This package provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in generalized linear models with categorical responses. The pre-fit methods apply on binomial-response generalized liner models such as logit, probit and cloglog regression, and can be directly supplied as fitting methods to the glm() function. The post-fit methods apply to models with categorical responses, including binomial-response generalized linear models and multinomial-response models, such as baseline category logits and adjacent category logits models; for example, the models implemented in the brglm2 package. The post-fit methods successively refit the model with increasing number of iteratively reweighted least squares iterations, and monitor the ratio of the estimated standard error for each parameter to what it has been in the first iteration.

This package provides a polycross is the pollination by natural hybridization of a group of genotypes, generally selected, grown in isolation from other compatible genotypes in such a way to promote random open pollination. A particular practical application of the polycross method occurs in the production of a synthetic variety resulting from cross-pollinated plants. Laying out these experiments in appropriate designs, known as polycross designs, would not only save experimental resources but also gather more information from the experiment. Different experimental situations may arise in polycross nurseries which may be requiring different polycross designs (Varghese et. al. (2015) <doi:10.1080/02664763.2015.1043860>. " Experimental designs for open pollination in polycross trials"). This package contains a function named PD() which generates nine types of polycross designs suitable for various experimental situations.

This package provides functions to estimate the proportion of treatment effect on a censored primary outcome that is explained by the treatment effect on a censored surrogate outcome/event. All methods are described in detail in Parast, Tian, Cai (2020) "Assessing the Value of a Censored Surrogate Outcome" <doi:10.1007/s10985-019-09473-1>. The main functions are (1) R.q.event() which calculates the proportion of the treatment effect (the difference in restricted mean survival time at time t) explained by surrogate outcome information observed up to a selected landmark time, (2) R.t.estimate() which calculates the proportion of the treatment effect explained by primary outcome information only observed up to a selected landmark time, and (3) IV.event() which calculates the incremental value of the surrogate outcome information.

This r-physicalactivity package provides a function wearingMarking for classification of monitored wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plots of accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. The revised package version 0.2-1 improved the functions regarding speed, robustness and add better support for time zones and daylight saving. In addition, several functions were added:

1. the markDelivery can classify days for ActiGraph delivery by mail;

2. the markPAI can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts.

It also supports importing ActiGraph (AGD) files with readActigraph and queryActigraph functions.

An R interface to the Julia package NeuralEstimators.jl'. The package facilitates the user-friendly development of neural Bayes estimators, which are neural networks that map data to a point summary of the posterior distribution (Sainsbury-Dale et al., 2024, <doi:10.1080/00031305.2023.2249522>). These estimators are likelihood-free and amortised, in the sense that, once the neural networks are trained on simulated data, inference from observed data can be made in a fraction of the time required by conventional approaches. The package also supports amortised Bayesian or frequentist inference using neural networks that approximate the posterior or likelihood-to-evidence ratio (Zammit-Mangion et al., 2025, Sec. 3.2, 5.2, <doi:10.48550/arXiv.2404.12484>). The package accommodates any model for which simulation is feasible by allowing users to define models implicitly through simulated data.

This package provides a comprehensive suite of functions for processing, analyzing, and visualizing textual data from tweets is offered. Users can clean tweets, analyze their sentiments, visualize data, and examine the correlation between sentiments and environmental data such as weather conditions. Main features include text processing, sentiment analysis, data visualization, correlation analysis, and synthetic data generation. Text processing involves cleaning and preparing tweets by removing textual noise and irrelevant words. Sentiment analysis extracts and accurately analyzes sentiments from tweet texts using advanced algorithms. Data visualization creates various charts like word clouds and sentiment polarity graphs for visual representation of data. Correlation analysis examines and calculates the correlation between tweet sentiments and environmental variables such as weather conditions. Additionally, random tweets can be generated for testing and evaluating the performance of analyses, empowering users to effectively analyze and interpret Twitter data for research and commercial purposes.

Point mutations occurring in a genome can be divided into 96 categories based on the base being mutated, the base it is mutated into and its two flanking bases. Therefore, for any patient, it is possible to represent all the point mutations occurring in that patient's tumor as a vector of length 96, where each element represents the count of mutations for a given category in the patient. A mutational signature represents the pattern of mutations produced by a mutagen or mutagenic process inside the cell. Each signature can also be represented by a vector of length 96, where each element represents the probability that this particular mutagenic process generates a mutation of the 96 above mentioned categories. In this R package, we provide a set of functions to extract and visualize the mutational signatures that best explain the mutation counts of a large number of patients.

Treemaps are a visually appealing graphical representation of numerical data using a space-filling approach. A plane or map is subdivided into smaller areas called cells. The cells in the map are scaled according to an underlying metric which allows to grasp the hierarchical organization and relative importance of many objects at once. This package contains two different implementations of treemaps, Voronoi treemaps and Sunburst treemaps. The Voronoi treemap function subdivides the plot area in polygonal cells according to the highest hierarchical level, then continues to subdivide those parental cells on the next lower hierarchical level, and so on. The Sunburst treemap is a computationally less demanding treemap that does not require iterative refinement, but simply generates circle sectors that are sized according to predefined weights. The Voronoi tesselation is based on functions from Paul Murrell (2012) <https://www.stat.auckland.ac.nz/~paul/Reports/VoronoiTreemap/voronoiTreeMap.html>.

This package provides a dynamic programming algorithm for optimal clustering multidimensional data with sequential constraint. The algorithm minimizes the sum of squares of within-cluster distances. The sequential constraint allows only subsequent items of the input data to form a cluster. The sequential constraint is typically required in clustering data streams or items with time stamps such as video frames, GPS signals of a vehicle, movement data of a person, e-pen data, etc. The algorithm represents an extension of Ckmeans.1d.dp to multiple dimensional spaces. Similarly to the one-dimensional case, the algorithm guarantees optimality and repeatability of clustering. Method clustering.sc.dp() can find the optimal clustering if the number of clusters is known. Otherwise, methods findwithinss.sc.dp() and backtracking.sc.dp() can be used. See Szkaliczki, T. (2016) "clustering.sc.dp: Optimal Clustering with Sequential Constraint by Using Dynamic Programming" <doi: 10.32614/RJ-2016-022> for more information.

The Percentage of Importance Indice (Percentage_I.I.) bases in magnitudes, frequencies, and distributions of occurrence of an event (DEMOLIN-LEITE, 2021) <http://cjascience.com/index.php/CJAS/article/view/1009/1350>. This index can detect the key loss sources (L.S) and solution sources (S.S.), classifying them according to their importance in terms of loss or income gain, on the productive system. The Percentage_I.I. = [(ks1 x c1 x ds1)/SUM (ks1 x c1 x ds1) + (ks2 x c2 x ds2) + (ksn x cn x dsn)] x 100. key source (ks) is obtained using simple regression analysis and magnitude (abundance). Constancy (c) is SUM of occurrence of L.S. or S.S. on the samples (absence = 0 or presence = 1), and distribution source (ds) is obtained using chi-square test. This index has derivations: i.e., i) Loss estimates and solutions effectiveness and ii) Attention and non-attention levels (DEMOLIN-LEITE,2024) <DOI: 10.1590/1519-6984.253215>.

This simple daemon feeds entropy from the CPU Jitter RNG core to the kernel Linux's entropy estimator. This prevents the /dev/random device from blocking and should benefit users of the preferred /dev/urandom and getrandom() interfaces too.

The CPU Jitter RNG itself is part of the kernel and claims to provide good entropy by collecting and magnifying differences in CPU execution time as measured by the high-resolution timer built into modern CPUs. It requires no additional hardware or external entropy source.

The random bit stream generated by jitterentropy-rngd is not processed by a cryptographically secure whitening function. Nonetheless, its authors believe it to be a suitable source of cryptographically secure key material or other cryptographically sensitive data.

If you agree with them, start this daemon as early as possible to provide properly seeded random numbers to services like SSH or those using TLS during early boot when entropy may be low, especially in virtualised environments.

Cleans and formats language transcripts guided by a series of transformation options (e.g., lemmatize words, omit stopwords, split strings across rows). SemanticDistance computes two distinct metrics of cosine semantic distance (experiential and embedding). These values reflect pairwise cosine distance between different elements or chunks of a language sample. SemanticDistance can process monologues (e.g., stories, ordered text), dialogues (e.g., conversation transcripts), word pairs arrayed in columns, and unordered word lists. Users specify options for how they wish to chunk distance calculations. These options include: rolling ngram-to-word distance (window of n-words to each new word), ngram-to-ngram distance (2-word chunk to the next 2-word chunk), pairwise distance between words arrayed in columns, matrix comparisons (i.e., all possible pairwise distances between words in an unordered list), turn-by-turn distance (talker to talker in a dialogue transcript). SemanticDistance includes visualization options for analyzing distances as time series data and simple semantic network dynamics (e.g., clustering, undirected graph network).

Data collected on movement behavior is often in the form of time- stamped latitude/longitude coordinates sampled from the underlying movement behavior. These data can be compressed into a set of segments via the Top- Down Time Ratio Segmentation method described in Meratnia and de By (2004) <doi:10.1007/978-3-540-24741-8_44> which, with some loss of information, can both reduce the size of the data as well as provide corrective smoothing mechanisms to help reduce the impact of measurement error. This is an improvement on the well-known Douglas-Peucker algorithm for segmentation that operates not on the basis of perpendicular distances. Top-Down Time Ratio segmentation allows for disparate sampling time intervals by calculating the distance between locations and segments with respect to time. Provided a trajectory with timestamps, tdtr() returns a set of straight- line segments that can represent the full trajectory. McCool, Lugtig, and Schouten (2022) <doi:10.1007/s11116-022-10328-2> describe this method as implemented here in more detail.

This package provides functions to estimate the optimal threshold of diagnostic markers or treatment selection markers. The optimal threshold is the marker value that maximizes the utility of the marker based-strategy (for diagnostic or treatment selection) in a given population. The utility function depends on the type of marker (diagnostic or treatment selection), but always takes into account the preferences of the patients or the physician in the decision process. For estimating the optimal threshold, ones must specify the distributions of the marker in different groups (defined according to the type of marker, diagnostic or treatment selection) and provides data to estimate the parameters of these distributions. Ones must also provide some features of the target populations (disease prevalence or treatment efficacies) as well as the preferences of patients or physicians. The functions rely on Bayesian inference which helps producing several indicators derived from the optimal threshold. See Blangero, Y, Rabilloud, M, Ecochard, R, and Subtil, F (2019) <doi:10.1177/0962280218821394> for the original article that describes the estimation method for treatment selection markers and Subtil, F, and Rabilloud, M (2019) <doi:10.1002/bimj.200900242> for diagnostic markers.

An implementation of metaheuristic algorithms for continuous optimization. Currently, the package contains the implementations of 21 algorithms, as follows: particle swarm optimization (Kennedy and Eberhart, 1995), ant lion optimizer (Mirjalili, 2015 <doi:10.1016/j.advengsoft.2015.01.010>), grey wolf optimizer (Mirjalili et al., 2014 <doi:10.1016/j.advengsoft.2013.12.007>), dragonfly algorithm (Mirjalili, 2015 <doi:10.1007/s00521-015-1920-1>), firefly algorithm (Yang, 2009 <doi:10.1007/978-3-642-04944-6_14>), genetic algorithm (Holland, 1992, ISBN:978-0262581110), grasshopper optimisation algorithm (Saremi et al., 2017 <doi:10.1016/j.advengsoft.2017.01.004>), harmony search algorithm (Mahdavi et al., 2007 <doi:10.1016/j.amc.2006.11.033>), moth flame optimizer (Mirjalili, 2015 <doi:10.1016/j.knosys.2015.07.006>, sine cosine algorithm (Mirjalili, 2016 <doi:10.1016/j.knosys.2015.12.022>), whale optimization algorithm (Mirjalili and Lewis, 2016 <doi:10.1016/j.advengsoft.2016.01.008>), clonal selection algorithm (Castro, 2002 <doi:10.1109/TEVC.2002.1011539>), differential evolution (Das & Suganthan, 2011), shuffled frog leaping (Eusuff, Landsey & Pasha, 2006), cat swarm optimization (Chu et al., 2006), artificial bee colony algorithm (Karaboga & Akay, 2009), krill-herd algorithm (Gandomi & Alavi, 2012), cuckoo search (Yang & Deb, 2009), bat algorithm (Yang, 2012), gravitational based search (Rashedi et al., 2009) and black hole optimization (Hatamlou, 2013).

Generate continuous (normal or non-normal), binary, ordinal, and count (Poisson or Negative Binomial) variables with a specified correlation matrix. It can also produce a single continuous variable. This package can be used to simulate data sets that mimic real-world situations (i.e. clinical or genetic data sets, plasmodes). All variables are generated from standard normal variables with an imposed intermediate correlation matrix. Continuous variables are simulated by specifying mean, variance, skewness, standardized kurtosis, and fifth and sixth standardized cumulants using either Fleishman's third-order (<DOI:10.1007/BF02293811>) or Headrick's fifth-order (<DOI:10.1016/S0167-9473(02)00072-5>) polynomial transformation. Binary and ordinal variables are simulated using a modification of the ordsample() function from GenOrd'. Count variables are simulated using the inverse cdf method. There are two simulation pathways which differ primarily according to the calculation of the intermediate correlation matrix. In Correlation Method 1, the intercorrelations involving count variables are determined using a simulation based, logarithmic correlation correction (adapting Yahav and Shmueli's 2012 method, <DOI:10.1002/asmb.901>). In Correlation Method 2, the count variables are treated as ordinal (adapting Barbiero and Ferrari's 2015 modification of GenOrd, <DOI:10.1002/asmb.2072>). There is an optional error loop that corrects the final correlation matrix to be within a user-specified precision value of the target matrix. The package also includes functions to calculate standardized cumulants for theoretical distributions or from real data sets, check if a target correlation matrix is within the possible correlation bounds (given the distributions of the simulated variables), summarize results (numerically or graphically), to verify valid power method pdfs, and to calculate lower standardized kurtosis bounds.

Automatically runs 18 individual models and 14 ensembles on numeric data, for a total of 32 models. The package automatically returns complete results on all 32 models, 30 charts and six tables. The user simply provides the tidy data, and answers a few questions (for example, how many times would you like to resample the data). From there the package randomly splits the data into train, test and validation sets, fits each of models on the training data, makes predictions on the test and validation sets, measures root mean squared error (RMSE), removes features above a user-set level of Variance Inflation Factor, and has several optional features including scaling all numeric data, four different ways to handle strings in the data. Perhaps the most significant feature is the package's ability to make predictions using the 32 pre trained models on totally new (untrained) data if the user selects that feature. This feature alone represents a very effective solution to the issue of reproducibility of models in data science. The package can also randomly resample the data as many times as the user sets, thus giving more accurate results than a single run. The graphs provide many results that are not typically found. For example, the package automatically calculates the Kolmogorov-Smirnov test for each of the 32 models and plots a bar chart of the results, a bias bar chart of each of the 32 models, as well as several plots for exploratory data analysis (automatic histograms of the numeric data, automatic histograms of the numeric data). The package also automatically creates a summary report that can be both sorted and searched for each of the 32 models, including RMSE, bias, train RMSE, test RMSE, validation RMSE, overfitting and duration. The best results on the holdout data typically beat the best results in data science competitions and published results for the same data set.

Ruby bindings.

Rust compiler symbol demangling.

Documentation at https://melpa.org/#/ruby-refactor

This package provides Rust compiler symbol demangling.

Documentation at https://melpa.org/#/org-re-reveal

This package provides rust library for formatting dynamic strings.

Rubygems-task provides Rake tasks for managing and releasing Ruby Gems.