R-universe search: population

idem-lab

conmat:Builds Contact Matrices using GAMs and Population Data

Builds contact matrices using GAMs and population data. This package incorporates data that is copyright Commonwealth of Australia (Australian Electoral Commission and Australian Bureau of Statistics) 2020.

Maintained by Nicholas Tierney. Last updated 5 days ago.

contact-matrices infectious-diseases population-data public-health

75.4 match 19 stars 7.21 score 47 scripts

poissonconsulting

ypr:Yield Per Recruit

An implementation of equilibrium-based yield per recruit methods. Yield per recruit methods can used to estimate the optimal yield for a fish population as described by Walters and Martell (2004) <isbn:0-691-11544-3>. The yield can be based on the number of fish caught (or harvested) or biomass caught for all fish or just large (trophy) individuals.

Maintained by Joe Thorley. Last updated 2 months ago.

yield-per-recruit

63.2 match 7 stars 7.84 score 55 scripts 1 dependents

daphnegiorgi

IBMPopSim:Individual Based Model Population Simulation

Simulation of the random evolution of heterogeneous populations using stochastic Individual-Based Models (IBMs) <doi:10.48550/arXiv.2303.06183>. The package enables users to simulate population evolution, in which individuals are characterized by their age and some characteristics, and the population is modified by different types of events, including births/arrivals, death/exit events, or changes of characteristics. The frequency at which an event can occur to an individual can depend on their age and characteristics, but also on the characteristics of other individuals (interactions). Such models have a wide range of applications. For instance, IBMs can be used for simulating the evolution of a heterogeneous insurance portfolio with selection or for validating mortality forecasts. This package overcomes the limitations of time-consuming IBMs simulations by implementing new efficient algorithms based on thinning methods, which are compiled using the 'Rcpp' package while providing a user-friendly interface.

Maintained by Daphné Giorgi. Last updated 5 months ago.

cpp

82.7 match 8 stars 5.83 score 14 scripts

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.

56.7 match 11 stars 8.17 score 62 scripts 1 dependents

bodkan

slendr:A Simulation Framework for Spatiotemporal Population Genetics

A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis.

Maintained by Martin Petr. Last updated 11 days ago.

popgen population-genetics simulations spatial-statistics

44.0 match 56 stars 9.15 score 88 scripts

uupharmacometrics

xpose4:Diagnostics for Nonlinear Mixed-Effect Models

A model building aid for nonlinear mixed-effects (population) model analysis using NONMEM, facilitating data set checkout, exploration and visualization, model diagnostics, candidate covariate identification and model comparison. The methods are described in Keizer et al. (2013) <doi:10.1038/psp.2013.24>, and Jonsson et al. (1999) <doi:10.1016/s0169-2607(98)00067-4>.

Maintained by Andrew C. Hooker. Last updated 1 years ago.

diagnostics nonmem pharmacometrics population-model xpose

48.9 match 35 stars 7.30 score 315 scripts

grunwaldlab

poppr:Genetic Analysis of Populations with Mixed Reproduction

Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the 'adegenet' package. Originally described in Kamvar, Tabima, and Grünwald (2014) <doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and Grünwald (2015) <doi:10.3389/fgene.2015.00208>.

Maintained by Zhian N. Kamvar. Last updated 10 months ago.

clonality genetic-analysis genetic-distances minimum-spanning-networks multilocus-genotypes multilocus-lineages population-genetics populations openmp

30.1 match 69 stars 10.84 score 672 scripts

gaynorr

AlphaSimR:Breeding Program Simulations

The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].

Maintained by Chris Gaynor. Last updated 4 months ago.

breeding genomics simulation openblas cpp openmp

31.9 match 47 stars 10.22 score 534 scripts 2 dependents

humaniverse

demographr:R package for mapping UK demographics

A package to distribute UK demographic data.

Maintained by Mike Page. Last updated 5 days ago.

73.4 match 2 stars 4.38 score 67 scripts

damianobaldan

RAC:R Package for Aqua Culture

Solves the individual bioenergetic balance for different aquaculture sea fish (Sea Bream and Sea Bass; Brigolin et al., 2014 <doi:10.3354/aei00093>) and shellfish (Mussel and Clam; Brigolin et al., 2009 <doi:10.1016/j.ecss.2009.01.029>; Solidoro et al., 2000 <doi:10.3354/meps199137>). Allows for spatialized model runs and population simulations.

Maintained by Baldan D.. Last updated 2 years ago.

69.8 match 4.54 score

myaseen208

PakPC2023:Pakistan Population Census 2023

Provides data sets and functions for exploration of Pakistan Population Census 2023 (<https://www.pbs.gov.pk/>).

Maintained by Muhammad Yaseen. Last updated 4 months ago.

74.1 match 1 stars 4.18 score 2 scripts 1 dependents

cbiit

LDlinkR:Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest

Provides access to the 'LDlink' API (<https://ldlink.nih.gov/?tab=apiaccess>) using the R console. This programmatic access facilitates researchers who are interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393> data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying germline variants in human population groups of interest. For more details, please see Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.

Maintained by Timothy A. Myers. Last updated 11 months ago.

ld-calculator ldlink ldlink-api ldlink-webtool linkage-disequilibrium population-genetics

31.5 match 58 stars 9.21 score 206 scripts 1 dependents

knausb

vcfR:Manipulate and Visualize VCF Data

Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.

Maintained by Brian J. Knaus. Last updated 21 days ago.

genomics population-genetics population-genomics rcpp vcf-data visualization zlib cpp

20.6 match 254 stars 13.59 score 3.1k scripts 19 dependents

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.

meta-population-models cpp

40.6 match 18 stars 6.66 score 84 scripts

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 19 days ago.

biogeography population-model process-based

33.3 match 10 stars 8.05 score 59 scripts 2 dependents

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.

20.3 match 182 stars 12.60 score 1.9k scripts 29 dependents

green-striped-gecko

dartR.base:Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism') and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility', maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages. To install the other packages, we recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'. If you want to cite 'dartR', you find the information by typing citation('dartR.base') in the console.

Maintained by Bernd Gruber. Last updated 11 days ago.

66.5 match 3.84 score 17 scripts 5 dependents

jgx65

hierfstat:Estimation and Tests of Hierarchical F-Statistics

Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) <https://academic.oup.com/genetics/article/144/4/1933/6017091>). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) <https://academic.oup.com/genetics/article/206/4/2085/6072590>.

Maintained by Jerome Goudet. Last updated 4 months ago.

devtools fstatistics gwas hierfstat kinship population-genetics population-genomics quantitative-genetics simulations

23.0 match 25 stars 10.94 score 560 scripts 4 dependents

myaseen208

PakPC2017:Pakistan Population Census 2017

Provides data sets and functions for exploration of Pakistan Population Census 2017 (<http://www.pbscensus.gov.pk/>).

Maintained by Muhammad Yaseen. Last updated 5 months ago.

43.9 match 7 stars 5.66 score 22 scripts 2 dependents

cristianetaniguti

onemap:Construction of Genetic Maps in Experimental Crosses

Analysis of molecular marker data from model (backcrosses, F2 and recombinant inbred lines) and non-model systems (i. e. outcrossing species). For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu et al. (2002) <doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint approaches using hidden Markov models.

Maintained by Cristiane Taniguti. Last updated 2 months ago.

cpp

37.6 match 3 stars 6.58 score 183 scripts

psirusteam

TeachingSampling:Selection of Samples and Parameter Estimation in Finite Population

Allows the user to draw probabilistic samples and make inferences from a finite population based on several sampling designs.

Maintained by Hugo Andres Gutierrez Rojas. Last updated 5 years ago.

42.3 match 4 stars 5.80 score 217 scripts 4 dependents

atsa-es

MARSS:Multivariate Autoregressive State-Space Modeling

The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models, including partially deterministic models. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Fitting available via Expectation-Maximization (EM), BFGS (using optim), and 'TMB' (using the 'marssTMB' companion package). Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, model selection criteria including bootstrap AICb, confidences intervals via the Hessian approximation or bootstrapping, and all conditional residual types. See the user guide for examples of dynamic factor analysis, dynamic linear models, outlier and shock detection, and multivariate AR-p models. Online workshops (lectures, eBook, and computer labs) at <https://atsa-es.github.io/>.

Maintained by Elizabeth Eli Holmes. Last updated 1 years ago.

multivariate-timeseries state-space-models statistics time-series

23.1 match 52 stars 10.34 score 596 scripts 3 dependents

rfsaldanha

brpop:Brazilian Population Estimatives

Functions to handle and aggregate population estimates for Brazilian municipalities by sex and age groups.

Maintained by Raphael Saldanha. Last updated 19 days ago.

46.0 match 16 stars 4.78 score 15 scripts

fishr-core-team

FSA:Simple Fisheries Stock Assessment Methods

A variety of simple fish stock assessment methods.

Maintained by Derek H. Ogle. Last updated 2 months ago.

fish fisheries fisheries-management fisheries-stock-assessment population-dynamics stock-assessment

19.7 match 68 stars 11.08 score 1.7k scripts 6 dependents

andrewhooker

PopED:Population (and Individual) Optimal Experimental Design

Optimal experimental designs for both population and individual studies based on nonlinear mixed-effect models. Often this is based on a computation of the Fisher Information Matrix. This package was developed for pharmacometric problems, and examples and predefined models are available for these types of systems. The methods are described in Nyberg et al. (2012) <doi:10.1016/j.cmpb.2012.05.005>, and Foracchia et al. (2004) <doi:10.1016/S0169-2607(03)00073-7>.

Maintained by Andrew C. Hooker. Last updated 5 months ago.

nlme optimal-design pharmacodynamics pharmacokinetics pharmacometrics pkpd population population-model

22.7 match 33 stars 9.58 score 300 scripts 1 dependents

dormancy1

lefko3:Historical and Ahistorical Population Projection Matrix Analysis

Complete analytical environment for the construction and analysis of matrix population models and integral projection models. Includes the ability to construct historical matrices, which are 2d matrices comprising 3 consecutive times of demographic information. Estimates both raw and function-based forms of historical and standard ahistorical matrices. It also estimates function-based age-by-stage matrices and raw and function-based Leslie matrices.

Maintained by Richard P. Shefferson. Last updated 2 days ago.

openblas cpp

64.1 match 3.30 score 11 scripts

therneau

survival:Survival Analysis

Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

Maintained by Terry M Therneau. Last updated 3 months ago.

10.0 match 400 stars 20.43 score 29k scripts 3.9k dependents

bioc

flowWorkspace:Infrastructure for representing and interacting with gated and ungated cytometry data sets.

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Maintained by Greg Finak. Last updated 8 days ago.

immunooncology flowcytometry dataimport preprocessing datarepresentation zlib openblas cpp

25.7 match 7.89 score 576 scripts 10 dependents

covaruber

sommer:Solving Mixed Model Equations in R

Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.

Maintained by Giovanny Covarrubias-Pazaran. Last updated 20 days ago.

average-information mixed-models rcpparmadillo openblas cpp openmp

15.9 match 43 stars 12.70 score 300 scripts 9 dependents

marshalllab

MGDrivE:Mosquito Gene Drive Explorer

Provides a model designed to be a reliable testbed where various gene drive interventions for mosquito-borne diseases control. It is being developed to accommodate the use of various mosquito-specific gene drive systems within a population dynamics framework that allows migration of individuals between patches in landscape. Previous work developing the population dynamics can be found in Deredec et al. (2001) <doi:10.1073/pnas.1110717108> and Hancock & Godfray (2007) <doi:10.1186/1475-2875-6-98>, and extensions to accommodate CRISPR homing dynamics in Marshall et al. (2017) <doi:10.1038/s41598-017-02744-7>.

Maintained by Héctor Manuel Sánchez Castellanos. Last updated 4 years ago.

cpp

28.7 match 6 stars 7.06 score 61 scripts

bemts-hhs

nemsqar:National Emergency Medical Service Quality Alliance Measure Calculations

Designed to automate the calculation of Emergency Medical Service (EMS) quality metrics, 'nemsqar' implements measures defined by the National EMS Quality Alliance (NEMSQA). By providing reliable, evidence-based quality assessments, the package supports EMS agencies, healthcare providers, and researchers in evaluating and improving patient outcomes. Users can find details on all approved NEMSQA measures at <https://www.nemsqa.org/measures>. Full technical specifications, including documentation and pseudocode used to develop 'nemsqar', are available on the NEMSQA website after creating a user profile at <https://www.nemsqa.org>.

Maintained by Nicolas Foss. Last updated 1 days ago.

ems nemsqa quality trauma

42.0 match 5 stars 4.70 score

guyabel

migest:Methods for the Indirect Estimation of Bilateral Migration

Tools for estimating, measuring and working with migration data.

Maintained by Guy J. Abel. Last updated 1 months ago.

demography migration population

33.9 match 32 stars 5.80 score 86 scripts

yuanmingzhang

SEA:Segregation Analysis

A few major genes and a series of polygene are responsive for each quantitative trait. Major genes are individually identified while polygene is collectively detected. This is mixed major genes plus polygene inheritance analysis or segregation analysis (SEA). In the SEA, phenotypes from a single or multiple bi-parental segregation populations along with their parents are used to fit all the possible models and the best model of the trait for population phenotypic distributions is viewed as the model of the trait. There are fourteen types of population combinations available. Zhang Yuan-Ming, Gai Jun-Yi, Yang Yong-Hua (2003, <doi:10.1017/S0016672303006141>).

Maintained by Yuan-Ming Zhang. Last updated 3 years ago.

83.2 match 2.26 score 18 scripts

mayer79

confintr:Confidence Intervals

Calculates classic and/or bootstrap confidence intervals for many parameters such as the population mean, variance, interquartile range (IQR), median absolute deviation (MAD), skewness, kurtosis, Cramer's V, odds ratio, R-squared, quantiles (incl. median), proportions, different types of correlation measures, difference in means, quantiles and medians. Many of the classic confidence intervals are described in Smithson, M. (2003, ISBN: 978-0761924999). Bootstrap confidence intervals are calculated with the R package 'boot'. Both one- and two-sided intervals are supported.

Maintained by Michael Mayer. Last updated 8 months ago.

bootstrap confidence-intervals statistical-inference statistics

21.6 match 15 stars 8.50 score 104 scripts 16 dependents

merck

metalite:ADaM Metadata Structure

A metadata structure for clinical data analysis and reporting based on Analysis Data Model (ADaM) datasets. The package simplifies clinical analysis and reporting tool development by defining standardized inputs, outputs, and workflow. The package can be used to create analysis and reporting planning grid, mock table, and validated analysis and reporting results based on consistent inputs.

Maintained by Yujie Zhao. Last updated 7 months ago.

cdisc clinical-trials metadata

20.3 match 15 stars 9.01 score 57 scripts 5 dependents

usepa

httk:High-Throughput Toxicokinetics

Pre-made models that can be rapidly tailored to various chemicals and species using chemical-specific in vitro data and physiological information. These tools allow incorporation of chemical toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE") into bioinformatics, as described by Pearce et al. (2017) (<doi:10.18637/jss.v079.i04>). Chemical-specific in vitro data characterizing toxicokinetics have been obtained from relatively high-throughput experiments. The chemical-independent ("generic") physiologically-based ("PBTK") and empirical (for example, one compartment) "TK" models included here can be parameterized with in vitro data or in silico predictions which are provided for thousands of chemicals, multiple exposure routes, and various species. High throughput toxicokinetics ("HTTK") is the combination of in vitro data and generic models. We establish the expected accuracy of HTTK for chemicals without in vivo data through statistical evaluation of HTTK predictions for chemicals where in vivo data do exist. The models are systems of ordinary differential equations that are developed in MCSim and solved using compiled (C-based) code for speed. A Monte Carlo sampler is included for simulating human biological variability (Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>) and propagating parameter uncertainty (Wambaugh et al., 2019 <doi:10.1093/toxsci/kfz205>). Empirically calibrated methods are included for predicting tissue:plasma partition coefficients and volume of distribution (Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>). These functions and data provide a set of tools for using IVIVE to convert concentrations from high-throughput screening experiments (for example, Tox21, ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK") (Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).

Maintained by John Wambaugh. Last updated 1 months ago.

comptox ord

17.4 match 27 stars 10.22 score 307 scripts 1 dependents

statistikat

simPop:Simulation of Complex Synthetic Data Information

Tools and methods to simulate populations for surveys based on auxiliary data. The tools include model-based methods, calibration and combinatorial optimization algorithms, see Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v079.i10>) and Templ (2017) <doi:10.1007/978-3-319-50272-4>. The package was developed with support of the International Household Survey Network, DFID Trust Fund TF011722 and funds from the World bank.

Maintained by Matthias Templ. Last updated 4 months ago.

cpp

26.6 match 31 stars 6.51 score 104 scripts

murrayefford

secr:Spatially Explicit Capture-Recapture

Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.

Maintained by Murray Efford. Last updated 23 hours ago.

cpp

16.8 match 3 stars 10.18 score 410 scripts 5 dependents

rostats

RSurveillance:Design and Analysis of Disease Surveillance Activities

A range of functions for the design and analysis of disease surveillance activities. These functions were originally developed for animal health surveillance activities but can be equally applied to aquatic animal, wildlife, plant and human health surveillance activities. Utilities are included for sample size calculation and analysis of representative surveys for disease freedom, risk-based studies for disease freedom and for prevalence estimation. This package is based on Cameron A., Conraths F., Frohlich A., Schauer B., Schulz K., Sergeant E., Sonnenburg J., Staubach C. (2015). R package of functions for risk-based surveillance. Deliverable 6.24, WP 6 - Decision making tools for implementing risk-based surveillance, Grant Number no. 310806, RISKSUR (<https://www.fp7-risksur.eu/sites/default/files/documents/Deliverables/RISKSUR_%28310806%29_D6.24.pdf>). Many of the 'RSurveillance' functions are incorporated into the 'epitools' website: Sergeant, ESG, 2019. Epitools epidemiological calculators. Ausvet Pty Ltd. Available at: <http://epitools.ausvet.com.au>.

Maintained by Rohan Sadler. Last updated 5 years ago.

42.1 match 3.98 score 64 scripts

adeverse

ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.

Maintained by Aurélie Siberchicot. Last updated 11 days ago.

openblas cpp

10.9 match 39 stars 14.96 score 2.2k scripts 256 dependents

finnishcancerregistry

popEpi:Functions for Epidemiological Analysis using Population Data

Enables computation of epidemiological statistics, including those where counts or mortality rates of the reference population are used. Currently supported: excess hazard models (Dickman, Sloggett, Hills, and Hakulinen (2012) <doi:10.1002/sim.1597>), rates, mean survival times, relative/net survival (in particular the Ederer II (Ederer and Heise (1959)) and Pohar Perme (Pohar Perme, Stare, and Esteve (2012) <doi:10.1111/j.1541-0420.2011.01640.x>) estimators), and standardized incidence and mortality ratios, all of which can be easily adjusted for by covariates such as age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi') and other computations achieved using 'data.table'.

Maintained by Joonas Miettinen. Last updated 1 months ago.

adjust-estimates age-adjusting direct-adjusting epidemiology indirect-adjusting survival

20.2 match 8 stars 8.05 score 117 scripts 1 dependents

mikldk

malan:MAle Lineage ANalysis

MAle Lineage ANalysis by simulating genealogies backwards and imposing short tandem repeats (STR) mutations forwards. Intended for forensic Y chromosomal STR (Y-STR) haplotype analyses. Numerous analyses are possible, e.g. number of matches and meiotic distance to matches. Refer to papers mentioned in citation("malan") (DOI's: <doi:10.1371/journal.pgen.1007028>, <doi:10.21105/joss.00684> and <doi:10.1016/j.fsigen.2018.10.004>).

Maintained by Mikkel Meyer Andersen. Last updated 1 years ago.

openblas cpp

36.2 match 4.48 score 6 scripts

slwu89

MicroMoB:Discrete Time Simulation of Mosquito-Borne Pathogen Transmission

Provides a framework based on S3 dispatch for constructing models of mosquito-borne pathogen transmission which are constructed from submodels of various components (i.e. immature and adult mosquitoes, human populations). A consistent mathematical expression for the distribution of bites on hosts means that different models (stochastic, deterministic, etc.) can be coherently incorporated and updated over a discrete time step.

Maintained by Sean L. Wu. Last updated 2 years ago.

38.6 match 4.16 score 32 scripts

mappinguniverse

mapping:Automatic Download, Linking, Manipulating Coordinates for Maps

Maps are an important tool to visualise variables distribution across different spatial objects. The mapping process requires to link the data with coordinates and then generate the correspondent map. This package provide coordinates, linking and mapping functions for an automatic, flexible and easy approach of external functions. The package provides an easy, flexible and automatic unit. Geographical coordinates are provided in the package and automatically linked with the input data to generate maps with internal provided functions or external functions. Provide an easy, flexible and automatic approach to potentially download updated coordinates, to link statistical units with coordinates and to aggregate variables based on the spatial hierarchy of units. The object returned from the package can be used for thematic maps with the build-in functions provided in mapping or with other packages already available.

Maintained by Alessio Serafini. Last updated 1 years ago.

33.3 match 4 stars 4.79 score 31 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.

16.1 match 4 stars 9.65 score 708 scripts 11 dependents

bioc

RAIDS:Accurate Inference of Genetic Ancestry from Cancer Sequences

This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.

Maintained by Pascal Belleau. Last updated 5 months ago.

genetics software sequencing wholegenome principalcomponent geneticvariability dimensionreduction biocviews ancestry cancer-genomics exome-sequencing genomics inference r-language rna-seq rna-sequencing whole-genome-sequencing

24.8 match 5 stars 6.23 score 19 scripts

ropengov

geofi:Access Finnish Geospatial Data

Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.

Maintained by Markus Kainu. Last updated 1 months ago.

ropengov ggplot2

18.8 match 20 stars 8.17 score 61 scripts

sizespectrum

mizer:Dynamic Multi-Species Size Spectrum Modelling

A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.

Maintained by Gustav Delius. Last updated 2 months ago.

ecosystem-model fish-population-dynamics fisheries fisheries-management marine-ecosystem population-dynamics simulation size-structure species-interactions transport-equation cpp

16.0 match 38 stars 9.43 score 207 scripts

hanase

wpp2019:World Population Prospects 2019

Provides data from the United Nation's World Population Prospects 2019.

Maintained by Hana Sevcikova. Last updated 5 years ago.

46.8 match 1 stars 3.17 score 99 scripts 5 dependents

kfarleigh

PopGenHelpR:Streamline Population Genomic and Genetic Analyses

Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.

Maintained by Keaka Farleigh. Last updated 8 months ago.

diversity fst heterozygosity interpolation neis population-genetics population-genomics private-alleles snmf structure vcf

28.7 match 3 stars 5.17 score 14 scripts

ropensci

beautier:'BEAUti' from R

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.

Maintained by Richèl J.C. Bilderbeek. Last updated 21 days ago.

bayesian beast beast2 beauti phylogenetic-inference phylogenetics

16.9 match 13 stars 8.76 score 198 scripts 5 dependents

slequime

nosoi:A Forward Agent-Based Transmission Chain Simulator

The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. Methods in Ecology and Evolution 11:1002-1007). It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. 'nosoi' is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.

Maintained by Sebastian Lequime. Last updated 2 months ago.

20.0 match 8 stars 7.26 score 30 scripts

jangraffelman

HardyWeinberg:Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi:10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots. The functionality of the package is explained in detail in a related JSS paper <doi:10.18637/jss.v064.i03>.

Maintained by Jan Graffelman. Last updated 11 months ago.

cpp

23.0 match 6.30 score 167 scripts 4 dependents

nikkrieger

USpopcenters:United States Centers of Population (Centroids)

Centers of population (centroid) data for census areas in the United States.

Maintained by Nik Krieger. Last updated 2 years ago.

53.3 match 1 stars 2.70 score 2 scripts

alarm-redist

redist:Simulation Methods for Legislative Redistricting

Enables researchers to sample redistricting plans from a pre-specified target distribution using Sequential Monte Carlo and Markov Chain Monte Carlo algorithms. The package allows for the implementation of various constraints in the redistricting process such as geographic compactness and population parity requirements. Tools for analysis such as computation of various summary statistics and plotting functionality are also included. The package implements the SMC algorithm of McCartan and Imai (2023) <doi:10.1214/23-AOAS1763>, the enumeration algorithm of Fifield, Imai, Kawahara, and Kenny (2020) <doi:10.1080/2330443X.2020.1791773>, the Flip MCMC algorithm of Fifield, Higgins, Imai and Tarr (2020) <doi:10.1080/10618600.2020.1739532>, the Merge-split/Recombination algorithms of Carter et al. (2019) <arXiv:1911.01503> and DeFord et al. (2021) <doi:10.1162/99608f92.eb30390f>, and the Short-burst optimization algorithm of Cannon et al. (2020) <arXiv:2011.02288>.

Maintained by Christopher T. Kenny. Last updated 2 months ago.

geospatial gerrymandering redistricting sampling openblas cpp openmp

15.5 match 68 stars 9.17 score 259 scripts

hneth

riskyr:Rendering Risk Literacy more Transparent

Risk-related information (like the prevalence of conditions, the sensitivity and specificity of diagnostic tests, or the effectiveness of interventions or treatments) can be expressed in terms of frequencies or probabilities. By providing a toolbox of corresponding metrics and representations, 'riskyr' computes, translates, and visualizes risk-related information in a variety of ways. Adopting multiple complementary perspectives provides insights into the interplay between key parameters and renders teaching and training programs on risk literacy more transparent.

Maintained by Hansjoerg Neth. Last updated 10 months ago.

2x2-matrix bayesian-inference contingency-table representation risk risk-literacy visualization

19.2 match 19 stars 7.36 score 80 scripts

epiverse-trace

epidemics:Composable Epidemic Scenario Modelling

A library of compartmental epidemic models taken from the published literature, and classes to represent affected populations, public health response measures including non-pharmaceutical interventions on social contacts, non-pharmaceutical and pharmaceutical interventions that affect disease transmissibility, vaccination regimes, and disease seasonality, which can be combined to compose epidemic scenario models.

Maintained by Rosalind Eggo. Last updated 9 months ago.

decision-support epidemic-modelling epidemic-simulations epidemiology epiverse infectious-disease-dynamics model-library non-pharmaceutical-interventions rcpp rcppeigen scenario-analysis vaccination cpp

18.5 match 9 stars 7.48 score 59 scripts

pdil

usmap:US Maps Including Alaska and Hawaii

Obtain United States map data frames of varying region types (e.g. county, state). The map data frames include Alaska and Hawaii conveniently placed to the bottom left, as they appear in most maps of the US. Convenience functions for plotting choropleths, visualizing spatial data, and working with FIPS codes are also provided.

Maintained by Paolo Di Lorenzo. Last updated 3 months ago.

counties data fips geodata mapping states usa

12.2 match 75 stars 11.22 score 1.7k scripts 2 dependents

evolecolgroup

tidypopgen:Tidy Population Genetics

We provide a tidy grammar of population genetics, facilitating the manipulation and analysis of data on biallelic single nucleotide polymorphisms (SNPs).

Maintained by Andrea Manica. Last updated 2 days ago.

openblas zlib cpp openmp

23.3 match 4 stars 5.83 score 8 scripts

isciences

exactextractr:Fast Extraction from Raster Datasets using Polygons

Quickly and accurately summarizes raster values over polygonal areas ("zonal statistics").

Maintained by Daniel Baston. Last updated 7 months ago.

gis raster rcpp geos cpp

11.0 match 286 stars 12.13 score 1.4k scripts 14 dependents

rstudio

gt:Easily Create Presentation-Ready Display Tables

Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.

Maintained by Richard Iannone. Last updated 10 days ago.

docx easy-to-use html latex rtf summary-tables

7.2 match 2.1k stars 18.36 score 20k scripts 112 dependents

gtonkinhill

rhierbaps:Clustering Genetic Sequence Data Using the HierBAPS Algorithm

Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences from multiple sequence alignments in FASTA format. The implementation includes improved defaults and plotting capabilities and unlike the original 'MATLAB' version removes singleton SNPs by default.

Maintained by Gerry Tonkin-Hill. Last updated 4 years ago.

population-genetics population-genomics population-structure

23.0 match 34 stars 5.66 score 27 scripts

vincentgarin

mppR:Multi-Parent Population QTL Analysis

Analysis of experimental multi-parent populations to detect regions of the genome (called quantitative trait loci, QTLs) influencing phenotypic traits measured in unique and multiple environments. The population must be composed of crosses between a set of at least three parents (e.g. factorial design, 'diallel', or nested association mapping). The functions cover data processing, QTL detection, and results visualization. The implemented methodology is described in Garin, Wimmer, Mezmouk, Malosetti and van Eeuwijk (2017) <doi:10.1007/s00122-017-2923-3>, in Garin, Malosetti and van Eeuwijk (2020) <doi: 10.1007/s00122-020-03621-0>, and in Garin, Diallo, Tekete, Thera, ..., and Rami (2024) <doi: 10.1093/genetics/iyae003>.

Maintained by Vincent Garin. Last updated 1 years ago.

24.2 match 2 stars 5.35 score 28 scripts

andybega

spduration:Split-Population Duration (Cure) Regression

An implementation of split-population duration regression models. Unlike regular duration models, split-population duration models are mixture models that accommodate the presence of a sub-population that is not at risk for failure, e.g. cancer patients who have been cured by treatment. This package implements Weibull and Loglogistic forms for the duration component, and focuses on data with time-varying covariates. These models were originally formulated in Boag (1949) and Berkson and Gage (1952), and extended in Schmidt and Witte (1989).

Maintained by Andreas Beger. Last updated 1 years ago.

mixture-model regression split-population survival-analysis cpp

23.7 match 4 stars 5.38 score 40 scripts

eriqande

CKMRpop:Forward-in-Time Simulation and Tallying of Pairwise Relationships

Provides an R wrapper around the program 'spip' (<https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1471-8286.2005.00884.x>), a C program for the simulation of pedigrees within age-structured populations with user-specified life histories. Also includes a variety of functions to parse 'spip' output to compile information about related pairs amongst simulated, sampled individuals, to assess the feasibility and potential accuracy of close-kin mark-recapture (CKMR). Full documentation and vignettes are mirrored at <https://eriqande.github.io/CKMRpop/index.html> and can be read online there.

Maintained by Eric C. Anderson. Last updated 1 years ago.

noaa-omics-software cpp

23.5 match 4 stars 5.38 score 24 scripts

highlanderlab

SIMplyBee:'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes

An extension of the 'AlphaSimR' package (<https://cran.r-project.org/package=AlphaSimR>) for stochastic simulations of honeybee populations and breeding programmes. 'SIMplyBee' enables simulation of individual bees that form a colony, which includes a queen, fathers (drones the queen mated with), virgin queens, workers, and drones. Multiple colony can be merged into a population of colonies, such as an apiary or a whole country of colonies. Functions enable operations on castes, colony, or colonies, to ease 'R' scripting of whole populations. All 'AlphaSimR' functionality with respect to genomes and genetic and phenotype values is available and further extended for honeybees, including haplo-diploidy, complementary sex determiner locus, colony events (swarming, supersedure, etc.), and colony phenotype values.

Maintained by Jana Obšteter. Last updated 6 months ago.

cpp openmp

20.1 match 2 stars 6.24 score 18 scripts

gchapron

population:Models for Simulating Populations

Run population simulations using an Individual-Based Model (IBM) compiled in C.

Maintained by Guillaume Chapron. Last updated 3 years ago.

62.4 match 2.00 score 5 scripts

doi-usgs

EGRET:Exploration and Graphics for RivEr Trends

Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).

Maintained by Laura DeCicco. Last updated 4 months ago.

usgs water-quality water-quality-data

11.6 match 90 stars 10.72 score 362 scripts 1 dependents

alexkychen

assignPOP:Population Assignment using Genetic, Non-Genetic or Integrated Data in a Machine Learning Framework

Use Monte-Carlo and K-fold cross-validation coupled with machine- learning classification algorithms to perform population assignment, with functionalities of evaluating discriminatory power of independent training samples, identifying informative loci, reducing data dimensionality for genomic data, integrating genetic and non-genetic data, and visualizing results.

Maintained by Kuan-Yu (Alex) Chen. Last updated 1 years ago.

cross-validation data-integration gbs machine-learning population-assignment population-genomics radseq

23.3 match 17 stars 5.33 score 25 scripts

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 5 days ago.

8.1 match 100 stars 15.36 score 1.4k scripts 36 dependents

emmanuelparadis

pegas:Population and Evolutionary Genetics Analysis System

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

Maintained by Emmanuel Paradis. Last updated 1 years ago.

16.5 match 7.53 score 576 scripts 18 dependents

jonesor

mpmsim:Simulation of Matrix Population Models with Defined Life History Characteristics

Allows users to simulate matrix population models with particular characteristics based on aspects of life history such as mortality trajectories and fertility trajectories. Also allows the exploration of sampling error due to small sample size.

Maintained by Owen Jones. Last updated 8 days ago.

20.4 match 5 stars 6.03 score 16 scripts

hanase

wpp2017:World Population Prospects 2017

Provides data from the United Nation's World Population Prospects 2017.

Maintained by Hana Sevcikova. Last updated 5 years ago.

46.8 match 1 stars 2.56 score 30 scripts 4 dependents

r-forge

surveillance:Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. twinSIR() models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hoehle (2009) <doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) <doi:10.18637/jss.v077.i11>.

Maintained by Sebastian Meyer. Last updated 17 hours ago.

cpp

11.0 match 2 stars 10.68 score 446 scripts 3 dependents

drj001

ASMap:Linkage Map Construction using the MSTmap Algorithm

Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).

Maintained by Julian Taylor. Last updated 4 months ago.

cpp

17.2 match 2 stars 6.73 score 79 scripts

bioc

GENESIS:GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.

Maintained by Stephanie M. Gogarten. Last updated 1 months ago.

snp geneticvariability genetics statisticalmethod dimensionreduction principalcomponent genomewideassociation qualitycontrol biocviews

10.7 match 36 stars 10.44 score 342 scripts 1 dependents

rcppcore

Rcpp:Seamless R and C++ Integration

The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013, <doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018, <doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.

Maintained by Dirk Eddelbuettel. Last updated 2 days ago.

c-plus-plus c-plus-plus-11 c-plus-plus-14 c-plus-plus-17 c-plus-plus-20 rcpp cpp

4.8 match 753 stars 22.58 score 11k scripts 13k dependents

richardli

SUMMER:Small-Area-Estimation Unit/Area Models and Methods for Estimation in R

Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645>, Wu et al. (DHS Spatial Analysis Reports No. 21, 2021), and Li et al. (2023) <doi:10.48550/arXiv.2007.05117>.

Maintained by Zehang R Li. Last updated 2 months ago.

bayesian-inference small-area-estimation space-time

10.3 match 23 stars 10.28 score 134 scripts 2 dependents

r4epi

apyramid:Visualize Population Pyramids Aggregated by Age

Provides a quick method for visualizing non-aggregated line-list or aggregated census data stratified by age and one or two categorical variables (e.g. gender and health status) with any number of values. It returns a 'ggplot' object, allowing the user to further customize the output. This package is part of the 'R4Epis' project <https://r4epis.netlify.app/>.

Maintained by Zhian N. Kamvar. Last updated 2 years ago.

17.0 match 20 stars 6.18 score 51 scripts 1 dependents

murrayefford

openCR:Open Population Capture-Recapture

Non-spatial and spatial open-population capture-recapture analysis.

Maintained by Murray Efford. Last updated 5 months ago.

cpp

17.5 match 4 stars 5.98 score 53 scripts

ald0405

SangerTools:Tools for Population Health Management Analytics

Created for population health analytics and monitoring. The functions in this package work best when working with patient level Master Patient Index-like datasets . Built to be used by NHS bodies and other health service providers.

Maintained by Asif Laldin. Last updated 1 years ago.

nhs nhs-r-community population-health prevalence

20.5 match 5 stars 5.05 score 45 scripts

poissonconsulting

bbouretro:Traditional Survival, Recruitment and Population Growth Methods

Estimates annual survival, recruitment and population growth using the traditional methods. This package is part of the bbou suite of tools.

Maintained by Ayla Pearson. Last updated 2 months ago.

19.7 match 5.26 score 3 scripts 1 dependents

poissonconsulting

bbousims:Simulate Boreal Caribou Survival, Recruitment and Population Growth

Simulates survival and recruitment data for boreal caribou populations using hierarchical Bayesian models.

Maintained by Seb Dalgarno. Last updated 4 months ago.

21.3 match 4.78 score 6 scripts 1 dependents

fzao

caRamel:Automatic Calibration by Evolutionary Multi Objective Algorithm

The caRamel optimizer has been developed to meet the requirement for an automatic calibration procedure that delivers a family of parameter sets that are optimal with regard to a multi-objective target (Monteil et al. <doi:10.5194/hess-24-3189-2020>).

Maintained by Fabrice Zaoui. Last updated 8 months ago.

fortran

14.5 match 12 stars 7.01 score 41 scripts

cran

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.

16.1 match 6.24 score 1.0k scripts 5 dependents

sahirbhatnagar

casebase:Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression

Fit flexible and fully parametric hazard regression models to survival data with single event type or multiple competing causes via logistic and multinomial regression. Our formulation allows for arbitrary functional forms of time and its interactions with other predictors for time-dependent hazards and hazard ratios. From the fitted hazard model, we provide functions to readily calculate and plot cumulative incidence and survival curves for a given covariate profile. This approach accommodates any log-linear hazard function of prognostic time, treatment, and covariates, and readily allows for non-proportionality. We also provide a plot method for visualizing incidence density via population time plots. Based on the case-base sampling approach of Hanley and Miettinen (2009) <DOI:10.2202/1557-4679.1125>, Saarela and Arjas (2015) <DOI:10.1111/sjos.12125>, and Saarela (2015) <DOI:10.1007/s10985-015-9352-x>.

Maintained by Sahir Bhatnagar. Last updated 7 months ago.

competing-risks cox-regression regression-models survival-analysis

14.0 match 9 stars 7.16 score 94 scripts

zilong-li

vcfppR:Rapid Manipulation of the Variant Call Format (VCF)

The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.

Maintained by Zilong Li. Last updated 1 days ago.

bioinformatics fastr htslib population-genetics population-genomics vcf vcf-data visulization libdeflate zlib bzip2 xz-utils curl cpp

15.0 match 13 stars 6.70 score 16 scripts

cran

sae:Small Area Estimation

Functions for small area estimation.

Maintained by Yolanda Marhuenda. Last updated 5 years ago.

18.3 match 6 stars 5.49 score 83 scripts 8 dependents

diondetterer

epinetr:Epistatic Network Modelling with Forward-Time Simulation

Allows for forward-in-time simulation of epistatic networks with associated phenotypic output.

Maintained by Dion Detterer. Last updated 3 years ago.

cpp

27.1 match 3.70 score 9 scripts

alinamateikondylis

sampling:Survey Sampling

Functions to draw random samples using different sampling schemes are available. Functions are also provided to obtain (generalized) calibration weights, different estimators, as well some variance estimators.

Maintained by Alina Matei. Last updated 1 years ago.

12.5 match 2 stars 7.98 score 772 scripts 29 dependents

r-forge

carData:Companion to Applied Regression Data Sets

Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage (2019).

Maintained by John Fox. Last updated 5 months ago.

8.0 match 12.41 score 944 scripts 919 dependents

lamho86

phylolm:Phylogenetic Linear Regression

Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.

Maintained by Lam Si Tung Ho. Last updated 4 months ago.

9.2 match 33 stars 10.79 score 318 scripts 14 dependents

cszang

treeclim:Numerical Calibration of Proxy-Climate Relationships

Bootstrapped response and correlation functions, seasonal correlations and evaluation of reconstruction skills for use in dendroclimatology and dendroecology, see Zang and Biondi (2015) <doi:10.1111/ecog.01335>.

Maintained by Christian Zang. Last updated 3 months ago.

climate-relationships dendroclimatology dendroecology openblas cpp

17.0 match 18 stars 5.66 score 36 scripts

jinghuazhao

gap:Genetic Analysis Package

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

Maintained by Jing Hua Zhao. Last updated 15 days ago.

genetics imputation lmm fortran

8.1 match 12 stars 11.88 score 448 scripts 16 dependents

walkerke

tidycensus:Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames

An integrated R interface to several United States Census Bureau APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping and spatial analysis.

Maintained by Kyle Walker. Last updated 2 months ago.

6.6 match 647 stars 14.27 score 7.5k scripts 10 dependents

alanarnholt

BSDA:Basic Statistics and Data Analysis

Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.

Maintained by Alan T. Arnholt. Last updated 2 years ago.

10.3 match 7 stars 9.11 score 1.3k scripts 6 dependents

bioc

microbiome:Microbiome Analytics

Utilities for microbiome analysis.

Maintained by Leo Lahti. Last updated 5 months ago.

metagenomics microbiome sequencing systemsbiology hitchip hitchip-atlas human-microbiome microbiology microbiome-analysis phyloseq population-study

7.5 match 290 stars 12.50 score 2.0k scripts 5 dependents

vavrycuk-zz

PoDBAY:Vaccine Efficacy Estimation Package

Set of functions that implement the PoDBAY method, described in the publication 'A method to estimate probability of disease and vaccine efficacy from clinical trial immunogenicity data' by Julie Dudasova, Regina Laube, Chandni Valiathan, Matthew C. Wiener, Ferdous Gheyas, Pavel Fiser, Justina Ivanauskaite, Frank Liu and Jeffrey R. Sachs (NPJ Vaccines, 2021), <doi:10.1038/s41541-021-00377-6>.

Maintained by Julie Dudasova (MSD). Last updated 3 years ago.

cpp

28.1 match 3.30 score 10 scripts

adamtclark

gauseR:Lotka-Volterra Models for Gause's 'Struggle for Existence'

A collection of tools and data for analyzing the Gause microcosm experiments, and for fitting Lotka-Volterra models to time series data. Includes methods for fitting single-species logistic growth, and multi-species interaction models, e.g. of competition, predator/prey relationships, or mutualism. See documentation for individual functions for examples. In general, see the lv_optim() function for examples of how to fit parameter values in multi-species systems. Note that the general methods applied here, as well as the form of the differential equations that we use, are described in detail in the Quantitative Ecology textbook by Lehman et al., available at <http://hdl.handle.net/11299/204551>, and in Lina K. Mühlbauer, Maximilienne Schulze, W. Stanley Harpole, and Adam T. Clark. 'gauseR': Simple methods for fitting Lotka-Volterra models describing Gause's 'Struggle for Existence' in the journal Ecology and Evolution.

Maintained by Adam Clark. Last updated 1 years ago.

24.1 match 6 stars 3.82 score 11 scripts

arilamstein

choroplethr:Simplify the Creation of Choropleth Maps in R

Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. This package simplifies this process by 1. Providing ready-made functions for creating choropleths of common maps. 2. Providing data and API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. 4. Overlaying those maps over reference maps from Google Maps.

Maintained by Ari Lamstein. Last updated 1 years ago.

13.5 match 3 stars 6.85 score 860 scripts 1 dependents

pharmaverse

admiral:ADaM in R Asset Library

A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).

Maintained by Ben Straub. Last updated 3 days ago.

cdisc clinical-trials open-source

6.6 match 236 stars 13.89 score 486 scripts 4 dependents

ropensci

historydata:Datasets for Historians

These sample data sets are intended for historians learning R. They include population, institutional, religious, military, and prosopographical data suitable for mapping, quantitative analysis, and network analysis.

Maintained by Lincoln Mullen. Last updated 7 months ago.

14.8 match 87 stars 6.19 score 118 scripts

kwstat

agridat:Agricultural Datasets

Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.

Maintained by Kevin Wright. Last updated 26 days ago.

data

8.2 match 125 stars 11.02 score 1.7k scripts 2 dependents

eriqande

rubias:Bayesian Inference from the Conditional Genetic Stock Identification Model

Implements Bayesian inference for the conditional genetic stock identification model. It allows inference of mixed fisheries and also simulation of mixtures to predict accuracy. A full description of the underlying methods is available in a recently published article in the Canadian Journal of Fisheries and Aquatic Sciences: <doi:10.1139/cjfas-2018-0016>.

Maintained by Eric C. Anderson. Last updated 1 years ago.

noaa-omics-software cpp

15.3 match 3 stars 5.90 score 89 scripts

bioc

openCyto:Hierarchical Gating Pipeline for flow cytometry data

This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

Maintained by Mike Jiang. Last updated 5 months ago.

immunooncology flowcytometry dataimport preprocessing datarepresentation cpp

11.7 match 7.62 score 404 scripts 1 dependents

robjohnnoble

ggmuller:Create Muller Plots of Evolutionary Dynamics

Create plots that combine a phylogeny and frequency dynamics. Phylogenetic input can be a generic adjacency matrix or a tree of class "phylo". Inspired by similar plots in publications of the labs of RE Lenski and JE Barrick. Named for HJ Muller (who popularised such plots) and H Wickham (whose code this package exploits).

Maintained by Robert Noble. Last updated 1 years ago.

12.1 match 65 stars 7.29 score 50 scripts

poissonconsulting

bboudata:Data for bbou Project

This package contains boreal caribou demographic data which can be used as validation for the associated shiny-app and analysis. The overall goal of the bbou packages is to develop a more standardized and consistent method for the comparison of boreal caribou survival rates, recruitment and population dynamics across Canada.

Maintained by Ayla Pearson. Last updated 2 months ago.

23.5 match 3.73 score 8 scripts 3 dependents

wjbraun

DAAG:Data Analysis and Graphics Data and Functions

Functions and data sets used in examples and exercises in the text Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data Analysis and Graphics Using R", and in an upcoming Maindonald, Braun, and Andrews text that builds on this earlier text.

Maintained by W. John Braun. Last updated 11 months ago.

10.5 match 8.25 score 1.2k scripts 1 dependents

tidyverse

tidyr:Tidy Messy Data

Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).

Maintained by Hadley Wickham. Last updated 12 days ago.

tidy-data cpp

3.8 match 1.4k stars 22.88 score 168k scripts 5.5k dependents

albgarre

biogrowth:Modelling of Population Growth

Modelling of population growth under static and dynamic environmental conditions. Includes functions for model fitting and making prediction under isothermal and dynamic conditions. The methods (algorithms & models) are based on predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).

Maintained by Alberto Garre. Last updated 14 hours ago.

12.7 match 5 stars 6.71 score 44 scripts

yelleknek

MBESS:The MBESS R Package

Implements methods that are useful in designing research studies and analyzing data, with particular emphasis on methods that are developed for or used within the behavioral, educational, and social sciences (broadly defined). That being said, many of the methods implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a suite of functions for a variety of related topics, such as effect sizes, confidence intervals for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size planning (from the accuracy in parameter estimation [AIPE], power analytic, equivalence, and minimum-risk point estimation perspectives), mediation analysis, various properties of distributions, and a variety of utility functions. MBESS (pronounced 'em-bes') was originally an acronym for 'Methods for the Behavioral, Educational, and Social Sciences,' but MBESS became more general and now contains methods applicable and used in a wide variety of fields and is an orphan acronym, in the sense that what was an acronym is now literally its name. MBESS has greatly benefited from others, see <https://www3.nd.edu/~kkelley/site/MBESS.html> for a detailed list of those that have contributed and other details.

Maintained by Ken Kelley. Last updated 1 years ago.

10.4 match 2 stars 8.21 score 274 scripts 23 dependents

junlingm

ABM:Agent Based Model Simulation Framework

A high-performance, flexible and extensible framework to develop continuous-time agent based models. Its high performance allows it to simulate millions of agents efficiently. Agents are defined by their states (arbitrary R lists). The events are handled in chronological order. This avoids the multi-event interaction problem in a time step of discrete-time simulations, and gives precise outcomes. The states are modified by provided or user-defined events. The framework provides a flexible and customizable implementation of state transitions (either spontaneous or caused by agent interactions), making the framework suitable to apply to epidemiology and ecology, e.g., to model life history stages, competition and cooperation, and disease and information spread. The agent interactions are flexible and extensible. The framework provides random mixing and network interactions, and supports multi-level mixing patterns. It can be easily extended to other interactions such as inter- and intra-households (or workplaces and schools) by subclassing an R6 class. It can be used to study the effect of age-specific, group-specific, and contact- specific intervention strategies, and complex interactions between individual behavior and population dynamics. This modeling concept can also be used in business, economical and political models. As a generic event based framework, it can be applied to many other fields. More information about the implementation and examples can be found at <https://github.com/junlingm/ABM>.

Maintained by Junling Ma. Last updated 2 months ago.

cpp

17.1 match 28 stars 4.92 score 12 scripts

barcaroli

SamplingStrata:Optimal Stratification of Sampling Frames for Multipurpose Sampling Surveys

In the field of stratified sampling design, this package offers an approach for the determination of the best stratification of a sampling frame, the one that ensures the minimum sample cost under the condition to satisfy precision constraints in a multivariate and multidomain case. This approach is based on the use of the genetic algorithm: each solution (i.e. a particular partition in strata of the sampling frame) is considered as an individual in a population; the fitness of all individuals is evaluated applying the Bethel-Chromy algorithm to calculate the sampling size satisfying precision constraints on the target estimates. Functions in the package allows to: (a) analyse the obtained results of the optimisation step; (b) assign the new strata labels to the sampling frame; (c) select a sample from the new frame accordingly to the best allocation. Functions for the execution of the genetic algorithm are a modified version of the functions in the 'genalg' package.

Maintained by Giulio Barcaroli. Last updated 13 days ago.

cpp

11.0 match 15 stars 7.60 score 178 scripts

mrc-ide

popim:POPulation IMmunity: Run a Demographic Model of Vaccine Exposure Over Time

Tools for setting up an age-structured population, applying vaccination activities to it, and tracking vaccine-induced immunity through time.

Maintained by Tini Garske. Last updated 2 months ago.

20.1 match 1 stars 4.15 score 4 scripts

openintrostat

openintro:Datasets and Supplemental Functions from 'OpenIntro' Textbooks and Labs

Supplemental functions and data for 'OpenIntro' resources, which includes open-source textbooks and resources for introductory statistics (<https://www.openintro.org/>). The package contains datasets used in our open-source textbooks along with custom plotting functions for reproducing book figures. Note that many functions and examples include color transparency; some plotting elements may not show up properly (or at all) when run in some versions of Windows operating system.

Maintained by Mine Çetinkaya-Rundel. Last updated 2 months ago.

data openintro

7.3 match 240 stars 11.39 score 6.0k scripts

bodkan

admixr:An Interface for Running 'ADMIXTOOLS' Analyses

An interface for performing all stages of 'ADMIXTOOLS' analyses (<https://reich.hms.harvard.edu/software>) entirely from R. Wrapper functions (D, f4, f3, etc.) completely automate the generation of intermediate configuration files, run 'ADMIXTOOLS' programs on the command-line, and parse output files to extract values of interest. This allows users to focus on the analysis itself instead of worrying about low-level technical details. A set of complementary functions for processing and filtering of data in the 'EIGENSTRAT' format is also provided.

Maintained by Martin Petr. Last updated 25 days ago.

bioinformatics popgen population-genetics

11.1 match 29 stars 7.42 score 91 scripts

middleton-lab

abd:The Analysis of Biological Data

The abd package contains data sets and sample code for The Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009; Roberts & Company Publishers).

Maintained by Kevin M. Middleton. Last updated 11 months ago.

14.9 match 6 stars 5.53 score 182 scripts 1 dependents

stan-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.

bayesian bayesian-data-analysis bayesian-inference bayesian-methods bayesian-statistics multilevel-models rstan rstanarm stan statistical-modeling cpp

5.2 match 393 stars 15.65 score 5.0k scripts 12 dependents

darwin-eu

IncidencePrevalence:Estimate Incidence and Prevalence using the OMOP Common Data Model

Calculate incidence and prevalence using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Incidence and prevalence can be estimated for the total population in a database or for a stratification cohort.

Maintained by Edward Burn. Last updated 5 days ago.

10.3 match 9 stars 7.96 score 102 scripts 1 dependents

lvclark

polyRAD:Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>. A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.

Maintained by Lindsay V. Clark. Last updated 7 days ago.

bioinformatics dna-sequencing genotype-likelihoods genotyping-by-sequencing hacktoberfest rad-seq rad-sequencing snp-genotyping cpp

11.7 match 28 stars 6.98 score 85 scripts

biodiverse

unmarked:Models for Data from Unmarked Animals

Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.

Maintained by Ken Kellner. Last updated 1 months ago.

openblas cpp openmp

6.2 match 4 stars 13.02 score 652 scripts 12 dependents

pik-piam

mrdrivers:Create GDP and Population Scenarios

Create GDP and population scenarios This package constructs the GDP and population scenarios used as drivers in both the REMIND and MAgPIE models.

Maintained by Johannes Koch. Last updated 23 days ago.

12.6 match 6.38 score 5 scripts 19 dependents

pedrosfig

BayesSampling:Bayes Linear Estimators for Finite Population

Allows the user to apply the Bayes Linear approach to finite population with the Simple Random Sampling - BLE_SRS() - and the Stratified Simple Random Sampling design - BLE_SSRS() - (both without replacement), to the Ratio estimator (using auxiliary information) - BLE_Ratio() - and to categorical data - BLE_Categorical(). The Bayes linear estimation approach is applied to a general linear regression model for finite population prediction in BLE_Reg() and it is also possible to achieve the design based estimators using vague prior distributions. Based on Gonçalves, K.C.M, Moura, F.A.S and Migon, H.S.(2014) <https://www150.statcan.gc.ca/n1/en/catalogue/12-001-X201400111886>.

Maintained by Pedro Soares Figueiredo. Last updated 4 years ago.

bayesian estimator sampling

17.4 match 1 stars 4.56 score 12 scripts

cran

PracTools:Designing and Weighting Survey Samples

Functions and datasets to support Valliant, Dever, and Kreuter (2018), <doi:10.1007/978-3-319-93632-1>, "Practical Tools for Designing and Weighting Survey Samples". Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.

Maintained by Richard Valliant. Last updated 9 months ago.

17.6 match 1 stars 4.48 score 101 scripts 1 dependents

bmcclintock

multimark:Capture-Mark-Recapture Analysis using Multiple Non-Invasive Marks

Traditional and spatial capture-mark-recapture analysis with multiple non-invasive marks. The models implemented in 'multimark' combine encounter history data arising from two different non-invasive "marks", such as images of left-sided and right-sided pelage patterns of bilaterally asymmetrical species, to estimate abundance and related demographic parameters while accounting for imperfect detection. Bayesian models are specified using simple formulae and fitted using Markov chain Monte Carlo. Addressing deficiencies in currently available software, 'multimark' also provides a user-friendly interface for performing Bayesian multimodel inference using non-spatial or spatial capture-recapture data consisting of a single conventional mark or multiple non-invasive marks. See McClintock (2015) <doi:10.1002/ece3.1676> and Maronde et al. (2020) <doi:10.1002/ece3.6990>.

Maintained by Brett T. McClintock. Last updated 2 years ago.

21.5 match 1 stars 3.65 score 30 scripts

epiverse-trace

finalsize:Calculate the Final Size of an Epidemic

Calculate the final size of a susceptible-infectious-recovered epidemic in a population with demographic variation in contact patterns and susceptibility to disease, as discussed in Miller (2012) <doi:10.1007/s11538-012-9749-6>.

Maintained by Rosalind Eggo. Last updated 30 days ago.

epidemic-modelling epidemiology epiverse outbreak-analysis rcpp sdg-3 cpp

9.7 match 11 stars 8.11 score 46 scripts

spedygiorgio

lifecontingencies:Financial and Actuarial Mathematics for Life Contingencies

Classes and methods that allow the user to manage life table, actuarial tables (also multiple decrements tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein. See Spedicato (2013) <doi:10.18637/jss.v055.i10>.

Maintained by Giorgio Alfredo Spedicato. Last updated 6 months ago.

actuarial financial life-contingencies life-insurance cpp

11.0 match 62 stars 7.09 score 156 scripts

tobiasschoch

robsurvey:Robust Survey Statistics Estimation

Robust (outlier-resistant) estimators of finite population characteristics like of means, totals, ratios, regression, etc. Available methods are M- and GM-estimators of regression, weight reduction, trimming, and winsorization. The package extends the 'survey' <https://CRAN.R-project.org/package=survey> package.

Maintained by Tobias Schoch. Last updated 3 months ago.

openblas

12.6 match 9 stars 6.16 score 5 scripts

adeckmyn

maps:Draw Geographical Maps

Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').

Maintained by Alex Deckmyn. Last updated 2 months ago.

5.3 match 24 stars 14.70 score 19k scripts 490 dependents

privefl

bigsnpr:Analysis of Massive SNP Arrays

Easy-to-use, efficient, flexible and scalable tools for analyzing massive SNP arrays. Privé et al. (2018) <doi:10.1093/bioinformatics/bty185>.

Maintained by Florian Privé. Last updated 9 days ago.

big-data bioinformatics memory-mapped-file parallel-computing polygenic-scores population-structure-inference snp-data statistical-methods openblas zlib cpp openmp

6.7 match 200 stars 11.44 score 1.5k scripts 3 dependents

cran

agricolae:Statistical Procedures for Agricultural Research

Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.

Maintained by Felipe de Mendiburu. Last updated 1 years ago.

10.8 match 7 stars 7.01 score 15 dependents

nsaph-software

CausalGPS:Matching on Generalized Propensity Scores with Continuous Exposures

Provides a framework for estimating causal effects of a continuous exposure using observational data, and implementing matching and weighting on the generalized propensity score. Wu, X., Mealli, F., Kioumourtzoglou, M.A., Dominici, F. and Braun, D., 2022. Matching on generalized propensity scores with continuous exposures. Journal of the American Statistical Association, pp.1-29.

Maintained by Naeem Khoshnevis. Last updated 9 months ago.

cpp openmp

9.9 match 24 stars 7.67 score 39 scripts

michaellli

evalITR:Evaluating Individualized Treatment Rules

Provides various statistical methods for evaluating Individualized Treatment Rules under randomized data. The provided metrics include Population Average Value (PAV), Population Average Prescription Effect (PAPE), Area Under Prescription Effect Curve (AUPEC). It also provides the tools to analyze Individualized Treatment Rules under budget constraints. Detailed reference in Imai and Li (2019) <arXiv:1905.05389>.

Maintained by Michael Lingzhi Li. Last updated 2 years ago.

11.0 match 14 stars 6.78 score 36 scripts

covaruber

lme4breeding:Relationship-Based Mixed-Effects Models

Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the 'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.

Maintained by Giovanny Covarrubias-Pazaran. Last updated 20 days ago.

14.2 match 6 stars 5.23 score 7 scripts

frbcesab

popbayes:Bayesian Model to Estimate Population Trends from Counts Series

Infers the trends of one or several animal populations over time from series of counts. It does so by accounting for count precision (provided or inferred based on expert knowledge, e.g. guesstimates), smoothing the population rate of increase over time, and accounting for the maximum demographic potential of species. Inference is carried out in a Bayesian framework. This work is part of the FRB-CESAB working group AfroBioDrivers <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/afrobiodrivers/>.

Maintained by Nicolas Casajus. Last updated 1 years ago.

animal bayesian counts population precision temporal-trend jags cpp

17.2 match 1 stars 4.30 score

thijsjanzen

GenomeAdmixR:Simulate Admixture of Genomes

Individual-based simulations forward in time, simulating how patterns in ancestry along the genome change after admixture. Full description can be found in Janzen (2021) <doi:10.1111/2041-210X.13612>.

Maintained by Thijs Janzen. Last updated 1 years ago.

cpp

14.1 match 5 stars 5.24 score 14 scripts

epiverse-trace

simulist:Simulate Disease Outbreak Line List and Contacts Data

Tools to simulate realistic raw case data for an epidemic in the form of line lists and contacts using a branching process. Simulated outbreaks are parameterised with epidemiological parameters and can have age-structured populations, age-stratified hospitalisation and death risk and time-varying case fatality risk.

Maintained by Joshua W. Lambert. Last updated 2 days ago.

epidemiology epiverse linelist outbreaks

9.3 match 9 stars 7.86 score 27 scripts

capnrefsmmat

regressinator:Simulate and Diagnose (Generalized) Linear Models

Simulate samples from populations with known covariate distributions, generate response variables according to common linear and generalized linear model families, draw from sampling distributions of regression estimates, and perform visual inference on diagnostics from model fits.

Maintained by Alex Reinhart. Last updated 5 months ago.

statistics

11.9 match 4 stars 6.08 score 25 scripts

thomas-neitmann

ggcharts:Get You to Your Desired Plot Faster

Streamlines the creation of common charts by taking care of a lot of data preprocessing and plot customization for the user. Provides a high-level interface for creating plots using 'ggplot2'.

Maintained by Thomas Neitmann. Last updated 3 years ago.

data-visualization ggplot2 plots

8.5 match 291 stars 8.49 score 119 scripts 1 dependents

yonicd

sinew:Package Development Documentation and Namespace Management

Manage package documentation and namespaces from the command line. Programmatically attach namespaces in R and Rmd script, populates Roxygen2 skeletons with information scraped from within functions and populate the Imports field of the DESCRIPTION file.

Maintained by Jonathan Sidi. Last updated 1 years ago.

8.4 match 166 stars 8.54 score 88 scripts

joelkilty

MMAC:Data for Mathematical Modeling and Applied Calculus

Contains the data sets for the textbook "Mathematical Modeling and Applied Calculus" by Joel Kilty and Alex M. McAllister. The book will be published by Oxford University Press in 2018 with ISBN-13: 978-019882472.

Maintained by Joel Kilty. Last updated 7 years ago.

28.8 match 2.50 score 63 scripts

minatonakazawa

fmsb:Functions for Medical Statistics Book with some Demographic Data

Several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.

Maintained by Minato Nakazawa. Last updated 1 years ago.

9.3 match 3 stars 7.74 score 1.9k scripts 23 dependents

john-harrold

formods:'Shiny' Modules for General Tasks

'Shiny' apps can often make use of the same key elements, this package provides modules for common tasks (data upload, wrangling data, figure generation and saving the app state), and also a framework for developing. These modules can react and interact as well as generate code to create reproducible analyses.

Maintained by John Harrold. Last updated 5 days ago.

9.0 match 8 stars 7.94 score 100 scripts 1 dependents

willekens

VirtualPop:Simulation of Populations by Sampling Waiting-Time Distributions

Generates lifespans and fertility histories in continuous time using individual-level state transition (multi-state) models and data from the Human Mortality Database and the Human Fertility Database. To facilitate virtual population analysis, data on virtual individuals are stored in a data structure commonly used in sample surveys. Life histories are generated for multiple generations. The genealogies that result facilitate the study of family ties.

Maintained by Frans Willekens. Last updated 2 years ago.

demography life-histories multistate-models simulation

13.0 match 14 stars 5.45 score 2 scripts

mjanuario

evolved:Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries

"Evolutionary Virtual Education" - 'evolved' - provides multiple tools to help educators (especially at the graduate level or in advanced undergraduate level courses) apply inquiry-based learning in general evolution classes. In particular, the tools provided include functions that simulate evolutionary processes (e.g., genetic drift, natural selection within a single locus) or concepts (e.g. Hardy-Weinberg equilibrium, phylogenetic distribution of traits). More than only simulating, the package also provides tools for students to analyze (e.g., measuring, testing, visualizing) datasets with characteristics that are common to many fields related to evolutionary biology. Importantly, the package is heavily oriented towards providing tools for inquiry-based learning - where students follow scientific practices to actively construct knowledge. For additional details, see package's vignettes.

Maintained by Matheus Januario. Last updated 1 months ago.

10.5 match 3 stars 6.73 score 23 scripts

simsem

semTools:Useful Tools for Structural Equation Modeling

Provides miscellaneous tools for structural equation modeling, many of which extend the 'lavaan' package. For example, latent interactions can be estimated using product indicators (Lin et al., 2010, <doi:10.1080/10705511.2010.488999>) and simple effects probed; analytical power analyses can be conducted (Jak et al., 2021, <doi:10.3758/s13428-020-01479-0>); and scale reliability can be estimated based on estimated factor-model parameters.

Maintained by Terrence D. Jorgensen. Last updated 2 days ago.

5.1 match 79 stars 13.74 score 1.1k scripts 31 dependents

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 2 years ago.

14.4 match 13 stars 4.88 score 59 scripts

ohdsi

PatientLevelPrediction:Develop Clinical Prediction Models Using the Common Data Model

A user friendly way to create patient level prediction models using the Observational Medical Outcomes Partnership Common Data Model. Given a cohort of interest and an outcome of interest, the package can use data in the Common Data Model to build a large set of features. These features can then be used to fit a predictive model with a number of machine learning algorithms. This is further described in Reps (2017) <doi:10.1093/jamia/ocy032>.

Maintained by Egill Fridgeirsson. Last updated 7 days ago.

hades openjdk

6.4 match 190 stars 10.85 score 297 scripts

john-harrold

ubiquity:PKPD, PBPK, and Systems Pharmacology Modeling Tools

Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.

Maintained by John Harrold. Last updated 15 days ago.

modeling pkpd

9.7 match 13 stars 7.14 score 33 scripts

inseefr

icarus:Calibrates and Reweights Units in Samples

Provides user-friendly tools for calibration in survey sampling. The package is production-oriented, and its interface is inspired by the famous popular macro 'Calmar' for SAS, so that 'Calmar' users can quickly get used to 'icarus'. In addition to calibration (with linear, raking and logit methods), 'icarus' features functions for calibration on tight bounds and penalized calibration.

Maintained by Antoine Rebecq. Last updated 2 years ago.

calibration icarus sampling stats survey-sampling

18.6 match 10 stars 3.70 score

cran

FlowerMate:Reciprocity Indices for Style-Polymorphic Plants

Computes unidimensional and multidimensional Reciprocity and Inaccuracy indices. These indices are applicable to common heterostylous populations and to any other type of stylar dimorphic and trimorphic populations, such as in enantiostylous and three-dimensional heterostylous plants. Simón-Porcar, V., A. J. Muñoz-Pajares, J. Arroyo, and S. D. Johnson. (in press) "FlowerMate: multidimensional reciprocity and inaccuracy indices for style-polymorphic plant populations."

Maintained by A. J. Muñoz-Pajares Developer. Last updated 9 months ago.

34.4 match 2.00 score

wch

gcookbook:Data for "R Graphics Cookbook"

Data sets used in the book "R Graphics Cookbook" by Winston Chang, published by O'Reilly Media.

Maintained by Winston Chang. Last updated 6 years ago.

10.2 match 10 stars 6.77 score 1.3k scripts 1 dependents

ncn-foreigners

singleRcapture:Single-Source Capture-Recapture Models

Implementation of single-source capture-recapture methods for population size estimation using zero-truncated, zero-one truncated and zero-truncated one-inflated Poisson, Geometric and Negative Binomial regression as well as Zelterman's and Chao's regression. Package includes point and interval estimators for the population size with variances estimated using analytical or bootstrap method. Details can be found in: van der Heijden et all. (2003) <doi:10.1191/1471082X03st057oa>, Böhning and van der Heijden (2019) <doi:10.1214/18-AOAS1232>, Böhning et al. (2020) Capture-Recapture Methods for the Social and Medical Sciences or Böhning and Friedl (2021) <doi:10.1007/s10260-021-00556-8>.

Maintained by Maciej Beręsewicz. Last updated 30 days ago.

11.0 match 11 stars 6.16 score 29 scripts

willekens

Families:Kinship Ties in Virtual Populations

Tools to study kinship networks, grandparenthood, and double burden (presence of children and oldest old parents) in virtual population produced by 'VirtualPop'.

Maintained by Frans Willekens. Last updated 3 years ago.

demography families kinship simulation

14.9 match 6 stars 4.48 score 1 scripts

mrc-ide

naomi:Naomi Model for Subnational HIV Estimates

This package implements the Naomi model for subnational HIV estimates.

Maintained by Jeff Eaton. Last updated 5 days ago.

cpp

8.6 match 9 stars 7.74 score 54 scripts 2 dependents

poissonconsulting

bboutools:Boreal Caribou Survival, Recruitment and Population Growth

Estimates annual survival, recruitment and population growth for boreal caribou populations using Bayesian and Maximum Likelihood models with fixed and random effects.

Maintained by Seb Dalgarno. Last updated 2 months ago.

12.9 match 1 stars 5.15 score 13 scripts 2 dependents

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.

environment eo gis mapme spatial sustainability

7.1 match 35 stars 9.24 score 287 scripts

soerenpannier

emdi:Estimating and Mapping Disaggregated Indicators

Functions that support estimating, assessing and mapping regional disaggregated indicators. So far, estimation methods comprise direct estimation, the model-based unit-level approach Empirical Best Prediction (see "Small area estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>), the area-level model (see "Estimates of income for small places: An application of James-Stein procedures to Census Data" by Fay and Herriot (1979) <doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance estimation methods, log and arcsin transformation, spatial, robust and measurement error models), as well as their precision estimates. The assessment of the used model is supported by a summary and diagnostic plots. For a suitable presentation of estimates, map plots can be easily created. Furthermore, results can easily be exported to excel. For a detailed description of the package and the methods used see "The R Package emdi for Estimating and Mapping Regionally Disaggregated Indicators" by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07> and the second package vignette "A Framework for Producing Small Area Estimates Based on Area-Level Models in R".

Maintained by Soeren Pannier. Last updated 1 years ago.

9.0 match 15 stars 7.26 score 45 scripts 1 dependents

distancedevelopment

dsims:Distance Sampling Simulations

Performs distance sampling simulations. 'dsims' repeatedly generates instances of a user defined population within a given survey region. It then generates realisations of a survey design and simulates the detection process. The data are then analysed so that the results can be compared for accuracy and precision across all replications. This process allows users to optimise survey designs for their specific set of survey conditions. The effects of uncertainty in population distribution or parameters can be investigated under a number of simulations so that users can be confident that they have achieved a robust survey design before deploying vessels into the field. The distance sampling designs used in this package from 'dssd' are detailed in Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008, ISBN-13: 978-0199225873). General distance sampling methods are detailed in Introduction to Distance Sampling: Estimating Abundance of Biological Populations, Buckland et. al. (2004, ISBN-13: 978-0198509271). Find out more about estimating animal/plant abundance with distance sampling at <https://distancesampling.org/>.

Maintained by Laura Marshall. Last updated 1 months ago.

13.0 match 2 stars 4.93 score 71 scripts

brechtdv

cystiSim:Agent-Based Model for Taenia_solium Transmission and Control

The cystiSim package provides an agent-based model for Taenia solium transmission and control. cystiSim was developed within the framework of CYSTINET, the European Network on taeniosis/cysticercosis, COST ACTION TD1302.

Maintained by Brecht Devleesschauwer. Last updated 5 years ago.

18.0 match 3.54 score 2 scripts

bioc

ggcyto:Visualize Cytometry data with ggplot

With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.

Maintained by Mike Jiang. Last updated 5 months ago.

immunooncology flowcytometry cellbasedassays infrastructure visualization

5.6 match 58 stars 11.25 score 362 scripts 5 dependents

usdaforestservice

FIESTA:Forest Inventory Estimation and Analysis

A research estimation tool for analysts that work with sample-based inventory data from the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) Program.

Maintained by Grayson White. Last updated 2 days ago.

8.8 match 30 stars 7.24 score 62 scripts

mdlincoln

europop:Historical Populations of European Cities, 1500-1800

This dataset contains population estimates of all European cities with at least 10,000 inhabitants during the period 1500-1800. These data are adapted from Jan De Vries, "European Urbanization, 1500-1800" (1984).

Maintained by Matthew Lincoln. Last updated 8 years ago.

data history population

17.0 match 9 stars 3.69 score 11 scripts

tdruet

RZooRoH:Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes

Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017) <doi:10.1111/mec.14324>.

Maintained by Tom Druet. Last updated 1 years ago.

fortran

19.6 match 1 stars 3.18 score 38 scripts

moderndive

moderndive:Tidyverse-Friendly Introductory Linear Regression

Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.

Maintained by Albert Y. Kim. Last updated 3 months ago.

5.5 match 88 stars 11.35 score 1.8k scripts

usdaforestservice

FIESTAutils:Utility Functions for Forest Inventory Estimation and Analysis

A set of tools for data wrangling, spatial data analysis, statistical modeling (including direct, model-assisted, photo-based, and small area tools), and USDA Forest Service data base tools. These tools are aimed to help Foresters, Analysts, and Scientists extract and perform analyses on USDA Forest Service data.

Maintained by Grayson White. Last updated 7 hours ago.

cpp

9.8 match 8 stars 6.33 score 1 dependents

bioc

flowGraph:Identifying differential cell populations in flow cytometry data accounting for marker frequency

Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.

Maintained by Alice Yue. Last updated 5 months ago.

flowcytometry statisticalmethod immunooncology software cellbasedassays visualization

15.5 match 4.00 score 10 scripts

mblumuga

abc.data:Data Only: Tools for Approximate Bayesian Computation (ABC)

Contains data which are used by functions of the 'abc' package.

Maintained by Blum Michael. Last updated 12 months ago.

17.4 match 3.53 score 6 scripts 10 dependents

gilberto-sassi

statBasics:Basic Functions to Statistical Methods Course

Basic statistical methods with some modifications for the course Statistical Methods at Federal University of Bahia (Brazil). All methods in this packages are explained in the text book of Montgomery and Runger (2010) <ISBN: 978-1-119-74635-5>.

Maintained by Gilberto Sassi. Last updated 1 years ago.

16.2 match 3.78 score 120 scripts

rafapereirabr

aopdata:Data from the 'Access to Opportunities Project (AOP)'

Download data from the 'Access to Opportunities Project (AOP)'. The 'aopdata' package brings annual estimates of access to employment, health, education and social assistance services by transport mode, as well as data on the spatial distribution of population, jobs, health care, schools and social assistance facilities at a fine spatial resolution for all cities included in the project. More info on the 'AOP' website <https://www.ipea.gov.br/acessooportunidades/en/>.

Maintained by Rafael H. M. Pereira. Last updated 2 months ago.

12.9 match 4.70 score 72 scripts

atorus-research

Tplyr:A Traceability Focused Grammar of Clinical Data Summary

A traceability focused tool created to simplify the data manipulation necessary to create clinical summaries.

Maintained by Mike Stackhouse. Last updated 1 years ago.

pharma tables

6.4 match 95 stars 9.49 score 138 scripts 2 dependents

epiforecasts

socialmixr:Social Mixing Matrices for Infectious Disease Modelling

Provides methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.

Maintained by Sebastian Funk. Last updated 5 months ago.

6.2 match 38 stars 9.74 score 227 scripts 1 dependents

paul-buerkner

brms:Bayesian Regression Models using 'Stan'

Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include both theory-driven and data-driven non-linear terms, auto-correlation structures, censoring and truncation, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their prior knowledge. Models can easily be evaluated and compared using several methods assessing posterior or prior predictions. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Bürkner (2018) <doi:10.32614/RJ-2018-017>; Bürkner (2021) <doi:10.18637/jss.v100.i05>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.

Maintained by Paul-Christian Bürkner. Last updated 1 days ago.

bayesian-inference brms multilevel-models stan statistical-models

3.6 match 1.3k stars 16.61 score 13k scripts 34 dependents

homerhanumat

tigerstats:R Functions for Elementary Statistics

A collection of data sets and functions that are useful in the teaching of statistics at an elementary level to students who may have little or no previous experience with the command line. The functions for elementary inferential procedures follow a uniform interface for user input. Some of the functions are instructional applets that can only be run on the R Studio integrated development environment with package 'manipulate' installed. Other instructional applets are Shiny apps that may be run locally. In teaching the package is used alongside of package 'mosaic', 'mosaicData' and 'abd', which are therefore listed as dependencies.

Maintained by Homer White. Last updated 4 years ago.

10.3 match 16 stars 5.77 score 327 scripts

hanase

wpp2015:World Population Prospects 2015

Provides data from the United Nation's World Population Prospects 2015.

Maintained by Hana Sevcikova. Last updated 6 years ago.

39.1 match 1.52 score 33 scripts

dwinter

mmod:Modern Measures of Population Differentiation

Provides functions for measuring population divergence from genotypic data.

Maintained by David Winter. Last updated 8 years ago.

7.2 match 11 stars 8.25 score 116 scripts 2 dependents

musajajorge

popPyramid:Population Pyramids

Functions that facilitate the elaboration of population pyramids.

Maintained by Jorge L. C. Musaja. Last updated 2 years ago.

population pyramids

22.0 match 2.70 score 1 scripts

guyabel

wcde:Download Data from the Wittgenstein Centre Human Capital Data Explorer

Download and plot education specific demographic data from the Wittgenstein Centre for Demography and Human Capital Data Explorer <http://dataexplorer.wittgensteincentre.org/>.

Maintained by Guy J. Abel. Last updated 1 years ago.

demography demograpic-data population-data

13.9 match 2 stars 4.26 score 18 scripts

richardli

surveyPrev:Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas

Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.

Maintained by Qianyu Dong. Last updated 4 days ago.

10.2 match 1 stars 5.76 score 11 scripts

jarretrt

tci:Target Controlled Infusion (TCI)

Implementation of target-controlled infusion algorithms for compartmental pharmacokinetic and pharmacokinetic-pharmacodynamic models. Jacobs (1990) <doi:10.1109/10.43622>; Marsh et al. (1991) <doi:10.1093/bja/67.1.41>; Shafer and Gregg (1993) <doi:10.1007/BF01070999>; Schnider et al. (1998) <doi:10.1097/00000542-199805000-00006>; Abuhelwa, Foster, and Upton (2015) <doi:10.1016/j.vascn.2015.03.004>; Eleveld et al. (2018) <doi:10.1016/j.bja.2018.01.018>.

Maintained by Ryan Jarrett. Last updated 2 years ago.

cpp openmp

16.9 match 6 stars 3.48 score 8 scripts

jakobbossek

ecr:Evolutionary Computation in R

Framework for building evolutionary algorithms for both single- and multi-objective continuous or discrete optimization problems. A set of predefined evolutionary building blocks and operators is included. Moreover, the user can easily set up custom objective functions, operators, building blocks and representations sticking to few conventions. The package allows both a black-box approach for standard tasks (plug-and-play style) and a much more flexible white-box approach where the evolutionary cycle is written by hand.

Maintained by Jakob Bossek. Last updated 1 years ago.

combinatorial-optimization evolutionary-algorithm evolutionary-algorithms evolutionary-strategy genetic-algorithm-framework metaheuristics multi-objective-optimization optimization optimization-framework cpp

7.9 match 43 stars 7.36 score 89 scripts 2 dependents

marekslenker

MorphoTools2:Multivariate Morphometric Analysis

Tools for multivariate analyses of morphological data, wrapped in one package, to make the workflow convenient and fast. Statistical and graphical tools provide a comprehensive framework for checking and manipulating input data, statistical analyses, and visualization of results. Several methods are provided for the analysis of raw data, to make the dataset ready for downstream analyses. Integrated statistical methods include hierarchical classification, principal component analysis, principal coordinates analysis, non-metric multidimensional scaling, and multiple discriminant analyses: canonical, stepwise, and classificatory (linear, quadratic, and the non-parametric k nearest neighbours). The philosophy of the package is described in Šlenker et al. 2022.

Maintained by Marek Šlenker. Last updated 5 months ago.

11.5 match 7 stars 5.02 score 9 scripts

japilo

colorednoise:Simulate Temporally Autocorrelated Populations

Temporally autocorrelated populations are correlated in their vital rates (growth, death, etc.) from year to year. It is very common for populations, whether they be bacteria, plants, or humans, to be temporally autocorrelated. This poses a challenge for stochastic population modeling, because a temporally correlated population will behave differently from an uncorrelated one. This package provides tools for simulating populations with white noise (no temporal autocorrelation), red noise (positive temporal autocorrelation), and blue noise (negative temporal autocorrelation). The algebraic formulation for autocorrelated noise comes from Ruokolainen et al. (2009) <doi:10.1016/j.tree.2009.04.009>. Models for unstructured populations and for structured populations (matrix models) are available.

Maintained by July Pilowsky. Last updated 11 months ago.

openblas cpp

10.6 match 10 stars 5.43 score 18 scripts

ipeagit

censobr:Download Data from Brazil's Population Census

Easy access to data from Brazil's population censuses. The package provides a simple and efficient way to download and read the data sets and the documentation of all the population censuses taken in and after 1960 in the country. The package is built on top of the 'Arrow' platform <https://arrow.apache.org/docs/r/>, which allows users to work with larger-than-memory census data using 'dplyr' familiar functions. <https://arrow.apache.org/docs/r/articles/arrow.html#analyzing-arrow-data-with-dplyr>.

Maintained by Rafael H. M. Pereira. Last updated 15 days ago.

brazil census census-data microdados microdata

6.9 match 39 stars 8.38 score 79 scripts

bioc

flowStats:Statistical methods for the analysis of flow cytometry data

Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.

Maintained by Greg Finak. Last updated 5 months ago.

immunooncology flowcytometry cellbasedassays

7.0 match 13 stars 8.24 score 195 scripts 1 dependents

r-forge

latticeExtra:Extra Graphical Utilities Based on Lattice

Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.

Maintained by Deepayan Sarkar. Last updated 3 years ago.

5.6 match 10.18 score 2.6k scripts 233 dependents

civilstat

RankingProject:The Ranking Project: Visualizations for Comparing Populations

Functions to generate plots and tables for comparing independently-sampled populations. Companion package to "A Primer on Visualizations for Comparing Populations, Including the Issue of Overlapping Confidence Intervals" by Wright, Klein, and Wieczorek (2019) <DOI:10.1080/00031305.2017.1392359> and "A Joint Confidence Region for an Overall Ranking of Populations" by Klein, Wright, and Wieczorek (2020) <DOI:10.1111/rssc.12402>.

Maintained by Jerzy Wieczorek. Last updated 3 years ago.

11.4 match 7 stars 5.02 score 10 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.

11.7 match 10 stars 4.88 score 15 scripts

viralemergence

epizootic:Spatially Explicit Population Models of Disease Transmission in Wildlife

This extension of the pattern-oriented modeling framework of the 'poems' package provides a collection of modules and functions customized for modeling disease transmission on a population scale in a spatiotemporally explicit manner. This includes seasonal time steps, dispersal functions that track disease state of dispersers, results objects that store disease states, and a population simulator that includes disease dynamics.

Maintained by July Pilowsky. Last updated 6 months ago.

cpp

10.4 match 4 stars 5.45 score 5 scripts

lbbe-software

fitdistrplus:Help to Fit of a Parametric Distribution to Non-Censored or Censored Data

Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit estimation (MGE) and maximum spacing estimation (MSE) methods (available only for non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g. Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction to parametric estimation.

Maintained by Aurélie Siberchicot. Last updated 11 days ago.

3.5 match 54 stars 16.15 score 4.5k scripts 153 dependents

rspatial

geodata:Download Geographic Data

Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.

Maintained by Robert J. Hijmans. Last updated 1 months ago.

5.3 match 162 stars 10.75 score 1.5k scripts 7 dependents

storeylab

popkin:Estimate Kinship and FST under Arbitrary Population Structure

Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.

Maintained by Alejandro Ochoa. Last updated 5 months ago.

9.2 match 20 stars 6.11 score 65 scripts

capnrefsmmat

covidcast:Client for Delphi's 'COVIDcast Epidata' API

Tools for Delphi's 'COVIDcast Epidata' API: data access, maps and time series plotting, and basic signal processing. The API includes a collection of numerous indicators relevant to the COVID-19 pandemic in the United States, including official reports, de-identified aggregated medical claims data, large-scale surveys of symptoms and public behavior, and mobility data, typically updated daily and at the county level. All data sources are documented at <https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html>.

Maintained by Alex Reinhart. Last updated 2 years ago.

11.5 match 4.86 score 293 scripts

kenkellner

IPMbook:Functions and Data for the Book 'Integrated Population Models'

Provides functions and data sets to accompany the book 'Integrated Population Models: Theory and Ecological Applications with R and JAGS' by Michael Schaub and Marc Kéry (ISBN: 9780128205648).

Maintained by Ken Kellner. Last updated 1 months ago.

14.2 match 1 stars 3.95 score 177 scripts

iainmstott

popdemo:Demographic Modelling Using Projection Matrices

Tools for modelling populations and demography using matrix projection models, with deterministic and stochastic model implementations. Includes population projection, indices of short- and long-term population size and growth, perturbation analysis, convergence to stability or stationarity, and diagnostic and manipulation tools.

Maintained by Iain Stott. Last updated 3 years ago.

10.8 match 5.16 score 172 scripts 7 dependents

kjhealy

gssrdoc:Document General Social Survey Variable

The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.

Maintained by Kieran Healy. Last updated 11 months ago.

24.4 match 2.28 score 38 scripts

jfieberg

SightabilityModel:Wildlife Sightability Modeling

Uses logistic regression to model the probability of detection as a function of covariates. This model is then used with observational survey data to estimate population size, while accounting for uncertain detection. See Steinhorst and Samuel (1989).

Maintained by Schwarz Carl James. Last updated 2 years ago.

11.2 match 1 stars 4.96 score 23 scripts

cran

epiR:Tools for the Analysis of Epidemiological Data

Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.

Maintained by Mark Stevenson. Last updated 1 months ago.

6.8 match 10 stars 8.18 score 10 dependents

jrmccombs

RHPCBenchmark:Benchmarks for High-Performance Computing Environments

Microbenchmarks for determining the run time performance of aspects of the R programming environment and packages relevant to high-performance computation. The benchmarks are divided into three categories: dense matrix linear algebra kernels, sparse matrix linear algebra kernels, and machine learning functionality.

Maintained by James McCombs. Last updated 8 years ago.

18.2 match 3.02 score 21 scripts

fbertran

sageR:Applied Statistics for Economics and Management with R

Datasets and functions for the book "Statistiques pour l’économie et la gestion", "Théorie et applications en entreprise", F. Bertrand, Ch. Derquenne, G. Dufrénot, F. Jawadi and M. Maumy, C. Borsenberger editor, (2021, ISBN:9782807319448, De Boeck Supérieur, Louvain-la-Neuve). The first chapter of the book is dedicated to an introduction to statistics and their world. The second chapter deals with univariate exploratory statistics and graphics. The third chapter deals with bivariate and multivariate exploratory statistics and graphics. The fourth chapter is dedicated to data exploration with Principal Component Analysis. The fifth chapter is dedicated to data exploration with Correspondance Analysis. The sixth chapter is dedicated to data exploration with Multiple Correspondance Analysis. The seventh chapter is dedicated to data exploration with automatic clustering. The eighth chapter is dedicated to an introduction to probability theory and classical probability distributions. The ninth chapter is dedicated to an estimation theory, one-sample and two-sample tests. The tenth chapter is dedicated to an Gaussian linear model. The eleventh chapter is dedicated to an introduction to time series. The twelfth chapter is dedicated to an introduction to probit and logit models. Various example datasets are shipped with the package as well as some new functions.

Maintained by Frederic Bertrand. Last updated 2 years ago.

13.1 match 2 stars 4.18 score 15 scripts