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>.
Last updated 4 days ago
13.67 score 38 stars 254 packages 2.4k scripts 38k downloadsadegenet - 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.
Last updated 2 years ago
12.35 score 168 stars 28 packages 2.1k scripts 11k downloadsadegenet - 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.
Last updated 2 years ago
12.32 score 166 stars 28 packages 2.0k scripts 11k downloadsincidence - Compute, Handle, Plot and Model Incidence of Dated Events
Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Last updated 4 months ago
outbreak
11.97 score 58 stars 11 packages 492 scripts 1.6k downloadshierfstat - 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>.
Last updated 2 days ago
devtoolsfstatisticsgwashierfstatkinshippopulation-geneticspopulation-genomicsquantitative-geneticssimulations
10.79 score 24 stars 4 packages 514 scripts 5.2k downloads
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>.
Last updated 6 months ago
clonalitygenetic-analysisgenetic-distancesminimum-spanning-networksmultilocus-genotypesmultilocus-lineagespopulation-geneticspopulations
10.67 score 68 stars 576 scripts 4.6k downloads
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>.
Last updated 6 months ago
clonalitygenetic-analysisgenetic-distancesminimum-spanning-networksmultilocus-genotypesmultilocus-lineagespopulation-geneticspopulations
10.67 score 68 stars 576 scripts 4.6k downloadstinkr - Cast '(R)Markdown' Files to 'XML' and Back Again
Parsing '(R)Markdown' files with numerous regular expressions can be fraught with peril, but it does not have to be this way. Converting '(R)Markdown' files to 'XML' using the 'commonmark' package allows in-memory editing via of 'markdown' elements via 'XPath' through the extensible 'R6' class called 'yarn'. These modified 'XML' representations can be written to '(R)Markdown' documents via an 'xslt' stylesheet which implements an extended version of 'GitHub'-flavoured 'markdown' so that you can tinker to your hearts content.
Last updated 10 days ago
commonmarkxmlxpath
7.89 score 57 stars 3 packages 4 scripts 175 downloadsaweek - Convert Dates to Arbitrary Week Definitions
Which day a week starts depends heavily on the either the local or professional context. This package is designed to be a lightweight solution to easily switching between week-based date definitions.
Last updated 4 years ago
date-formattingdatesepidemiologytimeseriesweek
7.88 score 17 stars 15 packages 118 scripts 1.7k downloadsaweek - Convert Dates to Arbitrary Week Definitions
Which day a week starts depends heavily on the either the local or professional context. This package is designed to be a lightweight solution to easily switching between week-based date definitions.
Last updated 4 years ago
date-formattingdatesepidemiologytimeseriesweek
7.88 score 17 stars 15 packages 118 scripts 1.7k downloadsepikit - Miscellaneous helper tools for epidemiologists
Contains tools for formatting inline code, renaming redundant columns, aggregating age categories, adding survey weights, finding the earliest date of an event, plotting z-curves, generating population counts and calculating proportions with confidence intervals. This is part of the 'R4Epis' project <https://r4epis.netlify.com>.
Last updated 2 years ago
6.30 score 9 stars 2 packages 21 scripts 1.2k downloadstinkr - Cast (R)Markdown Files to XML and Back Again
Casts (R)Markdown files to XML and back to allow their editing via XPath.
Last updated 3 years ago
commonmarkxmlxpath
6.19 score 57 stars 3 packages 4 scripts 150 downloadsapyramid - 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/>.
Last updated 2 years ago
6.17 score 20 stars 1 packages 49 scripts 890 downloadsapyramid - 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/>.
Last updated 2 years ago
6.14 score 20 stars 1 packages 46 scripts 859 downloadsmatchmaker - Flexible Dictionary-Based Cleaning
Provides flexible dictionary-based cleaning that allows users to specify implicit and explicit missing data, regular expressions for both data and columns, and global matches, while respecting ordering of factors. This package is part of the 'RECON' (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Last updated 5 years ago
5.43 score 9 stars 2 packages 9 scripts 509 downloadsmatchmaker - Flexible Dictionary-Based Cleaning
Provides flexible dictionary-based cleaning that allows users to specify implicit and explicit missing data, regular expressions for both data and columns, and global matches, while respecting ordering of factors. This package is part of the 'RECON' (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Last updated 5 years ago
5.43 score 9 stars 2 packages 9 scripts 519 downloadsstrataG - Summaries and Population Structure Analyses of Genetic Data
A toolkit for analyzing stratified population genetic data. Functions are provided for summarizing and checking loci (haploid, diploid, and polyploid), single stranded DNA sequences, calculating most population subdivision metrics, and running external programs such as structure and fastsimcoal. The package is further described in Archer et al (2016) <doi:10.1111/1755-0998.12559>.
Last updated 6 months ago
dna-sequencesgeneticslocus-summariesmicrosatellitespopulation-geneticspopulation-genomicspopulation-structuresnp-datasnps
5.07 score 25 stars 310 scripts 76 downloadsepidict - Epidemiology data dictionaries and random data generators
The 'R4EPIs' project <https://R4epis.netlify.com> seeks to provide a set of standardized tools for analysis of outbreak and survey data in humanitarian aid settings. This package currently provides standardized data dictionaries from MSF OCA for four outbreak scenarios (Acute Jaundice Syndrome, Cholera, Measles, Meningitis) and three surveys (Retrospective mortality and access to care, Malnutrition, and Vaccination coverage). In addition, a data generator from these dictionaries is provided.
Last updated 2 years ago
4.13 score 3 stars 1 packages 5 scripts
sitrep - Report templates and helper functions for applied epidemiology
Report templates and helper functions for applied epidemiology
Last updated 2 years ago
epidemiologymsfoutbreaksreport-generator
4.08 score 40 stars 9 scriptsezec - Easy Interface to Effective Concentration Calculations
Because fungicide resistance is an important phenotypic trait for fungi and oomycetes, it is necessary to have a standardized method of statistically analyzing the Effective Concentration (EC) values. This package is designed for those who are not terribly familiar with R to be able to analyze and plot an entire set of isolates using the 'drc' package.
Last updated 8 years ago
3.70 score 1 stars 6 scripts 183 downloadsepitabulate - Tables for Epidemiological Analysis
Produces tables for descriptive epidemiological analysis. These tables describe counts of variables in either line-list or survey data (with appropriate confidence intervals), with additional functionality to calculate odds, risk, and incidence rate ratios directly from a linelist across several variables. This package is part of the 'R4EPIs' project <https://R4epis.netlify.com>.
Last updated 2 years ago
3.38 score 8 stars 1 packages 3 scriptsbeaverdown - An updated R Markdown thesis template for Oregon State University using the bookdown package
Using the bookdown package and LaTeX and Word thesis templates from Oregon State University, this package was derived from Chester Ismay's package "thesisdown"
Last updated 8 years ago
2.93 score 17 stars 2 scriptsrepvar - Extract Samples to Represent All Variables
In population genetics, it's not uncommon to re-genotype sets of samples to use as positive controls in future studies or for diagnostic panels. To save cost, it's often desireable to have the minimum number of samples that represent all of the alleles in the data. This package provides a procedure that will select these samples with alternative options. The name 'repvar' stands for 'REPresent VARiables'.
Last updated 7 years ago
allelesgeneticsmicrosatellite
2.70 score 1 scriptsggcompoplot - Plot Posterior Assignment Values From a 'DAPC' Analysis
The package 'adegenet' calculates posterior population assignments, which can be plotted as a stacked bar chart. This package creates a 'ggplot2' version of this bar chart, facetted by population.
Last updated 8 years ago
1.70 score 1 stars 3 scripts