|
r-selfingtree
|
public |
A probability tree allows to compute probabilities of complex events, such as genotype probabilities in intermediate generations of inbreeding through recurrent self-fertilization (selfing). This package implements functionality to compute probability trees for two- and three-marker genotypes in the F2 to F7 selfing generations. The conditional probabilities are derived automatically and in symbolic form. The package also provides functionality to extract and evaluate the relevant probabilities.
|
2025-03-25 |
|
r-seleniumpipes
|
public |
The W3C WebDriver specification defines a way for out-of-process programs to remotely instruct the behaviour of web browsers. It is detailed at <https://w3c.github.io/webdriver/webdriver-spec.html>. This package provides an R client implementing the W3C specification.
|
2025-03-25 |
|
r-selemix
|
public |
Detection of outliers and influential errors using a latent variable model.
|
2025-03-25 |
|
r-selectmeta
|
public |
Publication bias, the fact that studies identified for inclusion in a meta analysis do not represent all studies on the topic of interest, is commonly recognized as a threat to the validity of the results of a meta analysis. One way to explicitly model publication bias is via selection models or weighted probability distributions. In this package we provide implementations of several parametric and nonparametric weight functions. The novelty in Rufibach (2011) is the proposal of a non-increasing variant of the nonparametric weight function of Dear & Begg (1992). The new approach potentially offers more insight in the selection process than other methods, but is more flexible than parametric approaches. To maximize the log-likelihood function proposed by Dear & Begg (1992) under a monotonicity constraint we use a differential evolution algorithm proposed by Ardia et al (2010a, b) and implemented in Mullen et al (2009). In addition, we offer a method to compute a confidence interval for the overall effect size theta, adjusted for selection bias as well as a function that computes the simulation-based p-value to assess the null hypothesis of no selection as described in Rufibach (2011, Section 6).
|
2025-03-25 |
|
r-selectiongain
|
public |
Multi-stage selection is practiced in numerous fields of life and social sciences and particularly in breeding. A special characteristic of multi-stage selection is that candidates are evaluated in successive stages with increasing intensity and effort, and only a fraction of the superior candidates is selected and promoted to the next stage. For the optimum design of such selection programs, the selection gain plays a crucial role. It can be calculated by integration of a truncated multivariate normal (MVN) distribution. While mathematical formulas for calculating the selection gain and the variance among selected candidates were developed long time ago, solutions for numerical calculation were not available. This package can also be used for optimizing multi-stage selection programs for a given total budget and different costs of evaluating the candidates in each stage.
|
2025-03-25 |
|
r-selectapref
|
public |
Provides indices such as Manly's alpha, foraging ratio, and Ivlev's selectivity to allow for analysis of dietary selectivity and preference. Can accommodate multiple experimental designs such as constant prey number of prey depletion. Please contact the package maintainer with any publications making use of this package in an effort to maintain a repository of dietary selections studies.
|
2025-03-25 |
|
r-sejong
|
public |
Sejong(http://www.sejong.or.kr/) corpus and Hannanum(http://semanticweb.kaist.ac.kr/home/index.php/HanNanum) dictionaries for KoNLP
|
2025-03-25 |
|
r-seismic
|
public |
An implementation of self-exciting point process model for information cascades, which occurs when many people engage in the same acts after observing the actions of others (e.g. post resharings on Facebook or Twitter). It provides functions to estimate the infectiousness of an information cascade and predict its popularity given the observed history. See <http://snap.stanford.edu/seismic/> for more information and datasets.
|
2025-03-25 |
|
r-segregation
|
public |
Computes segregation indices, including the Index of Dissimilarity, as well as the information-theoretic indices developed by Theil (1971) <isbn:978-0471858454>, namely the Mutual Information Index (M) and Theil's Information Index (H). The M, further described by Mora and Ruiz-Castillo (2011) <doi:10.1111/j.1467-9531.2011.01237.x> and Frankel and Volij (2011) <doi:10.1016/j.jet.2010.10.008>, is a measure of segregation that is highly decomposable. The package provides tools to decompose the index by units and groups (local segregation), and by within and between terms. The package also provides a method to decompose differences in segregation as described by Elbers (2021) <doi:10.1177/0049124121986204>. The package includes standard error estimation by bootstrapping, which also corrects for small sample bias. The package also contains functions for visualizing segregation patterns.
|
2025-03-25 |
|
r-segmented
|
public |
Given a regression model, segmented `updates' it by adding one or more segmented (i.e., piece-wise linear) relationships. Several variables with multiple breakpoints are allowed. The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>). Segmented mixed models, i.e. random effects in the change point, are discussed in in Muggeo (2014, <doi:10.1177/1471082X13504721>).
|
2025-03-25 |
|
r-seermapperwest
|
public |
Provides supplemental 2000 census tract boundaries for the 13 states without Seer Registries that are west of the Mississippi river for use with the 'SeerMapper' package. The data contained in this package is derived from U.S. 2000 Census data and is in the public domain. Updated to Alber Equal Area projection.
|
2025-03-25 |
|
r-seermapperregs
|
public |
Provides supplemental 2000 census tract boundaries for the 19 states containing Seer Registries for use with the 'SeerMapper' package. The data contained in this package is derived from U.S. Census data and is in the public domain.
|
2025-03-25 |
|
r-seermappereast
|
public |
Provides supplemental 2000 census tract boundaries for the 20 states, district and territory without Seer Registries that are east of the Mississippi river for use with the 'SeerMapper' package. The data contained in this package is derived from U.S. Census data and is in the public domain.
|
2025-03-25 |
|
r-seermapper2010west
|
public |
Provides supplemental 2010 census tract boundaries for the 13 states without Seer Registries that are west of the Mississippi river for use with the 'SeerMapper' package. The data contained in this package is derived from U.S. 2010 Census data and is in public domain.
|
2025-03-25 |
|
r-seermapper2010regs
|
public |
Provides supplemental 2010 census tract boundaries of the 19 states containing Seer Registries for use with the 'SeerMapper' package. The data contained in this package is derived from U.S. 2010 Census data and is in public domain.
|
2025-03-25 |
|
r-seermapper2010east
|
public |
Provides supplemental 2010 census tract boundary package for 20 states without Seer Registries that are east of the Mississippi river for use with the 'SeerMapper' package. The data contained in this package is derived from U.S. Census data and is in public domain.
|
2025-03-25 |
|
r-seer2r
|
public |
read and write SEER*STAT data files
|
2025-03-25 |
|
r-seedwater
|
public |
Bringing together tools for modeling drying and soaking (rehydration) kinetics of seeds. This package contains several widely used predictive models (e.g.: da Silva et al., 2018). As these are nonlinear, the functions are interactive-based and easy-to-use. Least squares estimates are obtained with just a few visual adjustments of the initial parameter values. Reference: da Silva AR et al. (2018) <doi:10.2134/agronj2017.07.0373>.
|
2025-03-25 |
|
r-seedcalc
|
public |
Functions to calculate seed germination and seedling emergence and growth indexes. The main indexes for germination and seedling emergence, considering the time for seed germinate are: T10, T50 and T90, in Farooq et al. (2005) <10.1111/j.1744-7909.2005.00031.x>; and MGT, in Labouriau (1983). Considering the germination speed are: Germination Speed Index, in Maguire (1962), Mean Germination Rate, in Labouriau (1983); considering the homogeneity of germination are: Coefficient of Variation of the Germination Time, in Carvalho et al. (2005) <10.1590/S0100-84042005000300018>, and Variance of Germination, in Labouriau (1983); Uncertainty, in Labouriau and Valadares (1976) <ISSN:0001-3765>; and Synchrony, in Primack (1980). The main seedling indexes are Growth, in Sako (2001), Uniformity, in Sako (2001) and Castan et al. (2018) <doi:10.1590/1678-992x-2016-0401>; and Vigour, in Medeiros and Pereira (2018) <doi:10.1590/1983-40632018v4852340>.
|
2025-03-25 |
|
r-seeclickfixr
|
public |
Provides a wrapper to access data from the SeeClickFix web API for R. SeeClickFix is a central platform employed by many cities that allows citizens to request their city's services. This package creates several functions to work with all the built-in calls to the SeeClickFix API. Allows users to download service request data from numerous locations in easy-to-use dataframe format manipulable in standard R functions.
|
2025-03-25 |
|
r-secret
|
public |
Allow sharing sensitive information, for example passwords, 'API' keys, etc., in R packages, using public key cryptography.
|
2025-03-25 |
|
r-seasonal
|
public |
Easy-to-use interface to X-13-ARIMA-SEATS, the seasonal adjustment software by the US Census Bureau. It offers full access to almost all options and outputs of X-13, including X-11 and SEATS, automatic ARIMA model search, outlier detection and support for user defined holiday variables, such as Chinese New Year or Indian Diwali. A graphical user interface can be used through the 'seasonalview' package. Uses the X-13-binaries from the 'x13binary' package.
|
2025-03-25 |
|
r-seasic
|
public |
This package conducts Score Equity Assessment (SEA; Dorans, 2004) by calculating and plotting multiple SEA indices as introduced by a variety of authors and summarized by Huggins and Penfield (2012).
|
2025-03-25 |
|
r-searcher
|
public |
Provides a search interface to look up terms on 'Google', 'Bing', 'DuckDuckGo', 'Startpage', 'Ecosia', 'rseek', 'Twitter', 'StackOverflow', 'RStudio Community', 'GitHub', and 'BitBucket'. Upon searching, a browser window will open with the aforementioned search results.
|
2025-03-25 |
|
r-searchable
|
public |
Provides functionality for searching / subsetting and slicing named objects using 'stringr/i'-style modifiers by case (in)sensitivity, regular expressions or fixed expressions; searches uses the standard '[' operator and allows specification of default search behavior to either the search target (named object) and/or the search pattern.
|
2025-03-25 |
|
r-sealasso
|
public |
Standard error adjusted adaptive lasso (SEA-lasso) is a version of the adaptive lasso, which incorporates OLS standard error to the L1 penalty weight. This method is intended for variable selection under linear regression settings (n > p). This new weight assignment strategy is especially useful when the collinearity of the design matrix is a concern.
|
2025-03-25 |
|
r-sdtoolkit
|
public |
Implements algorithms to help with scenario discovery - currently only modified version of the the Patient Rule Induction Method.
|
2025-03-25 |
|
r-sdt
|
public |
Functions for self-determination motivation theory (SDT) to compute measures of motivation internalization, motivation simplex structure, and of the original and adjusted self-determination or relative autonomy index. SDT was introduced by Deci and Ryan (1985) <doi:10.1007/978-1-4899-2271-7>. See package?SDT for an overview.
|
2025-03-25 |
|
r-sdmvspecies
|
public |
A software package help user to create virtual species for species distribution modelling. It includes several methods to help user to create virtual species distribution map. Those maps can be used for Species Distribution Modelling (SDM) study. SDM use environmental data for sites of occurrence of a species to predict all the sites where the environmental conditions are suitable for the species to persist, and may be expected to occur.
|
2025-03-25 |
|
r-sdm
|
public |
An extensible framework for developing species distribution models using individual and community-based approaches, generate ensembles of models, evaluate the models, and predict species potential distributions in space and time. For more information, please check the following paper: Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
|
2025-03-25 |
|
r-sdef
|
public |
Performs two tests to evaluate if the experiments are associated and returns a list of interesting features common to all the experiments.
|
2025-03-25 |
|
r-sddpack
|
public |
The semidiscrete decomposition (SDD) approximates a matrix as a weighted sum of outer products formed by vectors with entries constrained to be in the set {-1, 0, 1}.
|
2025-03-25 |
|
r-sdcspatial
|
public |
Privacy protected raster maps can be created from spatial point data. Protection methods include smoothing of dichotomous variables by de Jonge and de Wolf (2016) <doi:10.1007/978-3-319-45381-1_9>, continuous variables by de Wolf and de Jonge (2018) <doi:10.1007/978-3-319-99771-1_23>, suppressing revealing values and a generalization of the quad tree method by Suñé, Rovira, Ibáñez and Farré (2017) <doi:10.2901/EUROSTAT.C2017.001>.
|
2025-03-25 |
|
r-sdaa
|
public |
Functions and Datasets from Lohr, S. (1999), Sampling: Design and Analysis, Duxbury.
|
2025-03-25 |
|
r-scrt
|
public |
Design single-case phase, alternation and multiple-baseline experiments, and conduct randomization tests on data gathered by means of such designs, as discussed in Bulte and Onghena (2013) <doi:10.22237/jmasm/1383280020>.
|
2025-03-25 |
|
r-scrselect
|
public |
Contains four functions used in the DIC-tau_g procedure. SCRSELECT() and SCRSELECTRUN() uses Stochastic Search Variable Selection to select important covariates in the three hazard functions of a semi-competing risks model. These functions perform the Gibbs sampler for variable selection and a Metropolis-Hastings-Green sampler for the number of split points and parameters for the three baseline hazard function. The function SCRSELECT() returns the posterior sample of all quantities sampled in the Gibbs sampler after a burn-in period to a desired file location, while the function SCRSELECTRUN() returns posterior values of important quantities to the DIC-Tau_g procedure in a list. The function DICTAUG() returns a list containing the DIC values for the unique models visited by the DIC-Tau_g grid search. The function ReturnModel() uses SCRSELECTRUN() and DICTAUG() to return a summary of the posterior coefficient vectors for the optimal model along with saving this posterior sample to a desired path location.
|
2025-03-25 |
|
r-scrobbler
|
public |
'Last.fm'<https://www.last.fm> is a music platform focussed on building a detailed profile of a users listening habits. It does this by 'scrobbling' (recording) every track you listen to on other platforms ('spotify', 'youtube', 'soundcloud' etc) and transferring them to your 'Last.fm' database. This allows 'Last.fm' to act as a complete record of your entire listening history. 'scrobbler' provides helper functions to download and analyse your listening history in R.
|
2025-03-25 |
|
r-scripturs
|
public |
Full text, in data frames containing one row per verse, of the Standard Works of The Church of Jesus Christ of Latter-day Saints (LDS). These are the Old Testament, (KJV), the New Testament (KJV), the Book of Mormon, the Doctrine and Covenants, and the Pearl of Great Price.
|
2025-03-25 |
|
r-scriptname
|
public |
A small set of functions wrapping up the call stack and command line inspection needed to determine a running script's filename from within the script itself.
|
2025-03-25 |
|
r-scriptexec
|
public |
Run complex native scripts with a single command, similar to system commands.
|
2025-03-25 |
|
r-scriptests
|
public |
Support for using .Rt (transcript) tests in the tests directory of a package. Provides more convenience and features than the standard .R/.Rout.save tests. Tests can be run under R CMD check and also interactively. Provides source.pkg() for quickly loading code, DLLs, and data from a package for use in an edit/compile/test development cycle.
|
2025-03-25 |
|
r-scrime
|
public |
Tools for the analysis of high-dimensional data developed/implemented at the group "Statistical Complexity Reduction In Molecular Epidemiology" (SCRIME). Main focus is on SNP data. But most of the functions can also be applied to other types of categorical data.
|
2025-03-25 |
|
r-screenclean
|
public |
Routines for a collection of screen-and-clean type variable selection procedures, including UPS and GS.
|
2025-03-25 |
|
r-scraper
|
public |
Tools for Scraping Data from Web-Based Documents
|
2025-03-25 |
|
r-scraep
|
public |
Tools for scraping information from webpages and other XML contents, using XPath or CSS selectors.
|
2025-03-25 |
|
r-scrabblescore
|
public |
Given a word will produce that word's scrabble score. Unlike many naive implementations this package takes into consideration the distribution of letter in scrabble. So a word like 'zzz' will be scored '10' rather than '30'.
|
2025-03-25 |
|
r-scperf
|
public |
Implements different inventory models, the bullwhip effect and other supply chain performance variables. Marchena Marlene (2010) <arXiv:1009.3977>.
|
2025-03-25 |
|
r-scottknott
|
public |
Perform the balanced (Scott and Knott, 1974) and unbalanced <doi:10.1590/1984-70332017v17n1a1> Scott & Knott algorithm.
|
2025-03-25 |
|
r-scoring
|
public |
Evaluating probabilistic forecasts via proper scoring rules. scoring implements the beta, power, and pseudospherical families of proper scoring rules, along with ordered versions of the latter two families. Included among these families are popular rules like the Brier (quadratic) score, logarithmic score, and spherical score. For two-alternative forecasts, also includes functionality for plotting scores that one would obtain under specific scoring rules.
|
2025-03-25 |
|
r-scorer2
|
public |
This package contains the functions necessary to run the SCORER 2.0 algorithm. SCORER 2.0 can be used to differentiate between parallel dimeric and trimeric coiled-coil sequence, which are the two most more frequent coiled-coil structures observed naturally. As such, SCORER 2.0 is particularly useful for researchers looking to characterize novel coiled-coil sequences. It may also be used to assist in the structural characterization of synthetic coiled-coil sequences. Also included in this package are functions that allows the user to retrain the SCORER 2.0 algorithm using user-defined training data.
|
2025-03-25 |
