Showing 31 of total 31 results (show query)
stemangiola
tidyHeatmap:A Tidy Implementation of Heatmap
This is a tidy implementation for heatmap. At the moment it is based on the (great) package 'ComplexHeatmap'. The goal of this package is to interface a tidy data frame with this powerful tool. Some of the advantages are: Row and/or columns colour annotations are easy to integrate just specifying one parameter (column names). Custom grouping of rows is easy to specify providing a grouped tbl. For example: df %>% group_by(...). Labels size adjusted by row and column total number. Default use of Brewer and Viridis palettes.
Maintained by Stefano Mangiola. Last updated 1 months ago.
assaydomaininfrastructurebrewercomplexheatmapcustom-palettedplyrgraphvizheatmapmtcarsplottingrstudioscaletibbletidytidy-data-frametidybulktidyverseviridis
11.0 match 335 stars 10.23 score 197 scripts 1 dependents
bioc
Rgraphviz:Provides plotting capabilities for R graph objects
Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.
Maintained by Kasper Daniel Hansen. Last updated 4 days ago.
graphandnetworkvisualizationzlib
8.1 match 10.14 score 1.2k scripts 109 dependents
tbates
umx:Structural Equation Modeling and Twin Modeling in R
Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Maintained by Timothy C. Bates. Last updated 2 days ago.
behavior-geneticsgeneticsopenmxpsychologysemstatisticsstructural-equation-modelingtutorialstwin-modelsumx
5.3 match 44 stars 9.45 score 472 scripts
statnet
ndtv:Network Dynamic Temporal Visualizations
Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Maintained by Skye Bender-deMoll. Last updated 9 months ago.
5.3 match 52 stars 8.36 score 254 scripts 1 dependents
david-cortes
isotree:Isolation-Based Outlier Detection
Fast and multi-threaded implementation of isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>), extended isolation forest (Hariri, Kind, Brunner (2018) <doi:10.48550/arXiv.1811.02141>), SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>), fair-cut forest (Cortes (2021) <doi:10.48550/arXiv.2110.13402>), robust random-cut forest (Guha, Mishra, Roy, Schrijvers (2016) <http://proceedings.mlr.press/v48/guha16.html>), and customizable variations of them, for isolation-based outlier detection, clustered outlier detection, distance or similarity approximation (Cortes (2019) <doi:10.48550/arXiv.1910.12362>), isolation kernel calculation (Ting, Zhu, Zhou (2018) <doi:10.1145/3219819.3219990>), and imputation of missing values (Cortes (2019) <doi:10.48550/arXiv.1911.06646>), based on random or guided decision tree splitting, and providing different metrics for scoring anomalies based on isolation depth or density (Cortes (2021) <doi:10.48550/arXiv.2111.11639>). Provides simple heuristics for fitting the model to categorical columns and handling missing data, and offers options for varying between random and guided splits, and for using different splitting criteria.
Maintained by David Cortes. Last updated 14 days ago.
anomaly-detectionimputationisolation-forestoutlier-detectioncppopenmp
4.0 match 203 stars 10.41 score 115 scripts 6 dependents
rich-iannone
DiagrammeRsvg:Export DiagrammeR Graphviz Graphs as SVG
Allows for export of DiagrammeR Graphviz objects to SVG.
Maintained by Richard Iannone. Last updated 5 years ago.
3.6 match 29 stars 9.56 score 462 scripts 18 dependents
jinghuazhao
gap:Genetic Analysis Package
As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).
Maintained by Jing Hua Zhao. Last updated 16 days ago.
2.0 match 12 stars 11.88 score 448 scripts 16 dependents
gluc
data.tree:General Purpose Hierarchical Data Structure
Create tree structures from hierarchical data, and traverse the tree in various orders. Aggregate, cumulate, print, plot, convert to and from data.frame and more. Useful for decision trees, machine learning, finance, conversion from and to JSON, and many other applications.
Maintained by Christoph Glur. Last updated 5 months ago.
1.7 match 209 stars 12.84 score 1.1k scripts 88 dependents
d-gaspar
grPipe:Graphviz Pipeline Plot Based on Grids (grPipe: Graphviz Pipeline)
Create a grid-based graphviz using the following functions: 1 - Creating the data.frame where the nodes are; 2 - Adding and editing nodes; 3 - Plotting these nodes.
Maintained by Daniel Gaspar Gonçalves. Last updated 3 years ago.
6.9 match 2.70 score
yannabraham
Radviz:Project Multidimensional Data in 2D Space
An implementation of the radviz projection in R. It enables the visualization of multidimensional data while maintaining the relation to the original dimensions. This package provides functions to create and plot radviz projections, and a number of summary plots that enable comparison and analysis. For reference see Ankerst *et al.* (1996) (<https://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.68.1811>) for original implementation, see Di Caro *et al* (2012) (<https://link.springer.com/chapter/10.1007/978-3-642-13672-6_13>) for the original method for dimensional anchor arrangements, see Demsar *et al.* (2007) (<doi:10.1016/j.jbi.2007.03.010>) for the original Freeviz implementation.
Maintained by Yann Abraham. Last updated 3 years ago.
high-dimensional-dataradvizsciencevisualizationcpp
2.9 match 10 stars 6.19 score 52 scripts
peleplay
integr:An Implementation of Interaction Graphs of Aleks Jakulin
Generates a 'Graphviz' graph of the most significant 3-way interaction gains (i.e. conditional information gains) based on a provided discrete data frame. Various output formats are supported ('Graphviz', SVG, PNG, PDF, PS). For references, see the webpage of Aleks Jakulin <http://stat.columbia.edu/~jakulin/Int/>.
Maintained by Petar Markovic. Last updated 6 years ago.
3.8 match 3 stars 4.18 score 3 scripts
terminological
dtrackr:Track your Data Pipelines
Track and document 'dplyr' data pipelines. As you filter, mutate, and join your way through a data set, 'dtrackr' seamlessly keeps track of your data flow and makes publication ready documentation of a data pipeline simple.
Maintained by Robert Challen. Last updated 5 months ago.
1.8 match 69 stars 8.78 score 362 scripts 1 dependents
handcock
RDS:Respondent-Driven Sampling
Provides functionality for carrying out estimation with data collected using Respondent-Driven Sampling. This includes Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential Sampling estimator. The package is part of the "RDS Analyst" suite of packages for the analysis of respondent-driven sampling data. See Gile and Handcock (2010) <doi:10.1111/j.1467-9531.2010.01223.x>, Gile and Handcock (2015) <doi:10.1111/rssa.12091> and Gile, Beaudry, Handcock and Ott (2018) <doi:10.1146/annurev-statistics-031017-100704>.
Maintained by Mark S. Handcock. Last updated 6 months ago.
3.9 match 1 stars 3.87 score 82 scripts 3 dependentsbioc
veloviz:VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
VeloViz uses each cell’s current observed and predicted future transcriptional states inferred from RNA velocity analysis to build a nearest neighbor graph between cells in the population. Edges are then pruned based on a cosine correlation threshold and/or a distance threshold and the resulting graph is visualized using a force-directed graph layout algorithm. VeloViz can help ensure that relationships between cell states are reflected in the 2D embedding, allowing for more reliable representation of underlying cellular trajectories.
Maintained by Lyla Atta. Last updated 5 months ago.
transcriptomicsvisualizationgeneexpressionsequencingrnaseqdimensionreductioncpp
3.3 match 4.00 score 6 scripts
sem-in-r
seminr:Building and Estimating Structural Equation Models
A powerful, easy to syntax for specifying and estimating complex Structural Equation Models. Models can be estimated using Partial Least Squares Path Modeling or Covariance-Based Structural Equation Modeling or covariance based Confirmatory Factor Analysis. Methods described in Ray, Danks, and Valdez (2021).
Maintained by Nicholas Patrick Danks. Last updated 3 years ago.
common-factorscompositesconstructpls-models
1.8 match 62 stars 7.46 score 284 scripts
furrer-lab
abn:Modelling Multivariate Data with Additive Bayesian Networks
The 'abn' R package facilitates Bayesian network analysis, a probabilistic graphical model that derives from empirical data a directed acyclic graph (DAG). This DAG describes the dependency structure between random variables. The R package 'abn' provides routines to help determine optimal Bayesian network models for a given data set. These models are used to identify statistical dependencies in messy, complex data. Their additive formulation is equivalent to multivariate generalised linear modelling, including mixed models with independent and identically distributed (iid) random effects. The core functionality of the 'abn' package revolves around model selection, also known as structure discovery. It supports both exact and heuristic structure learning algorithms and does not restrict the data distribution of parent-child combinations, providing flexibility in model creation and analysis. The 'abn' package uses Laplace approximations for metric estimation and includes wrappers to the 'INLA' package. It also employs 'JAGS' for data simulation purposes. For more resources and information, visit the 'abn' website.
Maintained by Matteo Delucchi. Last updated 5 days ago.
bayesian-networkbinomialcategorical-datagaussiangrouped-datasetsmixed-effectsmultinomialmultivariatepoissonstructure-learninggslopenblascppopenmpjags
1.9 match 6 stars 6.94 score 90 scripts
cran
sna:Tools for Social Network Analysis
A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.
Maintained by Carter T. Butts. Last updated 6 months ago.
1.9 match 8 stars 6.78 score 94 dependentsbioc
gatom:Finding an Active Metabolic Module in Atom Transition Network
This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.
Maintained by Alexey Sergushichev. Last updated 5 months ago.
geneexpressiondifferentialexpressionpathwaysnetwork
1.8 match 6 stars 5.26 score 8 scripts
louisaslett
maths.genealogy:Mathematics PhD Genealogy Data and Plotting
Query, extract, and plot genealogical data from The Mathematics Genealogy Project <https://mathgenealogy.org/>. Data is gathered from the 'WebSocket' server run by the 'geneagrapher-core' project <https://github.com/davidalber/geneagrapher-core>.
Maintained by Louis Aslett. Last updated 4 days ago.
1.9 match 2 stars 4.95 score
mbq
vistla:Detecting Influence Paths with Information Theory
Traces information spread through interactions between features, utilising information theory measures and a higher-order generalisation of the concept of widest paths in graphs. In particular, 'vistla' can be used to better understand the results of high-throughput biomedical experiments, by organising the effects of the investigated intervention in a tree-like hierarchy from direct to indirect ones, following the plausible information relay circuits. Due to its higher-order nature, 'vistla' can handle multi-modality and assign multiple roles to a single feature.
Maintained by Miron B. Kursa. Last updated 25 days ago.
1.8 match 4.78 score 3 scripts
ltierney
proftools:Profile Output Processing Tools for R
Tools for examining Rprof profile output.
Maintained by Luke Tierney. Last updated 5 years ago.
1.7 match 4.58 score 128 scripts 1 dependentscran
datarobot:'DataRobot' Predictive Modeling API
For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Maintained by AJ Alon. Last updated 1 years ago.
1.8 match 2 stars 3.48 score
alishinski
lavaanPlot:Path Diagrams for 'Lavaan' Models via 'DiagrammeR'
Plots path diagrams from models in 'lavaan' using the plotting functionality from the 'DiagrammeR' package. 'DiagrammeR' provides nice path diagrams via 'Graphviz', and these functions make it easy to generate these diagrams from a 'lavaan' path model without having to write the DOT language graph specification.
Maintained by Alex Lishinski. Last updated 1 years ago.
0.5 match 40 stars 8.33 score 294 scripts
jkhaukka
cohorttools:Cohort Data Analyses
Functions to make lifetables and to calculate hazard function estimate using Poisson regression model with splines. Includes function to draw simple flowchart of cohort study. Function boxesLx() makes boxes of transition rates between states. It utilizes 'Epi' package 'Lexis' data.
Maintained by Jari Haukka. Last updated 2 years ago.
3.7 match 1.00 score 1 scripts
jackdunnnz
iai:Interface to 'Interpretable AI' Modules
An interface to the algorithms of 'Interpretable AI' <https://www.interpretable.ai> from the R programming language. 'Interpretable AI' provides various modules, including 'Optimal Trees' for classification, regression, prescription and survival analysis, 'Optimal Imputation' for missing data imputation and outlier detection, and 'Optimal Feature Selection' for exact sparse regression. The 'iai' package is an open-source project. The 'Interpretable AI' software modules are proprietary products, but free academic and evaluation licenses are available.
Maintained by Jack Dunn. Last updated 5 months ago.
1.7 match 1 stars 2.00 score 7 scripts
r-forge
gridGraphviz:Drawing Graphs with 'grid'
Functions for drawing node-and-edge graphs that have been laid out by 'graphviz'. This provides an alternative rendering to that provided by the 'Rgraphviz' package, with two main advantages: the rendering provided by 'gridGraphviz' should be more similar to what 'graphviz' itself would draw; and rendering with 'grid' allows for post-hoc customisations using the named viewports and grobs that 'gridGraphviz' produces.
Maintained by Paul Murrell. Last updated 3 years ago.
0.8 match 2.78 score 2 scripts 1 dependents
harrelfe
qreport:Statistical Reporting with 'Quarto'
Provides statistical components, tables, and graphs that are useful in 'Quarto' and 'RMarkdown' reports and that produce 'Quarto' elements for special formatting such as tabs and marginal notes and graphs. Some of the functions produce entire report sections with tabs, e.g., the missing data report created by missChk(). Functions for inserting variables and tables inside 'graphviz' and 'mermaid' diagrams are included, and so are special clinical trial graphics for adverse event reporting.
Maintained by Frank Harrell. Last updated 10 months ago.
0.5 match 2.70 score 32 scripts
deweyme
latdiag:Draws Diagrams Useful for Checking Latent Scales
A graph proposed by Rosenbaum is useful for checking some properties of various sorts of latent scale, this program generates commands to obtain the graph using 'dot' from 'graphviz'.
Maintained by Michael Dewey. Last updated 5 years ago.
0.5 match 2.00 score 3 scripts