moi_duplicatefinder

Sample IDs need to be uniquely assigned to
 samples. This function checks if a sample ID is
 assigned to two or more different samples. Similarly,
 the marker labels need to be uniquely defined. This
 function is also used to check forbidden marker label
 repetitions.

internal

The implemented methods reach out to scientists that seek to estimate multiplicity of infection (MOI) and lineage (allele) frequencies and prevalences at molecular markers using the maximum-likelihood method described in Schneider (2018) <doi:10.1371/journal.pone.0194148>, and Schneider and Escalante (2014) <doi:10.1371/journal.pone.0097899>. Users can import data from Excel files in various formats, and perform maximum-likelihood estimation on the imported data by the package's moimle() function.

Meraj Hashemi

MLMOI

Estimating Frequencies, Prevalence and Multiplicity of Infection

Kristan Schneider

moi_duplicatefinder function

<dl><dt>total</dt>
<dd>string vector; vector of sample IDs.</dd>
<dt>sam_mark</dt>
<dd>string; a string which is either "Sample
ID" or "Marker".</dd>
<dt>nummtd</dt>
<dd>numeric; number of metadata columns plus 2.</dd>
<dt>rw_col</dt>
<dd>string vector; variable used to switch
between row and column in case of transposed data.
Namely, <code>c("rows ", "row ", "column ", "columns
")</code>.</dd></dl>

Arguments

Finds forbidden sample ID repetitions — moi_duplicatefinder

<dl>

<dt>total</dt>
<dd>string vector; vector of sample IDs.</dd>


<dt>sam_mark</dt>
<dd>string; a string which is either "Sample
ID" or "Marker".</dd>


<dt>nummtd</dt>
<dd>numeric; number of metadata columns plus 2.</dd>


<dt>rw_col</dt>
<dd>string vector; variable used to switch
between row and column in case of transposed data.
Namely, <code>c("rows ", "row ", "column ", "columns
")</code>.</dd>

</dl>

moi_duplicatefinder: Finds forbidden sample ID repetitions

Description

Usage

Value

Arguments

See Also