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r-phylin
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The spatial interpolation of genetic distances between samples is based on a modified kriging method that accepts a genetic distance matrix and generates a map of probability of lineage presence. This package also offers tools to generate a map of potential contact zones between groups with user-defined thresholds in the tree to account for old and recent divergence. Additionally, it has functions for IDW interpolation using genetic data and midpoints.
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2024-01-16 |
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r-photobiology
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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>.
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2024-01-16 |
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r-phuassess
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Assessment of habitat selection by means of the permutation-based combination of sign tests (Fattorini et al., 2014 <DOI:10.1007/s10651-013-0250-7>). To exemplify the application of this procedure, habitat selection is assessed for a population of European Brown Hares settled in central Italy.
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2024-01-16 |
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r-phaser
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Performs a qualitative analysis of one- and two-dimensional autonomous ordinary differential equation systems, using phase plane methods. Programs are available to identify and classify equilibrium points, plot the direction field, and plot trajectories for multiple initial conditions. In the one-dimensional case, a program is also available to plot the phase portrait. Whilst in the two-dimensional case, programs are additionally available to plot nullclines and stable/unstable manifolds of saddle points. Many example systems are provided for the user. For further details can be found in Grayling (2014) <doi:10.32614/RJ-2014-023>.
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2024-01-16 |
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r-phontools
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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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2024-01-16 |
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r-pharmaversesdtm
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A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) datasets inside the pharmaverse family of packages. SDTM dataset specifications are described in: CDISC Submission Data Standards Team (2021) <https://www.cdisc.org/system/files/members/standard/foundational/SDTMIG%20v3.4-FINAL_2022-07-21.pdf>.
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2024-01-16 |
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r-phonenumber
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Convert English letters to numbers or numbers to English letters as on a telephone keypad. When converting letters to numbers, a character vector is returned with "A," "B," or "C" becoming 2, "D," "E", or "F" becoming 3, etc. When converting numbers to letters, a character vector is returned with multiple elements (i.e., "2" becomes a vector of "A," "B," and "C").
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2024-01-16 |
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r-phidelta
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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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2024-01-16 |
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r-pgirmess
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Set of tools for reading, writing and transforming spatial and seasonal data, model selection and specific statistical tests for ecologists. It includes functions to interpolate regular positions of points between landmarks, to discretize polylines into regular point positions, link distant observations to points and convert a bounding box in a spatial object. It also provides miscellaneous functions for field ecologists such as spatial statistics and inference on diversity indexes, writing data.frame with Chinese characters.
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2024-01-16 |
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r-pheval
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Provides tools for the evaluation of the goodness of fit and the predictive capacity of the proportional hazards model.
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2024-01-16 |
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r-pheatmap
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public |
Implementation of heatmaps that offers more control over dimensions and appearance.
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2024-01-16 |
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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, Thoresen and Finos (2021) <doi:10.1080/00949655.2020.1836183>.
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2024-01-16 |
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r-pglm
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Estimation of panel models for glm-like models: this includes binomial models (logit and probit), count models (poisson and negbin) and ordered models (logit and probit), as described in: Baltagi (2013) Econometric Analysis of Panel Data, ISBN-13:978-1-118-67232-7, Hsiao (2014) Analysis of Panel Data <doi:10.1017/CBO9781139839327> and Croissant and Millo (2018), Panel Data Econometrics with R, ISBN:978-1-118-94918-4.
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2024-01-16 |
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r-pgm2
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Construction method of nested resolvable designs from a projective geometry defined on Galois field of order 2. The obtained Resolvable designs are used to build uniform design. The presented results are based on <https://eudml.org/doc/219563> and A. Boudraa et al. (See references).
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2024-01-16 |
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r-ph2mult
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Provide multinomial design methods under intersection-union test (IUT) and union-intersection test (UIT) scheme for Phase II trial. The design types include : Minimax (minimize the maximum sample size), Optimal (minimize the expected sample size), Admissible (minimize the Bayesian risk) and Maxpower (maximize the exact power level).
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2024-01-16 |
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r-pgnorm
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Evaluation of the pdf and the cdf of the univariate, noncentral, p-generalized normal distribution. Sampling from the univariate, noncentral, p-generalized normal distribution using either the p-generalized polar method, the p-generalized rejecting polar method, the Monty Python method, the Ziggurat method or the method of Nardon and Pianca. The package also includes routines for the simulation of the bivariate, p-generalized uniform distribution and the simulation of the corresponding angular distribution.
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2024-01-16 |
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r-perry
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Tools that allow developers to write functions for prediction error estimation with minimal programming effort and assist users with model selection in regression problems.
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2024-01-16 |
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r-permutes
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Helps you determine the analysis window to use when analyzing densely-sampled time-series data, such as EEG data, using permutation testing (Maris & Oostenveld, 2007) <doi:10.1016/j.jneumeth.2007.03.024>. These permutation tests can help identify the timepoints where significance of an effect begins and ends, and the results can be plotted in various types of heatmap for reporting. Mixed-effects models are supported using an implementation of the approach by Lee & Braun (2012) <doi:10.1111/j.1541-0420.2011.01675.x>.
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2024-01-16 |
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r-pgee
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Fits penalized generalized estimating equations to longitudinal data with high-dimensional covariates.
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2024-01-16 |
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r-pesel
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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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2024-01-16 |
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r-petitr
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Calculates the relative growth rate (RGR) of a series of individuals by building a life table and solving the Lotka-Birch equation. (See Birch, L. C. 1948. The intrinsic rate of natural increase of an insect population. - Journal of Animal Ecology 17: 15-26) <doi:10.2307/1605>.
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2024-01-16 |
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r-petfinder
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Wrapper of the 'Petfinder API' <https://www.petfinder.com/developers/v2/docs/> that implements methods for interacting with and extracting data from the 'Petfinder' database. The 'Petfinder REST API' allows access to the 'Petfinder' database, one of the largest online databases of adoptable animals and animal welfare organizations across North America.
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2024-01-16 |
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r-pequod
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Moderated regression with mean and residual centering and simple slopes analysis.
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2024-01-16 |
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r-persianstemmer
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Allows users to stem Persian texts for text analysis.
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2024-01-16 |
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r-performance
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Utilities for computing measures to assess model quality, which are not directly provided by R's 'base' or 'stats' packages. These include e.g. measures like r-squared, intraclass correlation coefficient (Nakagawa, Johnson & Schielzeth (2017) <doi:10.1098/rsif.2017.0213>), root mean squared error or functions to check models for overdispersion, singularity or zero-inflation and more. Functions apply to a large variety of regression models, including generalized linear models, mixed effects models and Bayesian models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
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2024-01-16 |
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r-permute
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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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2024-01-16 |
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r-pedquant
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Provides an interface to access public economic and financial data for economic research and quantitative analysis. The data sources including NBS, FRED, Sina, Eastmoney and etc. It also provides quantitative functions for trading strategies based on the 'data.table', 'TTR', 'PerformanceAnalytics' and etc packages.
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2024-01-16 |
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r-permgs
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Permutational group-sequential tests for time-to-event data based on the log-rank test statistic. Supports exact permutation test when the censoring distributions are equal in the treatment and the control group and approximate imputation-permutation methods when the censoring distributions are different.
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2024-01-16 |
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r-permalgo
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This version of the permutational algorithm generates a dataset in which event and censoring times are conditional on an user-specified list of covariates, some or all of which are time-dependent.
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2024-01-16 |
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r-perm
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Perform Exact or Asymptotic permutation tests [see Fay and Shaw <doi:10.18637/jss.v036.i02>].
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2024-01-16 |
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r-periodictable
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Provides a dataset containing properties for chemical elements. Helper functions are also provided to access some atomic properties.
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2024-01-16 |
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r-perc
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To find the certainty of dominance interactions with indirect interactions being considered.
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2024-01-16 |
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r-pegrouptesting
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The population proportion using group testing can be estimated by different methods. Four functions including p.mle(), p.gart(), p.burrow() and p.order() are provided to implement four estimating methods including the maximum likelihood estimate, Gart's estimate, Burrow's estimate, and order statistic estimate.
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2024-01-16 |
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r-pepsavims
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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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2024-01-16 |
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r-pdfetch
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Download economic and financial time series from public sources, including the St Louis Fed's FRED system, Yahoo Finance, the US Bureau of Labor Statistics, the US Energy Information Administration, the World Bank, Eurostat, the European Central Bank, the Bank of England, the UK's Office of National Statistics, Deutsche Bundesbank, and INSEE.
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2024-01-16 |
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r-pchc
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Bayesian network learning using the PCHC algorithm. PCHC stands for PC Hill-Climbing, a new hybrid algorithm that uses PC to construct the skeleton of the BN and then applies the Hill-Climbing greedy search. More algorithms and variants have been added, such as MMHC, FEDHC, and the Tabu search variants, PCTABU, MMTABU and FEDTABU. The relevant papers are: a) Tsagris M. (2021). A new scalable Bayesian network learning algorithm with applications to economics. Computational Economics, 57(1): 341-367. <doi:10.1007/s10614-020-10065-7>. b) Tsagris M. (2022). The FEDHC Bayesian Network Learning Algorithm. Mathematics 2022, 10(15): 2604. <doi:10.3390/math10152604>.
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2024-01-16 |
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r-peerperformance
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Provides functions to perform the peer performance analysis of funds' returns as described in Ardia and Boudt (2018) <doi:10.1016/j.jbankfin.2017.10.014>.
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2024-01-16 |
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r-pearsonica
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The Pearson-ICA algorithm is a mutual information-based method for blind separation of statistically independent source signals. It has been shown that the minimization of mutual information leads to iterative use of score functions, i.e. derivatives of log densities. The Pearson system allows adaptive modeling of score functions. The flexibility of the Pearson system makes it possible to model a wide range of source distributions including asymmetric distributions. The algorithm is designed especially for problems with asymmetric sources but it works for symmetric sources as well.
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2024-01-16 |
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r-pearson7
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Supports maximum likelihood inference for the Pearson VII distribution with shape parameter 3/2 and free location and scale parameters. This distribution is relevant when estimating the velocity of processive motor proteins with random detachment.
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2024-01-16 |
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r-peakram
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When working with big data sets, RAM conservation is critically important. However, it is not always enough to just monitor the size of the objects created. So-called "copy-on-modify" behavior, characteristic of R, means that some expressions or functions may require an unexpectedly large amount of RAM overhead. For example, replacing a single value in a matrix duplicates that matrix in the back-end, making this task require twice as much RAM as that used by the matrix itself. This package makes it easy to monitor the total and peak RAM used so that developers can quickly identify and eliminate RAM hungry code.
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2024-01-16 |
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r-peacock.test
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The original definition of the two and three dimensional Kolmogorov-Smirnov two-sample test statistics given by Peacock (1983) is implemented. Two R-functions: peacock2 and peacock3, are provided to compute the test statistics in two and three dimensional spaces, respectively. Note the Peacock test is different from the Fasano and Franceschini test (1987). The latter is a variant of the Peacock test.
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2024-01-16 |
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r-pdshiny
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Interactive shiny application for working with Probability Distributions. Calculations and Graphs are provided.
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2024-01-16 |
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r-pder
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Data sets for the Panel Data Econometrics with R <doi:10.1002/9781119504641> book.
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2024-01-16 |
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r-pdm
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Measures real distances in pictures. With PDM() function, you can choose one '*.jpg' file, select the measure in mm of scale, starting and and finishing point in the graphical scale, the name of the measure, and starting and and finishing point of the measures. After, ask the user for a new measure.
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2024-01-16 |
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r-pdftables
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Allows the user to convert PDF tables to formats more amenable to analysis ('.csv', '.xml', or '.xlsx') by wrapping the PDFTables API. In order to use the package, the user needs to sign up for an API account on the PDFTables website (<https://pdftables.com/pdf-to-excel-api>). The package works by taking a PDF file as input, uploading it to PDFTables, and returning a file with the extracted data.
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2024-01-16 |
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r-pcsinr
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Parallel Constraint Satisfaction (PCS) models are an increasingly common class of models in Psychology, with applications to reading and word recognition (McClelland & Rumelhart, 1981), judgment and decision making (Glöckner & Betsch, 2008; Glöckner, Hilbig, & Jekel, 2014), and several other fields (e.g. Read, Vanman, & Miller, 1997). In each of these fields, they provide a quantitative model of psychological phenomena, with precise predictions regarding choice probabilities, decision times, and often the degree of confidence. This package provides the necessary functions to create and simulate basic Parallel Constraint Satisfaction networks within R.
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2024-01-16 |
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r-pcse
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A function to estimate panel-corrected standard errors. Data may contain balanced or unbalanced panels.
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2024-01-16 |
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r-pco
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Computation of the Pedroni (1999) panel cointegration test statistics. Reported are the empirical and the standardized values.
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2024-01-16 |
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r-pch
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Piecewise constant hazard models for survival data. The package allows for right-censored, left-truncated, and interval-censored data.
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2024-01-16 |
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r-pcg
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The package solves linear system of equations Ax=b by using Preconditioned Conjugate Gradient Algorithm where A is real symmetric positive definite matrix. A suitable preconditioner matrix may be provided by user. This can also be used to minimize quadratic function (x'Ax)/2-bx for unknown x.
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2024-01-16 |
