Package: mispitools 1.2.0

mispitools: Missing Person Identification Tools

An open source software package written in R statistical language. It consist in a set of decision making tools to conduct missing person searches. Particularly, it allows computing optimal LR threshold for declaring potential matches in DNA-based database search. More recently 'mispitools' incorporates preliminary investigation data based LRs. Statistical weight of different traces of evidence such as biological sex, age and hair color are presented. For citing mispitools please use the following references: Marsico and Caridi, 2023 <doi:10.1016/j.fsigen.2023.102891> and Marsico, Vigeland et al. 2021 <doi:10.1016/j.fsigen.2021.102519>.

Authors:Franco Marsico [aut, cre]

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

# Install 'mispitools' in R:
install.packages('mispitools', repos = c('https://marsicofl.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/marsicofl/mispitools/issues

Datasets:
  • Argentina - STRs allelic frequencies from specified country.
  • Asia - STRs allelic frequencies from specified country.
  • Austria - STRs allelic frequencies from specified country.
  • BosniaHerz - STRs allelic frequencies from specified country.
  • China - STRs allelic frequencies from specified country.
  • Europe - STRs allelic frequencies from specified country.
  • Japan - STRs allelic frequencies from specified country.
  • USA - STRs allelic frequencies from specified country.

On CRAN:

6.52 score 34 stars 1 packages 18 scripts 354 downloads 30 exports 134 dependencies

Last updated 2 months agofrom:d531f7639b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-winOKNov 08 2024
R-4.5-linuxOKNov 08 2024
R-4.4-winOKNov 08 2024
R-4.4-macOKNov 08 2024
R-4.3-winOKNov 08 2024
R-4.3-macOKNov 08 2024

Exports:bidirectionalKLCmodelcombLRcompute_LRs_colorsconditionedPropCondPlotCPT_MPCPT_POPdeplotDeTgetfreqsklPIELRageLRcolLRcolorsLRdateLRdistLRsexmakeMPprelimmakePOIgenmakePOIprelimmispiAppmulti_kl_divergencepostSimrefPropsimLR2dataframesimLRgensimLRprelimsimRefTrates

Dependencies:askpassbackportsbase64encbitbit64blobbroombslibcachemcallrcellrangerclicliprcolorspacecommonmarkconflictedcpp11crayoncurldata.tableDBIdbplyrdigestDirichletRegdplyrdtplyrevaluatefansifarverfastmapfontawesomeforcatsFormulaforrelfsgarglegenericsggplot2gluegoogledrivegooglesheets4gtablehavenhighrhmshtmltoolshttpuvhttridsisobandjquerylibjsonlitekinship2knitrlabelinglaterlatticelifecyclelubridatemagrittrMASSMatrixmaxLikmemoisemgcvmimemiscToolsmodelrmunsellnlmeopensslpatchworkpbapplypedFamiliaspedmutpedprobrpedtoolspillarpkgconfigplyrprettyunitsprocessxprogresspromisespspurrrquadprogR6raggrappdirsRColorBrewerRcppreadrreadxlrematchrematch2reprexreshape2ribdrlangrmarkdownrstudioapirvestsandwichsassscalesselectrshinyslamsourcetoolsstringistringrsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetinytextzdbutf8uuidvctrsverbalisrviridisLitevroomwithrxfunxml2xtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
STRs allelic frequencies from specified country.Argentina
STRs allelic frequencies from specified country.Asia
STRs allelic frequencies from specified country.Austria
Kullback-Leibler Divergence Calculation for Genetic MarkersbidirectionalKL
STRs allelic frequencies from specified country.BosniaHerz
STRs allelic frequencies from specified country.China
Epsilon hair color matrixCmodel
Combine LRs: a function for combining LRs obtained from simulations.combLR
Compute Likelihood Ratios based con color characteristicscompute_LRs_colors
Compute Conditioned Proportions for UPsconditionedProp
General plot for condiionted probabilities and LR combining variablesCondPlot
Missing person based conditioned probabilityCPT_MP
Population based conditioned probabilityCPT_POP
Decision making plot: a function for plotting false positive and false negative rates for each LR threshold.deplot
Decision Threshold: a function for computing likelihood ratio decision threshold.DeT
STRs allelic frequencies from specified country.Europe
Function for getting STR allele frequencies from different world populations.getfreqs
STRs allelic frequencies from specified country.Japan
Calculate Kullback-Leibler Divergence with Base 10 LogarithmklPIE
Likelihood ratio for age variableLRage
Likelihood ratio for color variableLRcol
Simulate LR values considering H1 and H2LRcolors
Likelihood ratio for birth date in missing person searchesLRdate
Likelihood ratio distribution: a function for plotting expected log10(LR) distributions under relatedness and unrelatedness.LRdist
Likelihood ratio for sex variableLRsex
Make preliminary investigation MP data simulations: a function for obtaining a database of preliminary investigation data for a missing person search.makeMPprelim
Make POIs gen: a function for obtaining a database with genetic information from simulated POIs or UHRs.makePOIgen
Make preliminary investigation POI/UHR data simulations: a function for obtaining a database of preliminary investigation data for a missing person search.makePOIprelim
Missing person shiny appmispiApp
Multi-dataset Kullback-Leibler Divergence Calculationmulti_kl_divergence
postSim: A function for simulating posterior oddspostSim
Generate a dataframe with hair colour, skin colour, eye colour and their specific combination frequenciesrefProp
simLR2dataframe: A function for extracting LR distributions in a dataframe from simLRgen() output.simLR2dataframe
Simulate likelihoods ratio (LRs) based on genetic data: a function for obtaining expected LRs under relatedness and unrelatedness kinship hypothesis.simLRgen
Simulate likelihoods ratio (LRs) based on preliminary investigation data: a function for obtaining expected LRs under relatedness and unrelatedness kinship hypothesis.simLRprelim
Generate Reference Properties for a Hypothetical PopulationsimRef
Threshold rates: a function for computing error rates and Matthews correlation coefficient of a specific LR threshold.Trates
STRs allelic frequencies from specified country.USA