Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K .idat files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.
Implementation of the EPA's Ecological Exposure Research Division (EERD) tools (discontinued in 1999) for Probit and Trimmed Spearman-Karber Analysis. Probit and Spearman-Karber methods from Finney's book "Probit analysis a statistical treatment of the sigmoid response curve" with options for most accurate results or identical results to the book. Probit and all the tables from Finney's book (code-generated, not copied) with the generating functions included. Control correction: Abbott, Schneider-Orelli, Henderson-Tilton, Sun-Shepard. Toxicity scales: Horsfall-Barratt, Archer, Gauhl-Stover, Fullerton-Olsen, etc.
The general workflow of most imputation methods is quite similar. The aim of this package is to provide parts of this general workflow to make the implementation of imputation methods easier. The heart of an imputation method is normally the used model. These models can be defined using the parsnip package or customized specifications. The rest of an imputation method are more technical specification e.g. which columns and rows should be used for imputation and in which order. These technical specifications can be set inside the imputation functions.
An R interface to version 0.3 of the ROPTLIB optimization library (see <https://www.math.fsu.edu/~whuang2/> for more information). Optimize real-valued functions over manifolds such as Stiefel, Grassmann, and symmetric positive definite matrices. For details see Martin et al. (2020) <doi:10.18637/jss.v093.i01>. Note that the optional ldr package used in some of this package's examples can be obtained from either the article <doi:10.18637/jss.v061.i03> or from the ldr package <https://cran.r-project.org/package=ldr>.
Guile-Reader is a simple framework for building readers for GNU Guile.
The idea is to make it easy to build procedures that extend Guile’s read procedure. Readers supporting various syntax variants can easily be written, possibly by re-using existing “token readers” of a standard Scheme readers. For example, it is used to implement Skribilo’s R5RS-derived document syntax.
Guile-Reader’s approach is similar to Common Lisp’s “read table”, but hopefully more powerful and flexible (for instance, one may instantiate as many readers as needed).
Randomly select samples using simple random sampling (SRS), systematic sampling, and various probability proportional to size (PPS) methods, including systematic PPS and sequential PPS (i.e., Chromy's method). Also includes functionality to allocate sample sizes across strata using proportional, power, Neyman, and optimal allocation methods, and to select samples within strata. Designed to make survey sample design and selection reproducible, efficient, and transparent for survey statisticians and researchers. Sampling methods follow Kalton (1983) <doi:10.4135/9781412984683> and Chromy (1979) <http://www.asasrms.org/Proceedings/papers/1979_081.pdf>.
DoubletFinder identifies doublets by generating artificial doublets from existing scRNA-seq data and defining which real cells preferentially co-localize with artificial doublets in gene expression space. Other DoubletFinder package functions are used for fitting DoubletFinder to different scRNA-seq datasets. For example, ideal DoubletFinder performance in real-world contexts requires optimal pK selection and homotypic doublet proportion estimation. pK selection is achieved using pN-pK parameter sweeps and maxima identification in mean-variance-normalized bimodality coefficient distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies.
This package provides a very fast and robust interface to ArcGIS Geocoding Services'. Provides capabilities for reverse geocoding, finding address candidates, character-by-character search autosuggestion, and batch geocoding. The public ArcGIS World Geocoder is accessible for free use via arcgisgeocode for all services except batch geocoding. arcgisgeocode also integrates with arcgisutils to provide access to custom locators or private ArcGIS World Geocoder hosted on ArcGIS Enterprise'. Learn more in the Geocode service API reference <https://developers.arcgis.com/rest/geocode/api-reference/overview-world-geocoding-service.htm>.
Stock, Options and Futures Trading Strategies for Traders and Investors with Bullish Outlook are represented here through their Graphs. The graphic indicators, strategies, calculations, functions and all the discussions are for academic, research, and educational purposes only and should not be construed as investment advice and come with absolutely no Liability. Guy Cohen (â The Bible of Options Strategies (2nd ed.)â , 2015, ISBN: 9780133964028). Zura Kakushadze, Juan A. Serur (â 151 Trading Strategiesâ , 2018, ISBN: 9783030027919). John C. Hull (â Options, Futures, and Other Derivatives (11th ed.)â , 2022, ISBN: 9780136939979).
Pacote para a analise de experimentos havendo duas variaveis explicativas quantitativas e uma variavel dependente quantitativa. Os experimentos podem ser sem repeticoes ou com delineamento estatistico. Sao ajustados 12 modelos de regressao multipla e plotados graficos de superficie resposta (Hair JF, 2016) <ISBN:13:978-0138132637>.(Package for the analysis of experiments having two explanatory quantitative variables and one quantitative dependent variable. The experiments can be without repetitions or with a statistical design. Twelve multiple regression models are fitted and response surface graphs are plotted (Hair JF, 2016) <ISBN:13:978-0138132637>).
This package provides a tool for interactive exploration of the results from omics experiments to facilitate novel discoveries from high-throughput biology. The software includes R functions for the bioinformatician to deposit study metadata and the outputs from statistical analyses (e.g. differential expression, enrichment). These results are then exported to an interactive JavaScript dashboard that can be interrogated on the user's local machine or deployed online to be explored by collaborators. The dashboard includes sortable tables, interactive plots including network visualization, and fine-grained filtering based on statistical significance.
Extras and extensions for xaringan slides. Navigate your slides with tile view. Make your slides editable, live! Announce slide changes with subtle tones. Animate slide transitions with animate.css'. Add tabbed panels to slides with panelset'. Use the Tachyons CSS utility toolkit for rapid slide development. Scribble on your slides. Add a copy button to your code chunks with clipboard'. Add a logo or top or bottom banner to every slide. Broadcast slides to stay in sync with remote viewers. Include yourself in your slides with webcam'. Plus a whole lot more!
The leader clustering algorithm provides a means for clustering a set of data points. Unlike many other clustering algorithms it does not require the user to specify the number of clusters, but instead requires the approximate radius of a cluster as its primary tuning parameter. The package provides a fast implementation of this algorithm in n-dimensions using Lp-distances (with special cases for p=1,2, and infinity) as well as for spatial data using the Haversine formula, which takes latitude/longitude pairs as inputs and clusters based on great circle distances.
Learned Pattern Similarity (LPS) for time series, as described in Baydogan and Runger (2016) <doi:10.1007/s10618-015-0425-y>. Implements an approach to model the dependency structure in time series that generalizes the concept of autoregression to local auto-patterns. Generates a pattern-based representation of time series along with a similarity measure called Learned Pattern Similarity (LPS). Introduces a generalized autoregressive kernel. This package adapts C code from the randomForest package by Andy Liaw and Matthew Wiener, itself based on original Fortran code by Leo Breiman and Adele Cutler.
Market odds from from Pinnacle, an online sports betting bookmaker (see <https://www.pinnacle.com> for more information). Included are datasets for the Major League Baseball (MLB) 2016 season and the USA election 2016. These datasets can be used to build models and compare statistical information with the information from prediction markets.The Major League Baseball (MLB) 2016 dataset can be used for sabermetrics analysis and also can be used in conjunction with other popular Major League Baseball (MLB) datasets such as Retrosheets or the Lahman package by merging by GameID.
Noise Repellent is an LV2 plugin to reduce noise. It has the following features:
Spectral gating and spectral subtraction suppression rule
Adaptive and manual noise thresholds estimation
Adjustable noise floor
Adjustable offset of thresholds to perform over-subtraction
Time smoothing and a masking estimation to reduce artifacts
Basic onset detector to avoid transients suppression
Whitening of the noise floor to mask artifacts and to recover higher frequencies
Option to listen to the residual signal
Soft bypass
Noise profile saved with the session
An application for analysis of Adverse Events, as described in Chen, et al., (2023) <doi:10.3390/cancers15092521>. The required data for the application includes demographics, follow up, adverse event, drug administration and optional tumor measurement data. The app can produce swimmers plots of adverse events, Kaplan-Meier plots and Cox Proportional Hazards model results for the association of adverse event biomarkers and overall survival and progression free survival. The adverse event biomarkers include occurrence of grade 3, low grade (1-2), and treatment related adverse events. Plots and tables of results are downloadable.
The official website of the Trends in International Mathematics and Science Study (TIMSS) 2023 provides Student Process Data Files for Grade 4 in RData format. However, the data are presented exclusively in numerical form. This package converts the numeric values into categorical variables, allowing for easier interpretation and reducing ambiguity in statistical analysis. The category labels are presented in Bahasa Indonesia. This effort also supports the promotion of Bahasa Indonesia in programming, in line with its recognition as one of the official languages of the United Nations. For further information, visit <https://timss2023.org/>.
Imports causal and system-dynamics models from Vensim', Stella / iThink and Powersim Studio ('XMILE'), AnyLogic and GoldSim (exported XML'), and converts them into a two-column edge list of cause-to-effect links. Vensim models are read from their native diagram files; Powersim Studio and GoldSim are also now read from their native diagram files in addition to exported XMILE or XML'. Provides an RStudio add-in with a simple point-and-click interface, together with command-line functions that return a data frame or write it to CSV or Excel'.
Exploratory analysis of a data base. Using the functions of this package is possible to filter the data set detecting atypical values (outliers) and to perform exploratory analysis through visual inspection or dispersion measures. With this package you can explore the structure of your data using several parameters at the same time joining statistical parameters with different graphics. Finally, this package aid to confirm or reject the hypothesis that your data structure presents a normal distribution. Therefore this package is useful to get a previous insight of your data before to carry out statistical analysis.
The function forAD() implements the adaptive forecasting procedure of Giraitis, Kapetanios and Price (2013) <doi:10.1016/j.jeconom.2013.04.003>. The method can be iterated (e.g., adapt²) and combined with autoregressive (AR) forecasting. These approaches are computationally simple and adapt automatically to structural changes without requiring prior specification of the underlying data-generating process. They are applicable to both stationary and non-stationary time series. The numerical and graphical outputs assist in selecting an appropriate forecasting method, particularly one that minimises mean squared forecast error (MSFE) and yields uncorrelated forecast errors.
This package performs modeling and forecasting of park visitor counts using social media data and (partial) on-site visitor counts. Specifically, the model is built based on an automatic decomposition of the trend and seasonal components of the social media-based park visitor counts, from which short-term forecasts of the visitor counts and percent changes in the visitor counts can be made. A reference for the underlying model that VisitorCounts uses can be found at Russell Goebel, Austin Schmaltz, Beth Ann Brackett, Spencer A. Wood, Kimihiro Noguchi (2023) <doi:10.1002/for.2965> .
Query for enriched data such as country, region, city, latitude & longitude, ZIP code, time zone, Autonomous System, Internet Service Provider, domain, net speed, International direct dialing (IDD) code, area code, weather station data, mobile data, elevation, usage type, address type, advertisement category, fraud score, and proxy data with an IP address. You can also query a list of hosted domain names for the IP address too. This package uses the IP2Location.io API to query this data. To get started with a free API key, sign up here <https://www.ip2location.io/sign-up?ref=1>.
This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.