Package: coiaf 0.1.2

Aris Paschalidis

coiaf: Complexity of Infection Estimation with Allele Frequencies

Provides a direct method for estimating complexity of infection using easily calculated measures from sequence read depth data.

Authors:Aris Paschalidis [aut, cre], OJ Watson [aut]

coiaf_0.1.2.tar.gz
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coiaf.pdf |coiaf.html✨
coiaf/json (API)
NEWS

# Install 'coiaf' in R:

install.packages('coiaf', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bailey-lab/coiaf/issues

Datasets:

example_real_data - Example real data

On CRAN:

allele-frequencies coi complexity-of-infection estimation

4.18 score 3 stars 25 scripts 23 exports 74 dependencies

Last updated 2 years agofrom:3df5509ceb. Checks:OK: 7. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 01 2024
R-4.5-win	OK	Nov 01 2024
R-4.5-linux	OK	Nov 01 2024
R-4.4-win	OK	Nov 01 2024
R-4.4-mac	OK	Nov 01 2024
R-4.3-win	OK	Nov 01 2024
R-4.3-mac	OK	Nov 01 2024

Exports::=.data %>%as_label as_name bootstrap_ci compute_coi compute_coi_regression cont_sensitivity disc_sensitivity enquo enquos error_plot likelihood optimize_coi optimize_coi_regression process_real process_sim sensitivity_plot sim_biallelic theme_coiaf theoretical_coi world_map

Dependencies:backports base64enc boot broom bslib cachem checkmate cli cluster colorspace cpp11 data.table digest dplyr evaluate fansi farver fastmap fontawesome foreign Formula fs generics ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS mathjaxr Matrix memoise mgcv mime munsell nlme nnet pillar pkgconfig purrr R6 rappdirs RColorBrewer rlang rmarkdown rpart rstudioapi sass scales stringi stringr tibble tidyr tidyselect tinytex utf8 vctrs viridis viridisLite withr xfun yaml

Continuous sensitivity analysis

Rendered fromsensitivity_analysis_continuous.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-04-13
Started: 2021-12-27

Discrete sensitivity analysis

Rendered fromsensitivity_analysis_discrete.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-04-13
Started: 2021-12-27

Real data example

Rendered fromexample_real_data.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2022-12-15
Started: 2020-07-08

Simulator details

Rendered fromsimulator_details.Rmdusingknitr::rmarkdownon Nov 01 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generate bootstrapped CI	bootstrap_ci bootstrap_ci.default bootstrap_ci.sim
Predict the COI	compute_coi
Compute COI based on residuals of all loci against theoretical curves	compute_coi_regression
Continuous sensitivity analysis	cont_sensitivity
Discrete Sensitivity analysis	disc_sensitivity
Error plot	error_plot
Example real data	example_real_data
Likelihood of a COI	likelihood
Optimize the COI	optimize_coi
Compute COI based on all points fitted to best fitting curve for COI	optimize_coi_regression
Plot simulated data	autoplot.sim plot-simulation plot.sim
Process real data	process_real
Process simulated data	process_sim
Sensitivity plot	sensitivity_plot
Simulate biallelic data	sim_biallelic
Custom ggplot2 theme	theme_coiaf
Theoretical COI	theoretical_coi
World map plot	world_map

Usage by other packages (reverse dependencies)