Package: imprinting 0.1.1

Alex Byrnes

imprinting: Calculate Birth Year-Specific Probabilities of Immune Imprinting to Influenza

Reconstruct birth-year specific probabilities of immune imprinting to influenza A, using the methods of Gostic et al. (2016) <doi:10.1126/science.aag1322>. Plot, save, or export the calculated probabilities for use in your own research. By default, the package calculates subtype-specific imprinting probabilities, but with user-provided frequency data, it is possible to calculate probabilities for arbitrary kinds of primary exposure to influenza A, including primary vaccination and exposure to specific clades, strains, etc.

Authors:Katelyn Gostic [aut], Alex Byrnes [ctb, cre]

imprinting_0.1.1.tar.gz
imprinting_0.1.1.zip(r-4.7-any)imprinting_0.1.1.zip(r-4.6-any)imprinting_0.1.1.zip(r-4.5-any)
imprinting_0.1.1.tgz(r-4.6-any)imprinting_0.1.1.tgz(r-4.5-any)
imprinting_0.1.1.tar.gz(r-4.7-any)imprinting_0.1.1.tar.gz(r-4.6-any)
imprinting_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
imprinting/json (API)

# Install 'imprinting' in R:
install.packages('imprinting', repos = c('https://cobeylab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cobeylab/imprinting/issues

Pkgdown/docs site:https://cobeylab.github.io

On CRAN:

Conda:

ceirr-cmc

4.20 score 16 scripts 352 downloads 12 exports 30 dependencies

Last updated from:266f9cdf2f. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE193
source / vignettesOK223
linux-releaseNOTE137
macos-releaseNOTE191
macos-oldrelNOTE146
windows-develNOTE93
windows-releaseNOTE104
windows-oldrelNOTE102
wasm-releaseOK124

Exports:get_country_cocirculation_dataget_country_inputs_1997_to_presentget_country_intensity_dataget_imprinting_probabilitiesget_p_infection_yearget_regional_inputs_1997_to_presentget_template_dataget_WHO_regionplot_many_country_yearsplot_one_country_yearshow_available_countriesshow_available_regions

Dependencies:clicowplotcpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

custom-imprinting-types
Generate probabilities of imprinting to custom subsets of influenza A viruses | Input the custom frequencies into get_imprinting_probabilities()
Rendered fromcustom-imprinting-types.Rmdusingknitr::rmarkdown

Last update: 2022-11-17
Started: 2022-08-25

intro-to-imprinting
1. Install the imprinting package | 1.1 Install the devtools package | 1.2 Load the devtools package | 1.3 Install the imprinting package from github | 1.4 Load the imprinting package | 2. Use the package to calculate imprinting probabilities | 2.1 Calculate imprinting probabilities for one country and year of observation | 2.2 Why do we specify the observation_year? | 2.2 View a list of the available countries | 2.3 Generate probabilities for many countries and observation years | 3. Plot the outputs | 3.1 Plot the first country-year combination in the output data frame | Select a specific country and year to plot | 3.2 Plot up to five countires at a time | 4. Explore the underlying data and components of the imprinting probabilities | Get the probability that an individual imprinted 0, 1, 2, ... 12 years after birth
Rendered fromintro-to-imprinting.Rmdusingknitr::rmarkdown

Last update: 2022-11-17
Started: 2022-08-03