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>.
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openblascpp
13.75 score 45 stars 290 dependents 2.7k scripts 58k 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.
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12.81 score 201 stars 29 dependents 2.8k scripts 18k 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.
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12.79 score 201 stars 29 dependents 2.6k scripts 18k 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.
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outbreak
11.46 score 57 stars 11 dependents 562 scripts 1.4k 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>.
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devtoolsfstatisticsgwashierfstatkinshippopulation-geneticspopulation-genomicsquantitative-geneticssimulations
10.97 score 27 stars 5 dependents 780 scripts 7.4k 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>.
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clonalitygenetic-analysisgenetic-distancesminimum-spanning-networksmultilocus-genotypesmultilocus-lineagespopulation-geneticspopulationsopenmp
10.25 score 72 stars 848 scripts 11k downloadspoppr - 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>.
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clonalitygenetic-analysisgenetic-distancesminimum-spanning-networksmultilocus-genotypesmultilocus-lineagespopulation-geneticspopulationsopenmp
10.25 score 72 stars 848 scripts 11k 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.
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commonmarkxmlxpath
8.00 score 62 stars 4 dependents 4 scripts 334 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.
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commonmarkxmlxpath
8.00 score 62 stars 4 dependents 4 scripts 334 downloads
sitrep - Report Templates and Helper Functions for Applied Epidemiology
A meta-package that loads the complete sitrep ecosystem for applied epidemiology analysis. This package provides report templates and automatically loads companion packages, including 'epitabulate' (for epidemiological tables), 'epidict' (for data dictionaries), 'epikit' (for epidemiological utilities), and 'apyramid' (for age-sex pyramids). Simply load 'sitrep' to access all functions from the ecosystem.
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epidemiologymsfoutbreaksreport-generator
8.00 score 45 stars 7 scripts 211 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.
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date-formattingdatesepidemiologytimeseriesweek
7.92 score 17 stars 13 dependents 155 scripts 1.6k 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.
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date-formattingdatesepidemiologytimeseriesweek
7.89 score 17 stars 13 dependents 142 scripts 1.6k 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>.
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dna-sequencesgeneticslocus-summariesmicrosatellitespopulation-geneticspopulation-genomicspopulation-structuresnp-datasnpscpp
7.51 score 26 stars 392 scripts 13 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 formatting proportions with confidence intervals. This is part of the 'R4Epis' project <https://r4epi.github.io/sitrep/>.
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6.77 score 10 stars 2 dependents 24 scripts 1.4k 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/>.
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6.19 score 20 stars 1 dependents 52 scripts 927 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/>.
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6.19 score 20 stars 1 dependents 52 scripts 797 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.
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5.16 score 8 stars 1 dependents 12 scripts 447 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.
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5.08 score 8 stars 1 dependents 9 scripts 513 downloadsepitabulate - Tables for Epidemiological Analysis
Produces tables for descriptive epidemiological analysis. These tables include attack rates, case fatality ratios, and mortality rates (with appropriate confidence intervals), with additional functionality to calculate Mantel-Haenszel odds, risk, and incidence rate ratios. The methods implemented follow standard epidemiological approaches described in Rothman et al. (2008, ISBN:978-0-19-513554-2). This package is part of the 'R4EPIs' project <https://R4EPI.github.io/sitrep/>.
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4.98 score 8 stars 1 dependents 3 scripts 224 downloadsbeaverdown - 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"
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2.95 score 18 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'.
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allelesgeneticsmicrosatellite
2.70 score 1 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.
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2.70 score 1 stars 8 scripts 500 downloadsggcompoplot - 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.
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1.70 score 1 stars 3 scripts