ys_VHX_BPD

Previously-published microsatellite data on P. vivax parasites
extracted from study participants enrolled in the Best Primaquine Dose (BPD) and Vivax
History (VHX) trials; see
Taylor &amp; Watson et al. 2019 (tools:::Rd_expr_doi("doi:10.1038/s41467-019-13412-x"))
for more details of the genetic data; for more details of the VHX and BPD trials, see
Chu et al. 2018a (tools:::Rd_expr_doi("doi:10.1093/cid/ciy319")) and
Chu et al. 2018b (tools:::Rd_expr_doi("doi:10.1093/cid/ciy735")).

datasets

Plot malaria parasite genetic data on two or more episodes.
Compute per-person posterior probabilities that each
Plasmodium vivax (Pv) recurrence is a recrudescence, relapse,
or reinfection (3Rs) using per-person P. vivax genetic data on two or
more episodes and a statistical model described in
Taylor, Foo and White (2022) <doi:10.1101/2022.11.23.22282669>.
Plot per-recurrence posterior probabilities.

Aimee Taylor

Pv3Rs

Estimate the Cause of Recurrent Vivax Malaria using Genetic Data

Yong See Foo

Tymoteusz Kwiecinski

Duncan Murdoch

Mans Magnusson

Institut Pasteur 

European Union, Project 101110393 

ys_VHX_BPD function

A list of 217 study participants; for each study participant, a list of one or more
episodes; for each episode, a list of three or more microsatellite markers;
for each marker, a vector of observed alleles (repeat lengths). For example:<dl>
<dt>BPD_103</dt>
<dd>Study participant identifier: study participant 103 in the BPD trial</dd><dt>BPD_103_1</dt>
<dd>Episode identifier: episode one of study participant 103 in the BPD trial</dd><dt>PV.3.27</dt>
<dd>Marker identifier: P. vivax 3.27</dd><dt>18</dt>
<dd>Allele identifier: 18 repeat lengths</dd>
</dl>

Format

Example Plasmodium vivax data — ys_VHX_BPD

A list of 217 study participants; for each study participant, a list of one or more
episodes; for each episode, a list of three or more microsatellite markers;
for each marker, a vector of observed alleles (repeat lengths). For example:<dl>
<dt>BPD_103</dt>
<dd>Study participant identifier: study participant 103 in the BPD trial</dd>

<dt>BPD_103_1</dt>
<dd>Episode identifier: episode one of study participant 103 in the BPD trial</dd>

<dt>PV.3.27</dt>
<dd>Marker identifier: P. vivax 3.27</dd>

<dt>18</dt>
<dd>Allele identifier: 18 repeat lengths</dd>


</dl>

ys_VHX_BPD: Example Plasmodium vivax data

Description

Usage

Arguments

Format