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:
imprinting_0.1.1.tar.gz
imprinting_0.1.1.zip(r-4.5)imprinting_0.1.1.zip(r-4.4)imprinting_0.1.1.zip(r-4.3)
imprinting_0.1.1.tgz(r-4.4-any)imprinting_0.1.1.tgz(r-4.3-any)
imprinting_0.1.1.tar.gz(r-4.5-noble)imprinting_0.1.1.tar.gz(r-4.4-noble)
imprinting_0.1.1.tgz(r-4.4-emscripten)imprinting_0.1.1.tgz(r-4.3-emscripten)
imprinting.pdf |imprinting.html✨
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
Last updated 2 years agofrom:266f9cdf2f. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 24 2024 |
| R-4.5-win | NOTE | Aug 24 2024 |
| R-4.5-linux | NOTE | Aug 24 2024 |
| R-4.4-win | NOTE | Aug 24 2024 |
| R-4.4-mac | NOTE | Aug 24 2024 |
| R-4.3-win | OK | Aug 24 2024 |
| R-4.3-mac | OK | Aug 24 2024 |
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:clicolorspacecowplotcpp11dplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get data on the relative circulation of each influenza A subtype | get_country_cocirculation_data |
| Return raw flu surveillance data for a specific country | get_country_inputs_1997_to_present |
| Get the relative intensity of influenza A circulation | get_country_intensity_data |
| Calculate imprinting probabilities | get_imprinting_probabilities |
| Calculate the probability imprinting occurs n years after birth | get_p_infection_year |
| Return raw flu surveillance data for a specific WHO region | get_regional_inputs_1997_to_present |
| Get country-independent flu circulation data for 1918-1996 | get_template_data |
| Look up a country's WHO region | get_WHO_region |
| Plot imprinting probabilities for up to five country-years | plot_many_country_years |
| Plot imprinting probabilities for a single country and year | plot_one_country_year |
| Show a list of all available countries | show_available_countries |
| Show all WHO regions | show_available_regions |
