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 1 months ago

openblascpp

13.65 score 38 stars 254 dependents 2.3k scripts 38k downloads

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.

Last updated 2 years ago

12.37 score 174 stars 28 dependents 2.1k scripts 11k downloads

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.

Last updated 2 years ago

12.34 score 169 stars 28 dependents 1.9k scripts 11k downloads

incidence - 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 5 months ago

outbreak

12.02 score 58 stars 11 dependents 496 scripts 1.8k downloads

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>.

Last updated 1 months ago

devtoolsfstatisticsgwashierfstatkinshippopulation-geneticspopulation-genomicsquantitative-geneticssimulations

10.79 score 24 stars 4 dependents 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 7 months ago

clonalitygenetic-analysisgenetic-distancesminimum-spanning-networksmultilocus-genotypesmultilocus-lineagespopulation-geneticspopulationsopenmp

10.71 score 68 stars 576 scripts 5.1k 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 7 months ago

clonalitygenetic-analysisgenetic-distancesminimum-spanning-networksmultilocus-genotypesmultilocus-lineagespopulation-geneticspopulationsopenmp

10.71 score 68 stars 576 scripts 5.1k downloads

tinkr - 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 1 months ago

commonmarkxmlxpath

8.01 score 57 stars 4 dependents 4 scripts 146 downloads

aweek - 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

7.90 score 17 stars 14 dependents 116 scripts 1.9k downloads

aweek - 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

7.90 score 17 stars 14 dependents 115 scripts 1.9k downloads

tinkr - 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 1 months ago

commonmarkxmlxpath

7.89 score 57 stars 3 dependents 4 scripts 180 downloads

epikit - 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

6.23 score 9 stars 2 dependents 21 scripts 808 downloads

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/>.

Last updated 2 years ago

6.18 score 20 stars 1 dependents 50 scripts 838 downloads

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/>.

Last updated 2 years ago

6.18 score 20 stars 1 dependents 50 scripts 905 downloads

matchmaker - 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 dependents 9 scripts 558 downloads

matchmaker - 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 dependents 9 scripts 489 downloads

strataG - 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 7 months ago

dna-sequencesgeneticslocus-summariesmicrosatellitespopulation-geneticspopulation-genomicspopulation-structuresnp-datasnpscppjags

5.08 score 25 stars 318 scripts 79 downloads

epidict - 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 dependents 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 scripts

ezec - 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 9 years ago

3.70 score 1 stars 6 scripts 141 downloads

epitabulate - 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 dependents 3 scripts

beaverdown - 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 scripts

repvar - 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 scripts

ggcompoplot - 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