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Package: Pv3Rs 0.0.0.9000

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Pv3Rs: What the Package Does (One Line, Title Case)

What the package does (one paragraph).

Authors:First Last [aut, cre]

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Pv3Rs.pdf |Pv3Rs.html✨
Pv3Rs/json (API)

# Install 'Pv3Rs' in R:

install.packages('Pv3Rs', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aimeertaylor/pv3rs/issues

Datasets:

fs_VHX_BPD - Allele frequencies computed from example Plasmodium vivax data
ys_VHX_BPD - Example Plasmodium vivax data

On CRAN:

3.28 score 13 scripts 20 exports 37 dependencies

Last updated 3 months agofrom:d5dcc95136. Checks:1 ERROR, 6 WARNING. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	FAIL	Jan 07 2025
R-4.5-win	WARNING	Jan 07 2025
R-4.5-linux	WARNING	Jan 07 2025
R-4.4-win	WARNING	Jan 07 2025
R-4.4-mac	WARNING	Jan 07 2025
R-4.3-win	WARNING	Jan 07 2025
R-4.3-mac	WARNING	Jan 07 2025

Exports:compatible_rstrs compute_posterior determine_MOIs enumerate_alleles enumerate_CPs enumerate_halfsib_alleles enumerate_IPs_RG enumerate_RGs hash.IP locus_type_summary plot_data plot_RG plot_simplex prep_data project2D recombine_parent_ids RG_inference RG_to_igraph sample_RG split_two

Dependencies:cli cpp11 dotCall64 dplyr fansi fields generics glue gmp igraph lattice lifecycle magrittr maps mathjaxr Matrix matrixStats multicool partitions pillar pkgconfig polynom purrr R6 rbibutils RColorBrewer Rcpp Rdpack rlang sets spam tibble tidyselect utf8 vctrs viridisLite withr

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Find all vectors of recurrence states compatible with relationship graph	compatible_rstrs
Compute posterior probabilities of _P. vivax_ recurrent states	compute_posterior
Determine MOIs from unphased data	determine_MOIs
Find all allele assignments for genotypes within the same infection	enumerate_alleles
Enumerate partitions induced by clonal relationships	enumerate_CPs
List all allelic draws for three half siblings	enumerate_halfsib_alleles
Enumerate IBD partitions consistent with a given relationship graph	enumerate_IPs_RG
Enumerate transitive relationship graphs	enumerate_RGs
Allele frequencies computed from example Plasmodium vivax data	fs_VHX_BPD
Convert IBD partition to a unique string for hashing	hash.IP
Summarise locus-wise data types	locus_type_summary
Message progress bar	msg_progress_bar msg_progress_bar-class
Plots the data	plot_data
Plot a relationship graph (RG)	plot_RG
Plots a 2D simplex	plot_simplex
Pre-process data to remove repeats and 'NA's	prep_data
Project 3D probability coordinates onto 2D simplex coordinates	project2D
Generate parental allocations for a meiotic tetrad	recombine_parent_ids
Computes the likelihood of all relationship graphs	RG_inference
Converts relationship graph to an 'igraph' object	RG_to_igraph
Sample a transitive relationship graph	sample_RG
Partition a vector into at most two subvectors	split_two
Example Plasmodium vivax data	ys_VHX_BPD