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

What the package does (one paragraph).

moire - Multiplicity of Infection and Allele Frequency Recovery from Noisy Polyallelic Genetics Data

A Markov Chain Monte Carlo (MCMC) based approach to Bayesian estimation of individual level multiplicity of infection, within host relatedness, and population allele frequencies from polyallelic genetic data.

magenta - Individual-Based Simulation Model of Malaria Epidemiology and Genomics

Individual-based simulation model of malaria epidemiology and genomics. magenta extends the imperial malaria model by tracking the infection history of individuals. With this additional genetic characteristics of the parasite can be assessed, including resistance.

dcifer - Genetic Relatedness Between Polyclonal Infections

An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results. Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.

polySimIBD - Structured Wright Fisher Simulator for Malaria Genetics

Unique features of the malaria life-cycle and transmission dynamics requires extensions of typical population genetic simulators. Using a spatial discrete-loci, discrete-time structured Wright Fisher framework, we simulate malaria population genetics forwards in time. Users are then able to capture the full Ancestral Recombination Graph.

PGEhammer - What the Package Does (Title Case)

A series of utility functions that improve the experience of working with other software tools in Plasmodium genomic epidemiology. This includes functions for wrangling data and visualising outputs. Part of the PGEforge set of resources.

pixelate.fork - Pixelate spatial predictions as per their average uncertainty

Pixelate spatially continuous predictions as per their average uncertainty. The package pixelate centres around a single function also called pixelate. The function pixelate groups predictions into a specified number of large pixels; computes the average uncertainty within each large pixel; then, for each large pixel, depending on its average uncertainty, either averages the predictions across it or across smaller pixels nested within it. The averaged predictions can then be plotted. The resulting plot of averaged predictions is selectively pixelated, similar to a photo that is deliberately pixelated to disguise a person’s identity. Areas of high average uncertainty in the pixelated plot are unresolved, while areas with high average certainty are resolved, similar to information poor versus rich regions of a satellite map.

DRpower - Study design and analysis for pfhrp2/3 deletion prevalence studies

This package can be used in the design and/or analysis stages of Plasmodium falciparum pfhrp2/3 deletion prevalence studies. We assume that the study takes the form of a clustered prevalence survey, meaning the data consists of a numerator (number of deletions found) and denominator (number tested) over multiple clusters. We are interested in estimating the study-level prevalence, i.e. over all clusters, while accounting for the possibility of high intra-cluster correlation. The analysis approach uses a Bayesian random effects model to estimate prevalence and intra-cluster correlation. The approach to power analysis is simulation-based, running the analysis many times on simulated data and estimating empirical power. This method can be used to establish a minimum sample size required to achieve a given target power.

PlasmoSim - Simulation of Plasmodium genetic data

A basic Plasmodium simulator. Contains functions to simulate epidemiological and genetic data from a simple model of Plasmodium falciparum transmission.

MIPanalyzer - Filtering and analysis of MIP data

Filtering and analysis of MIP data.

discent - Estimation of Deme Inbreeding Spatial Coefficients with Gradient Descent

In the early 1970s, Malécot described the relationship between genetic relatedness and physical distance, forming the framework of isolation by distance, or -- put simply -- pairs that are far apart are less likely to mate. Capitalizing on this framework by using measures of Identity by Descent, we produce a deme inbreeding spatial coefficient (DISC) using "vanilla" gradient descent. For the mathematical formulation of the of DISC, see: <TODO>. Briefly, we assume that the relatedness between two locations (demes) in space is given by the average pairwise IBD between the two locations conditional on the distance that seperates them. Further, we assume that geographic distance is scaled by a migration rate, which is a global parameter among all spatial locations.

hierfstat - Estimation and Tests of Hierarchical F-Statistics

Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) <https://academic.oup.com/genetics/article/144/4/1933/6017091>). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) <https://academic.oup.com/genetics/article/206/4/2085/6072590>.

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.

SIMPLEGEN -

paneljudge - Judge the performance of a panel of genetic markers using simulated data

An R package to judge the performance of a panel of genetic markers using data simulated for pairs of haploid genotypes. The data are simulated under a hidden Markov model of relatedness (described in Taylor, A.R., Jacob, P.E., Neafsey, D.E. and Buckee, C.O., 2019. Estimating relatedness between malaria parasites. Genetics, 212(4), pp.1337-1351) using allele frequency estimates provided by the user and inter-marker distances. The markers are treated as categorical random variables whose realisations (alleles) are unordered. The effective cardinalities and diversities of the markers can be computed using the input allele frequency estimates. Panel performance can be judged in terms of the root mean square error (RMSE) and confidence interval width of estimated relatedness, where relatedness is estimated under the same model used to simulate the data. At present, the examples we provide do not consider model misspecification; do not account for uncertainty around input allele frequency estimates; do not consider relatedness between pairs of haploid genotypes simulated using different allele frequencies; do not account for marker drop-out (markers that fail to produce useful data, e.g. because they a monomorphic). Otherwise stated, in the examples provided, the performance of a panel is judged in its most favourable light; it will likely perform less well in reality.

pixelate -

McCOILR - Rcpp implementation of THE REAL McCOIL

Wrapper for THE REAL McCOIL in Rcpp. Becuase R is easieR.

hmmibdr - HMM Identity by Descent

Wrapper for HMMIBD in Rcpp.

DEploid - Deconvolute Mixed Genomes with Unknown Proportions

Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.

MALECOT - Joint estimation of COI and population structure for malaria genetic data

Carries out joint estimation of complexity of infection (COI) and population structure on malaria genetic data. Assumes a simple model in which individuals have genotypes sampled from one or more subpopulations, and the number of genotypes in an individual is equal to the COI, which is also unknown. All unknown parameters are inferred using MCMC.

isoRelate - Identity-by-Descent Inference of Haploid Recombining Organisms

Pairwise identity by descent inference of haploid species using single nucleotide polymorphism data. isoRelate can detect IBD in the presence of multi-clonal infections and also provides a function for identifying loci under recent positive selection.