samples z-test: See Derrick, Dobson-Mckittrick, Toher and White (2015), Test statistics for comparing two proportions with partially overlapping samples. Journal of Applied Quantitative Methods, 10(3).
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2023-06-16 |
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r-paperplanes
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public |
This is a data only package, that provides distances from a paper plane experiment.
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2023-06-16 |
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r-pampe
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public |
Implements the Panel Data Approach Method for program evaluation as developed in Hsiao, Ching and Ki Wan (2012). pampe estimates the effect of an intervention by comparing the evolution of the outcome for a unit affected by an intervention or treatment to the evolution of the unit had it not been affected by the intervention.
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2023-06-16 |
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r-paleots
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public |
Facilitates analysis of paleontological sequences of trait values. Functions are provided to fit, using maximum likelihood, simple evolutionary models (including unbiased random walks, directional evolution,stasis, Ornstein-Uhlenbeck, covariate-tracking) and complex models (punctuation, mode shifts).
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2023-06-16 |
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r-pakpmics2014hh
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public |
Provides data set and function for exploration of Multiple Indicator Cluster Survey (MICS) 2014 Household questionnaire data for Punjab, Pakistan (<http://www.mics.unicef.org/surveys>).
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2023-06-16 |
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r-painter
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public |
Functions for creating color palettes, visualizing palettes, modifying colors, and assigning colors for plotting.
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2023-06-16 |
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r-oz
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public |
Functions for plotting Australia's coastline and state boundaries.
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2023-06-16 |
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r-outliers
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public |
A collection of some tests commonly used for identifying outliers.
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2023-06-16 |
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r-osmose
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public |
The multispecies and individual-based model (IBM) 'OSMOSE' (Shin and Curry (2001) <doi:10.1016/S0990-7440(01)01106-8> and Shin and Curry (2004) <doi:10.1139/f03-154>) focuses on fish species. This model assumes opportunistic predation based on spatial co-occurrence and size adequacy between a predator and its prey (size-based opportunistic predation). It represents fish individuals grouped into schools, which are characterized by their size, weight, age, taxonomy and geographical location (2D model), and which undergo major processes of fish life cycle (growth, explicit predation, natural and starvation mortalities, reproduction and migration) and fishing exploitation. The model needs basic biological parameters that are often available for a wide range of species, and which can be found in 'FishBase' for instance (see <http://www.fishbase.org/search.php>), and fish spatial distribution data. This package provides tools to build and run simulations using the 'OSMOSE' model.
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2023-06-16 |
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r-orclus
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public |
Functions to perform subspace clustering and classification.
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2023-06-16 |
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r-optimx
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public |
Provides a replacement and extension of the optim() function to call to several function minimization codes in R in a single statement. These methods handle smooth, possibly box constrained functions of several or many parameters. Note that function 'optimr()' was prepared to simplify the incorporation of minimization codes going forward. Also implements some utility codes and some extra solvers, including safeguarded Newton methods. Many methods previously separate are now included here.
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2023-06-16 |
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r-oompadata
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public |
This is a data-only package to provide example data for other packages that are part of the "Object-Oriented Microrray and Proteomics Analysis" suite of packages. These are described in more detail at the package URL.
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2023-06-16 |
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r-oner
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public |
Implements the One Rule (OneR) Machine Learning classification algorithm (Holte, R.C. (1993) <doi:10.1023/A:1022631118932>) with enhancements for sophisticated handling of numeric data and missing values together with extensive diagnostic functions. It is useful as a baseline for machine learning models and the rules are often helpful heuristics.
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2023-06-16 |
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r-nptest
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public |
Robust permutation tests for location, correlation, and regression problems, as described in Helwig (2019) <doi:10.1002/wics.1457>. Univariate and multivariate tests are supported. For each problem, exact tests and Monte Carlo approximations are available. Parallel computing is implemented via the 'parallel' package.
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2023-06-16 |
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r-npreg
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public |
Multiple and generalized nonparametric regression using smoothing spline ANOVA models and generalized additive models. Includes support for Gaussian and non-Gaussian responses, smoothers for multiple types of predictors, interactions between smoothers of mixed types, and eight different methods for smoothing parameter selection.
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2023-06-16 |
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r-ohpl
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public |
Ordered homogeneity pursuit lasso (OHPL) algorithm for group variable selection proposed in Lin et al. (2017) <DOI:10.1016/j.chemolab.2017.07.004>. The OHPL method exploits the homogeneity structure in high-dimensional data and enjoys the grouping effect to select groups of important variables automatically. This feature makes it particularly useful for high-dimensional datasets with strongly correlated variables, such as spectroscopic data.
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2023-06-16 |
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r-numkm
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public |
To add the table of numbers at risk below the Kaplan-Meier plot.
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2023-06-16 |
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r-nsgp
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public |
A Gaussian process regression using a Gaussian kernel for both one-sample and two-sample cases. Includes non-stationary Gaussian kernel (exponential decay function) and several likelihood ratio tests for differential testing along target points.
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2023-06-16 |
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r-phontools
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public |
Contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the creation and manipulation of WAVE audio files.
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2023-06-16 |
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r-phidelta
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public |
Analysis of features by phi delta diagrams. In particular, functions for reading data and calculating phi and delta as well as the functionality to plot it. Moreover it is possible to do further analysis on the data by generating rankings. For more information on phi delta diagrams, see also Giuliano Armano (2015) <doi:10.1016/j.ins.2015.07.028>.
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2023-06-16 |
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r-phd
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public |
Provides permutation methods for testing in high-dimensional linear models. The tests are often robust against heteroscedasticity and non-normality and usually perform well under anti-sparsity. See Hemerik and Goeman (2018) <doi:10.1007/s11749-017-0571-1>.
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2023-06-16 |
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r-perturb
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public |
Use the perturb() function to evaluates collinearity by adding random noise to selected variables (Hendrickx & Pelzer 2004). The colldiag function() calculates condition numbers and variance decomposition proportions to test for collinearity and uncover its sources (Belsley 1980).
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2023-06-16 |
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r-permute
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public |
A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.
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2023-06-16 |
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r-pbs
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public |
Periodic B Splines Basis
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2023-06-16 |
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r-paws.common
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public |
Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).
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2023-06-16 |
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r-pawacc
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public |
This is a collection of functions to process, format and store accelerometer data.
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2023-06-16 |
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r-piggyback
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public |
Because larger (> 50 MB) data files cannot easily be committed to git, a different approach is required to manage data associated with an analysis in a GitHub repository. This package provides a simple work-around by allowing larger (up to 2 GB) data files to piggyback on a repository as assets attached to individual GitHub releases. These files are not handled by git in any way, but instead are uploaded, downloaded, or edited directly by calls through the GitHub API. These data files can be versioned manually by creating different releases. This approach works equally well with public or private repositories. Data can be uploaded and downloaded programmatically from scripts. No authentication is required to download data from public repositories.
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2023-06-16 |
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r-pesel
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public |
Automatic estimation of number of principal components in PCA with PEnalized SEmi-integrated Likelihood (PESEL). See Piotr Sobczyk, Malgorzata Bogdan, Julie Josse 'Bayesian dimensionality reduction with PCA using penalized semi-integrated likelihood' (2017) <doi:10.1080/10618600.2017.1340302>.
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2023-06-16 |
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r-pbibd
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public |
The PBIB designs are important type of incomplete block designs having wide area of their applications for example in agricultural experiments, in plant breeding, in sample surveys etc. This package constructs various series of PBIB designs and assists in checking all the necessary conditions of PBIB designs and the association scheme on which these designs are based on. It also assists in calculating the efficiencies of PBIB designs with any number of associate classes. The package also constructs Youden-m square designs which are Row-Column designs for the two-way elimination of heterogeneity. The incomplete columns of these Youden-m square designs constitute PBIB designs. With the present functionality, the package will be of immense importance for the researchers as it will help them to construct PBIB designs, to check if their PBIB designs and association scheme satisfy various necessary conditions for the existence, to calculate the efficiencies of PBIB designs based on any association scheme and to construct Youden-m square designs for the two-way elimination of heterogeneity. R. C. Bose and K. R. Nair (1939) <http://www.jstor.org/stable/40383923>.
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2023-06-16 |
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r-pastis
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public |
A pre-processor for mrBayes that assimilates sequences, taxonomic information and tree constraints as per xxx. The main functions of interest for most users will be pastis_simple, pastis_main and conch. The main analysis is conducted with pastis_simple or pastis_main followed by a manual execution of mrBayes (>3.2). The placement of taxa not contained in the tree constraint can be investigated using conch.
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2023-06-16 |
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r-params
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public |
An interface to simplify organizing parameters used in a package, using external configuration files. This attempts to provide a cleaner alternative to options().
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2023-06-16 |
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r-p2distance
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public |
The welfare's synthetic indicator provides an ideal tool for measuring multi-dimensional concepts such as welfare, development, living standards, etc. It enables information from the various indicators to be aggregated into a single synthetic measure.
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2023-06-16 |
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r-ops
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public |
Comparison of data by Pearson product-moment correlation coefficients is prone to outliers. The problem can be alleviated by normalizing data with outliers before computing the Pearson correlation coefficient. The sample provides such normalization by optimal power space transformation.
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2023-06-16 |
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r-oligospecificitysystem
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public |
Calculate the theorical specificity of a system of multiple primers used for PCR, qPCR primers or degenerated primer design
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2023-06-16 |
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r-ods
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public |
Outcome-dependent sampling (ODS) schemes are cost-effective ways to enhance study efficiency. In ODS designs, one observes the exposure/covariates with a probability that depends on the outcome variable. Popular ODS designs include case-control for binary outcome, case-cohort for time-to-event outcome, and continuous outcome ODS design (Zhou et al. 2002) <doi: 10.1111/j.0006-341X.2002.00413.x>. Because ODS data has biased sampling nature, standard statistical analysis such as linear regression will lead to biases estimates of the population parameters. This package implements four statistical methods related to ODS designs: (1) An empirical likelihood method analyzing the primary continuous outcome with respect to exposure variables in continuous ODS design (Zhou et al., 2002). (2) A partial linear model analyzing the primary outcome in continuous ODS design (Zhou, Qin and Longnecker, 2011) <doi: 10.1111/j.1541-0420.2010.01500.x>. (3) Analyze a secondary outcome in continuous ODS design (Pan et al. 2018) <doi: 10.1002/sim.7672>. (4) An estimated likelihood method analyzing a secondary outcome in case-cohort data (Pan et al. 2017) <doi: 10.1111/biom.12838>.
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2023-06-16 |
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r-nscancor
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public |
Two implementations of canonical correlation analysis (CCA) that are based on iterated regression. By choosing the appropriate regression algorithm for each data domain, it is possible to enforce sparsity, non-negativity or other kinds of constraints on the projection vectors. Multiple canonical variables are computed sequentially using a generalized deflation scheme, where the additional correlation not explained by previous variables is maximized. 'nscancor' is used to analyze paired data from two domains, and has the same interface as the 'cancor' function from the 'stats' package (plus some extra parameters). 'mcancor' is appropriate for analyzing data from three or more domains. See <http://sigg-iten.ch/learningbits/2014/01/20/canonical-correlation-analysis-under-constraints/> and Sigg et al. (2007) <doi:10.1109/MLSP.2007.4414315> for more details.
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2023-06-16 |
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r-npmr
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public |
Fit multinomial logistic regression with a penalty on the nuclear norm of the estimated regression coefficient matrix, using proximal gradient descent. Reference: Powers S, Hastie T and Tibshirani R (2018) <doi:10.1177/1471082X18777669>.
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2023-06-16 |
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r-nozzle.r1
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public |
The Nozzle package provides an API to generate HTML reports with dynamic user interface elements based on JavaScript and CSS (Cascading Style Sheets). Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big data sets. The package can be applied to any project where user-friendly reports need to be created.
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2023-06-16 |
