The purpose of **dvir** is to implement state-of-the-art
algorithms for DNA-based disaster victim identification (DVI). In
particular, **dvir** performs *joint* identification
of multiple victims.

The methodology and algorithms of **dvir** are described
in Vigeland
& Egeland (2021): DNA-based Disaster Victim Identification.

The **dvir** package is part of the pedsuite, a collection
of R packages for pedigree analysis. Much of the machinery behind
**dvir** is imported from other pedsuite packages,
especially **pedtools** for handling pedigree data, and
**forrel** for the calculation of likelihood ratios. A
comprehensive presentation of these packages, and much more, can be
found in the book Pedigree
Analysis in R.

To get the current official version of **dvir**, install
from CRAN as follows:

`install.packages("dvir")`

Alternatively, the latest development version may be obtained from GitHub:

```
# install.packages("remotes")
::install_github("magnusdv/dvir") remotes
```

In the following we will use a toy DVI example from the paper
(see above) to illustrate how to use **dvir**.

To get started, we load the **dvir** package.

```
library(dvir)
#> Loading required package: pedtools
```

We consider the DVI problem shown below, in which three victim samples (V1, V2, V3) are to be matched against three missing persons (M1, M2, M3) belonging to two different families.

The hatched symbols indicate genotyped individuals. In this simple example we consider only a single marker, with 10 equifrequent alleles denoted 1, 2,…, 10. The available genotypes are shown in the figure.

DNA profiles from victims are generally referred to as *post
mortem* (PM) data, while the *ante mortem* (AM) data contains
profiles from the reference individuals R1 and R2.

A possible solution to the DVI problem is called an
*assignment*. In our toy example, there are *a priori* 14
possible assignments, which can be listed as follows:

```
#> V1 V2 V3
#> 1 * * *
#> 2 * * M3
#> 3 * M1 *
#> 4 * M1 M3
#> 5 * M2 *
#> 6 * M2 M3
#> 7 M1 * *
#> 8 M1 * M3
#> 9 M1 M2 *
#> 10 M1 M2 M3
#> 11 M2 * *
#> 12 M2 * M3
#> 13 M2 M1 *
#> 14 M2 M1 M3
```

Each row indicates the missing persons corresponding to V1, V2 and V3
(in that order) with `*`

meaning *not identified*. For
example, the first line contains the *null model* corresponding
to none of the victims being identified, while the last line gives the
assignment where `(V1, V2, V3) = (M1, M2, M3)`

, For each
assignment `a`

we can calculate the likelihood, denoted
`L(a)`

. The null likelihood is denoted `L0`

.

We consider the following to be two of the main goals in the analysis of a DVI case with multiple missing persons:

- Rank the assignments according to how likely they are. We measure
this by calculating the LR comparing each assignment
`a`

to the null model:`LR = L(a)/L0`

. - Find the
*posterior pairing probabilities*`P(Vi = Mj | data)`

for all combinations of i and j, and the*posterior non-pairing probabilities*`P(Vi = '*' | data)`

for all i.

The pedigrees and genotypes for this toy example are available within
**dvir** as a built-in dataset, under the name
`example2`

.

```
example2#> DVI dataset:
#> 3 victims (2M/1F): V1, V2, V3
#> 3 missing (2M/1F): M1, M2, M3
#> 2 typed refs: R1, R2
#> 2 ref families: 1, 2
#> Number of markers, PM and AM: 1
```

Internally, all DVI datasets in **dvir** have the
structure of a list, with elements `pm`

(the victim data),
`am`

(the reference data) and `missing`

(a vector
naming the missing persons): We can inspect the data by printing each
object. For instance, in this case `am`

is a list of two
pedigrees:

```
$am
example2#> [[1]]
#> id fid mid sex L1
#> M1 * * 1 -/-
#> R1 * * 2 2/2
#> M2 M1 R1 1 -/-
#>
#> [[2]]
#> id fid mid sex L1
#> R2 * * 1 3/3
#> MO2 * * 2 -/-
#> M3 R2 MO2 2 -/-
```

Note that the two pedigrees are printed in so-called *ped
format*, with columns `id`

(ID label), `fid`

(father), `mid`

(mother), `sex`

(1 = male; 2 =
female) and `L1`

(genotypes at locus `L1`

).

The code generating this dataset can be found in the github
repository of **dvir**, more specifically here: https://github.com/magnusdv/dvir/blob/master/data-raw/example2.R.

A great way to inspect a DVI dataset is to plot it with the function
`plotDVI()`

.

`plotDVI(example2)`

The `plotDVI()`

function offers many parameters for
tweaking the plot; see the help page `?plotDVI()`

for
details.

The `jointDVI()`

function performs joint identification of
all three victims, given the data. It returns a data frame ranking all
assignments with nonzero likelihood:

```
= jointDVI(example2, verbose = FALSE)
jointRes
# Print the result
jointRes#> V1 V2 V3 loglik LR posterior
#> 1 M1 M2 M3 -16.11810 250 0.718390805
#> 2 M1 M2 * -17.72753 50 0.143678161
#> 3 * M2 M3 -18.42068 25 0.071839080
#> 4 M1 * M3 -20.03012 5 0.014367816
#> 5 * M1 M3 -20.03012 5 0.014367816
#> 6 * M2 * -20.03012 5 0.014367816
#> 7 * * M3 -20.03012 5 0.014367816
#> 8 M1 * * -21.63956 1 0.002873563
#> 9 * M1 * -21.63956 1 0.002873563
#> 10 * * * -21.63956 1 0.002873563
```

The output shows that the most likely joint solution is (V1, V2, V3) = (M1, M2, M3), with an LR of 250 compared to the null model.

The function `plotSolution()`

shows the most likely
solution:

`plotSolution(example2, jointRes, marker = 1)`

By default, the plot displays the assignment in the first row of
`jointRes`

. To examine the second most likely, add
`k = 2`

(and so on to go further down the list).

Next, we compute the posterior pairing (and non-pairing)
probabilities. This is done by feeding the output from
`jointDVI()`

into the function `Bmarginal()`

.

```
Bmarginal(jointRes, example2$missing, prior = NULL)
#> M1 M2 M3 *
#> V1 0.87931034 0.0000000 0.0000000 0.12068966
#> V2 0.01724138 0.9482759 0.0000000 0.03448276
#> V3 0.00000000 0.0000000 0.8333333 0.16666667
```

Here we used a default flat prior for simplicity, assigning equal prior probabilities to all assignments.

we see that the posterior pairing probabilities for the most likely solution are

*P*(V1 = M1 | data) = 0.88,*P*(V2 = M2 | data) = 0.95,*P*(V3 = M2 | data) = 0.83.