Package: snp.slicer 0.1.0

Maxwell Murphy

snp.slicer: Bayesian Nonparametric Resolution of Multi-Strain Infections

Implementation of SNP-Slice, a Bayesian nonparametric method for resolving multi-strain infections using slice sampling with stick-breaking construction. The algorithm simultaneously estimates strain haplotypes and links them to hosts from sequencing data. Supports multiple observation models including categorical, Poisson, binomial, and negative binomial distributions.

Authors:Nianqiao Ju [aut], Maxwell Murphy [cre]

snp.slicer_0.1.0.tar.gz
snp.slicer_0.1.0.zip(r-4.7)snp.slicer_0.1.0.zip(r-4.6)snp.slicer_0.1.0.zip(r-4.5)
snp.slicer_0.1.0.tgz(r-4.6-any)snp.slicer_0.1.0.tgz(r-4.5-any)
snp.slicer_0.1.0.tar.gz(r-4.7-any)snp.slicer_0.1.0.tar.gz(r-4.6-any)
snp.slicer_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
snp.slicer/json (API)

# Install 'snp.slicer' in R:

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

Bug tracker:https://github.com/plasmogenepi/snp.slicer/issues

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

Datasets:

example_read0 - Example Read Count Data - Reference Alleles
example_read1 - Example Read Count Data - Alternate Alleles
example_snp_data - Example SNP Data

On CRAN:

3.30 score 1 scripts 16 exports 30 dependencies

Last updated from:303bfd83dd. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	190
source / vignettes	OK	209
linux-release-x86_64	ERROR	188
macos-release-arm64	ERROR	148
macos-oldrel-arm64	ERROR	136
windows-devel	ERROR	165
windows-release	ERROR	143
windows-oldrel	ERROR	127
wasm-release	OK	133

Exports:calculate_allele_frequencies calculate_allele_frequencies_by_sets calculate_individual_coi clear_performance_log effective_sample_size extract_allocations extract_strains get_performance_summary load_example_results plot_convergence print_performance_summary snp_slice snp_slice_binomial snp_slice_categorical snp_slice_negative_binomial snp_slice_poisson

Dependencies:bit bit64 cli clipr cpp11 crayon dplyr generics glue hms lifecycle magrittr pillar pkgconfig prettyunits progress purrr R6 readr rlang stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs vroom withr

Introduction to SNP-Slice

Maxwell Murphy

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-03-02
Started: 2025-08-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate Allele Frequencies from MCMC Results	calculate_allele_frequencies
Calculate allele frequencies for multiple target sets	calculate_allele_frequencies_by_sets
Calculate estimated individual COI with uncertainty	calculate_individual_coi
Clear performance log	clear_performance_log
Calculate effective sample size for MCMC diagnostics	effective_sample_size
Example Read Count Data - Reference Alleles	example_read0
Example Read Count Data - Alternate Alleles	example_read1
Example SNP Data	example_snp_data
Extract allocation information from SNP-Slice results	extract_allocations
Extract strain information from SNP-Slice results	extract_strains
Get performance summary	get_performance_summary
Load Example Analysis Results	load_example_results
Performance Logger for SNP-Slice	performance_env
Plot convergence diagnostics	plot_convergence
Print performance summary	print_performance_summary
Print comprehensive ESS results for all parameters	print.ess_all_results
Print effective sample size results	print.ess_result
Print SNP-Slice results	print.snp_slice_results
Bayesian Nonparametric Resolution of Multi-Strain Infections	snp_slice snp_slice_binomial snp_slice_categorical snp_slice_negative_binomial snp_slice_poisson
Print summary of SNP-Slice results	summary.snp_slice_results