zkamvar r-universe repositoryhttps://zkamvar.r-universe.devPackage updated in zkamvarcranlike-server 0.14.14https://github.com/zkamvar.png?size=400zkamvar r-universe repositoryhttps://zkamvar.r-universe.devFri, 03 Feb 2023 21:55:45 GMT[zkamvar] renv 0.16.0-63kevin@rstudio.com (Kevin Ushey)A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.https://github.com/r-universe/zkamvar/actions/runs/4088233946Fri, 03 Feb 2023 21:55:45 GMTrenv0.16.0-63failurehttps://zkamvar.r-universe.devhttps://github.com/rstudio/renv[zkamvar] sitrep 0.2.3aspina@appliedepi.org (Alexander Spina)Report templates and helper functions for applied epidemiologyhttps://github.com/r-universe/zkamvar/actions/runs/4087098300Fri, 03 Feb 2023 18:52:03 GMTsitrep0.2.3successhttps://zkamvar.r-universe.devhttps://github.com/r4epi/sitrep[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/4086700110Fri, 03 Feb 2023 17:54:52 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] 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/4041751375Mon, 30 Jan 2023 07:57:05 GMTade41.7-22successhttps://zkamvar.r-universe.devhttps://github.com/sdray/ade4[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/4029256952Sat, 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/4029288942Sat, 28 Jan 2023 00:12:40 GMTadegenet2.1.10successhttps://thibautjombart.r-universe.devhttps://github.com/thibautjombart/adegenet[carpentries] pegboard 0.4.3zkamvar@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/4018300772Thu, 26 Jan 2023 18:00:35 GMTpegboard0.4.3successhttps://carpentries.r-universe.devhttps://github.com/carpentries/pegboard[zkamvar] pegboard 0.4.3zkamvar@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/zkamvar/actions/runs/4017881718Thu, 26 Jan 2023 18:00:35 GMTpegboard0.4.3successhttps://zkamvar.r-universe.devhttps://github.com/carpentries/pegboard[carpentries] sandpaper 0.11.4zkamvar@carpentries.org (Zhian N. Kamvar)We provide tools to build a Carpentries-themed lesson repository
into an accessible standalone static website. These include local tools and
those designed to be used in a continuous integration context so that all the
lesson author needs to focus on is writing the content of the actual lesson.https://github.com/r-universe/carpentries/actions/runs/4017863916Wed, 25 Jan 2023 22:38:52 GMTsandpaper0.11.4successhttps://carpentries.r-universe.devhttps://github.com/carpentries/sandpaperbuilding-with-renv.Rmdbuilding-with-renv.htmlBuilding Lessons With A Package Cache2021-09-16 19:44:002021-12-03 01:43:40automated-pull-requests.Rmdautomated-pull-requests.htmlWorking with Automated Pull Requests2021-09-16 19:44:002022-11-08 16:29:32[zkamvar] sandpaper 0.11.4zkamvar@carpentries.org (Zhian N. Kamvar)We provide tools to build a Carpentries-themed lesson repository
into an accessible standalone static website. These include local tools and
those designed to be used in a continuous integration context so that all the
lesson author needs to focus on is writing the content of the actual lesson.https://github.com/r-universe/zkamvar/actions/runs/4010690715Wed, 25 Jan 2023 22:38:52 GMTsandpaper0.11.4failurehttps://zkamvar.r-universe.devhttps://github.com/carpentries/sandpaper[zkamvar] varnish 0.2.14zkamvar@carpentries.org (Zhian N. Kamvar)This package does nothing but contain template HTML CSS and JS files.https://github.com/r-universe/zkamvar/actions/runs/3970510414Fri, 20 Jan 2023 18:35:10 GMTvarnish0.2.14successhttps://zkamvar.r-universe.devhttps://github.com/carpentries/varnish[carpentries] varnish 0.2.14zkamvar@carpentries.org (Zhian N. Kamvar)This package does nothing but contain template HTML CSS and JS files.https://github.com/r-universe/carpentries/actions/runs/3970528927Fri, 20 Jan 2023 18:35:10 GMTvarnish0.2.14successhttps://carpentries.r-universe.devhttps://github.com/carpentries/varnish[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/4041121151Tue, 30 Aug 2022 16:03:07 GMTstrataG2.5.01successhttps://zkamvar.r-universe.devhttps://github.com/EricArcher/strataGgtypes.Rmdgtypes.htmlCreating and manipulating gtypes2015-07-18 17:41:532020-02-05 17:21:44summaries.Rmdsummaries.htmlGenotype and sequence summaries2015-07-18 17:41:532020-02-05 17:21:44external.programs.Rmdexternal.programs.htmlInstalling External Programs2016-03-22 17:26:442020-02-05 17:21:44sequences.Rmdsequences.htmlWorking with sequences2015-07-18 17:41:532020-02-05 17:21:44[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/3860712194Tue, 30 Aug 2022 07:58:01 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] 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/4035306511Fri, 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/4081180088Tue, 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[zkamvar] poppr 2.9.3zkamvar@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/4040966942Tue, 07 Sep 2021 14:46:33 GMTpoppr2.9.3successhttps://zkamvar.r-universe.devhttps://github.com/grunwaldlab/poppralgo.Rnwalgo.pdfAlgorightms and Equations2014-05-24 06:29:352017-08-20 22:20:39[grunwaldlab] poppr 2.9.3zkamvar@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/4050901206Tue, 07 Sep 2021 14:46:33 GMTpoppr2.9.3successhttps://grunwaldlab.r-universe.devhttps://github.com/grunwaldlab/poppralgo.Rnwalgo.pdfAlgorightms and Equations2014-05-24 06:29:352017-08-20 22:20:39[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/3880270733Sun, 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] 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/3880270762Sun, 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] incidence 1.7.3tim.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/3978213287Tue, 03 Nov 2020 17:18:51 GMTincidence1.7.3successhttps://zkamvar.r-universe.devhttps://github.com/reconhub/incidenceconversions.Rmdconversions.htmlConversions2017-04-03 15:55:232020-11-03 17:18:51customize_plot.Rmdcustomize_plot.htmlCustomise graphics2016-10-25 08:33:252020-11-03 17:18:51incidence_class.Rmdincidence_class.htmlIncidence class2016-10-25 08:33:372020-11-03 17:18:51incidence_fit_class.Rmdincidence_fit_class.htmlIncidence fit class2018-08-21 13:31:042018-11-30 10:08:39overview.Rmdoverview.htmlOverview2016-10-17 11:51:172020-11-03 17:18:51[zkamvar] epibuffet 0.0.0.9005zkamvar@gmail.com (Zhian N. Kamvar)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/3890046664Mon, 07 Sep 2020 22:10:55 GMTepibuffet0.0.0.9005successhttps://zkamvar.r-universe.devhttps://github.com/r4epi/epibuffet[zkamvar] apyramid 0.1.2zkamvar@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.com>.https://github.com/r-universe/zkamvar/actions/runs/3983471248Fri, 08 May 2020 14:44:23 GMTapyramid0.1.2successhttps://zkamvar.r-universe.devhttps://github.com/r4epi/apyramidintro.Rmdintro.htmlIntroduction to {apyramid}2020-01-13 15:59:402020-01-13 15:59:40[r4epi] apyramid 0.1.2zkamvar@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.com>.https://github.com/r-universe/r4epi/actions/runs/4002996568Fri, 08 May 2020 14:44:23 GMTapyramid0.1.2successhttps://r4epi.r-universe.devhttps://github.com/r4epi/apyramidintro.Rmdintro.htmlIntroduction to {apyramid}2020-01-13 15:59:402020-01-13 15:59:40[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/3852744472Fri, 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[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/3936748146Fri, 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] 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/3870959408Thu, 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/3853017568Wed, 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/3927565746Thu, 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/4021844888Sun, 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