Multiple tools are now available for inferring the personalised germ line set from an adaptive immune receptor repertoire. Output from these tools is converted to a single format and supplemented with rich data such as usage and characterisation of novel germ line alleles. This data can be particularly useful when considering the validity of novel inferences. Use of the analysis provided is described in <doi:10.3389/fimmu.2019.00435>.

This package provides an end-to-end workflow for integrative analysis of two omics layers using sparse canonical correlation analysis (sCCA), including sample alignment, feature selection, network edge construction, and visualization of gene-metabolite relationships. The underlying methods are based on penalized matrix decomposition and sparse CCA (Witten, Tibshirani and Hastie (2009) <doi:10.1093/biostatistics/kxp008>), with design principles inspired by multivariate integrative frameworks such as mixOmics (Rohart et al. (2017) <doi:10.1371/journal.pcbi.1005752>).

Developed to help researchers who need to model the kinetics of carbon dioxide (CO2) production in alcoholic fermentation of wines, beers and other fermented products. The following models are available for modeling the carbon dioxide production curve as a function of time: 5PL, Gompertz and 4PL. This package has different functions, which applied can: perform the modeling of the data obtained in the fermentation and return the coefficients, analyze the model fit and return different statistical metrics, and calculate the kinetic parameters: Maximum production of carbon dioxide; Maximum rate of production of carbon dioxide; Moment in which maximum fermentation rate occurs; Duration of the latency phase for carbon dioxide production; Carbon dioxide produced until maximum fermentation rate occurs. In addition, a function that generates graphs with the observed and predicted data from the models, isolated and combined, is available. Gava, A., Borsato, D., & Ficagna, E. (2020)."Effect of mixture of fining agents on the fermentation kinetics of base wine for sparkling wine production: Use of methodology for modeling". <doi:10.1016/j.lwt.2020.109660>.

This package provides a method that analyzes quality control metrics from multi-sample genomic sequencing studies and nominates poor quality samples for exclusion. Per sample quality control data are transformed into z-scores and aggregated. The distribution of aggregated z-scores are modelled using parametric distributions. The parameters of the optimal model, selected either by goodness-of-fit statistics or user-designation, are used for outlier nomination. Two implementations of the Cosine Similarity Outlier Detection algorithm are provided with flexible parameters for dataset customization.

Open Location Codes <http://openlocationcode.com/> are a Google-created standard for identifying geographic locations. olctools provides utilities for validating, encoding and decoding entries that follow this standard.

We proposes a framework that provides real time support for early detection of anomalous series within a large collection of streaming time series data. By definition, anomalies are rare in comparison to a system's typical behaviour. We define an anomaly as an observation that is very unlikely given the forecast distribution. The algorithm first forecasts a boundary for the system's typical behaviour using a representative sample of the typical behaviour of the system. An approach based on extreme value theory is used for this boundary prediction process. Then a sliding window is used to test for anomalous series within the newly arrived collection of series. Feature based representation of time series is used as the input to the model. To cope with concept drift, the forecast boundary for the system's typical behaviour is updated periodically. More details regarding the algorithm can be found in Talagala, P. D., Hyndman, R. J., Smith-Miles, K., et al. (2019) <doi:10.1080/10618600.2019.1617160>.

Fits ordinal regression models with elastic net penalty. Supported model families include cumulative probability, stopping ratio, continuation ratio, and adjacent category. These families are a subset of vector glm's which belong to a model class we call the elementwise link multinomial-ordinal (ELMO) class. Each family in this class links a vector of covariates to a vector of class probabilities. Each of these families has a parallel form, which is appropriate for ordinal response data, as well as a nonparallel form that is appropriate for an unordered categorical response, or as a more flexible model for ordinal data. The parallel model has a single set of coefficients, whereas the nonparallel model has a set of coefficients for each response category except the baseline category. It is also possible to fit a model with both parallel and nonparallel terms, which we call the semi-parallel model. The semi-parallel model has the flexibility of the nonparallel model, but the elastic net penalty shrinks it toward the parallel model. For details, refer to Wurm, Hanlon, and Rathouz (2021) <doi:10.18637/jss.v099.i06>.

This package performs one-way tests in independent groups designs including homoscedastic and heteroscedastic tests. These are one-way analysis of variance (ANOVA), Welch's heteroscedastic F test, Welch's heteroscedastic F test with trimmed means and Winsorized variances, Brown-Forsythe test, Alexander-Govern test, James second order test, Kruskal-Wallis test, Scott-Smith test, Box F test, Johansen F test, Generalized tests equivalent to Parametric Bootstrap and Fiducial tests, Alvandi's F test, Alvandi's generalized p-value, approximate F test, B square test, Cochran test, Weerahandi's generalized F test, modified Brown-Forsythe test, adjusted Welch's heteroscedastic F test, Welch-Aspin test, Permutation F test. The package performs pairwise comparisons and graphical approaches. Also, the package includes Student's t test, Welch's t test and Mann-Whitney U test for two samples. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots (Dag et al., 2018, <https://journal.r-project.org/archive/2018/RJ-2018-022/RJ-2018-022.pdf>).

Implementation of optimistic optimization methods for global optimization of deterministic or stochastic functions. The algorithms feature guarantees of the convergence to a global optimum. They require minimal assumptions on the (only local) smoothness, where the smoothness parameter does not need to be known. They are expected to be useful for the most difficult functions when we have no information on smoothness and the gradients are unknown or do not exist. Due to the weak assumptions, however, they can be mostly effective only in small dimensions, for example, for hyperparameter tuning.

Intended to create standard human-in-the-loop validity tests for typical automated content analysis such as topic modeling and dictionary-based methods. This package offers a standard workflow with functions to prepare, administer and evaluate a human-in-the-loop validity test. This package provides functions for validating topic models using word intrusion, topic intrusion (Chang et al. 2009, <https://papers.nips.cc/paper/3700-reading-tea-leaves-how-humans-interpret-topic-models>) and word set intrusion (Ying et al. 2021) <doi:10.1017/pan.2021.33> tests. This package also provides functions for generating gold-standard data which are useful for validating dictionary-based methods. The default settings of all generated tests match those suggested in Chang et al. (2009) and Song et al. (2020) <doi:10.1080/10584609.2020.1723752>.

This package provides unified workflows for quality control, normalization, and visualization of proteomic and metabolomic data. The package simplifies preprocessing through automated imputation, scaling, and principal component analysis (PCA)-based exploratory analysis, enabling researchers to prepare omics datasets efficiently for downstream statistical and machine learning analyses.

This package provides functions for creating ensembles of optimal trees for regression, classification (Khan, Z., Gul, A., Perperoglou, A., Miftahuddin, M., Mahmoud, O., Adler, W., & Lausen, B. (2019). (2019) <doi:10.1007/s11634-019-00364-9>) and class membership probability estimation (Khan, Z, Gul, A, Mahmoud, O, Miftahuddin, M, Perperoglou, A, Adler, W & Lausen, B (2016) <doi:10.1007/978-3-319-25226-1_34>) are given. A few trees are selected from an initial set of trees grown by random forest for the ensemble on the basis of their individual and collective performance. Three different methods of tree selection for the case of classification are given. The prediction functions return estimates of the test responses and their class membership probabilities. Unexplained variations, error rates, confusion matrix, Brier scores, etc. are also returned for the test data.

Solves penalized least squares problems for big tall data using the orthogonalizing EM algorithm of Xiong et al. (2016) <doi:10.1080/00401706.2015.1054436>. The main fitting function is oem() and the functions cv.oem() and xval.oem() are for cross validation, the latter being an accelerated cross validation function for linear models. The big.oem() function allows for out of memory fitting. A description of the underlying methods and code interface is described in Huling and Chien (2022) <doi:10.18637/jss.v104.i06>.

This package provides a data set package with the "Orsi" and "Park/Durand" fronts as SpatialLinesDataFrame objects. The Orsi et al. (1995) fronts are published at the Southern Ocean Atlas Database Page, and the Park et al. (2019) fronts are published at the SEANOE Altimetry-derived Antarctic Circumpolar Current fronts page, please see package CITATION for details.

Simplified odds ratio calculation of GAM(M)s & GLM(M)s. Provides structured output (data frame) of all predictors and their corresponding odds ratios and confident intervals for further analyses. It helps to avoid false references of predictors and increments by specifying these parameters in a list instead of using exp(coef(model)) (standard approach of odds ratio calculation for GLMs) which just returns a plain numeric output. For GAM(M)s, odds ratio calculation is highly simplified with this package since it takes care of the multiple predict() calls of the chosen predictor while holding other predictors constant. Also, this package allows odds ratio calculation of percentage steps across the whole predictor distribution range for GAM(M)s. In both cases, confident intervals are returned additionally. Calculated odds ratio of GAM(M)s can be inserted into the smooth function plot.

This package implements the out-of-treatment testing from Kuelpmann and Kuzmics (2020) <doi:10.2139/ssrn.3441675> based on the Vuong Test introduced in Vuong (1989) <doi:10.2307/1912557>. Out-of treatment testing allows for a direct, pairwise likelihood comparison of theories, calibrated with pre-existing data.

This package provides a function for fitting various penalized Bayesian cumulative link ordinal response models when the number of parameters exceeds the sample size. These models have been described in Zhang and Archer (2021) <doi:10.1186/s12859-021-04432-w>.

Generating and validating One-time Password based on Hash-based Message Authentication Code (HOTP) and Time Based One-time Password (TOTP) according to RFC 4226 <https://datatracker.ietf.org/doc/html/rfc4226> and RFC 6238 <https://datatracker.ietf.org/doc/html/rfc6238>.

Incorporates functions for image preprocessing, filtering and image recognition. The package takes advantage of RcppArmadillo to speed up computationally intensive functions. The histogram of oriented gradients descriptor is a modification of the findHOGFeatures function of the SimpleCV computer vision platform, the average_hash(), dhash() and phash() functions are based on the ImageHash python library. The Gabor Feature Extraction functions are based on Matlab code of the paper, "CloudID: Trustworthy cloud-based and cross-enterprise biometric identification" by M. Haghighat, S. Zonouz, M. Abdel-Mottaleb, Expert Systems with Applications, vol. 42, no. 21, pp. 7905-7916, 2015, <doi:10.1016/j.eswa.2015.06.025>. The SLIC and SLICO superpixel algorithms were explained in detail in (i) "SLIC Superpixels Compared to State-of-the-art Superpixel Methods", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 34, num. 11, p. 2274-2282, May 2012, <doi:10.1109/TPAMI.2012.120> and (ii) "SLIC Superpixels", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, EPFL Technical Report no. 149300, June 2010.

This package implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. The methods implemented include InterVA4 by Byass et al (2012) <doi:10.3402/gha.v5i0.19281>, InterVA5 by Byass at al (2019) <doi:10.1186/s12916-019-1333-6>, InSilicoVA by McCormick et al (2016) <doi:10.1080/01621459.2016.1152191>, NBC by Miasnikof et al (2015) <doi:10.1186/s12916-015-0521-2>, and a replication of Tariff method by James et al (2011) <doi:10.1186/1478-7954-9-31> and Serina, et al. (2015) <doi:10.1186/s12916-015-0527-9>. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics. The NBC method is implemented by the nbc4va package that can be installed from <https://github.com/rrwen/nbc4va>. Note that this package was not developed by authors affiliated with the Institute for Health Metrics and Evaluation and thus unintentional discrepancies may exist in the implementation of the Tariff method.

Efficient Monte Carlo Algorithms for the price and the sensitivities of Asian and European Options under Geometric Brownian Motion.

Determine the sea area where the fishing boat operates. The latitude and longitude of geographic coordinates are used to match oceanic areas and economic sea areas. You can plot the distribution map with dotplot() function. Please refer to Flanders Marine Institute (2020) <doi:10.14284/403>.

The Ontario Marginalization Index is a socioeconomic model that is built on Statistics Canada census data. The model consists of four dimensions: In 2021, these dimensions were updated to "Material Resources" (previously called "Material Deprivation"), "Households and Dwellings" (previously called "Residential Instability"), "Age and Labour Force" (previously called "Dependency"), and "Racialized and Newcomer Populations" (previously called "Ethnic Concentration"). This update reflects a movement away from deficit-based language. 2021 data will load with these new dimension names, wheras 2011 and 2016 data will load with the historical dimension names. Each of these dimensions are imported for a variety of geographic levels (DA, CD, etc.) for the 2021, 2011 and 2016 administrations of the census. These data sets contribute to community analysis of equity with respect to Ontario's Anti-Racism Act. The Ontario Marginalization Index data is retrieved from the Public Health Ontario website: <https://www.publichealthontario.ca/en/data-and-analysis/health-equity/ontario-marginalization-index>. The shapefile data is retrieved from the Statistics Canada website: <https://www12.statcan.gc.ca/census-recensement/2011/geo/bound-limit/bound-limit-eng.cfm>.

This package provides an Interface to Open Collaboration Services OCS (<https://www.open-collaboration-services.org/>) REST API.