Clusters state sequences and weighted data. It provides an optimized weighted PAM algorithm as well as functions for aggregating replicated cases, computing cluster quality measures for a range of clustering solutions, sequence analysis typology validation using parametric bootstraps and plotting (fuzzy) clusters of state sequences. It further provides a fuzzy and crisp CLARA algorithm to cluster large database with sequence analysis, and a methodological framework for Robustness Assessment of Regressions using Cluster Analysis Typologies (RARCAT).

Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data. This package utilizes the shiny and plotly frameworks to provide a user friendly dashboard for interactive plotting.

Book is "Linear Mixed Models: A Practical Guide Using Statistical Software" published in 2006 by Chapman Hall / CRC Press.

This package performs Wilcoxon-Mann-Whitney test in the presence of missing data with controlled Type I error regardless of the values of missing data.

Imports WhatsApp chat logs and parses them into a usable dataframe object. The parser works on chats exported from Android or iOS phones and on Linux, macOS and Windows. The parser has multiple options for extracting smileys and emojis from the messages, extracting URLs and domains from the messages, extracting names and types of sent media files from the messages, extracting timestamps from messages, extracting and anonymizing author names from messages. Can be used to create anonymized versions of data.

Takes screenshots of web pages, including Shiny applications and R Markdown documents. webshot2 uses headless Chrome or Chromium as the browser back-end.

This package provides automated downloading, parsing and formatting of weather data for Australia through API endpoints provided by the Department of Primary Industries and Regional Development (DPIRD) of Western Australia and by the Science and Technology Division of the Queensland Government's Department of Environment and Science (DES). As well as the Bureau of Meteorology (BOM) of the Australian government precis and coastal forecasts, and downloading and importing radar and satellite imagery files. DPIRD weather data are accessed through public APIs provided by DPIRD, <https://www.dpird.wa.gov.au/online-tools/apis/>, providing access to weather station data from the DPIRD weather station network. Australia-wide weather data are based on data from the Australian Bureau of Meteorology (BOM) data and accessed through SILO (Scientific Information for Land Owners) Jeffrey et al. (2001) <doi:10.1016/S1364-8152(01)00008-1>. DPIRD data are made available under a Creative Commons Attribution 3.0 Licence (CC BY 3.0 AU) license <https://creativecommons.org/licenses/by/3.0/au/deed.en>. SILO data are released under a Creative Commons Attribution 4.0 International licence (CC BY 4.0) <https://creativecommons.org/licenses/by/4.0/>. BOM data are (c) Australian Government Bureau of Meteorology and released under a Creative Commons (CC) Attribution 3.0 licence or Public Access Licence (PAL) as appropriate, see <https://www.bom.gov.au/copyright> for further details.

This package provides a weather generator to simulate precipitation and temperature for regions with seasonality. Users input training data containing precipitation, temperature, and seasonality (up to 26 seasons). Including weather season as a training variable allows users to explore the effects of potential changes in season duration as well as average start- and end-time dates due to phenomena like climate change. Data for training should be a single time series but can originate from station data, basin averages, grid cells, etc. Bearup, L., Gangopadhyay, S., & Mikkelson, K. (2021). "Hydroclimate Analysis Lower Santa Cruz River Basin Study (Technical Memorandum No ENV-2020-056)." Bureau of Reclamation. Gangopadhyay, S., Bearup, L. A., Verdin, A., Pruitt, T., Halper, E., & Shamir, E. (2019, December 1). "A collaborative stochastic weather generator for climate impacts assessment in the Lower Santa Cruz River Basin, Arizona." Fall Meeting 2019, American Geophysical Union. <https://ui.adsabs.harvard.edu/abs/2019AGUFMGC41G1267G>.

ETS stands for Error, Trend, and Seasonality, and it is a popular time series forecasting method. Wavelet decomposition can be used for denoising, compression, and feature extraction of signals. By removing the high-frequency components, wavelet decomposition can remove noise from the data while preserving important features. A hybrid Wavelet ETS (Error Trend-Seasonality) model has been developed for time series forecasting using algorithm of Anjoy and Paul (2017) <DOI:10.1007/s00521-017-3289-9>.

This package provides function, wget_set(), to change the method (default to wget -c') using in download.file(). Using wget -c allowing continued downloading, which is especially useful for slow internet connection and for downloading large files. User can run wget_unset() to restore previous setting.

This package provides a prediction model is calibrated if, roughly, for any percentage x we can expect that x subjects out of 100 experience the event among all subjects that have a predicted risk of x%. A calibration plot provides a simple, yet useful, way of assessing the calibration assumption. The Wally plot consists of a sequence of usual calibration plots. Among the plots contained within the sequence, one is the actual calibration plot which has been obtained from the data and the others are obtained from similar simulated data under the calibration assumption. It provides the investigator with a direct visual understanding of the shape and sampling variability that are common under the calibration assumption. The original calibration plot from the data is included randomly among the simulated calibration plots, similarly to a police lineup. If the original calibration plot is not easily identified then the calibration assumption is not contradicted by the data. The method handles the common situations in which the data contain censored observations and occurrences of competing events.

Construct a Canonical Variate Analysis Biplot via the Generalised Singular Value Decomposition, for cases when the number of samples is less than the number of variables. For more information on biplots, see Gower JC, Lubbe SG, Le Roux NJ (2011) <doi:10.1002/9780470973196> and for more information on the generalised singular value decomposition, see Edelman A, Wang Y (2020) <doi:10.1137/18M1234412>.

This package implements Weighted-Average Least Squares model averaging for negative binomial regression models of Huynh (2024) <doi:10.48550/arXiv.2404.11324>, generalized linear models of De Luca, Magnus, Peracchi (2018) <doi:10.1016/j.jeconom.2017.12.007> and linear regression models of Magnus, Powell, Pruefer (2010) <doi:10.1016/j.jeconom.2009.07.004>, see also Magnus, De Luca (2016) <doi:10.1111/joes.12094>. Weighted-Average Least Squares for the linear regression model is based on the original MATLAB code by Magnus and De Luca <https://www.janmagnus.nl/items/WALS.pdf>, see also Kumar, Magnus (2013) <doi:10.1007/s13571-013-0060-9> and De Luca, Magnus (2011) <doi:10.1177/1536867X1201100402>.

The web version WebGestalt <https://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.

Select data analysis plots, under a standardized calling interface implemented on top of ggplot2 and plotly'. Plots of interest include: ROC', gain curve, scatter plot with marginal distributions, conditioned scatter plot with marginal densities, box and stem with matching theoretical distribution, and density with matching theoretical distribution.

Generate wordsearch and crossword puzzles using custom lists of words (and clues). Make them easy or hard, and print them to solve offline with paper and pencil!

Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data. Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted. Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format): MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>), Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>), MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>), OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>), Proline (Bouyssie et al 2020 <doi:10.1093/bioinformatics/btaa118>), AlphaPept (preprint Strauss et al <doi:10.1101/2021.07.23.453379>) and Wombat-P (Bouyssie et al 2023 <doi:10.1021/acs.jproteome.3c00636>. Meta-data provided by initial analysis software and/or in sdrf format can be integrated to the analysis. Quantitative proteomics measurements frequently contain multiple NA values, due to physical absence of given peptides in some samples, limitations in sensitivity or other reasons. Help is provided to inspect the data graphically to investigate the nature of NA-values via their respective replicate measurements and to help/confirm the choice of NA-replacement algorithms. Meta-data in sdrf-format (Perez-Riverol et al 2020 <doi:10.1021/acs.jproteome.0c00376>) or similar tabular formats can be imported and included. Missing values can be inspected and imputed based on the concept of NA-neighbours or other methods. Dedicated filtering and statistical testing using the framework of package limma <doi:10.18129/B9.bioc.limma> can be run, enhanced by multiple rounds of NA-replacements to provide robustness towards rare stochastic events. Multi-species samples, as frequently used in benchmark-tests (eg Navarro et al 2016 <doi:10.1038/nbt.3685>, Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>), can be run with special options considering such sub-groups during normalization and testing. Subsequently, ROC curves (Hand and Till 2001 <doi:10.1023/A:1010920819831>) can be constructed to compare multiple analysis approaches. As detailed example the data-set from Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>) quantified by MaxQuant, ProteomeDiscoverer, and Proline is provided with a detailed analysis of heterologous spike-in proteins.

This package implements a functional approximation of the four panel cointegration tests developed by Westerlund (2007) <doi:10.1111/j.1468-0084.2007.00477.x>. The tests are based on structural rather than residual dynamics and allow for heterogeneity in both the long-run cointegrating relationship and the short-run dynamics. The package includes logic for automated lag and lead selection via AIC/BIC, Bartlett kernel long-run variance estimation, and a bootstrap procedure to handle cross-sectional dependence. It also includes a bootstrapping distribution visualization function for diagnostic purposes.

Life data analysis in the graphical tradition of Waloddi Weibull. Methods derived from Robert B. Abernethy (2008, ISBN 0-965306-3-2), Wayne Nelson (1982, ISBN: 9780471094586), William Q. Meeker and Lois A. Escobar (1998, ISBN: 1-471-14328-6), John I. McCool, (2012, ISBN: 9781118217986).

Allows to generate on-demand or by batch, any R documentation file, whatever is kind, data, function, class or package. It populates documentation sections, either automatically or by considering your input. Input code could be standard R code or offensive programming code. Documentation content completeness depends on the type of code you use. With offensive programming code, expect generated documentation to be fully completed, from a format and content point of view. With some standard R code, you will have to activate post processing to fill-in any section that requires complements. Produced manual page validity is automatically tested against R documentation compliance rules. Documentation language proficiency, wording style, and phrasal adjustments remains your job.

This package provides functions for the import, transformation, and analysis of data from muscle physiology experiments. The work loop technique is used to evaluate the mechanical work and power output of muscle. Josephson (1985) <doi:10.1242/jeb.114.1.493> modernized the technique for application in comparative biomechanics. Although our initial motivation was to provide functions to analyze work loop experiment data, as we developed the package we incorporated the ability to analyze data from experiments that are often complementary to work loops. There are currently three supported experiment types: work loops, simple twitches, and tetanus trials. Data can be imported directly from .ddf files or via an object constructor function. Through either method, data can then be cleaned or transformed via methods typically used in studies of muscle physiology. Data can then be analyzed to determine the timing and magnitude of force development and relaxation (for isometric trials) or the magnitude of work, net power, and instantaneous power among other things (for work loops). Although we do not provide plotting functions, all resultant objects are designed to be friendly to visualization via either base-R plotting or tidyverse functions. This package has been peer-reviewed by rOpenSci (v. 1.1.0).

The Wavelet Decomposition followed by Random Forest Regression (RF) models have been applied for time series forecasting. The maximum overlap discrete wavelet transform (MODWT) algorithm was chosen as it works for any length of the series. The series is first divided into training and testing sets. In each of the wavelet decomposed series, the supervised machine learning approach namely random forest was employed to train the model. This package also provides accuracy metrics in the form of Root Mean Square Error (RMSE) and Mean Absolute Prediction Error (MAPE). This package is based on the algorithm of Ding et al. (2021) <DOI: 10.1007/s11356-020-12298-3>.

This package provides a collection of tools to fit and work with trophic Species Distribution Models. Trophic Species Distribution Models combine knowledge of trophic interactions with Bayesian structural equation models that model each species as a function of its prey (or predators) and environmental conditions. It exploits the topological ordering of the known trophic interaction network to predict species distribution in space and/or time, where the prey (or predator) distribution is unavailable. The method implemented by the package is described in Poggiato, Andréoletti, Pollock and Thuiller (2022) <doi:10.22541/au.166853394.45823739/v1>.

Supports systematic scrutiny, modification, and integration of data. The function status() counts rows that have missing values in grouping columns (returned by na() ), have non-unique combinations of grouping columns (returned by dup() ), and that are not locally sorted (returned by unsorted() ). Functions enumerate() and itemize() give sorted unique combinations of columns, with or without occurrence counts, respectively. Function ignore() drops columns in x that are present in y, and informative() drops columns in x that are entirely NA; constant() returns values that are constant, given a key. Data that have defined unique combinations of grouping values behave more predictably during merge operations.