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      /\ \         /\ \ /\ \     /\_\      / /\
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      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
     / /_ \ \   / / /\ \ \\ \___/ /     / / /\ \___\
    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
   / / /  \/_// / /   / / / \ \ \        \ \ \
  / / /      / / /   / / /   \ \ \   _    \ \ \
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/_/ /      / / /____\/ /       \ \_\\ \/___/ /
\_\/       \/_________/         \/_/ \_____\/
r-onmarg 1.0.3
Propagated dependencies: r-stringr@1.5.1 r-sf@1.0-19 r-readxl@1.4.3 r-httr@1.4.7 r-dplyr@1.1.4
Channel: guix-cran
Location: guix-cran/packages/o.scm (guix-cran packages o)
Home page: https://cran.r-project.org/package=onmaRg
Licenses: GPL 3
Synopsis: Import Public Health Ontario's Ontario Marginalization Index
Description:

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>.

r-mega2r 1.1.0
Propagated dependencies: r-skat@2.2.5 r-rsqlite@2.3.7 r-rcpp@1.0.13-1 r-pedgene@3.9 r-kinship2@1.9.6.1 r-genomeinfodb@1.42.0 r-gdsfmt@1.42.0 r-famskatrc@1.1.0 r-dbi@1.2.3 r-annotationdbi@1.68.0
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://watson.hgen.pitt.edu/mega2/mega2r/
Licenses: GPL 2
Synopsis: Accessing and Processing a 'Mega2' Genetic Database
Description:

Uses as input genetic data that have been reformatted and stored in a SQLite database; this database is initially created by the standalone mega2 C++ program (available freely from <https://watson.hgen.pitt.edu/register/>). Loads and manipulates data frames containing genotype, phenotype, and family information from the input SQLite database, and decompresses needed subsets of the genotype data, on the fly, in a memory efficient manner. We have also created several more functions that illustrate how to use the data frames as well as perform useful tasks: these permit one to run the pedgene package to carry out gene-based association tests on family data using selected marker subsets, to run the SKAT package to carry out gene-based association tests using selected marker subsets, to run the famSKATRC package to carry out gene-based association tests on families (optionally) and with rare or common variants using selected marker subsets, to output the Mega2R data as a VCF file and related files (for phenotype and family data), and to convert the data frames into CoreArray Genomic Data Structure (GDS) format.

r-amelia 1.8.3
Propagated dependencies: r-rlang@1.1.4 r-rcpparmadillo@14.0.2-1 r-rcpp@1.0.13-1 r-foreign@0.8-87
Channel: guix-cran
Location: guix-cran/packages/a.scm (guix-cran packages a)
Home page: https://gking.harvard.edu/amelia
Licenses: GPL 2+
Synopsis: Program for Missing Data
Description:

This package provides a tool that "multiply imputes" missing data in a single cross-section (such as a survey), from a time series (like variables collected for each year in a country), or from a time-series-cross-sectional data set (such as collected by years for each of several countries). Amelia II implements our bootstrapping-based algorithm that gives essentially the same answers as the standard IP or EMis approaches, is usually considerably faster than existing approaches and can handle many more variables. Unlike Amelia I and other statistically rigorous imputation software, it virtually never crashes (but please let us know if you find to the contrary!). The program also generalizes existing approaches by allowing for trends in time series across observations within a cross-sectional unit, as well as priors that allow experts to incorporate beliefs they have about the values of missing cells in their data. Amelia II also includes useful diagnostics of the fit of multiple imputation models. The program works from the R command line or via a graphical user interface that does not require users to know R.

r-omegag 1.0.1
Channel: guix-cran
Location: guix-cran/packages/o.scm (guix-cran packages o)
Home page: https://cran.r-project.org/package=OmegaG
Licenses: GPL 2
Synopsis: Omega-Generic: Composite Reliability of Multidimensional Measures
Description:

It is a computer tool to estimate the item-sum score's reliability (composite reliability, CR) in multidimensional scales with overlapping items. An item that measures more than one domain construct is called an overlapping item. The estimation is based on factor models allowing unlimited cross-factor loadings such as exploratory structural equation modeling (ESEM) and Bayesian structural equation modeling (BSEM). The factor models include correlated-factor models and bi-factor models. Specifically for bi-factor models, a type of hierarchical factor model, the package estimates the CR hierarchical subscale/hierarchy and CR subscale/scale total. The CR estimator Omega-generic was proposed by Mai, Srivastava, and Krull (2021) <https://whova.com/embedded/subsession/enars_202103/1450751/1452993/>. The current version can only handle continuous data. Yujiao Mai contributes to the algorithms, R programming, and application example. Deo Kumar Srivastava contributes to the algorithms and the application example. Kevin R. Krull contributes to the application example. The package OmegaG was sponsored by American Lebanese Syrian Associated Charities (ALSAC). However, the contents of OmegaG do not necessarily represent the policy of the ALSAC.

r-spte2m 1.0.3
Propagated dependencies: r-rmarkdown@2.29 r-mass@7.3-61 r-maps@3.4.2.1 r-mapproj@1.2.11 r-knitr@1.49 r-glmnet@4.1-8 r-ggplot2@3.5.1
Channel: guix-cran
Location: guix-cran/packages/s.scm (guix-cran packages s)
Home page: https://cran.r-project.org/package=SpTe2M
Licenses: GPL 3+
Synopsis: Nonparametric Modeling and Monitoring of Spatio-Temporal Data
Description:

Spatio-temporal data have become increasingly popular in many research fields. Such data often have complex structures that are difficult to describe and estimate. This package provides reliable tools for modeling complicated spatio-temporal data. It also includes tools of online process monitoring to detect possible change-points in a spatio-temporal process over time. More specifically, the package implements the spatio-temporal mean estimation procedure described in Yang and Qiu (2018) <doi:10.1002/sim.7622>, the spatio-temporal covariance estimation procedure discussed in Yang and Qiu (2019) <doi:10.1002/sim.8315>, the three-step method for the joint estimation of spatio-temporal mean and covariance functions suggested by Yang and Qiu (2022) <doi:10.1007/s10463-021-00787-2>, the spatio-temporal disease surveillance method discussed in Qiu and Yang (2021) <doi:10.1002/sim.9150> that can accommodate the covariate effect, the spatial-LASSO-based process monitoring method proposed by Qiu and Yang (2023) <doi:10.1080/00224065.2022.2081104>, and the online spatio-temporal disease surveillance method described in Yang and Qiu (2020) <doi:10.1080/24725854.2019.1696496>.

r-eyeris 1.0.0
Propagated dependencies: r-zoo@1.8-12 r-withr@3.0.2 r-tidyr@1.3.1 r-stringr@1.5.1 r-rlang@1.1.4 r-purrr@1.0.2 r-progress@1.2.3 r-gsignal@0.3-7 r-eyelinker@0.2.1 r-dplyr@1.1.4 r-data-table@1.16.2 r-cli@3.6.3
Channel: guix-cran
Location: guix-cran/packages/e.scm (guix-cran packages e)
Home page: https://shawnschwartz.com/eyeris/
Licenses: Expat
Synopsis: Flexible, Extensible, & Reproducible Processing of Pupil Data
Description:

Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states (see Clewett et al., 2020 <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie, 2018 <doi:10.3758/s13428-018-1075-y>; Strauch, 2024 <doi:10.1016/j.tins.2024.06.002>). Yet, despite decades of pupillometry research, many established packages and workflows to date unfortunately lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles (see Wilkinson et al., 2016 <doi:10.1038/sdata.2016.18> for more information). eyeris', on the other hand, follows a design philosophy that provides users with an intuitive, modular, performant, and extensible pupillometry data preprocessing framework out-of-the-box. eyeris introduces a Brain Imaging Data Structure (BIDS)-like organization for derivative (i.e., preprocessed) pupillometry data as well as an intuitive workflow for inspecting preprocessed pupil epochs using interactive output report files (Esteban et al., 2019 <doi:10.1038/s41592-018-0235-4>; Gorgolewski et al., 2016 <doi:10.1038/sdata.2016.44>).

r-export 0.3.0
Propagated dependencies: r-xtable@1.8-4 r-xml2@1.3.6 r-stargazer@5.2.3 r-rvg@0.3.5 r-rgl@1.3.12 r-openxlsx@4.2.7.1 r-officer@0.6.7 r-flextable@0.9.7 r-devemf@4.5-1 r-broom@1.0.7
Channel: guix-cran
Location: guix-cran/packages/e.scm (guix-cran packages e)
Home page: https://cran.r-project.org/package=export
Licenses: GPL 2
Synopsis: Streamlined Export of Graphs and Data Tables
Description:

Easily export R graphs and statistical output to Microsoft Office / LibreOffice', Latex and HTML Documents, using sensible defaults that result in publication-quality output with simple, straightforward commands. Output to Microsoft Office is in editable DrawingML vector format for graphs, and can use corporate template documents for styling. This enables the production of standardized reports and also allows for manual tidy-up of the layout of R graphs in Powerpoint before final publication. Export of graphs is flexible, and functions enable the currently showing R graph or the currently showing R stats object to be exported, but also allow the graphical or tabular output to be passed as objects. The package relies on package officer for export to Office documents,and output files are also fully compatible with LibreOffice'. Base R', ggplot2 and lattice plots are supported, as well as a wide variety of R stats objects, via wrappers to xtable(), broom::tidy() and stargazer(), including aov(), lm(), glm(), lme(), glmnet() and coxph() as well as matrices and data frames and many more...

r-gldreg 1.1.1
Propagated dependencies: r-gldex@2.0.0.9.3 r-ddst@1.4
Channel: guix-cran
Location: guix-cran/packages/g.scm (guix-cran packages g)
Home page: https://cran.r-project.org/package=GLDreg
Licenses: GPL 3+
Synopsis: Fit GLD Regression/Quantile/AFT Model to Data
Description:

Owing to the rich shapes of Generalised Lambda Distributions (GLDs), GLD standard/quantile/Accelerated Failure Time (AFT) regression is a competitive flexible model compared to standard/quantile/AFT regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. For AFT model, it also eliminates the needs to try several different AFT models, owing to the flexible shapes of GLD. The goodness of fit of the proposed model can be assessed via QQ plots and Kolmogorov-Smirnov tests and data driven smooth test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly from simulated data. References include the following: Su (2015) "Flexible Parametric Quantile Regression Model" <doi:10.1007/s11222-014-9457-1>, Su (2021) "Flexible parametric accelerated failure time model"<doi:10.1080/10543406.2021.1934854>.

r-protag 1.0.0
Propagated dependencies: r-rcolorbrewer@1.1-3 r-ggplot2@3.5.1 r-dplyr@1.1.4
Channel: guix-cran
Location: guix-cran/packages/p.scm (guix-cran packages p)
Home page: https://cran.r-project.org/package=protag
Licenses: GPL 2
Synopsis: Search Tagged Peptides & Draw Highlighted Mass Spectra
Description:

In a typical protein labelling procedure, proteins are chemically tagged with a functional group, usually at specific sites, then digested into peptides, which are then analyzed using matrix-assisted laser desorption ionization - time of flight mass spectrometry (MALDI-TOF MS) to generate peptide fingerprint. Relative to the control, peptides that are heavier by the mass of the labelling group are informative for sequence determination. Searching for peptides with such mass shifts, however, can be difficult. This package, designed to tackle this inconvenience, takes as input the mass list of two or multiple MALDI-TOF MS mass lists, and makes pairwise comparisons between the labeled groups vs. control, and restores centroid mass spectra with highlighted peaks of interest for easier visual examination. Particularly, peaks differentiated by the mass of the labelling group are defined as a â pairâ , those with equal masses as a â matchâ , and all the other peaks as a â mismatchâ .For more bioanalytical background information, refer to following publications: Jingjing Deng (2015) <doi:10.1007/978-1-4939-2550-6_19>; Elizabeth Chang (2016) <doi:10.7171/jbt.16-2702-002>.

r-braggr 0.1.1
Propagated dependencies: r-rcpp@1.0.13-1
Channel: guix-cran
Location: guix-cran/packages/b.scm (guix-cran packages b)
Home page: https://cran.r-project.org/package=braggR
Licenses: GPL 2
Synopsis: Calculate the Revealed Aggregator of Probability Predictions
Description:

Forecasters predicting the chances of a future event may disagree due to differing evidence or noise. To harness the collective evidence of the crowd, Ville Satopää (2021) "Regularized Aggregation of One-off Probability Predictions" <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3769945> proposes a Bayesian aggregator that is regularized by analyzing the forecasters disagreement and ascribing over-dispersion to noise. This aggregator requires no user intervention and can be computed efficiently even for a large numbers of predictions. The author evaluates the aggregator on subjective probability predictions collected during a four-year forecasting tournament sponsored by the US intelligence community. The aggregator improves the accuracy of simple averaging by around 20% and other state-of-the-art aggregators by 10-25%. The advantage stems almost exclusively from improved calibration. This aggregator -- know as "the revealed aggregator" -- inputs a) forecasters probability predictions (p) of a future binary event and b) the forecasters common prior (p0) of the future event. In this R-package, the function sample_aggregator(p,p0,...) allows the user to calculate the revealed aggregator. Its use is illustrated with a simple example.

r-dmrnet 0.4.0
Propagated dependencies: r-hclust1d@0.1.1 r-grpreg@3.5.0 r-glmnet@4.1-8
Channel: guix-cran
Location: guix-cran/packages/d.scm (guix-cran packages d)
Home page: https://github.com/SzymonNowakowski/DMRnet
Licenses: GPL 2
Synopsis: Delete or Merge Regressors Algorithms for Linear and Logistic Model Selection and High-Dimensional Data
Description:

Model selection algorithms for regression and classification, where the predictors can be continuous or categorical and the number of regressors may exceed the number of observations. The selected model consists of a subset of numerical regressors and partitions of levels of factors. Szymon Nowakowski, Piotr Pokarowski, Wojciech Rejchel and Agnieszka SoÅ tys, 2023. Improving Group Lasso for High-Dimensional Categorical Data. In: Computational Science â ICCS 2023. Lecture Notes in Computer Science, vol 14074, p. 455-470. Springer, Cham. <doi:10.1007/978-3-031-36021-3_47>. Aleksandra Maj-KaÅ ska, Piotr Pokarowski and Agnieszka Prochenka, 2015. Delete or merge regressors for linear model selection. Electronic Journal of Statistics 9(2): 1749-1778. <doi:10.1214/15-EJS1050>. Piotr Pokarowski and Jan Mielniczuk, 2015. Combined l1 and greedy l0 penalized least squares for linear model selection. Journal of Machine Learning Research 16(29): 961-992. <https://www.jmlr.org/papers/volume16/pokarowski15a/pokarowski15a.pdf>. Piotr Pokarowski, Wojciech Rejchel, Agnieszka SoÅ tys, MichaÅ Frej and Jan Mielniczuk, 2022. Improving Lasso for model selection and prediction. Scandinavian Journal of Statistics, 49(2): 831â 863. <doi:10.1111/sjos.12546>.

r-dtwumi 1.0
Propagated dependencies: r-rlist@0.4.6.2 r-lsa@0.73.3 r-entropy@1.3.1 r-e1071@1.7-16 r-dtwbi@1.1 r-dtw@1.23-1
Channel: guix-cran
Location: guix-cran/packages/d.scm (guix-cran packages d)
Home page: http://mawenzi.univ-littoral.fr/DTWUMI/
Licenses: GPL 2+
Synopsis: Imputation of Multivariate Time Series Based on Dynamic Time Warping
Description:

This package provides functions to impute large gaps within multivariate time series based on Dynamic Time Warping methods. Gaps of size 1 or inferior to a defined threshold are filled using simple average and weighted moving average respectively. Larger gaps are filled using the methodology provided by Phan et al. (2017) <DOI:10.1109/MLSP.2017.8168165>: a query is built immediately before/after a gap and a moving window is used to find the most similar sequence to this query using Dynamic Time Warping. To lower the calculation time, similar sequences are pre-selected using global features. Contrary to the univariate method (package DTWBI'), these global features are not estimated over the sequence containing the gap(s), but a feature matrix is built to summarize general features of the whole multivariate signal. Once the most similar sequence to the query has been identified, the adjacent sequence to this window is used to fill the gap considered. This function can deal with multiple gaps over all the sequences componing the input multivariate signal. However, for better consistency, large gaps at the same location over all sequences should be avoided.

r-seagle 1.0.1
Propagated dependencies: r-matrix@1.7-1 r-compquadform@1.4.3
Channel: guix-cran
Location: guix-cran/packages/s.scm (guix-cran packages s)
Home page: https://github.com/jocelynchi/SEAGLE
Licenses: GPL 3
Synopsis: Scalable Exact Algorithm for Large-Scale Set-Based Gene-Environment Interaction Tests
Description:

The explosion of biobank data offers immediate opportunities for gene-environment (GxE) interaction studies of complex diseases because of the large sample sizes and rich collection in genetic and non-genetic information. However, the extremely large sample size also introduces new computational challenges in GxE assessment, especially for set-based GxE variance component (VC) tests, a widely used strategy to boost overall GxE signals and to evaluate the joint GxE effect of multiple variants from a biologically meaningful unit (e.g., gene). We present SEAGLE', a Scalable Exact AlGorithm for Large-scale Set-based GxE tests, to permit GxE VC test scalable to biobank data. SEAGLE employs modern matrix computations to achieve the same â exactâ results as the original GxE VC tests, and does not impose additional assumptions nor relies on approximations. SEAGLE can easily accommodate sample sizes in the order of 10^5, is implementable on standard laptops, and does not require specialized equipment. The accompanying manuscript for this package can be found at Chi, Ipsen, Hsiao, Lin, Wang, Lee, Lu, and Tzeng. (2021+) <arXiv:2105.03228>.

r-klovan 0.1.0
Propagated dependencies: r-tidyselect@1.2.1 r-tibble@3.2.1 r-sp@2.1-4 r-pracma@2.4.4 r-metr@0.18.0 r-mass@7.3-61 r-magrittr@2.0.3 r-gstat@2.1-2 r-ggrepel@0.9.6 r-ggplot2@3.5.1 r-ggforce@0.4.2 r-ggally@2.2.1 r-fields@16.3 r-dplyr@1.1.4
Channel: guix-cran
Location: guix-cran/packages/k.scm (guix-cran packages k)
Home page: https://cran.r-project.org/package=klovan
Licenses: Expat
Synopsis: Geostatistics Methods and Klovan Data
Description:

This package provides a comprehensive set of geostatistical, visual, and analytical methods, in conjunction with the expanded version of the acclaimed J.E. Klovan's mining dataset, are included in klovan'. This makes the package an excellent learning resource for Principal Component Analysis (PCA), Factor Analysis (FA), kriging, and other geostatistical techniques. Originally published in the 1976 book Geological Factor Analysis', the included mining dataset was assembled by Professor J. E. Klovan of the University of Calgary. Being one of the first applications of FA in the geosciences, this dataset has significant historical importance. As a well-regarded and published dataset, it is an excellent resource for demonstrating the capabilities of PCA, FA, kriging, and other geostatistical techniques in geosciences. For those interested in these methods, the klovan datasets provide a valuable and illustrative resource. Note that some methods require the RGeostats package. Please refer to the README or Additional_repositories for installation instructions. This material is based upon research in the Materials Data Science for Stockpile Stewardship Center of Excellence (MDS3-COE), and supported by the Department of Energy's National Nuclear Security Administration under Award Number DE-NA0004104.

r-deepgp 1.1.3
Propagated dependencies: r-rcpparmadillo@14.0.2-1 r-rcpp@1.0.13-1 r-mvtnorm@1.3-2 r-matrix@1.7-1 r-gpgp@0.5.1 r-foreach@1.5.2 r-fnn@1.1.4.1 r-doparallel@1.0.17
Channel: guix-cran
Location: guix-cran/packages/d.scm (guix-cran packages d)
Home page: https://cran.r-project.org/package=deepgp
Licenses: LGPL 2.0+
Synopsis: Bayesian Deep Gaussian Processes using MCMC
Description:

This package performs Bayesian posterior inference for deep Gaussian processes following Sauer, Gramacy, and Higdon (2023, <doi:10.48550/arXiv.2012.08015>). See Sauer (2023, <http://hdl.handle.net/10919/114845>) for comprehensive methodological details and <https://bitbucket.org/gramacylab/deepgp-ex/> for a variety of coding examples. Models are trained through MCMC including elliptical slice sampling of latent Gaussian layers and Metropolis-Hastings sampling of kernel hyperparameters. Vecchia-approximation for faster computation is implemented following Sauer, Cooper, and Gramacy (2023, <doi:10.48550/arXiv.2204.02904>). Optional monotonic warpings are implemented following Barnett et al. (2024, <doi:10.48550/arXiv.2408.01540>). Downstream tasks include sequential design through active learning Cohn/integrated mean squared error (ALC/IMSE; Sauer, Gramacy, and Higdon, 2023), optimization through expected improvement (EI; Gramacy, Sauer, and Wycoff, 2022 <doi:10.48550/arXiv.2112.07457>), and contour location through entropy (Booth, Renganathan, and Gramacy, 2024 <doi:10.48550/arXiv.2308.04420>). Models extend up to three layers deep; a one layer model is equivalent to typical Gaussian process regression. Incorporates OpenMP and SNOW parallelization and utilizes C/C++ under the hood.

r-incdtw 1.1.4.4
Propagated dependencies: r-scales@1.3.0 r-rcppparallel@5.1.9 r-rcpparmadillo@14.0.2-1 r-rcpp@1.0.13-1 r-ggplot2@3.5.1 r-data-table@1.16.2
Channel: guix-cran
Location: guix-cran/packages/i.scm (guix-cran packages i)
Home page: https://cran.r-project.org/package=IncDTW
Licenses: GPL 2+
Synopsis: Incremental Calculation of Dynamic Time Warping
Description:

The Dynamic Time Warping (DTW) distance measure for time series allows non-linear alignments of time series to match similar patterns in time series of different lengths and or different speeds. IncDTW is characterized by (1) the incremental calculation of DTW (reduces runtime complexity to a linear level for updating the DTW distance) - especially for life data streams or subsequence matching, (2) the vector based implementation of DTW which is faster because no matrices are allocated (reduces the space complexity from a quadratic to a linear level in the number of observations) - for all runtime intensive DTW computations, (3) the subsequence matching algorithm runDTW, that efficiently finds the k-NN to a query pattern in a long time series, and (4) C++ in the heart. For details about DTW see the original paper "Dynamic programming algorithm optimization for spoken word recognition" by Sakoe and Chiba (1978) <DOI:10.1109/TASSP.1978.1163055>. For details about this package, Dynamic Time Warping and Incremental Dynamic Time Warping please see "IncDTW: An R Package for Incremental Calculation of Dynamic Time Warping" by Leodolter et al. (2021) <doi:10.18637/jss.v099.i09>.

r-carrot 3.0.2
Propagated dependencies: r-rdpack@2.6.1 r-nnet@7.3-19 r-foreach@1.5.2 r-doparallel@1.0.17
Channel: guix-cran
Location: guix-cran/packages/c.scm (guix-cran packages c)
Home page: https://cran.r-project.org/package=CARRoT
Licenses: GPL 2
Synopsis: Predicting Categorical and Continuous Outcomes Using One in Ten Rule
Description:

Predicts categorical or continuous outcomes while concentrating on a number of key points. These are Cross-validation, Accuracy, Regression and Rule of Ten or "one in ten rule" (CARRoT), and, in addition to it R-squared statistics, prior knowledge on the dataset etc. It performs the cross-validation specified number of times by partitioning the input into training and test set and fitting linear/multinomial/binary regression models to the training set. All regression models satisfying chosen constraints are fitted and the ones with the best predictive power are given as an output. Best predictive power is understood as highest accuracy in case of binary/multinomial outcomes, smallest absolute and relative errors in case of continuous outcomes. For binary case there is also an option of finding a regression model which gives the highest AUROC (Area Under Receiver Operating Curve) value. The option of parallel toolbox is also available. Methods are described in Peduzzi et al. (1996) <doi:10.1016/S0895-4356(96)00236-3> , Rhemtulla et al. (2012) <doi:10.1037/a0029315>, Riley et al. (2018) <doi:10.1002/sim.7993>, Riley et al. (2019) <doi:10.1002/sim.7992>.

r-dmcfun 4.0.1
Propagated dependencies: r-tidyr@1.3.1 r-rcpp@1.0.13-1 r-pbapply@1.7-2 r-dplyr@1.1.4 r-deoptim@2.2-8 r-bh@1.84.0-0
Channel: guix-cran
Location: guix-cran/packages/d.scm (guix-cran packages d)
Home page: https://github.com/igmmgi/DMCfun
Licenses: Expat
Synopsis: Diffusion Model of Conflict (DMC) in Reaction Time Tasks
Description:

DMC model simulation detailed in Ulrich, R., Schroeter, H., Leuthold, H., & Birngruber, T. (2015). Automatic and controlled stimulus processing in conflict tasks: Superimposed diffusion processes and delta functions. Cognitive Psychology, 78, 148-174. Ulrich et al. (2015) <doi:10.1016/j.cogpsych.2015.02.005>. Decision processes within choice reaction-time (CRT) tasks are often modelled using evidence accumulation models (EAMs), a variation of which is the Diffusion Decision Model (DDM, for a review, see Ratcliff & McKoon, 2008). Ulrich et al. (2015) introduced a Diffusion Model for Conflict tasks (DMC). The DMC model combines common features from within standard diffusion models with the addition of superimposed controlled and automatic activation. The DMC model is used to explain distributional reaction time (and error rate) patterns in common behavioural conflict-like tasks (e.g., Flanker task, Simon task). This R-package implements the DMC model and provides functionality to fit the model to observed data. Further details are provided in the following paper: Mackenzie, I.G., & Dudschig, C. (2021). DMCfun: An R package for fitting Diffusion Model of Conflict (DMC) to reaction time and error rate data. Methods in Psychology, 100074. <doi:10.1016/j.metip.2021.100074>.

r-mmtsne 0.1.0
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=mmtsne
Licenses: FSDG-compatible FSDG-compatible
Synopsis: Multiple Maps t-SNE
Description:

An implementation of multiple maps t-distributed stochastic neighbor embedding (t-SNE). Multiple maps t-SNE is a method for projecting high-dimensional data into several low-dimensional maps such that non-metric space properties are better preserved than they would be by a single map. Multiple maps t-SNE with only one map is equivalent to standard t-SNE. When projecting onto more than one map, multiple maps t-SNE estimates a set of latent weights that allow each point to contribute to one or more maps depending on similarity relationships in the original data. This implementation is a port of the original Matlab library by Laurens van der Maaten. See Van der Maaten and Hinton (2012) <doi:10.1007/s10994-011-5273-4>. This material is based upon work supported by the United States Air Force and Defense Advanced Research Project Agency (DARPA) under Contract No. FA8750-17-C-0020. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the United States Air Force and Defense Advanced Research Projects Agency. Distribution Statement A: Approved for Public Release; Distribution Unlimited.

r-lrcell 1.14.0
Propagated dependencies: r-magrittr@2.0.3 r-ggrepel@0.9.6 r-ggplot2@3.5.1 r-experimenthub@2.14.0 r-dplyr@1.1.4 r-biocparallel@1.40.0 r-annotationhub@3.14.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/LRcell
Licenses: Expat
Synopsis: Differential cell type change analysis using Logistic/linear Regression
Description:

The goal of LRcell is to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. To achieve this, LRcell utilizes sets of cell marker genes acquired from single-cell RNA-sequencing (scRNA-seq) as indicators for various cell types in the tissue of interest. Next, for each cell type, using its marker genes as indicators, we apply Logistic Regression on the complete set of genes with differential expression p-values to calculate a cell-type significance p-value. Finally, these p-values are compared to predict which one(s) are likely to be responsible for the differential gene expression pattern observed in the bulk RNA-seq experiments. LRcell is inspired by the LRpath[@sartor2009lrpath] algorithm developed by Sartor et al., originally designed for pathway/gene set enrichment analysis. LRcell contains three major components: LRcell analysis, plot generation and marker gene selection. All modules in this package are written in R. This package also provides marker genes in the Prefrontal Cortex (pFC) human brain region, human PBMC and nine mouse brain regions (Frontal Cortex, Cerebellum, Globus Pallidus, Hippocampus, Entopeduncular, Posterior Cortex, Striatum, Substantia Nigra and Thalamus).

r-granie 1.10.0
Propagated dependencies: r-viridis@0.6.5 r-topgo@2.58.0 r-tidyselect@1.2.1 r-tidyr@1.3.1 r-tibble@3.2.1 r-summarizedexperiment@1.36.0 r-stringr@1.5.1 r-scales@1.3.0 r-s4vectors@0.44.0 r-rlang@1.1.4 r-reshape2@1.4.4 r-readr@2.1.5 r-rcolorbrewer@1.1-3 r-progress@1.2.3 r-patchwork@1.3.0 r-matrixstats@1.4.1 r-matrix@1.7-1 r-magrittr@2.0.3 r-limma@3.62.1 r-igraph@2.1.1 r-gridextra@2.3 r-ggplot2@3.5.1 r-genomicranges@1.58.0 r-genomeinfodb@1.42.0 r-futile-logger@1.4.3 r-forcats@1.0.0 r-ensembldb@2.30.0 r-dplyr@1.1.4 r-deseq2@1.46.0 r-data-table@1.16.2 r-complexheatmap@2.22.0 r-colorspace@2.1-1 r-circlize@0.4.16 r-checkmate@2.3.2 r-biostrings@2.74.0 r-biomart@2.62.0 r-annotationhub@3.14.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://grp-zaugg.embl-community.io/GRaNIE
Licenses: Artistic License 2.0
Synopsis: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data
Description:

Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have cell-type specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using single-cell or bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally (Capture) Hi-C data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach.

r-amnlfa 1.1.2
Propagated dependencies: r-stringr@1.5.1 r-stringi@1.8.4 r-reshape2@1.4.4 r-plyr@1.8.9 r-mplusautomation@1.1.1 r-gridextra@2.3 r-ggplot2@3.5.1 r-dplyr@1.1.4 r-devtools@2.4.5
Channel: guix-cran
Location: guix-cran/packages/a.scm (guix-cran packages a)
Home page: https://cran.r-project.org/package=aMNLFA
Licenses: GPL 2
Synopsis: Automated Moderated Nonlinear Factor Analysis Using 'M-plus'
Description:

Automated generation, running, and interpretation of moderated nonlinear factor analysis models for obtaining scores from observed variables, using the method described by Gottfredson and colleagues (2019) <doi:10.1016/j.addbeh.2018.10.031>. This package creates M-plus input files which may be run iteratively to test two different types of covariate effects on items: (1) latent variable impact (both mean and variance); and (2) differential item functioning. After sequentially testing for all effects, it also creates a final model by including all significant effects after adjusting for multiple comparisons. Finally, the package creates a scoring model which uses the final values of parameter estimates to generate latent variable scores. \n\n This package generates TEMPLATES for M-plus inputs, which can and should be inspected, altered, and run by the user. In addition to being presented without warranty of any kind, the package is provided under the assumption that everyone who uses it is reading, interpreting, understanding, and altering every M-plus input and output file. There is no one right way to implement moderated nonlinear factor analysis, and this package exists solely to save users time as they generate M-plus syntax according to their own judgment.

r-whatif 1.5-10
Propagated dependencies: r-pbmcapply@1.5.1 r-lpsolve@5.6.22
Channel: guix-cran
Location: guix-cran/packages/w.scm (guix-cran packages w)
Home page: https://gking.harvard.edu/whatif
Licenses: GPL 3+
Synopsis: Software for Evaluating Counterfactuals
Description:

Inferences about counterfactuals are essential for prediction, answering what if questions, and estimating causal effects. However, when the counterfactuals posed are too far from the data at hand, conclusions drawn from well-specified statistical analyses become based largely on speculation hidden in convenient modeling assumptions that few would be willing to defend. Unfortunately, standard statistical approaches assume the veracity of the model rather than revealing the degree of model-dependence, which makes this problem hard to detect. WhatIf offers easy-to-apply methods to evaluate counterfactuals that do not require sensitivity testing over specified classes of models. If an analysis fails the tests offered here, then we know that substantive inferences will be sensitive to at least some modeling choices that are not based on empirical evidence, no matter what method of inference one chooses to use. WhatIf implements the methods for evaluating counterfactuals discussed in Gary King and Langche Zeng, 2006, "The Dangers of Extreme Counterfactuals," Political Analysis 14 (2) <DOI:10.1093/pan/mpj004>; and Gary King and Langche Zeng, 2007, "When Can History Be Our Guide? The Pitfalls of Counterfactual Inference," International Studies Quarterly 51 (March) <DOI:10.1111/j.1468-2478.2007.00445.x>.

r-orders 0.1.8
Propagated dependencies: r-vgam@1.1-12 r-newdistns@2.1 r-gamlss-dist@6.1-1 r-actuar@3.3-4
Channel: guix-cran
Location: guix-cran/packages/o.scm (guix-cran packages o)
Home page: https://cran.r-project.org/package=orders
Licenses: GPL 3
Synopsis: Sampling from k-th Order Statistics of New Families of Distributions
Description:

Set of tools to generate samples of k-th order statistics and others quantities of interest from new families of distributions. The main references for this package are: C. Kleiber and S. Kotz (2003) Statistical size distributions in economics and actuarial sciences; Gentle, J. (2009), Computational Statistics, Springer-Verlag; Naradajah, S. and Rocha, R. (2016), <DOI:10.18637/jss.v069.i10> and Stasinopoulos, M. and Rigby, R. (2015), <DOI:10.1111/j.1467-9876.2005.00510.x>. The families of distributions are: Benini distributions, Burr distributions, Dagum distributions, Feller-Pareto distributions, Generalized Pareto distributions, Inverse Pareto distributions, The Inverse Paralogistic distributions, Marshall-Olkin G distributions, exponentiated G distributions, beta G distributions, gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions, beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions, exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modified beta G distributions, exponentiated exponential Poisson G distributions, Poisson-inverse gaussian distributions, Skew normal type 1 distributions, Skew student t distributions, Singh-Maddala distributions, Sinh-Arcsinh distributions, Sichel distributions, Zero inflated Poisson distributions.

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