Showing 200 of total 456 results (show query)
r-transit
tidytransit:Read, Validate, Analyze, and Map GTFS Feeds
Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <https://gtfs.org/>.
Maintained by Flavio Poletti. Last updated 1 months ago.
gtfspublicpublic-transporttidyversetransittransit-datatransporttransportation
39.4 match 151 stars 10.47 score 272 scripts 1 dependents
jiefei-wang
aws.ecx:Communicating with AWS EC2 and ECS using AWS REST APIs
Providing the functions for communicating with Amazon Web Services(AWS) Elastic Compute Cloud(EC2) and Elastic Container Service(ECS). The functions will have the prefix 'ecs_' or 'ec2_' depending on the class of the API. The request will be sent via the REST API and the parameters are given by the function argument. The credentials can be set via 'aws_set_credentials'. The EC2 documentation can be found at <https://docs.aws.amazon.com/AWSEC2/latest/APIReference/Welcome.html> and ECS can be found at <https://docs.aws.amazon.com/AmazonECS/latest/APIReference/Welcome.html>.
Maintained by Jiefei Wang. Last updated 3 years ago.
97.9 match 1 stars 4.18 score 2 scripts
hesim-dev
hesim:Health Economic Simulation Modeling and Decision Analysis
A modular and computationally efficient R package for parameterizing, simulating, and analyzing health economic simulation models. The package supports cohort discrete time state transition models (Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>, N-state partitioned survival models (Glasziou et al. 1990) <doi:10.1002/sim.4780091106>, and individual-level continuous time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>, encompassing both Markov (time-homogeneous and time-inhomogeneous) and semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is quantified with standard graphical and tabular summaries of a probabilistic sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>, <doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table make individual-patient simulation, probabilistic sensitivity analysis, and incorporation of patient heterogeneity fast.
Maintained by Devin Incerti. Last updated 6 months ago.
health-economic-evaluationmicrosimulationsimulation-modelingcpp
46.0 match 67 stars 8.12 score 41 scripts
thomasp85
gganimate:A Grammar of Animated Graphics
The grammar of graphics as implemented in the 'ggplot2' package has been successful in providing a powerful API for creating static visualisation. In order to extend the API for animated graphics this package provides a completely new set of grammar, fully compatible with 'ggplot2' for specifying transitions and animations in a flexible and extensible way.
Maintained by Thomas Lin Pedersen. Last updated 1 years ago.
animationdata-visualizationggplot-extensionggplot2transition
23.1 match 2.0k stars 15.87 score 13k scripts 25 dependents
bioc
transite:RNA-binding protein motif analysis
transite is a computational method that allows comprehensive analysis of the regulatory role of RNA-binding proteins in various cellular processes by leveraging preexisting gene expression data and current knowledge of binding preferences of RNA-binding proteins.
Maintained by Konstantin Krismer. Last updated 5 months ago.
geneexpressiontranscriptiondifferentialexpressionmicroarraymrnamicroarraygeneticsgenesetenrichmentcpp
59.8 match 4.30 score 20 scripts
sonsoleslp
tna:Transition Network Analysis (TNA)
Provides tools for performing Transition Network Analysis (TNA) to study relational dynamics, including functions for building and plotting TNA models, calculating centrality measures, and identifying dominant events and patterns. TNA statistical techniques (e.g., bootstrapping and permutation tests) ensure the reliability of observed insights and confirm that identified dynamics are meaningful. See (Saqr et al., 2025) <doi:10.1145/3706468.3706513> for more details on TNA.
Maintained by Sonsoles López-Pernas. Last updated 2 days ago.
educational-data-mininglearning-analyticsmarkov-modeltemporal-analysis
35.0 match 4 stars 6.48 score 5 scripts
insightsengineering
simIDM:Simulating Oncology Trials using an Illness-Death Model
Based on the illness-death model a large number of clinical trials with oncology endpoints progression-free survival (PFS) and overall survival (OS) can be simulated, see Meller, Beyersmann and Rufibach (2019) <doi:10.1002/sim.8295>. The simulation set-up allows for random and event-driven censoring, an arbitrary number of treatment arms, staggered study entry and drop-out. Exponentially, Weibull and piecewise exponentially distributed survival times can be generated. The correlation between PFS and OS can be calculated.
Maintained by Alexandra Erdmann. Last updated 1 years ago.
multistate-modelssimulation-engine
34.7 match 13 stars 6.26 score 9 scripts
agrdatasci
gdistance:Distances and Routes on Geographical Grids
Provides classes and functions to calculate various distance measures and routes in heterogeneous geographic spaces represented as grids. The package implements measures to model dispersal histories first presented by van Etten and Hijmans (2010) <doi:10.1371/journal.pone.0012060>. Least-cost distances as well as more complex distances based on (constrained) random walks can be calculated. The distances implemented in the package are used in geographical genetics, accessibility indicators, and may also have applications in other fields of geospatial analysis.
Maintained by Andrew Marx. Last updated 1 years ago.
17.0 match 17 stars 10.34 score 478 scripts 23 dependents
hputter
mstate:Data Preparation, Estimation and Prediction in Multi-State Models
Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>.
Maintained by Hein Putter. Last updated 28 days ago.
13.5 match 11 stars 12.13 score 322 scripts 55 dependents
spedygiorgio
markovchain:Easy Handling Discrete Time Markov Chains
Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>. Some functions for continuous times Markov chains depend on the suggested ctmcd package.
Maintained by Giorgio Alfredo Spedicato. Last updated 4 months ago.
ctmcdtmcmarkov-chainmarkov-modelr-programmingrcppopenblascpp
12.5 match 104 stars 12.78 score 712 scripts 4 dependentsthomasp85
tweenr:Interpolate Data for Smooth Animations
In order to create smooth animation between states of data, tweening is necessary. This package provides a range of functions for creating tweened data that can be used as basis for animation. Furthermore it adds a number of vectorized interpolaters for common R data types such as numeric, date and colour.
Maintained by Thomas Lin Pedersen. Last updated 1 years ago.
animationplottingtransitiontweeningcpp
12.3 match 399 stars 12.80 score 440 scripts 319 dependentsr-transit
gtfsio:Read and Write General Transit Feed Specification (GTFS) Files
Tools for the development of packages related to General Transit Feed Specification (GTFS) files. Establishes a standard for representing GTFS feeds using R data types. Provides fast and flexible functions to read and write GTFS feeds while sticking to this standard. Defines a basic 'gtfs' class which is meant to be extended by packages that depend on it. And offers utility functions that support checking the structure of GTFS objects.
Maintained by Daniel Herszenhut. Last updated 6 days ago.
20.2 match 14 stars 7.49 score 13 scripts 5 dependents
statnet
ergm:Fit, Simulate and Diagnose Exponential-Family Models for Networks
An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.
Maintained by Pavel N. Krivitsky. Last updated 7 days ago.
9.0 match 100 stars 15.36 score 1.4k scripts 36 dependents
gforge
Gmisc:Descriptive Statistics, Transition Plots, and More
Tools for making the descriptive "Table 1" used in medical articles, a transition plot for showing changes between categories (also known as a Sankey diagram), flow charts by extending the grid package, a method for variable selection based on the SVD, Bézier lines with arrows complementing the ones in the 'grid' package, and more.
Maintained by Max Gordon. Last updated 2 years ago.
12.5 match 50 stars 10.40 score 233 scripts 2 dependents
arturstat
TPmsm:Estimation of Transition Probabilities in Multistate Models
Estimation of transition probabilities for the illness-death model and or the three-state progressive model.
Maintained by Artur Araujo. Last updated 1 years ago.
illness-death-modelkaplan-meiermonte-carlo-simulationmulti-state-modelsopenmp-parallelizationsurvival-analysistransition-probabilitiesopenblasopenmp
28.4 match 1 stars 4.52 score 22 scripts 1 dependents
aphp
heemod:Markov Models for Health Economic Evaluations
An implementation of the modelling and reporting features described in reference textbook and guidelines (Briggs, Andrew, et al. Decision Modelling for Health Economic Evaluation. Oxford Univ. Press, 2011; Siebert, U. et al. State-Transition Modeling. Medical Decision Making 32, 690-700 (2012).): deterministic and probabilistic sensitivity analysis, heterogeneity analysis, time dependency on state-time and model-time (semi-Markov and non-homogeneous Markov models), etc.
Maintained by Kevin Zarca. Last updated 6 months ago.
13.1 match 15 stars 8.81 score 204 scripts
chjackson
flexsurv:Flexible Parametric Survival and Multi-State Models
Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models, based on either cause-specific hazards or mixture models.
Maintained by Christopher Jackson. Last updated 2 months ago.
8.5 match 57 stars 13.31 score 632 scripts 43 dependents
igraph
igraph:Network Analysis and Visualization
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Maintained by Kirill Müller. Last updated 9 hours ago.
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphfortranlibxml2glpkopenblascpp
5.3 match 582 stars 21.11 score 31k scripts 1.9k dependents
elipousson
mapbaltimore:Make maps for Baltimore City with open data
This package provides data from the Baltimore City, the state of Maryland, and other sources, functions to access additional data, and function to create and modify simple maps of Baltimore neighborhoods using sf and ggplot2.
Maintained by Eli Pousson. Last updated 4 months ago.
27.4 match 17 stars 3.85 score 14 scripts
r-lum
RLumCarlo:Monte-Carlo Methods for Simulating Luminescence Phenomena
A collection of functions to simulate luminescence production in dosimetric materials using Monte Carlo methods. Implemented are models for delocalised transitions (e.g., Chen and McKeever (1997) <doi:10.1142/2781>), localised transitions (e.g., Pagonis et al. (2019) <doi:10.1016/j.jlumin.2018.11.024>) and tunnelling transitions (Jain et al. (2012) <doi:10.1088/0953-8984/24/38/385402> and Pagonis et al. (2019) <doi:10.1016/j.jlumin.2018.11.024>). Supported stimulation methods are thermal luminescence (TL), continuous-wave optically stimulated luminescence (CW-OSL), linearly-modulated optically stimulated luminescence (LM-OSL), linearly-modulated infrared stimulated luminescence (LM-IRSL), and isothermal luminescence (ITL or ISO-TL).
Maintained by Sebastian Kreutzer. Last updated 8 months ago.
feldspargeochronologyluminescenceluminescence-modelsmonte-carlo-simulationssimulationcpp
21.3 match 3 stars 4.95 score 5 scripts
merck
psm3mkv:Evaluate Partitioned Survival and State Transition Models
Fits and evaluates three-state partitioned survival analyses (PartSAs) and Markov models (clock forward or clock reset) to progression and overall survival data typically collected in oncology clinical trials. These model structures are typically considered in cost-effectiveness modeling in advanced/metastatic cancer indications. Muston (2024). "Informing structural assumptions for three state oncology cost-effectiveness models through model efficiency and fit". Applied Health Economics and Health Policy.
Maintained by Dominic Muston. Last updated 9 months ago.
15.7 match 10 stars 6.43 score 1 scripts
cran
icmstate:Interval Censored Multi-State Models
Allows for the non-parametric estimation of transition intensities in interval-censored multi-state models using the approach of Gomon and Putter (2024) <doi:10.48550/arXiv.2409.07176> or Gu et al. (2023) <doi:10.1093/biomet/asad073>.
Maintained by Daniel Gomon. Last updated 4 months ago.
26.6 match 3.65 score 15 scripts
acguidoum
Sim.DiffProc:Simulation of Diffusion Processes
It provides users with a wide range of tools to simulate, estimate, analyze, and visualize the dynamics of stochastic differential systems in both forms Ito and Stratonovich. Statistical analysis with parallel Monte Carlo and moment equations methods of SDEs <doi:10.18637/jss.v096.i02>. Enabled many searchers in different domains to use these equations to modeling practical problems in financial and actuarial modeling and other areas of application, e.g., modeling and simulate of first passage time problem in shallow water using the attractive center (Boukhetala K, 1996) ISBN:1-56252-342-2.
Maintained by Arsalane Chouaib Guidoum. Last updated 1 years ago.
dynamic-systemmoment-equationsmonte-carlo-simulationparallel-computingstochastic-calculusstochastic-differential-equationtransition-density
12.6 match 13 stars 7.69 score 86 scripts 4 dependents
opatp
GTFSwizard:Exploring and Manipulating 'GTFS' Files
Exploring, analyzing, and manipulating General Transit Feed Specification (GTFS) files, which represent public transportation schedules and geographic data. The package allows users to filter data by routes, trips, stops, and time, generate spatial visualizations, and perform detailed analyses of transit networks, including headway, dwell times, and route frequencies. Designed for transit planners, researchers, and data analysts, 'GTFSwizard' integrates functionalities from popular packages to enable efficient GTFS data manipulation and visualization.
Maintained by Nelson de O. Quesado Filho. Last updated 2 months ago.
21.7 match 1 stars 4.41 scorebioc
maftools:Summarize, Analyze and Visualize MAF Files
Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.
Maintained by Anand Mayakonda. Last updated 5 months ago.
datarepresentationdnaseqvisualizationdrivermutationvariantannotationfeatureextractionclassificationsomaticmutationsequencingfunctionalgenomicssurvivalbioinformaticscancer-genome-atlascancer-genomicsgenomicsmaf-filestcgacurlbzip2xz-utilszlib
6.5 match 459 stars 14.63 score 948 scripts 18 dependents
hkestler
BoolNet:Construction, Simulation and Analysis of Boolean Networks
Functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks <doi:10.1093/bioinformatics/btq124>.
Maintained by Hans A. Kestler. Last updated 1 years ago.
14.6 match 3 stars 5.90 score 122 scripts 6 dependents
uscbiostats
fmcmc:A friendly MCMC framework
Provides a friendly (flexible) Markov Chain Monte Carlo (MCMC) framework for implementing Metropolis-Hastings algorithm in a modular way allowing users to specify automatic convergence checker, personalized transition kernels, and out-of-the-box multiple MCMC chains using parallel computing. Most of the methods implemented in this package can be found in Brooks et al. (2011, ISBN 9781420079425). Among the methods included, we have: Haario (2001) <doi:10.1007/s11222-011-9269-5> Adaptive Metropolis, Vihola (2012) <doi:10.1007/s11222-011-9269-5> Robust Adaptive Metropolis, and Thawornwattana et al. (2018) <doi:10.1214/17-BA1084> Mirror transition kernels.
Maintained by George Vega Yon. Last updated 1 years ago.
adaptivebayesian-inferencemarkov-chain-monte-carlomcmcmetropolis-hastingsparallel-computing
12.4 match 16 stars 6.79 score 86 scripts 1 dependents
mclements
etm:Empirical Transition Matrix
The etm (empirical transition matrix) package permits to estimate the matrix of transition probabilities for any time-inhomogeneous multi-state model with finite state space using the Aalen-Johansen estimator. Functions for data preparation and for displaying are also included (Allignol et al., 2011 <doi:10.18637/jss.v038.i04>). Functionals of the Aalen-Johansen estimator, e.g., excess length-of-stay in an intermediate state, can also be computed (Allignol et al. 2011 <doi:10.1007/s00180-010-0200-x>).
Maintained by Arthur Allignol. Last updated 3 years ago.
9.7 match 8.09 score 110 scripts 13 dependentsbioc
RBGL:An interface to the BOOST graph library
A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.
Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.
8.9 match 8.59 score 320 scripts 132 dependents
traminer
TraMineR:Trajectory Miner: a Sequence Analysis Toolkit
Set of sequence analysis tools for manipulating, describing and rendering categorical sequences, and more generally mining sequence data in the field of social sciences. Although this sequence analysis package is primarily intended for state or event sequences that describe time use or life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and functions for extracting the most frequent event subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Maintained by Gilbert Ritschard. Last updated 3 months ago.
9.3 match 11 stars 8.24 score 534 scripts 13 dependents
munterfi
hereR:'sf'-Based Interface to the 'HERE' REST APIs
Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>: (1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API; (2) route directions, travel distance or time matrices and isolines using the 'Routing', 'Matrix Routing' and 'Isoline Routing' APIs; (3) request real-time traffic flow and incident information from the 'Traffic' API; (4) find request public transport connections and nearby stations from the 'Public Transit' API; (5) request intermodal routes using the 'Intermodal Routing' API; (6) get weather forecasts, reports on current weather conditions, astronomical information and alerts at a specific location from the 'Destination Weather' API. Locations, routes and isolines are returned as 'sf' objects.
Maintained by Merlin Unterfinger. Last updated 24 days ago.
apigeocodinggishere-technologiesisolineroutingrspatialtrafficweather
8.7 match 90 stars 8.70 score 63 scripts
mhahsler
rEMM:Extensible Markov Model for Modelling Temporal Relationships Between Clusters
Implements TRACDS (Temporal Relationships between Clusters for Data Streams), a generalization of Extensible Markov Model (EMM). TRACDS adds a temporal or order model to data stream clustering by superimposing a dynamically adapting Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN data stream clustering). Development of this package was supported in part by NSF IIS-0948893 and R21HG005912 from the National Human Genome Research Institute. Hahsler and Dunham (2010) <doi:10.18637/jss.v035.i05>.
Maintained by Michael Hahsler. Last updated 7 months ago.
clusteringdata-streamsequence-analysis
15.1 match 2 stars 4.79 score 31 scripts
smbc-nzp
MigConnectivity:Estimate Migratory Connectivity for Migratory Animals
Allows the user to estimate transition probabilities for migratory animals between any two phases of the annual cycle, using a variety of different data types. Also quantifies the strength of migratory connectivity (MC), a standardized metric to quantify the extent to which populations co-occur between two phases of the annual cycle. Includes functions to estimate MC and the more traditional metric of migratory connectivity strength (Mantel correlation) incorporating uncertainty from multiple sources of sampling error. For cross-species comparisons, methods are provided to estimate differences in migratory connectivity strength, incorporating uncertainty. See Cohen et al. (2018) <doi:10.1111/2041-210X.12916>, Cohen et al. (2019) <doi:10.1111/ecog.03974>, and Roberts et al. (2023) <doi:10.1002/eap.2788> for details on some of these methods.
Maintained by Jeffrey A. Hostetler. Last updated 12 months ago.
10.6 match 8 stars 6.77 score 41 scripts
saviviro
sstvars:Toolkit for Reduced Form and Structural Smooth Transition Vector Autoregressive Models
Penalized and non-penalized maximum likelihood estimation of smooth transition vector autoregressive models with various types of transition weight functions, conditional distributions, and identification methods. Constrained estimation with various types of constraints is available. Residual based model diagnostics, forecasting, simulations, and calculation of impulse response functions, generalized impulse response functions, and generalized forecast error variance decompositions. See Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>, Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>, Markku Lanne, Savi Virolainen (2025) <doi:10.48550/arXiv.2403.14216>, Savi Virolainen (2025) <doi:10.48550/arXiv.2404.19707>.
Maintained by Savi Virolainen. Last updated 16 days ago.
11.2 match 4 stars 6.36 score 41 scripts
thej022214
hisse:Hidden State Speciation and Extinction
Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.
Maintained by Jeremy Beaulieu. Last updated 1 months ago.
8.4 match 6 stars 8.45 score 152 scriptsbioc
netZooR:Unified methods for the inference and analysis of gene regulatory networks
netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.
Maintained by Tara Eicher. Last updated 9 days ago.
networkinferencenetworkgeneregulationgeneexpressiontranscriptionmicroarraygraphandnetworkgene-regulatory-networktranscription-factors
8.8 match 105 stars 7.98 score
nanxstats
protr:Generating Various Numerical Representation Schemes for Protein Sequences
Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042>. For full functionality, the software 'ncbi-blast+' is needed, see <https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html> for more information.
Maintained by Nan Xiao. Last updated 6 months ago.
bioinformaticsfeature-engineeringfeature-extractionmachine-learningpeptidesprotein-sequencessequence-analysis
7.0 match 52 stars 10.02 score 173 scripts 3 dependents
klausvigo
phangorn:Phylogenetic Reconstruction and Analysis
Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).
Maintained by Klaus Schliep. Last updated 1 months ago.
softwaretechnologyqualitycontrolphylogenetic-analysisphylogeneticsopenblascpp
4.2 match 206 stars 16.69 score 2.5k scripts 135 dependents
ajsims1704
rdecision:Decision Analytic Modelling in Health Economics
Classes and functions for modelling health care interventions using decision trees and semi-Markov models. Mechanisms are provided for associating an uncertainty distribution with each source variable and for ensuring transparency of the mathematical relationships between variables. The package terminology follows Briggs "Decision Modelling for Health Economic Evaluation" (2006, ISBN:978-0-19-852662-9).
Maintained by Andrew Sims. Last updated 1 months ago.
10.5 match 3 stars 6.46 score 22 scriptsbioc
dada2:Accurate, high-resolution sample inference from amplicon sequencing data
The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.
Maintained by Benjamin Callahan. Last updated 5 months ago.
immunooncologymicrobiomesequencingclassificationmetagenomicsampliconbioconductorbioinformaticsmetabarcodingtaxonomycpp
5.1 match 485 stars 13.17 score 3.0k scripts 4 dependents
marshalllab
MGDrivE2:Mosquito Gene Drive Explorer 2
A simulation modeling framework which significantly extends capabilities from the 'MGDrivE' simulation package via a new mathematical and computational framework based on stochastic Petri nets. For more information about 'MGDrivE', see our publication: <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13318>. Some of the notable capabilities of 'MGDrivE2' include: incorporation of human populations, epidemiological dynamics, time-varying parameters, and a continuous-time simulation framework with various sampling algorithms for both deterministic and stochastic interpretations. 'MGDrivE2' relies on the genetic inheritance structures provided in package 'MGDrivE', so we suggest installing that package initially.
Maintained by Sean L. Wu. Last updated 4 years ago.
10.4 match 6 stars 6.33 score 30 scripts
gobbios
EloRating:Animal Dominance Hierarchies by Elo Rating
Provides functions to quantify animal dominance hierarchies. The major focus is on Elo rating and its ability to deal with temporal dynamics in dominance interaction sequences. For static data, David's score and de Vries' I&SI are also implemented. In addition, the package provides functions to assess transitivity, linearity and stability of dominance networks. See Neumann et al (2011) <doi:10.1016/j.anbehav.2011.07.016> for an introduction.
Maintained by Christof Neumann. Last updated 8 months ago.
9.5 match 4 stars 6.86 score 61 scripts 1 dependents
polkas
cat2cat:Handling an Inconsistently Coded Categorical Variable in a Longitudinal Dataset
Unifying an inconsistently coded categorical variable between two different time points in accordance with a mapping table. The main rule is to replicate the observation if it could be assigned to a few categories. Then using frequencies or statistical methods to approximate the probabilities of being assigned to each of them. This procedure was invented and implemented in the paper by Nasinski, Majchrowska, and Broniatowska (2020) <doi:10.24425/cejeme.2020.134747>.
Maintained by Maciej Nasinski. Last updated 1 years ago.
categoriesencodingencodingsfactorlongitudinalmappingmappingspaneltransitions
14.9 match 4 stars 4.30 score 2 scripts
bupaverse
petrinetR:Building, Visualizing, Exporting and Replaying Petri Nets
Functions for the construction of Petri Nets. Petri Nets can be replayed by firing enabled transitions. Silent transitions will be hidden by the execution handler. Also includes functionalities for the visualization of Petri Nets and export of Petri Nets to PNML (Petri Net Markup Language) files.
Maintained by Gert Janssenswillen. Last updated 2 years ago.
14.3 match 4 stars 4.31 score 17 scripts 1 dependents
bcmullins
mobilityIndexR:Calculates Transition Matrices and Mobility Indices
Measures mobility in a population through transition matrices and mobility indices. Relative, mixed, and absolute transition matrices are supported. The Prais-Bibby, Absolute Movement, Origin Specific, and Weighted Group Mobility indices are supported. Example income and grade data are included.
Maintained by Brett Mullins. Last updated 3 years ago.
16.5 match 3.70 score 4 scripts
glenndavis52
zonohedra:Compute and Plot Zonohedra from Vector Generators
Computes a zonohedron from real vector generators. The package also computes zonogons (2D zonotopes) and zonosegs (1D zonotopes). An elementary S3 class for matroids is included, which supports matroids with rank 3, 2, and 1. Optimization methods are taken from Heckbert (1985) <https://www.cs.cmu.edu/~ph/zono.ps.gz>.
Maintained by Glenn Davis. Last updated 1 months ago.
19.9 match 3.00 score 8 scriptscran
popbio:Construction and Analysis of Matrix Population Models
Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).
Maintained by Chris Stubben. Last updated 12 months ago.
9.4 match 6.24 score 1.0k scripts 5 dependents
karlines
diagram:Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams
Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs, electrical networks, etc. Support for the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter M.J. Herman (2009), Springer. and the book "Solving Differential Equations in R" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer. Includes demo(flowchart), demo(plotmat), demo(plotweb).
Maintained by Karline Soetaert. Last updated 4 years ago.
5.8 match 10.06 score 598 scripts 487 dependents
ocean-tracking-network
glatos:A package for the Great Lakes Acoustic Telemetry Observation System
Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
Maintained by Christopher Holbrook. Last updated 6 months ago.
8.8 match 10 stars 6.38 score 112 scripts
spatial-ews
spatialwarnings:Spatial Early Warning Signals of Ecosystem Degradation
Tools to compute and assess significance of early-warnings signals (EWS) of ecosystem degradation on raster data sets. EWS are spatial metrics derived from raster data -- e.g. spatial autocorrelation -- that increase before an ecosystem undergoes a non-linear transition (Genin et al. (2018) <doi:10.1111/2041-210X.13058>).
Maintained by Alexandre Genin. Last updated 6 months ago.
catastrophiccriticalecologyindicatorspointsshiftsspacetransitionscpp
10.5 match 15 stars 5.32 score 46 scripts
egarpor
sdetorus:Statistical Tools for Toroidal Diffusions
Implementation of statistical methods for the estimation of toroidal diffusions. Several diffusive models are provided, most of them belonging to the Langevin family of diffusions on the torus. Specifically, the wrapped normal and von Mises processes are included, which can be seen as toroidal analogues of the Ornstein-Uhlenbeck diffusion. A collection of methods for approximate maximum likelihood estimation, organized in four blocks, is given: (i) based on the exact transition probability density, obtained as the numerical solution to the Fokker-Plank equation; (ii) based on wrapped pseudo-likelihoods; (iii) based on specific analytic approximations by wrapped processes; (iv) based on maximum likelihood of the stationary densities. The package allows the replicability of the results in García-Portugués et al. (2019) <doi:10.1007/s11222-017-9790-2>.
Maintained by Eduardo García-Portugués. Last updated 1 years ago.
circular-statisticsinferencemaximum-likelihoodreproducible-researchsdestatisticstoroidal-dataopenblascpp
14.3 match 5 stars 3.88 score 9 scripts 1 dependents
brockk
trialr:Clinical Trial Designs in 'rstan'
A collection of clinical trial designs and methods, implemented in 'rstan' and R, including: the Continual Reassessment Method by O'Quigley et al. (1990) <doi:10.2307/2531628>; EffTox by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the two-parameter logistic method of Neuenschwander, Branson & Sponer (2008) <doi:10.1002/sim.3230>; and the Augmented Binary method by Wason & Seaman (2013) <doi:10.1002/sim.5867>; and more. We provide functions to aid model-fitting and analysis. The 'rstan' implementations may also serve as a cookbook to anyone looking to extend or embellish these models. We hope that this package encourages the use of Bayesian methods in clinical trials. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a method you would like implemented, please get in touch.
Maintained by Kristian Brock. Last updated 1 years ago.
6.5 match 41 stars 8.55 score 106 scripts 3 dependentsthomasp85
transformr:Polygon and Path Transformations
In order to smoothly animate the transformation of polygons and paths, many aspects needs to be taken into account, such as differing number of control points, changing center of rotation, etc. The 'transformr' package provides an extensive framework for manipulating the shapes of polygons and paths and can be seen as the spatial brother to the 'tweenr' package.
Maintained by Thomas Lin Pedersen. Last updated 1 years ago.
animationdata-visualizationinterpolationmatching-shapestweeningcpp
5.5 match 116 stars 9.82 score 772 scripts 26 dependents
rsetienne
secsse:Several Examined and Concealed States-Dependent Speciation and Extinction
Simultaneously infers state-dependent diversification across two or more states of a single or multiple traits while accounting for the role of a possible concealed trait. See Herrera-Alsina et al. (2019) <doi:10.1093/sysbio/syy057>.
Maintained by Rampal S. Etienne. Last updated 11 months ago.
9.0 match 1 stars 5.83 score 34 scripts
ropensci
opentripplanner:Setup and connect to 'OpenTripPlanner'
Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>. OTP is an open source platform for multi-modal and multi-agency journey planning written in 'Java'. The package allows you to manage a local version or connect to remote OTP server to find walking, cycling, driving, or transit routes. This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).
Maintained by Malcolm Morgan. Last updated 3 months ago.
dataisochronesjavaopentripplannerotppublic-transportroutingtransporttransportation-planning
5.8 match 83 stars 8.94 score 147 scripts
goldingn
pop:A Flexible Syntax for Population Dynamic Modelling
Population dynamic models underpin a range of analyses and applications in ecology and epidemiology. The various approaches for analysing population dynamics models (MPMs, IPMs, ODEs, POMPs, PVA) each require the model to be defined in a different way. This makes it difficult to combine different modelling approaches and data types to solve a given problem. 'pop' aims to provide a flexible and easy to use common interface for constructing population dynamic models and enabling to them to be fitted and analysed in lots of different ways.
Maintained by Nick Golding. Last updated 9 years ago.
10.3 match 10 stars 4.88 score 15 scriptsbioc
mnem:Mixture Nested Effects Models
Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, ... and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm.
Maintained by Martin Pirkl. Last updated 4 months ago.
pathwayssystemsbiologynetworkinferencenetworkrnaseqpooledscreenssinglecellcrispratacseqdnaseqgeneexpressioncpp
8.5 match 4 stars 5.64 score 15 scripts 4 dependents
hongyuanjia
eplusr:A Toolkit for Using Whole Building Simulation Program 'EnergyPlus'
A rich toolkit of using the whole building simulation program 'EnergyPlus'(<https://energyplus.net>), which enables programmatic navigation, modification of 'EnergyPlus' models and makes it less painful to do parametric simulations and analysis.
Maintained by Hongyuan Jia. Last updated 8 months ago.
energy-simulationenergyplusenergyplus-modelseplusepwiddidfparametric-simulationr6simulation
6.6 match 72 stars 7.20 score 91 scripts 4 dependents
mu-sigma
HVT:Constructing Hierarchical Voronoi Tessellations and Overlay Heatmaps for Data Analysis
Facilitates building topology preserving maps for data analysis.
Maintained by "Mu Sigma, Inc.". Last updated 1 months ago.
7.5 match 4 stars 6.26 score 1 scriptsbioc
sRACIPE:Systems biology tool to simulate gene regulatory circuits
sRACIPE implements a randomization-based method for gene circuit modeling. It allows us to study the effect of both the gene expression noise and the parametric variation on any gene regulatory circuit (GRC) using only its topology, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises. sRACIPE provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation.
Maintained by Mingyang Lu. Last updated 20 days ago.
researchfieldsystemsbiologymathematicalbiologygeneexpressiongeneregulationgenetargetcpp
7.3 match 4 stars 6.40 score 209 scriptsbioc
BioTIP:BioTIP: An R package for characterization of Biological Tipping-Point
Adopting tipping-point theory to transcriptome profiles to unravel disease regulatory trajectory.
Maintained by Yuxi (Jennifer) Sun. Last updated 5 months ago.
sequencingrnaseqgeneexpressiontranscriptionsoftware
6.8 match 18 stars 6.84 score 37 scriptschjackson
msmbayes:Bayesian Multi-State Models for Intermittently-Observed Data
Bayesian multi-state models for intermittently-observed data. Markov and phase-type semi-Markov models, and misclassification hidden Markov models.
Maintained by Christopher Jackson. Last updated 4 months ago.
10.5 match 4 stars 4.26 score 3 scripts
r-lib
gargle:Utilities for Working with Google APIs
Provides utilities for working with Google APIs <https://developers.google.com/apis-explorer>. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.
Maintained by Jennifer Bryan. Last updated 2 years ago.
3.0 match 113 stars 14.88 score 266 scripts 192 dependents
reginalexavier
OpenLand:Quantitative Analysis and Visualization of LUCC
Tools for the analysis of land use and cover (LUC) time series. It includes support for loading spatiotemporal raster data and synthesized spatial plotting. Several LUC change (LUCC) metrics in regular or irregular time intervals can be extracted and visualized through one- and multistep sankey and chord diagrams. A complete intensity analysis according to Aldwaik and Pontius (2012) <doi:10.1016/j.landurbplan.2012.02.010> is implemented, including tools for the generation of standardized multilevel output graphics.
Maintained by Reginal Exavier. Last updated 11 months ago.
geographygeospatialintensity-analysisland-use-and-land-cover-changeluc-mapslulcplotrasters
7.3 match 22 stars 5.80 score 19 scripts
alexchristensen
NetworkToolbox:Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis
Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershgoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Maintained by Alexander Christensen. Last updated 2 years ago.
6.0 match 23 stars 6.99 score 101 scripts 4 dependents
msuchard
MultiBD:Multivariate Birth-Death Processes
Computationally efficient functions to provide direct likelihood-based inference for partially-observed multivariate birth-death processes. Such processes range from a simple Yule model to the complex susceptible-infectious-removed model in disease dynamics. Efficient likelihood evaluation facilitates maximum likelihood estimation and Bayesian inference.
Maintained by Marc A. Suchard. Last updated 10 months ago.
7.3 match 6 stars 5.76 score 24 scripts
squidlobster
castor:Efficient Phylogenetics on Large Trees
Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Maintained by Stilianos Louca. Last updated 4 months ago.
7.0 match 2 stars 5.75 score 450 scripts 9 dependents
k5cents
metro:Washington Metropolitan Area Transit Authority API
The Washington Metropolitan Area Transit Authority is a government agency operating light rail and passenger buses in the Washington D.C. area. With a free developer account, access their 'Metro Transparent Data Sets API' <https://developer.wmata.com/> to return data frames of transit data for easy analysis.
Maintained by Kiernan Nicholls. Last updated 1 years ago.
metropublic-transportationtransit-datawashington-dcwmatawmata-api
11.2 match 4 stars 3.60 score 7 scriptsropensci
comtradr:Interface with the United Nations Comtrade API
Interface with and extract data from the United Nations 'Comtrade' API <https://comtradeplus.un.org/>. 'Comtrade' provides country level shipping data for a variety of commodities, these functions allow for easy API query and data returned as a tidy data frame.
Maintained by Paul Bochtler. Last updated 4 months ago.
apicomtradepeer-reviewedsupply-chain
4.5 match 66 stars 8.67 score 70 scripts
thinhong
denim:Generate and Simulate Deterministic Discrete-Time Compartmental Models
R package to build and simulate deterministic discrete-time compartmental models that can be non-Markov. Length of stay in each compartment can be defined to follow a parametric distribution (d_exponential(), d_gamma(), d_weibull(), d_lognormal()) or a non-parametric distribution (nonparametric()). Other supported types of transition from one compartment to another includes fixed transition (constant()), multinomial (multinomial()), fixed transition probability (transprob()).
Maintained by Anh Phan. Last updated 6 days ago.
6.7 match 2 stars 5.82 score 8 scripts
skranz
RelationalContracts:Characterize relational contracts in repated or stochastic games
Characterize relational contracts in repated or stochastic games. Can also analyse repeated negotiation equilibria.
Maintained by Sebastian Kranz. Last updated 4 years ago.
dynamic-gameeconomicsgame-theoryhold-upnash-equilibriumrepeated-gamestochastic-game
15.4 match 4 stars 2.48 score 15 scripts
greta-dev
greta.dynamics:Modelling Structured Dynamical Systems in 'greta'
A 'greta' extension for analysing transition matrices and ordinary differential equations representing dynamical systems. Provides functions for analysing transition matrices by iteration, and solving ordinary differential equations. This is an extension to the 'greta' software, Golding (2019) <doi:10.21105/joss.01601>.
Maintained by Nicholas Tierney. Last updated 4 months ago.
6.5 match 6 stars 5.72 score 11 scripts
oscarperpinan
solaR:Radiation and Photovoltaic Systems
Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.
Maintained by Oscar Perpiñán Lamigueiro. Last updated 25 days ago.
7.0 match 38 stars 5.32 score 55 scripts
ivanwilli
DemoKin:Estimate Population Kin Distribution
Estimate population kin counts and its distribution by type, age and sex. The package implements one-sex and two-sex framework for studying living-death availability, with time varying rates or not, and multi-stage model.
Maintained by Iván Williams. Last updated 18 days ago.
6.8 match 23 stars 5.51 score 20 scripts
archaeostat
ArchaeoPhases:Post-Processing of Markov Chain Monte Carlo Simulations for Chronological Modelling
Statistical analysis of archaeological dates and groups of dates. This package allows to post-process Markov Chain Monte Carlo (MCMC) simulations from 'ChronoModel' <https://chronomodel.com/>, 'Oxcal' <https://c14.arch.ox.ac.uk/oxcal.html> or 'BCal' <https://bcal.shef.ac.uk/>. It provides functions for the study of rhythms of the long term from the posterior distribution of a series of dates (tempo and activity plot). It also allows the estimation and visualization of time ranges from the posterior distribution of groups of dates (e.g. duration, transition and hiatus between successive phases) as described in Philippe and Vibet (2020) <doi:10.18637/jss.v093.c01>.
Maintained by Anne Philippe. Last updated 11 months ago.
archaeologybayesian-statisticsgeochronologymarkov-chainradiocarbon-dates
5.4 match 10 stars 6.90 score 66 scripts
predictiveecology
SpaDES.tools:Additional Tools for Developing Spatially Explicit Discrete Event Simulation (SpaDES) Models
Provides GIS and map utilities, plus additional modeling tools for developing cellular automata, dynamic raster models, and agent based models in 'SpaDES'. Included are various methods for spatial spreading, spatial agents, GIS operations, random map generation, and others. See '?SpaDES.tools' for an categorized overview of these additional tools. The suggested package 'NLMR' can be installed from the following repository: (<https://PredictiveEcology.r-universe.dev>).
Maintained by Alex M Chubaty. Last updated 4 months ago.
4.8 match 4 stars 7.55 score 52 scripts 6 dependents
svmiller
peacesciencer:Tools and Data for Quantitative Peace Science Research
These are useful tools and data sets for the study of quantitative peace science. The goal for this package is to include tools and data sets for doing original research that mimics well what a user would have to previously get from a software package that may not be well-sourced or well-supported. Those software bundles were useful the extent to which they encourage replications of long-standing analyses by starting the data-generating process from scratch. However, a lot of the functionality can be done relatively quickly and more transparently in the R programming language.
Maintained by Steve Miller. Last updated 3 days ago.
6.6 match 29 stars 5.49 score 211 scripts
bxc147
Epi:Statistical Analysis in Epidemiology
Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.
Maintained by Bendix Carstensen. Last updated 2 months ago.
3.6 match 4 stars 9.65 score 708 scripts 11 dependents
stevenmmortimer
salesforcer:An Implementation of 'Salesforce' APIs Using Tidy Principles
Functions connecting to the 'Salesforce' Platform APIs (REST, SOAP, Bulk 1.0, Bulk 2.0, Metadata, Reports and Dashboards) <https://trailhead.salesforce.com/content/learn/modules/api_basics/api_basics_overview>. "API" is an acronym for "application programming interface". Most all calls from these APIs are supported as they use CSV, XML or JSON data that can be parsed into R data structures. For more details please see the 'Salesforce' API documentation and this package's website <https://stevenmmortimer.github.io/salesforcer/> for more information, documentation, and examples.
Maintained by Steven M. Mortimer. Last updated 4 months ago.
api-wrappersr-languager-programmingsalesforcesalesforce-apis
3.8 match 82 stars 9.27 score 191 scripts
brry
berryFunctions:Function Collection Related to Plotting and Hydrology
Draw horizontal histograms, color scattered points by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings, use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays, fit multiple functions.
Maintained by Berry Boessenkool. Last updated 1 months ago.
3.7 match 13 stars 9.43 score 350 scripts 16 dependents
ipeagit
gtfstools:General Transit Feed Specification (GTFS) Editing and Analysing Tools
Utility functions to read, manipulate, analyse and write transit feeds in the General Transit Feed Specification (GTFS) data format.
Maintained by Daniel Herszenhut. Last updated 2 months ago.
gtfspublic-transportpublictransportcpp
3.7 match 40 stars 9.31 score 126 scripts 3 dependents
bmcclintock
momentuHMM:Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models
Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, discrete- or continuous-time HMMs, continuous- or discrete-space movement models, approximate Langevin diffusion models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Maintained by Brett McClintock. Last updated 1 months ago.
4.0 match 43 stars 8.47 score 162 scripts
modal-inria
cfda:Categorical Functional Data Analysis
Package for the analysis of categorical functional data. The main purpose is to compute an encoding (real functional variable) for each state <doi:10.3390/math9233074>. It also provides functions to perform basic statistical analysis on categorical functional data.
Maintained by Quentin Grimonprez. Last updated 2 months ago.
categorical-datafunctional-data-analysishacktoberfest
7.3 match 4 stars 4.60 score 3 scripts
cotterell
TDCM:The Transition Diagnostic Classification Model Framework
Estimate the transition diagnostic classification model (TDCM) described in Madison & Bradshaw (2018) <doi:10.1007/s11336-018-9638-5>, a longitudinal extension of the log-linear cognitive diagnosis model (LCDM) in Henson, Templin & Willse (2009) <doi:10.1007/s11336-008-9089-5>. As the LCDM subsumes many other diagnostic classification models (DCMs), many other DCMs can be estimated longitudinally via the TDCM. The 'TDCM' package includes functions to estimate the single-group and multigroup TDCM, summarize results of interest including item parameters, growth proportions, transition probabilities, transitional reliability, attribute correlations, model fit, and growth plots.
Maintained by Michael E. Cotterell. Last updated 4 months ago.
7.4 match 4.54 score 5 scripts
mapme-initiative
mapme.biodiversity:Efficient Monitoring of Global Biodiversity Portfolios
Biodiversity areas, especially primary forest, serve a multitude of functions for local economy, regional functionality of the ecosystems as well as the global health of our planet. Recently, adverse changes in human land use practices and climatic responses to increased greenhouse gas emissions, put these biodiversity areas under a variety of different threats. The present package helps to analyse a number of biodiversity indicators based on freely available geographical datasets. It supports computational efficient routines that allow the analysis of potentially global biodiversity portfolios. The primary use case of the package is to support evidence based reporting of an organization's effort to protect biodiversity areas under threat and to identify regions were intervention is most duly needed.
Maintained by Darius A. Görgen. Last updated 3 months ago.
environmenteogismapmespatialsustainability
3.6 match 35 stars 9.24 score 287 scripts
dallenmidd
IxPopDyMod:Framework for Tick Population and Infection Modeling
Code to specify, run, and then visualize and analyze the results of Ixodidae (hard-bodied ticks) population and infection dynamics models. Such models exist in the literature, but the source code to run them is not always available. 'IxPopDyMod' provides an easy way for these models to be written and shared.
Maintained by Myles Stokowski. Last updated 4 months ago.
11.1 match 2 stars 3.00 score 6 scripts
theomichelot
moveHMM:Animal Movement Modelling using Hidden Markov Models
Provides tools for animal movement modelling using hidden Markov models. These include processing of tracking data, fitting hidden Markov models to movement data, visualization of data and fitted model, decoding of the state process, etc. <doi:10.1111/2041-210X.12578>.
Maintained by Theo Michelot. Last updated 1 years ago.
3.8 match 38 stars 8.63 score 112 scripts
stocnet
goldfish:Statistical Network Models for Dynamic Network Data
Tools for fitting statistical network models to dynamic network data. Can be used for fitting both dynamic network actor models ('DyNAMs') and relational event models ('REMs'). Stadtfeld, Hollway, and Block (2017a) <doi:10.1177/0081175017709295>, Stadtfeld, Hollway, and Block (2017b) <doi:10.1177/0081175017733457>, Stadtfeld and Block (2017) <doi:10.15195/v4.a14>, Hoffman et al. (2020) <doi:10.1017/nws.2020.3>.
Maintained by Alvaro Uzaheta. Last updated 6 months ago.
dynamnetwork-modellingremstatistical-network-analysisopenblascppopenmp
4.1 match 61 stars 7.91 score 44 scriptsbioc
GenVisR:Genomic Visualizations in R
Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.
Maintained by Zachary Skidmore. Last updated 5 months ago.
infrastructuredatarepresentationclassificationdnaseq
3.1 match 215 stars 9.87 score 76 scripts
ketchbrookanalytics
migrate:Create Credit State Migration (Transition) Matrices
Tools to help convert credit risk data at two timepoints into traditional credit state migration (aka, "transition") matrices. At a higher level, 'migrate' is intended to help an analyst understand how risk moved in their credit portfolio over a time interval. References to this methodology include: 1. Schuermann, T. (2008) <doi:10.1002/9780470061596.risk0409>. 2. Perederiy, V. (2017) <doi:10.48550/arXiv.1708.00062>.
Maintained by Michael Thomas. Last updated 8 months ago.
credit-riskfinancerisk-management
5.2 match 6 stars 5.89 score 13 scripts
mcandocia
keyToEnglish:Convert Data to Memorable Phrases
Convert keys and other values to memorable phrases. Includes some methods to build lists of words.
Maintained by Max Candocia. Last updated 4 years ago.
11.3 match 1 stars 2.70 score 3 scriptsmhahsler
markovDP:Infrastructure for Discrete-Time Markov Decision Processes (MDP)
Provides the infrastructure to work with Markov Decision Processes (MDPs) in R. The focus is on convenience in formulating MDPs, the support of sparse representations (using sparse matrices, lists and data.frames) and visualization of results. Some key components are implemented in C++ to speed up computation. Several popular solvers are implemented.
Maintained by Michael Hahsler. Last updated 3 days ago.
control-theorymarkov-decision-processoptimizationcpp
5.5 match 7 stars 5.51 score 4 scripts
jlaake
RMark:R Code for Mark Analysis
An interface to the software package MARK that constructs input files for MARK and extracts the output. MARK was developed by Gary White and is freely available at <http://www.phidot.org/software/mark/downloads/> but is not open source.
Maintained by Jeff Laake. Last updated 3 years ago.
6.1 match 4.90 score 366 scripts 4 dependents
urbananalyst
gtfsrouter:Routing with 'GTFS' (General Transit Feed Specification) Data
Use 'GTFS' (General Transit Feed Specification) data for routing from nominated start and end stations, for extracting 'isochrones', and travel times from any nominated start station to all other stations.
Maintained by Mark Padgham. Last updated 27 days ago.
gtfsgtfsrouterpublic-transportationroutercpp
3.4 match 89 stars 8.78 score 21 scripts 3 dependents
prabhanjan-tattar
ACSWR:A Companion Package for the Book "A Course in Statistics with R"
A book designed to meet the requirements of masters students. Tattar, P.N., Suresh, R., and Manjunath, B.G. "A Course in Statistics with R", J. Wiley, ISBN 978-1-119-15272-9.
Maintained by Prabhanjan Tattar. Last updated 10 years ago.
14.5 match 2.03 score 106 scripts
avdrark
mokken:Conducts Mokken Scale Analysis
Contains functions for performing Mokken scale analysis on test and questionnaire data. It includes an automated item selection algorithm, and various checks of model assumptions.
Maintained by L. Andries van der Ark. Last updated 9 months ago.
8.5 match 2 stars 3.45 score 68 scripts
bieneschwarze
MicSim:Performing Continuous-Time Microsimulation
This toolkit allows performing continuous-time microsimulation for a wide range of life science (demography, social sciences, epidemiology) applications. Individual life-courses are specified by a continuous-time multi-state model.
Maintained by Sabine Zinn. Last updated 2 years ago.
8.6 match 2 stars 3.41 score 13 scripts
danheck
MCMCprecision:Precision of Discrete Parameters in Transdimensional MCMC
Estimates the precision of transdimensional Markov chain Monte Carlo (MCMC) output, which is often used for Bayesian analysis of models with different dimensionality (e.g., model selection). Transdimensional MCMC (e.g., reversible jump MCMC) relies on sampling a discrete model-indicator variable to estimate the posterior model probabilities. If only few switches occur between the models, precision may be low and assessment based on the assumption of independent samples misleading. Based on the observed transition matrix of the indicator variable, the method of Heck, Overstall, Gronau, & Wagenmakers (2019, Statistics & Computing, 29, 631-643) <doi:10.1007/s11222-018-9828-0> draws posterior samples of the stationary distribution to (a) assess the uncertainty in the estimated posterior model probabilities and (b) estimate the effective sample size of the MCMC output.
Maintained by Daniel W. Heck. Last updated 9 months ago.
5.3 match 5.49 score 52 scripts 4 dependents
hanettools
Perc:Using Percolation and Conductance to Find Information Flow Certainty in a Direct Network
To find the certainty of dominance interactions with indirect interactions being considered.
Maintained by Jessica Vandeleest. Last updated 4 years ago.
4.9 match 5.88 score 38 scripts
solarization
solaR2:Radiation and Photovoltaic Systems
Provides tools for calculating solar geometry, solar radiation on horizontal and inclined planes, and simulating the performance of various photovoltaic (PV) systems. Supports daily and intradaily irradiation data, enabling detailed analysis of grid-connected and water-pumping PV systems, including shading effects and solar angle calculations.
Maintained by Francisco Delgado-López. Last updated 25 days ago.
7.0 match 1 stars 4.08 score 5 scripts
dstgithub
GrpString:Patterns and Statistical Differences Between Two Groups of Strings
Methods include converting series of event names to strings, finding common patterns in a group of strings, discovering featured patterns when comparing two groups of strings as well as the number and starting position of each pattern in each string, obtaining transition matrix, computing transition entropy, statistically comparing the difference between two groups of strings, and clustering string groups. Event names can be any action names or labels such as events in log files or areas of interest (AOIs) in eye tracking research.
Maintained by Hui (Tom) Tang. Last updated 7 years ago.
8.2 match 2 stars 3.48 score 30 scriptscran
evmix:Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation
The usual distribution functions, maximum likelihood inference and model diagnostics for univariate stationary extreme value mixture models are provided. Kernel density estimation including various boundary corrected kernel density estimation methods and a wide choice of kernels, with cross-validation likelihood based bandwidth estimator. Reasonable consistency with the base functions in the 'evd' package is provided, so that users can safely interchange most code.
Maintained by Carl Scarrott. Last updated 6 years ago.
10.0 match 2 stars 2.85 score 7 dependentsbioc
lipidr:Data Mining and Analysis of Lipidomics Datasets
lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, total chain length and unsaturation.
Maintained by Ahmed Mohamed. Last updated 5 months ago.
lipidomicsmassspectrometrynormalizationqualitycontrolvisualizationbioconductor
3.8 match 29 stars 7.44 score 40 scripts
jassler
socialranking:Social Ranking Solutions for Power Relations on Coalitions
The notion of power index has been widely used in literature to evaluate the influence of individual players (e.g., voters, political parties, nations, stockholders, etc.) involved in a collective decision situation like an electoral system, a parliament, a council, a management board, etc., where players may form coalitions. Traditionally this ranking is determined through numerical evaluation. More often than not however only ordinal data between coalitions is known. The package 'socialranking' offers a set of solutions to rank players based on a transitive ranking between coalitions, including through CP-Majority, ordinal Banzhaf or lexicographic excellence solution summarized by Tahar Allouche, Bruno Escoffier, Stefano Moretti and Meltem Öztürk (2020, <doi:10.24963/ijcai.2020/3>).
Maintained by Felix Fritz. Last updated 2 days ago.
5.4 match 6 stars 5.08 score 6 scripts
giabaio
survHE:Survival Analysis in Health Economic Evaluation
Contains a suite of functions for survival analysis in health economics. These can be used to run survival models under a frequentist (based on maximum likelihood) or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian Monte Carlo). To run the Bayesian models, the user needs to install additional modules (packages), i.e. 'survHEinla' and 'survHEhmc'. These can be installed using 'remotes::install_github' from their GitHub repositories: (<https://github.com/giabaio/survHEhmc> and <https://github.com/giabaio/survHEinla/> respectively). 'survHEinla' is based on the package INLA, which is available for download at <https://inla.r-inla-download.org/R/stable/>. The user can specify a set of parametric models using a common notation and select the preferred mode of inference. The results can also be post-processed to produce probabilistic sensitivity analysis and can be used to export the output to an Excel file (e.g. for a Markov model, as often done by modellers and practitioners). <doi:10.18637/jss.v095.i14>.
Maintained by Gianluca Baio. Last updated 9 days ago.
frequentisthamiltonian-monte-carlohealth-economic-evaluationinlaplotting-survival-curvesrstansurvival-analysissurvival-modelsuncertaintyopenjdk
4.0 match 42 stars 6.88 score 2 dependents
matthieustigler
tsDyn:Nonlinear Time Series Models with Regime Switching
Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Maintained by Matthieu Stigler. Last updated 5 months ago.
2.6 match 34 stars 10.56 score 684 scripts 3 dependents
marc-girondot
embryogrowth:Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Tools to analyze the embryo growth and the sexualisation thermal reaction norms. See <doi:10.7717/peerj.8451> for tsd functions; see <doi:10.1016/j.jtherbio.2014.08.005> for thermal reaction norm of embryo growth.
Maintained by Marc Girondot. Last updated 7 months ago.
11.0 match 1 stars 2.40 score 252 scripts
pik-piam
quitte:Bits and pieces of code to use with quitte-style data frames
A collection of functions for easily dealing with quitte-style data frames, doing multi-model comparisons and plots.
Maintained by Michaja Pehl. Last updated 2 days ago.
3.2 match 8.22 score 184 scripts 35 dependents
mikkoku
efdm:Simulate Forest Resources with the European Forestry Dynamics Model
An implementation of European Forestry Dynamics Model (EFDM) and an estimation algorithm for the transition probabilities. The EFDM is a large-scale forest model that simulates the development of the forest and estimates volume of wood harvested for any given forested area. This estimate can be broken down by, for example, species, site quality, management regime and ownership category. See Packalen et al. (2015) <doi:10.2788/153990>.
Maintained by Mikko Kuronen. Last updated 2 months ago.
6.8 match 3.78 score 12 scriptsbioc
epigraHMM:Epigenomic R-based analysis with hidden Markov models
epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.
Maintained by Pedro Baldoni. Last updated 5 months ago.
chipseqatacseqdnaseseqhiddenmarkovmodelepigeneticszlibopenblascppopenmp
5.1 match 4.94 score 88 scripts
rmi-pacta
pacta.multi.loanbook:Run 'PACTA' on Multiple Loan Books Easily
Run Paris Agreement Capital Transition Assessment ('PACTA') analyses on multiple loan books in a structured way. Provides access to standard 'PACTA' metrics and additional 'PACTA'-related metrics for multiple loan books. Results take the form of 'csv' files and plots and are exported to user-specified project paths.
Maintained by Jacob Kastl. Last updated 2 days ago.
climate-changepactapactaversesustainable-finance
3.9 match 6.48 score 4 scripts
thibautjombart
adegenet:Exploratory Analysis of Genetic and Genomic Data
Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
Maintained by Zhian N. Kamvar. Last updated 1 months ago.
2.0 match 182 stars 12.60 score 1.9k scripts 29 dependents
stan-dev
bayesplot:Plotting for Bayesian Models
Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow advocated in Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>. The package is designed not only to provide convenient functionality for users, but also a common set of functions that can be easily used by developers working on a variety of R packages for Bayesian modeling, particularly (but not exclusively) packages interfacing with 'Stan'.
Maintained by Jonah Gabry. Last updated 1 months ago.
bayesianggplot2mcmcpandocstanstatistical-graphicsvisualization
1.5 match 436 stars 16.69 score 6.5k scripts 98 dependents
crlsierra
SoilR:Models of Soil Organic Matter Decomposition
Functions for modeling Soil Organic Matter decomposition in terrestrial ecosystems with linear and nonlinear systems of differential equations. The package implements models according to the compartmental system representation described in Sierra and others (2012) <doi:10.5194/gmd-5-1045-2012> and Sierra and others (2014) <doi:10.5194/gmd-7-1919-2014>.
Maintained by Carlos A. Sierra. Last updated 1 years ago.
8.7 match 5 stars 2.88 score 153 scripts
steps-dev
steps:Spatially- and Temporally-Explicit Population Simulator
Software to simulate population change across space and time. Visintin et al. (2020) <doi:10.1111/2041-210X.13354>.
Maintained by Casey Visintin. Last updated 1 years ago.
3.8 match 18 stars 6.66 score 84 scriptsbioc
segmenter:Perform Chromatin Segmentation Analysis in R by Calling ChromHMM
Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin's underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation.
Maintained by Mahmoud Ahmed. Last updated 5 months ago.
softwarehistonemodificationbioconductorchromhmmsegmentation-an
6.9 match 4 stars 3.60 score 9 scripts
radicalcommecol
cxr:A Toolbox for Modelling Species Coexistence in R
Recent developments in modern coexistence theory have advanced our understanding on how species are able to persist and co-occur with other species at varying abundances. However, applying this mathematical framework to empirical data is still challenging, precluding a larger adoption of the theoretical tools developed by empiricists. This package provides a complete toolbox for modelling interaction effects between species, and calculate fitness and niche differences. The functions are flexible, may accept covariates, and different fitting algorithms can be used. A full description of the underlying methods is available in García-Callejas, D., Godoy, O., and Bartomeus, I. (2020) <doi:10.1111/2041-210X.13443>. Furthermore, the package provides a series of functions to calculate dynamics for stage-structured populations across sites.
Maintained by David Garcia-Callejas. Last updated 1 months ago.
3.8 match 10 stars 6.51 score 27 scripts
soodoku
guess:Adjust Estimates of Learning for Guessing
Adjust Estimates of Learning for Guessing. The package provides standard guessing correction, and a latent class model that leverages informative pre-post transitions. For details of the latent class model, see <http://gsood.com/research/papers/guess.pdf>.
Maintained by Gaurav Sood. Last updated 3 years ago.
5.7 match 3 stars 4.29 score 13 scripts
hidef-aerial-surveying
stochLAB:Stochastic Collision Risk Model
Collision Risk Models for avian fauna (seabird and migratory birds) at offshore wind farms. The base deterministic model is derived from Band (2012) <https://tethys.pnnl.gov/publications/using-collision-risk-model-assess-bird-collision-risks-offshore-wind-farms>. This was further expanded on by Masden (2015) <doi:10.7489/1659-1> and code used here is heavily derived from this work with input from Dr A. Cook at the British Trust for Ornithology. These collision risk models are useful for marine ornithologists who are working in the offshore wind industry, particularly in UK waters. However, many of the species included in the stochastic collision risk models (stoch_crm) can also be found in the North Atlantic in the United States and Canada, and could be applied there.
Maintained by Grant Humphries. Last updated 2 years ago.
collision-riskmigratoryspeciesoffshore-windseabirds
5.1 match 6 stars 4.78 score 10 scriptsipeagit
gtfs2emis:Estimating Public Transport Emissions from General Transit Feed Specification (GTFS) Data
A bottom up model to estimate the emission levels of public transport systems based on General Transit Feed Specification (GTFS) data. The package requires two main inputs: i) Public transport data in the GTFS standard format; and ii) Some basic information on fleet characteristics such as fleet age, technology, fuel and Euro stage. As it stands, the package estimates several pollutants at high spatial and temporal resolutions. Pollution levels can be calculated for specific transport routes, trips, time of the day or for the transport system as a whole. The output with emission estimates can be extracted in different formats, supporting analysis on how emission levels vary across space, time and by fleet characteristics. A full description of the methods used in the 'gtfs2emis' model is presented in Vieira, J. P. B.; Pereira, R. H. M.; Andrade, P. R. (2022) <doi:10.31219/osf.io/8m2cy>.
Maintained by Joao Bazzo. Last updated 2 months ago.
emissionsenvironmental-modellinggtfspublic-transportrspatialtransport
3.3 match 28 stars 7.47 score 29 scripts
higgi13425
medicaldata:Data Package for Medical Datasets
Provides access to well-documented medical datasets for teaching. Featuring several from the Teaching of Statistics in the Health Sciences website <https://www.causeweb.org/tshs/category/dataset/>, a few reconstructed datasets of historical significance in medical research, some reformatted and extended from existing R packages, and some data donations.
Maintained by Peter Higgins. Last updated 2 years ago.
3.3 match 48 stars 7.43 score 317 scripts
sdctools
ptable:Generation of Perturbation Tables for the Cell-Key Method
Tabular data from statistical institutes and agencies are mostly confidential and must be protected prior to publications. The cell-key method is a post-tabular Statistical Disclosure Control perturbation technique that adds random noise to tabular data. The statistical properties of the perturbations are defined by some noise probability distributions - also referred to as perturbation tables. This tool can be used to create the perturbation tables based on a maximum entropy approach as described for example in Giessing (2016) <doi:10.1007/978-3-319-45381-1_18>. The perturbation tables created can finally be used to apply a cell-key method to frequency count or magnitude tables.
Maintained by Tobias Enderle. Last updated 2 years ago.
5.3 match 1 stars 4.59 score 13 scripts 1 dependents
jonesor
Rage:Life History Metrics from Matrix Population Models
Functions for calculating life history metrics using matrix population models ('MPMs'). Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.
Maintained by Owen Jones. Last updated 3 months ago.
2.9 match 11 stars 8.17 score 62 scripts 1 dependents
nlmixr2
nlmixr2lib:A Model Library for 'nlmixr2'
A model library for 'nlmixr2'. The models include (and plan to include) pharmacokinetic, pharmacodynamic, and disease models used in pharmacometrics. Where applicable, references for each model are included in the meta-data for each individual model. The package also includes model composition and modification functions to make model updates easier.
Maintained by Bill Denney. Last updated 2 months ago.
3.8 match 6 stars 6.38 score 9 scripts
ingmarvisser
depmixS4:Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4
Fits latent (hidden) Markov models on mixed categorical and continuous (time series) data, otherwise known as dependent mixture models, see Visser & Speekenbrink (2010, <DOI:10.18637/jss.v036.i07>).
Maintained by Ingmar Visser. Last updated 4 years ago.
3.5 match 12 stars 6.87 score 308 scripts 4 dependentsglenndavis52
colorSpec:Color Calculations with Emphasis on Spectral Data
Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners. Build complex systems from simpler parts using a spectral product algebra. For light sources, compute CCT, CRI, SSI, and IES TM-30 reports. For object colors, compute optimal colors and Logvinenko coordinates. Work with the standard CIE illuminants and color matching functions, and read spectra from text files, including CGATS files. Estimate a spectrum from its response. A user guide and 9 vignettes are included.
Maintained by Glenn Davis. Last updated 1 months ago.
3.8 match 2 stars 6.34 score 73 scripts 5 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
4.5 match 6 stars 5.26 score 8 scripts
vgxhc
ntdr:Retrieve Data from the National Transit Database
Downloads the latest 'National Transit Database' data, processes it, and returns in a tidy data format.
Maintained by Harald Kliems. Last updated 5 months ago.
5.3 match 3 stars 4.48 score 7 scripts
ncss-tech
aqp:Algorithms for Quantitative Pedology
The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Maintained by Dylan Beaudette. Last updated 29 days ago.
digital-soil-mappingncss-technrcspedologypedometricssoilsoil-surveyusda
2.0 match 55 stars 11.77 score 1.2k scripts 2 dependentsstan-dev
rstanarm:Bayesian Applied Regression Modeling via Stan
Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
Maintained by Ben Goodrich. Last updated 9 months ago.
bayesianbayesian-data-analysisbayesian-inferencebayesian-methodsbayesian-statisticsmultilevel-modelsrstanrstanarmstanstatistical-modelingcpp
1.5 match 393 stars 15.68 score 5.0k scripts 13 dependents
ruibarrigana
ebmstate:Empirical Bayes Multi-State Cox Model
Implements an empirical Bayes, multi-state Cox model for survival analysis. Run "?'ebmstate-package'" for details. See also Schall (1991) <doi:10.1093/biomet/78.4.719>.
Maintained by Rui Costa. Last updated 5 months ago.
13.7 match 1.70 score 6 scripts
anespinosa
netmem:Social Network Measures using Matrices
Measures to describe and manipulate networks using matrices.
Maintained by Alejandro Espinosa-Rada. Last updated 5 days ago.
matricesmultilayer-networksnetwork-analysisnetwork-sciencesnasocial-networksocial-network-analysissociology
5.3 match 11 stars 4.33 score 13 scripts
jsanchezalv
WARDEN:Workflows for Health Technology Assessments in R using Discrete EveNts
Toolkit to support and perform discrete event simulations without resource constraints in the context of health technology assessments (HTA). The package focuses on cost-effectiveness modelling and aims to be submission-ready to relevant HTA bodies in alignment with 'NICE TSD 15' <https://www.sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>. More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.
Maintained by Javier Sanchez Alvarez. Last updated 3 months ago.
3.3 match 6 stars 6.69 score 9 scriptsjlaake
marked:Mark-Recapture Analysis for Survival and Abundance Estimation
Functions for fitting various models to capture-recapture data including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and the multi-variate state model structure for survival estimation and POPAN structured Jolly-Seber models for abundance estimation. There are also Hidden Markov model (HMM) implementations of CJS and multistate models with and without state uncertainty and a simulation capability for HMM models.
Maintained by Jeff Laake. Last updated 1 years ago.
5.4 match 1 stars 4.05 score 85 scripts 1 dependents
svizcaya
gems:Generalized Multistate Simulation Model
Simulate and analyze multistate models with general hazard functions. gems provides functionality for the preparation of hazard functions and parameters, simulation from a general multistate model and predicting future events. The multistate model is not required to be a Markov model and may take the history of previous events into account. In the basic version, it allows to simulate from transition-specific hazard function, whose parameters are multivariable normally distributed.
Maintained by Luisa Salazar Vizcaya. Last updated 8 years ago.
8.7 match 2.52 score 33 scripts
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.
5.6 match 1 stars 3.87 score 82 scripts 3 dependents
symbolixau
googleway:Accesses Google Maps APIs to Retrieve Data and Plot Maps
Provides a mechanism to plot a 'Google Map' from 'R' and overlay it with shapes and markers. Also provides access to 'Google Maps' APIs, including places, directions, roads, distances, geocoding, elevation and timezone.
Maintained by David Cooley. Last updated 6 months ago.
google-mapgoogle-mapsgoogle-maps-apigoogle-maps-javascript-apispatialspatial-analysis
2.3 match 236 stars 9.67 score 536 scripts 2 dependents
choi-phd
maat:Multiple Administrations Adaptive Testing
Provides an extension of the shadow-test approach to computerized adaptive testing (CAT) implemented in the 'TestDesign' package for the assessment framework involving multiple tests administered periodically throughout the year. This framework is referred to as the Multiple Administrations Adaptive Testing (MAAT) and supports multiple item pools vertically scaled and multiple phases (stages) of CAT within each test. Between phases and tests, transitioning from one item pool (and associated constraints) to another is allowed as deemed necessary to enhance the quality of measurement.
Maintained by Seung W. Choi. Last updated 9 months ago.
5.4 match 4.00 score 5 scripts
schochastics
netrankr:Analyzing Partial Rankings in Networks
Implements methods for centrality related analyses of networks. While the package includes the possibility to build more than 20 indices, its main focus lies on index-free assessment of centrality via partial rankings obtained by neighborhood-inclusion or positional dominance. These partial rankings can be analyzed with different methods, including probabilistic methods like computing expected node ranks and relative rank probabilities (how likely is it that a node is more central than another?). The methodology is described in depth in the vignettes and in Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Maintained by David Schoch. Last updated 1 months ago.
network-analysisnetwork-centralityopenblascppopenmp
2.3 match 49 stars 9.56 score 91 scripts 2 dependentsbioc
HPiP:Host-Pathogen Interaction Prediction
HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data unavailability for HP-PPI network reconstructions. Moreover, establishing computational frameworks in that regard will reveal mechanistic insights into infectious diseases and suggest potential HP-PPI targets, thus narrowing down the range of possible candidates for subsequent wet-lab experimental validations.
Maintained by Matineh Rahmatbakhsh. Last updated 5 months ago.
proteomicssystemsbiologynetworkinferencestructuralpredictiongenepredictionnetwork
4.3 match 3 stars 4.95 score 6 scripts
danielturek
nimbleSCR:Spatial Capture-Recapture (SCR) Methods Using 'nimble'
Provides utility functions, distributions, and fitting methods for Bayesian Spatial Capture-Recapture (SCR) and Open Population Spatial Capture-Recapture (OPSCR) modelling using the nimble package (de Valpine et al. 2017 <doi:10.1080/10618600.2016.1172487 >). Development of the package was motivated primarily by the need for flexible and efficient analysis of large-scale SCR data (Bischof et al. 2020 <doi:10.1073/pnas.2011383117 >). Computational methods and techniques implemented in nimbleSCR include those discussed in Turek et al. 2021 <doi:10.1002/ecs2.3385>; among others. For a recent application of nimbleSCR, see Milleret et al. (2021) <doi:10.1098/rsbl.2021.0128>.
Maintained by Daniel Turek. Last updated 2 years ago.
4.8 match 4.29 score 388 scriptsbioc
bnem:Training of logical models from indirect measurements of perturbation experiments
bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).
Maintained by Martin Pirkl. Last updated 5 months ago.
pathwayssystemsbiologynetworkinferencenetworkgeneexpressiongeneregulationpreprocessing
4.5 match 2 stars 4.60 score 5 scripts
epiforesite
facilityepimath:Analyze Mathematical Models of Healthcare Facility Transmission
Calculate useful quantities for a user-defined differential equation model of infectious disease transmission among individuals in a healthcare facility. Input rates of transition between states of individuals with and without the disease-causing organism, distributions of states at facility admission, relative infectivity of transmissible states, and the facility length of stay distribution. Calculate the model equilibrium and the basic facility reproduction number, as described in Toth et al. (2025) <doi:10.1101/2025.02.21.25322698>.
Maintained by Damon Toth. Last updated 5 days ago.
4.0 match 5.18 score
duncanobrien
EWSmethods:Forecasting Tipping Points at the Community Level
Rolling and expanding window approaches to assessing abundance based early warning signals, non-equilibrium resilience measures, and machine learning. See Dakos et al. (2012) <doi:10.1371/journal.pone.0041010>, Deb et al. (2022) <doi:10.1098/rsos.211475>, Drake and Griffen (2010) <doi:10.1038/nature09389>, Ushio et al. (2018) <doi:10.1038/nature25504> and Weinans et al. (2021) <doi:10.1038/s41598-021-87839-y> for methodological details. Graphical presentation of the outputs are also provided for clear and publishable figures. Visit the 'EWSmethods' website for more information, and tutorials.
Maintained by Duncan OBrien. Last updated 7 months ago.
3.8 match 8 stars 5.51 score 20 scripts
keefe-murphy
MEDseq:Mixtures of Exponential-Distance Models with Covariates
Implements a model-based clustering method for categorical life-course sequences relying on mixtures of exponential-distance models introduced by Murphy et al. (2021) <doi:10.1111/rssa.12712>. A range of flexible precision parameter settings corresponding to weighted generalisations of the Hamming distance metric are considered, along with the potential inclusion of a noise component. Gating covariates can be supplied in order to relate sequences to baseline characteristics and sampling weights are also accommodated. The models are fitted using the EM algorithm and tools for visualising the results are also provided.
Maintained by Keefe Murphy. Last updated 6 days ago.
distance-based-clusteringmixture-of-expertsmodel-based-clusteringsequence-analysis
3.8 match 5 stars 5.49 score 25 scriptsbioc
rBiopaxParser:Parses BioPax files and represents them in R
Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.
Maintained by Frank Kramer. Last updated 5 months ago.
3.5 match 10 stars 5.85 score 7 scripts
loelschlaeger
oeli:Utilities for Developing Data Science Software
Some general helper functions that I (and maybe others) find useful when developing data science software.
Maintained by Lennart Oelschläger. Last updated 4 months ago.
3.8 match 2 stars 5.42 score 1 scripts 4 dependents
kurthornik
relations:Data Structures and Algorithms for Relations
Data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.
Maintained by Kurt Hornik. Last updated 25 days ago.
4.0 match 5.04 score 58 scripts 14 dependents
ericpante
marmap:Import, Plot and Analyze Bathymetric and Topographic Data
Import xyz data from the NOAA (National Oceanic and Atmospheric Administration, <https://www.noaa.gov>), GEBCO (General Bathymetric Chart of the Oceans, <https://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Maintained by Benoit Simon-Bouhet. Last updated 8 months ago.
2.3 match 32 stars 8.86 score 524 scripts 1 dependents
kainhofer
MortalityTables:A Framework for Various Types of Mortality / Life Tables
Classes to implement, analyze and plot cohort life tables for actuarial calculations. Birth-year dependent cohort mortality tables using a yearly trend to extrapolate from a base year are implemented, as well as period life table, cohort life tables using an age shift, and merged life tables. Additionally, several data sets from various countries are included to provide widely-used tables out of the box.
Maintained by Reinhold Kainhofer. Last updated 1 years ago.
3.5 match 1 stars 5.70 score 84 scripts 2 dependentsbioc
StructuralVariantAnnotation:Variant annotations for structural variants
StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.
Maintained by Daniel Cameron. Last updated 5 months ago.
dataimportsequencingannotationgeneticsvariantannotation
3.2 match 6.26 score 102 scripts 2 dependents
tguillerme
treats:Trees and Traits Simulations
A modular package for simulating phylogenetic trees and species traits jointly. Trees can be simulated using modular birth-death parameters (e.g. changing starting parameters or algorithm rules). Traits can be simulated in any way designed by the user. The growth of the tree and the traits can influence each other through modifiers objects providing rules for affecting each other. Finally, events can be created to modify both the tree and the traits under specific conditions ( Guillerme, 2024 <DOI:10.1111/2041-210X.14306>).
Maintained by Thomas Guillerme. Last updated 2 months ago.
4.3 match 3 stars 4.63 score 19 scriptsbioc
atSNP:Affinity test for identifying regulatory SNPs
atSNP performs affinity tests of motif matches with the SNP or the reference genomes and SNP-led changes in motif matches.
Maintained by Sunyoung Shin. Last updated 5 months ago.
softwarechipseqgenomeannotationmotifannotationvisualizationcpp
3.4 match 1 stars 5.73 score 36 scripts
pauljohn32
kutils:Project Management Tools
Tools for data importation, recoding, and inspection. There are functions to create new project folders, R code templates, create uniquely named output directories, and to quickly obtain a visual summary for each variable in a data frame. The main feature here is the systematic implementation of the "variable key" framework for data importation and recoding. We are eager to have community feedback about the variable key and the vignette about it. In version 1.7, the function 'semTable' is removed. It was deprecated since 1.67. That is provided in a separate package, 'semTable'.
Maintained by Paul Johnson. Last updated 1 years ago.
3.3 match 5.85 score 110 scripts 20 dependents
loukiaspin
tracenma:Database for Developing Transitivity Methodology in Network Meta-Analysis
Functions to access the database of 217 data-frames with aggregate study-level characteristics (that may act as effect modifiers) extracted from published systematic reviews with network meta-analysis. The database shall only be used for developing and appraising the methodology to assess the transitivity assumption quantitatively.
Maintained by Loukia Spineli. Last updated 2 months ago.
5.1 match 1 stars 3.74 score 1 scriptsrmi-pacta
pacta.portfolio.audit:Functions for Calculating Audit Statistics for PACTA on Capital Transition Monitor
These utils include functions that facilitate calculation of useful audit statistics for PACTA on Capital Transition Monitor.
Maintained by CJ Yetman. Last updated 3 months ago.
climate-changepactapactaversesustainable-finance
5.1 match 1 stars 3.71 score 5 scripts 1 dependents
cranhaven
rock:Reproducible Open Coding Kit
The Reproducible Open Coding Kit ('ROCK', and this package, 'rock') was developed to facilitate reproducible and open coding, specifically geared towards qualitative research methods. Although it is a general-purpose toolkit, three specific applications have been implemented, specifically an interface to the 'rENA' package that implements Epistemic Network Analysis ('ENA'), means to process notes from Cognitive Interviews ('CIs'), and means to work with decentralized construct taxonomies ('DCTs'). The 'ROCK' and this 'rock' package are described in the ROCK book <https://rockbook.org> and more information, such as tutorials, is available at <https://rock.science>.
Maintained by Gjalt-Jorn Peters. Last updated 8 days ago.
5.5 match 5 stars 3.40 score
boehringer-ingelheim
oncomsm:Bayesian Multi-State Models for Early Oncology
Implements methods to fit a parametric Bayesian multi-state model to tumor response data. The model can be used to sample from the predictive distribution to impute missing data and calculate probability of success for custom decision criteria in early clinical trials during an ongoing trial. The inference is implemented using 'stan'.
Maintained by Kevin Kunzmann. Last updated 2 years ago.
3.2 match 8 stars 5.80 score 13 scripts
florianpein
stepR:Multiscale Change-Point Inference
Allows fitting of step-functions to univariate serial data where neither the number of jumps nor their positions is known by implementing the multiscale regression estimators SMUCE, simulataneous multiscale changepoint estimator, (K. Frick, A. Munk and H. Sieling, 2014) <doi:10.1111/rssb.12047> and HSMUCE, heterogeneous SMUCE, (F. Pein, H. Sieling and A. Munk, 2017) <doi:10.1111/rssb.12202>. In addition, confidence intervals for the change-point locations and bands for the unknown signal can be obtained.
Maintained by Pein Florian. Last updated 5 months ago.
5.2 match 1 stars 3.58 score 64 scripts
albertoarcagni
parsec:Partial Orders in Socio-Economics
Implements tools for the analysis of partially ordered data, with a particular focus on the evaluation of multidimensional systems of indicators and on the analysis of poverty. References, Fattore M. (2016) <doi:10.1007/s11205-015-1059-6> Fattore M., Arcagni A. (2016) <doi:10.1007/s11205-016-1501-4> Arcagni A. (2017) <doi:10.1007/978-3-319-45421-4_19>.
Maintained by Alberto Arcagni. Last updated 2 years ago.
8.3 match 1 stars 2.21 score 54 scripts 1 dependents
globalecologylab
poems:Pattern-Oriented Ensemble Modeling System
A framework of interoperable R6 classes (Chang, 2020, <https://CRAN.R-project.org/package=R6>) for building ensembles of viable models via the pattern-oriented modeling (POM) approach (Grimm et al.,2005, <doi:10.1126/science.1116681>). The package includes classes for encapsulating and generating model parameters, and managing the POM workflow. The workflow includes: model setup; generating model parameters via Latin hyper-cube sampling (Iman & Conover, 1980, <doi:10.1080/03610928008827996>); running multiple sampled model simulations; collating summary results; and validating and selecting an ensemble of models that best match known patterns. By default, model validation and selection utilizes an approximate Bayesian computation (ABC) approach (Beaumont et al., 2002, <doi:10.1093/genetics/162.4.2025>), although alternative user-defined functionality could be employed. The package includes a spatially explicit demographic population model simulation engine, which incorporates default functionality for density dependence, correlated environmental stochasticity, stage-based transitions, and distance-based dispersal. The user may customize the simulator by defining functionality for translocations, harvesting, mortality, and other processes, as well as defining the sequence order for the simulator processes. The framework could also be adapted for use with other model simulators by utilizing its extendable (inheritable) base classes.
Maintained by July Pilowsky. Last updated 20 days ago.
biogeographypopulation-modelprocess-based
2.3 match 10 stars 8.05 score 59 scripts 2 dependentscran
flexmsm:A General Framework for Flexible Multi-State Survival Modelling
A general estimation framework for multi-state Markov processes with flexible specification of the transition intensities. The log-transition intensities can be specified through Generalised Additive Models which allow for virtually any type of covariate effect. Elementary specifications such as time-homogeneous processes and simple parametric forms are also supported. There are no limitations on the type of process one can assume, with both forward and backward transitions allowed and virtually any number of states.
Maintained by Alessia Eletti. Last updated 8 months ago.
18.1 match 1.00 score 7 scripts
juba
scatterD3:D3 JavaScript Scatterplot from R
Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive features : panning, zooming, tooltips, etc.
Maintained by Julien Barnier. Last updated 7 months ago.
2.0 match 160 stars 8.98 score 125 scripts 4 dependents
sestelo
survidm:Inference and Prediction in an Illness-Death Model
Newly developed methods for the estimation of several probabilities in an illness-death model. The package can be used to obtain nonparametric and semiparametric estimates for: transition probabilities, occupation probabilities, cumulative incidence function and the sojourn time distributions. Additionally, it is possible to fit proportional hazards regression models in each transition of the Illness-Death Model. Several auxiliary functions are also provided which can be used for marginal estimation of the survival functions.
Maintained by Marta Sestelo. Last updated 4 years ago.
6.0 match 1 stars 2.95 score 18 scriptscran
clusTransition:Monitor Changes in Cluster Solutions of Dynamic Datasets
Monitor and trace changes in clustering solutions of accumulating datasets at successive time points. The clusters can adopt External and Internal transition at succeeding time points. The External transitions comprise of Survived, Merged, Split, Disappeared, and newly Emerged candidates. In contrast, Internal transition includes changes in location and cohesion of the survived clusters. The package uses MONIC framework developed by Spiliopoulou, Ntoutsi, Theodoridis, and Schult (2006)<doi:10.1145/1150402.1150491> .
Maintained by Muhammad Atif. Last updated 4 years ago.
17.8 match 1.00 score
rvlenth
lsmeans:Least-Squares Means
Obtain least-squares means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays. Least-squares means were proposed in Harvey, W (1960) "Least-squares analysis of data with unequal subclass numbers", Tech Report ARS-20-8, USDA National Agricultural Library, and discussed further in Searle, Speed, and Milliken (1980) "Population marginal means in the linear model: An alternative to least squares means", The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>. NOTE: lsmeans now relies primarily on code in the 'emmeans' package. 'lsmeans' will be archived in the near future.
Maintained by Russell Lenth. Last updated 6 years ago.
2.3 match 12 stars 7.82 score 1.8k scripts
maraab23
ggseqplot:Render Sequence Plots using 'ggplot2'
A set of wrapper functions that mainly re-produces most of the sequence plots rendered with TraMineR::seqplot(). Whereas 'TraMineR' uses base R to produce the plots this library draws on 'ggplot2'. The plots are produced on the basis of a sequence object defined with TraMineR::seqdef(). The package automates the reshaping and plotting of sequence data. Resulting plots are of class 'ggplot', i.e. components can be added and tweaked using '+' and regular 'ggplot2' functions.
Maintained by Marcel Raab. Last updated 4 months ago.
ggplot2sequence-analysistraminervisualization
3.1 match 14 stars 5.70 score 18 scriptsbioc
SeqVarTools:Tools for variant data
An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.
Maintained by Stephanie M. Gogarten. Last updated 5 months ago.
snpgeneticvariabilitysequencinggenetics
2.0 match 3 stars 8.76 score 384 scripts 2 dependents
dreamrs
billboarder:Create Interactive Chart with the JavaScript 'Billboard' Library
Provides an 'htmlwidgets' interface to 'billboard.js', a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.
Maintained by Victor Perrier. Last updated 5 months ago.
1.8 match 174 stars 9.74 score 96 scripts 4 dependents
nalimilan
logmult:Log-Multiplicative Models, Including Association Models
Functions to fit log-multiplicative models using 'gnm', with support for convenient printing, plots, and jackknife/bootstrap standard errors. For complex survey data, models can be fitted from design objects from the 'survey' package. Currently supported models include UNIDIFF (Erikson & Goldthorpe, 1992), a.k.a. log-multiplicative layer effect model (Xie, 1992) <doi:10.2307/2096242>, and several association models: Goodman (1979) <doi:10.2307/2286971> row-column association models of the RC(M) and RC(M)-L families with one or several dimensions; two skew-symmetric association models proposed by Yamaguchi (1990) <doi:10.2307/271086> and by van der Heijden & Mooijaart (1995) <doi:10.1177/0049124195024001002> Functions allow computing the intrinsic association coefficient (see Bouchet-Valat (2022) <doi:10.1177/0049124119852389>) and the Altham (1970) index <doi:10.1111/j.2517-6161.1970.tb00816.x>, including via the Bayes shrinkage estimator proposed by Zhou (2015) <doi:10.1177/0081175015570097>; and the RAS/IPF/Deming-Stephan algorithm.
Maintained by Milan Bouchet-Valat. Last updated 3 years ago.
log-linear-modelmodellingstatistics
3.3 match 4 stars 5.18 score 76 scripts
saitheinthantun
ibmcraftr:Toolkits to Develop Individual-Based Models in Infectious Disease
It provides a generic set of tools for initializing a synthetic population with each individual in specific disease states, and making transitions between those disease states according to the rates calculated on each timestep. The new version 1.0.0 has C++ code integration to make the functions run faster. It has also a higher level function to actually run the transitions for the number of timesteps that users specify. Additional functions will follow for changing attributes on demographic, health belief and movement.
Maintained by Sai Thein Than Tun. Last updated 8 years ago.
6.4 match 2.70 score 7 scripts
yulab-smu
TDbook:Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574, doi:10.1201/9781003279242)
The companion package that provides all the datasets used in the book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574, doi:10.1201/9781003279242).
Maintained by Guangchuang Yu. Last updated 3 years ago.
3.5 match 13 stars 4.88 score 59 scripts
dgrun
RaceID:Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).
Maintained by Dominic Grün. Last updated 4 months ago.
3.6 match 4.74 score 110 scripts
fmmattioni
whippr:Tools for Manipulating Gas Exchange Data
Set of tools for manipulating gas exchange data from cardiopulmonary exercise testing.
Maintained by Felipe Mattioni Maturana. Last updated 8 months ago.
4.0 match 12 stars 4.26 score 5 scripts
whalenjf
walkscoreAPI:Walk Score and Transit Score API
A collection of functions to perform the Application Programming Interface (API) calls associated with the Walk Score website (www.walkscore.com) within the R environment. These functions can be used to query the Walk Score and Transit Score database for a wide variety of information using R scripts. This package includes the simple Walk Score and Transit Score API calls, which return the scores associated with an input location, as well as calls which return some data used to calculate the scores. These functions are especially useful for mass data collection and gathering Walk Score and Transit Score values for large lists of locations.
Maintained by John Whalen. Last updated 13 years ago.
11.3 match 2 stars 1.51 score 16 scriptsbioc
paircompviz:Multiple comparison test visualization
This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.
Maintained by Michal Burda. Last updated 5 months ago.
5.1 match 3.30 score 3 scriptsbioc
wavClusteR:Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).
Maintained by Federico Comoglio. Last updated 5 months ago.
immunooncologysequencingtechnologyripseqrnaseqbayesian
3.7 match 4.60 score 3 scripts
edoardobaldoni
multilaterals:Transitive Index Numbers for Cross-Sections and Panel Data
Computing transitive (and non-transitive) index numbers (Coelli et al., 2005 <doi:10.1007/b136381>) for cross-sections and panel data. For the calculation of transitive indexes, the EKS (Coelli et al., 2005 <doi:10.1007/b136381>; Rao et al., 2002 <doi:10.1007/978-1-4615-0851-9_4>) and Minimum spanning tree (Hill, 2004 <doi:10.1257/0002828043052178>) methods are implemented. Traditional fixed-base and chained indexes, and their growth rates, can also be derived using the Paasche, Laspeyres, Fisher and Tornqvist formulas.
Maintained by Edoardo Baldoni. Last updated 8 years ago.
16.5 match 1.00 score 8 scripts
alexgenin
chouca:A Stochastic Cellular Automaton Engine
An engine for stochastic cellular automata. It provides a high-level interface to declare a model, which can then be simulated by various backends (Genin et al. (2023) <doi:10.1101/2023.11.08.566206>).
Maintained by Alexandre Genin. Last updated 7 months ago.
3.0 match 10 stars 5.48 score 3 scripts
christinayap
dtpcrm:Dose Transition Pathways for Continual Reassessment Method
Provides the dose transition pathways (DTP) to project in advance the doses recommended by a model-based design for subsequent patients (stay, escalate, deescalate or stop early) using all the accumulated toxicity information; See Yap et al (2017) <doi: 10.1158/1078-0432.CCR-17-0582>. DTP can be used as a design and an operational tool and can be displayed as a table or flow diagram. The 'dtpcrm' package also provides the modified continual reassessment method (CRM) and time-to-event CRM (TITE-CRM) with added practical considerations to allow stopping early when there is sufficient evidence that the lowest dose is too toxic and/or there is a sufficient number of patients dosed at the maximum tolerated dose.
Maintained by Christina Yap. Last updated 6 years ago.
8.2 match 2.00 score 10 scripts
gennaro-tedesco
Rdice:A Collection of Functions to Experiment Dice Rolls
A collection of functions to simulate dice rolls and the like. In particular, experiments and exercises can be performed looking at combinations and permutations of values in dice rolls and coin flips, together with the corresponding frequencies of occurrences. When applying each function, the user has to input the number of times (rolls, flips) to toss the dice. Needless to say, the more the tosses, the more the frequencies approximate the actual probabilities. Moreover, the package provides functions to generate non-transitive sets of dice (like Efron's) and to check whether a given set of dice is non-transitive with given probability.
Maintained by Gennaro Tedesco:. Last updated 8 years ago.
5.7 match 2.85 score 14 scripts
great-northern-diver
loon:Interactive Statistical Data Visualization
An extendable toolkit for interactive data visualization and exploration.
Maintained by R. Wayne Oldford. Last updated 2 years ago.
data-analysisdata-sciencedata-visualizationexploratory-analysisexploratory-data-analysishigh-dimensional-datainteractive-graphicsinteractive-visualizationsloonpythonstatistical-analysisstatistical-graphicsstatisticstcl-extensiontk
1.8 match 48 stars 9.00 score 93 scripts 5 dependentsbioc
CellScore:Tool for Evaluation of Cell Identity from Transcription Profiles
The CellScore package contains functions to evaluate the cell identity of a test sample, given a cell transition defined with a starting (donor) cell type and a desired target cell type. The evaluation is based upon a scoring system, which uses a set of standard samples of known cell types, as the reference set. The functions have been carried out on a large set of microarray data from one platform (Affymetrix Human Genome U133 Plus 2.0). In principle, the method could be applied to any expression dataset, provided that there are a sufficient number of standard samples and that the data are normalized.
Maintained by Nancy Mah. Last updated 5 months ago.
geneexpressiontranscriptionmicroarraymultiplecomparisonreportwritingdataimportvisualization
4.0 match 4.00 score 5 scripts
ocbe-uio
BayesMallows:Bayesian Preference Learning with the Mallows Rank Model
An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>; Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>; Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Maintained by Oystein Sorensen. Last updated 1 months ago.
mallows-modelopenblascppopenmp
2.0 match 21 stars 7.91 score 36 scripts 1 dependentsmhahsler
pomdp:Infrastructure for Partially Observable Markov Decision Processes (POMDP)
Provides the infrastructure to define and analyze the solutions of Partially Observable Markov Decision Process (POMDP) models. Interfaces for various exact and approximate solution algorithms are available including value iteration, point-based value iteration and SARSOP. Smallwood and Sondik (1973) <doi:10.1287/opre.21.5.1071>.
Maintained by Michael Hahsler. Last updated 3 months ago.
control-theorymarkov-decision-processesoptimizationcpp
2.3 match 19 stars 7.03 score 21 scripts
alexanderlange53
svars:Data-Driven Identification of SVAR Models
Implements data-driven identification methods for structural vector autoregressive (SVAR) models as described in Lange et al. (2021) <doi:10.18637/jss.v097.i05>. Based on an existing VAR model object (provided by e.g. VAR() from the 'vars' package), the structural impact matrix is obtained via data-driven identification techniques (i.e. changes in volatility (Rigobon, R. (2003) <doi:10.1162/003465303772815727>), patterns of GARCH (Normadin, M., Phaneuf, L. (2004) <doi:10.1016/j.jmoneco.2003.11.002>), independent component analysis (Matteson, D. S, Tsay, R. S., (2013) <doi:10.1080/01621459.2016.1150851>), least dependent innovations (Herwartz, H., Ploedt, M., (2016) <doi:10.1016/j.jimonfin.2015.11.001>), smooth transition in variances (Luetkepohl, H., Netsunajev, A. (2017) <doi:10.1016/j.jedc.2017.09.001>) or non-Gaussian maximum likelihood (Lanne, M., Meitz, M., Saikkonen, P. (2017) <doi:10.1016/j.jeconom.2016.06.002>)).
Maintained by Alexander Lange. Last updated 2 years ago.
2.2 match 46 stars 7.22 score 130 scriptsbioc
CIMICE:CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
CIMICE is a tool in the field of tumor phylogenetics and its goal is to build a Markov Chain (called Cancer Progression Markov Chain, CPMC) in order to model tumor subtypes evolution. The input of CIMICE is a Mutational Matrix, so a boolean matrix representing altered genes in a collection of samples. These samples are assumed to be obtained with single-cell DNA analysis techniques and the tool is specifically written to use the peculiarities of this data for the CMPC construction.
Maintained by Nicolò Rossi. Last updated 5 months ago.
softwarebiologicalquestionnetworkinferenceresearchfieldphylogeneticsstatisticalmethodgraphandnetworktechnologysinglecell
3.7 match 4.30 score 5 scripts
pakjiddat
wordpredictor:Develop Text Prediction Models Based on N-Grams
A framework for developing n-gram models for text prediction. It provides data cleaning, data sampling, extracting tokens from text, model generation, model evaluation and word prediction. For information on how n-gram models work we referred to: "Speech and Language Processing" <https://web.archive.org/web/20240919222934/https%3A%2F%2Fweb.stanford.edu%2F~jurafsky%2Fslp3%2F3.pdf>. For optimizing R code and using R6 classes we referred to "Advanced R" <https://adv-r.hadley.nz/r6.html>. For writing R extensions we referred to "R Packages", <https://r-pkgs.org/index.html>.
Maintained by Nadir Latif. Last updated 5 months ago.
n-gram-language-modelsnatural-language-processingr-programming
3.3 match 6 stars 4.78 score 9 scriptsbioc
Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.
Maintained by Nan Xiao. Last updated 5 months ago.
softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiologybioconductorbioinformaticsdrug-discoveryfeature-extractionfingerprintmolecular-descriptorsprotein-sequences
2.0 match 37 stars 7.81 score 29 scriptscran
TSA:Time Series Analysis
Contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan.
Maintained by Kung-Sik Chan. Last updated 3 years ago.
3.4 match 2 stars 4.47 score 5 dependents
vimc
vaultr:Vault Client for Secrets and Sensitive Data
Provides an interface to a 'HashiCorp' vault server over its http API (typically these are self-hosted; see <https://www.vaultproject.io>). This allows for secure storage and retrieval of secrets over a network, such as tokens, passwords and certificates. Authentication with vault is supported through several backends including user name/password and authentication via 'GitHub'.
Maintained by Rich FitzJohn. Last updated 1 years ago.
2.3 match 24 stars 6.78 score 2 scripts 1 dependents
uligges
klaR:Classification and Visualization
Miscellaneous functions for classification and visualization, e.g. regularized discriminant analysis, sknn() kernel-density naive Bayes, an interface to 'svmlight' and stepclass() wrapper variable selection for supervised classification, partimat() visualization of classification rules and shardsplot() of cluster results as well as kmodes() clustering for categorical data, corclust() variable clustering, variable extraction from different variable clustering models and weight of evidence preprocessing.
Maintained by Uwe Ligges. Last updated 1 years ago.
2.0 match 5 stars 7.61 score 1.4k scripts 13 dependents