zkamvar r-universe repositoryhttps://zkamvar.r-universe.devPackage updated in zkamvarcranlike-server 0.17.29https://github.com/zkamvar.png?size=400zkamvar r-universe repositoryhttps://zkamvar.r-universe.devTue, 18 Jun 2024 09:32:18 GMT[zkamvar] ade4 1.7-22aurelie.siberchicot@univ-lyon1.fr (Aurélie Siberchicot)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>.https://github.com/r-universe/zkamvar/actions/runs/9563309239Tue, 18 Jun 2024 09:32:18 GMTade41.7-22successhttps://zkamvar.r-universe.devhttps://github.com/sdray/ade4faq.Rmdfaq.htmlFAQ2023-05-17 08:35:532024-01-22 09:15:28[ropensci] tinkr 0.2.0.9000zkamvar@gmail.com (Zhian N. Kamvar)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.https://github.com/r-universe/ropensci/actions/runs/9523484405Fri, 14 Jun 2024 22:57:21 GMTtinkr0.2.0.9000successhttps://ropensci.r-universe.devhttps://github.com/ropensci/tinkrtinkr.Rmdtinkr.htmlIntroduction to the tinkr package2021-05-27 06:34:342021-05-27 06:34:34[grunwaldlab] poppr 2.9.6zkamvar@gmail.com (Zhian N. Kamvar)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>.https://github.com/r-universe/grunwaldlab/actions/runs/9525814635Thu, 16 May 2024 18:29:07 GMTpoppr2.9.6successhttps://grunwaldlab.r-universe.devhttps://github.com/grunwaldlab/poppralgo.Rnwalgo.pdfAlgorightms and Equations2014-05-24 06:29:352024-01-16 06:58:58[zkamvar] poppr 2.9.6zkamvar@gmail.com (Zhian N. Kamvar)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>.https://github.com/r-universe/zkamvar/actions/runs/9525814803Thu, 16 May 2024 18:29:07 GMTpoppr2.9.6successhttps://zkamvar.r-universe.devhttps://github.com/grunwaldlab/poppralgo.Rnwalgo.pdfAlgorightms and Equations2014-05-24 06:29:352024-01-16 06:58:58[zkamvar] incidence 1.7.4tim.taylor@hiddenelephants.co.uk (Tim Taylor)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.https://github.com/r-universe/zkamvar/actions/runs/9511007427Wed, 15 May 2024 12:06:11 GMTincidence1.7.4successhttps://zkamvar.r-universe.devhttps://github.com/reconhub/incidenceconversions.Rmdconversions.htmlConversions to and from the incidence class2017-04-03 15:55:232020-11-03 17:18:51customize_plot.Rmdcustomize_plot.htmlCustomize plots of incidence2016-10-25 08:33:252024-05-15 10:48:16incidence_class.Rmdincidence_class.htmlDetails of the incidence class2016-10-25 08:33:372020-11-03 17:18:51incidence_fit_class.Rmdincidence_fit_class.htmlDetails of the incidence_fit class2018-08-21 13:31:042018-11-30 10:08:39overview.Rmdoverview.htmlOverview of the incidence package2016-10-17 11:51:172024-05-15 10:48:16[zkamvar] strataG 2.5.01eric.archer@noaa.gov (Eric Archer)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>.https://github.com/r-universe/zkamvar/actions/runs/9532636783Tue, 14 May 2024 16:07:00 GMTstrataG2.5.01failurehttps://zkamvar.r-universe.devhttps://github.com/EricArcher/strataG[carpentries] pegboard 0.7.5zkamvar@carpentries.org (Zhian N. Kamvar)The Carpentries (<https://carpentries.org>) curricula is
made of of lessons that are hosted as websites. Each lesson
represents between a half day to two days of instruction and
contains several episodes, which are written as
'kramdown'-flavored 'markdown' documents and converted to HTML
using the 'Jekyll' static website generator. This package
builds on top of the 'tinkr' package; reads in these markdown
documents to 'XML' and stores them in R6 classes for convenient
exploration and manipulation of sections within episodes.https://github.com/r-universe/carpentries/actions/runs/9443236161Thu, 11 Apr 2024 11:28:45 GMTpegboard0.7.5successhttps://carpentries.r-universe.devhttps://github.com/carpentries/pegboard[zkamvar] hierfstat 0.5-11jerome.goudet@unil.ch (Jerome Goudet)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>.https://github.com/r-universe/zkamvar/actions/runs/9296520400Sun, 16 Apr 2023 14:02:57 GMThierfstat0.5-11successhttps://zkamvar.r-universe.devhttps://github.com/jgx65/hierfstathierfstat.Rmdhierfstat.htmlHierfstat latest features2015-12-03 15:36:152022-05-05 20:23:46import.Rmdimport.htmlImporting data in Hierfstat2016-08-24 07:04:272022-08-12 08:17:14[zkamvar] epitabulate 0.0.0.9007aspina@appliedepi.org (Alexander Spina)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>.https://github.com/r-universe/zkamvar/actions/runs/9441596303Sat, 18 Mar 2023 13:36:15 GMTepitabulate0.0.0.9007successhttps://zkamvar.r-universe.devhttps://github.com/r4epi/epitabulate[r4epi] apyramid 0.1.3zkamvar@gmail.com (Zhian N. Kamvar)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/>.https://github.com/r-universe/r4epi/actions/runs/9458748544Tue, 14 Feb 2023 17:11:25 GMTapyramid0.1.3successhttps://r4epi.r-universe.devhttps://github.com/r4epi/apyramidintro.Rmdintro.htmlIntroduction to {apyramid}2020-01-13 15:59:402020-01-13 15:59:40[zkamvar] apyramid 0.1.3zkamvar@gmail.com (Zhian N. Kamvar)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/>.https://github.com/r-universe/zkamvar/actions/runs/9425492228Tue, 14 Feb 2023 17:11:25 GMTapyramid0.1.3successhttps://zkamvar.r-universe.devhttps://github.com/r4epi/apyramidintro.Rmdintro.htmlIntroduction to {apyramid}2020-01-13 15:59:402020-01-13 15:59:40[zkamvar] epikit 0.1.4aspina@appliedepi.org (Alexander Spina)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>.https://github.com/r-universe/zkamvar/actions/runs/9330185339Sun, 05 Feb 2023 09:49:46 GMTepikit0.1.4successhttps://zkamvar.r-universe.devhttps://github.com/r4epi/epikitintro.Rmdintro.htmlIntroduction to epikit2020-01-28 10:20:452020-01-28 10:20:45[zkamvar] sitrep 0.2.3aspina@appliedepi.org (Alexander Spina)Report templates and helper functions for applied
epidemiologyhttps://github.com/r-universe/zkamvar/actions/runs/9262600679Fri, 03 Feb 2023 18:52:03 GMTsitrep0.2.3successhttps://zkamvar.r-universe.devhttps://github.com/r4epi/sitrep[zkamvar] adegenet 2.1.10zkamvar@gmail.com (Zhian N. Kamvar)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.https://github.com/r-universe/zkamvar/actions/runs/9608161681Sat, 28 Jan 2023 00:12:40 GMTadegenet2.1.10successhttps://zkamvar.r-universe.devhttps://github.com/thibautjombart/adegenet[thibautjombart] adegenet 2.1.10zkamvar@gmail.com (Zhian N. Kamvar)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.https://github.com/r-universe/thibautjombart/actions/runs/9559117785Sat, 28 Jan 2023 00:12:40 GMTadegenet2.1.10successhttps://thibautjombart.r-universe.devhttps://github.com/thibautjombart/adegenet[zkamvar] epidict 0.0.0.9001aspina@appliedepi.org (Alexander Spina)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.https://github.com/r-universe/zkamvar/actions/runs/9201385060Fri, 26 Aug 2022 09:56:41 GMTepidict0.0.0.9001successhttps://zkamvar.r-universe.devhttps://github.com/r4epi/epidictintro.Rmdintro.htmlIntroduction to epidict2020-02-11 18:06:332020-02-11 18:06:33Outbreaks.RmdOutbreaks.htmlMSF outbreak dictionaries2020-02-11 18:06:332021-12-16 21:25:33Surveys.RmdSurveys.htmlMSF Survey Dictionaries2020-02-11 18:06:332021-12-16 21:25:33[zkamvar] tinkr 0.0.0.9001zkamvar@gmail.com (Zhian N. Kamvar)Casts (R)Markdown files to XML and back to allow their
editing via XPath.https://github.com/r-universe/zkamvar/actions/runs/9262471442Tue, 08 Feb 2022 15:54:26 GMTtinkr0.0.0.9001successhttps://zkamvar.r-universe.devhttps://github.com/ropensci/tinkrtinkr.Rmdtinkr.htmlIntroduction to the tinkr package2021-05-27 06:34:342021-05-27 06:34:34[reconhub] aweek 1.0.2zkamvar@gmail.com (Zhian N. Kamvar)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.https://github.com/r-universe/reconhub/actions/runs/9343357346Sun, 21 Mar 2021 19:30:40 GMTaweek1.0.2successhttps://reconhub.r-universe.devhttps://github.com/reconhub/aweekintroduction.Rmdintroduction.htmlaweek means 'any week'2019-02-25 07:20:282021-03-21 19:30:40[zkamvar] aweek 1.0.2zkamvar@gmail.com (Zhian N. Kamvar)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.https://github.com/r-universe/zkamvar/actions/runs/9249704394Sun, 21 Mar 2021 19:30:40 GMTaweek1.0.2successhttps://zkamvar.r-universe.devhttps://github.com/reconhub/aweekintroduction.Rmdintroduction.htmlaweek means 'any week'2019-02-25 07:20:282021-03-21 19:30:40[reconhub] matchmaker 0.1.1zkamvar@gmail.com (Zhian N. Kamvar)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.https://github.com/r-universe/reconhub/actions/runs/9441595446Fri, 21 Feb 2020 20:44:05 GMTmatchmaker0.1.1successhttps://reconhub.r-universe.devhttps://github.com/reconhub/matchmakerintro.Rmdintro.htmlIntroduction to matchmaker2020-01-10 16:26:372020-01-16 11:44:09[zkamvar] matchmaker 0.1.1zkamvar@gmail.com (Zhian N. Kamvar)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.https://github.com/r-universe/zkamvar/actions/runs/9296256865Fri, 21 Feb 2020 20:44:05 GMTmatchmaker0.1.1successhttps://zkamvar.r-universe.devhttps://github.com/reconhub/matchmakerintro.Rmdintro.htmlIntroduction to matchmaker2020-01-10 16:26:372020-01-16 11:44:09[zkamvar] repvar 0.1.0zkamvar@gmail.com (Zhian N. Kamvar)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'.https://github.com/r-universe/zkamvar/actions/runs/9335013990Thu, 05 Apr 2018 22:15:37 GMTrepvar0.1.0successhttps://zkamvar.r-universe.devhttps://github.com/zkamvar/repvargetting-started.Rmdgetting-started.htmlGetting Started2018-04-04 20:33:292018-04-05 22:15:37[zkamvar] beaverdown 0.2.1zkamvar@gmail.com (Zhian N. Kamvar)Using the bookdown package and LaTeX and Word thesis
templates from Oregon State University, this package was
derived from Chester Ismay's package "thesisdown"https://github.com/r-universe/zkamvar/actions/runs/9296388195Wed, 05 Oct 2016 05:35:48 GMTbeaverdown0.2.1successhttps://zkamvar.r-universe.devhttps://github.com/zkamvar/beaverdown[zkamvar] ggcompoplot 0.1.0kamvarz@science.oregonstate.edu (Zhian N. Kamvar)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.https://github.com/r-universe/zkamvar/actions/runs/9433290753Thu, 21 Jul 2016 22:40:37 GMTggcompoplot0.1.0successhttps://zkamvar.r-universe.devhttps://github.com/zkamvar/ggcompoplot[grunwaldlab] ezec 1.0.0kamvarz@science.oregonstate.edu (Zhian N. Kamvar)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.https://github.com/r-universe/grunwaldlab/actions/runs/9590539831Sun, 12 Jun 2016 03:45:44 GMTezec1.0.0successhttps://grunwaldlab.r-universe.devhttps://github.com/grunwaldlab/ezecgetting_started.Rmdgetting_started.htmlGetting Started with EZEC2015-11-21 00:21:212016-06-10 18:29:12