Updates in euroformix_1.9.3: (09.09.17)

  • The function contLikMCMCpara has been added to the R-package:
    - It performs parallelization of the contLikMCMC function.
  • For LRsensitivity calculation:
    - The Hp/Hd plots for LR sensitivity has been removed.
    - Parallell processing is now performed by contLikMCMCpara to carry out more samples, using same number of parallels as the number of cores.
  • Added flexibility:
    - Allele names (not being AMEL) can now be strings. For these situations the stutter and degradation models will not work.
    - If kitname is not recognised, intensities for the samples are still plotted (sum per loci). In addition a goodness of fit QQ plot is given to check whether the intensities can be assumed being independent gamma-distributed.
  • For SNPs:
    - Degradation/stutters turned off automatically.
    - The allelenames can be strings.
  • In the loglikgamma.cpp code:
    - The value "INFVAL = std::numeric_limits::infinity()" is used instead for "log(0)".
    - The error caused by the function tgamma_lower(x,y) is now handled by adding a "try" block. Small/High non-negative values of x and y caused unexpected error.

Updates in euroformix_1.9.1: (15.06.17)

  • EFM changed from v1.8 to v1.9:
    - All markers in evidence are utilized even when references have missing markers. Implemented for Weight-of-Evidence, Deconvolution and Database searching.
    -> This indicates that users of EuroForMix should describe how they treat missing loci for references (i.e. whether they deselect evidence markers OR include missing markers for the references).
    - The version of euroformix R-package now follow the GUI version. I.e. the R-package starts from 1.9.0 for this current version (v1.9).
  • New feature for Generating data: degradation is now possible by adjusting the beta parameter (degradation slope).
    - beta has been added to Parameters in "Generate data"
  • New features for Deconvolution:
    -> Genotypes of references for missing markers are also inferred.
    -> The "Joint" table has been replaced.
    -> Marginal probability of each alleles also calculated.
  • New check feature for allele frequencies:
    - When EuroForMix starts, all allele frequency numbers for the selected allele frequency file are investigated. A warning message is given if any of these scenarios occur:
    -> Being negative.
    -> If a marker did not provide any allele frequency.
    -> If the sum of the allele frequncies are different from one (up to two decimals).
  • Cosmetic changes:
    - In Model validation: The main title now shows "PP-plot under Hp" under Hp and "PP-plot under Hd" for Hd.
    - "Plot EPG" in model setting changed to "Show"
    - "Model options" has been removed in Model specification for "Generate data"
  • Changes in functions:
    - Updated validMLEmodel: Also prints allele names for outliers.
    - Updated prepareC: Accepts refData to have 0 or 2 number of alleles per loci. This allows references to have zero alleles (i.e. a missing marker).
    - Updated genDataset: References with empty loci are substituted with a random individual.
    - Updated deconvolve:
    -- Input parameter "unknownonly" is removed. The genotype of all contributors are now shown.
    -- outputs rankG=deconvlist,pG=pG are removed
    -- table1 is now changed: Includes combined geno prob per marker.
    -- table3 and table 4 added: Includes marginal geno and allele prob per marker per contributors
    - Updated simDOdistr: Allele-list Element in refData[[loc]][[ref]] can now be NULL or numeric() => Supports missing loci. These are substituted with a random individual.
  • Bugs causing newest R versions (3.4.0) to give error is fixed.
    - We have replaced "<-glayout" with "<-gframe" at following lines in the code: Line 1407,Line 673,Line 2411,Line 2412,Line 2413,Line 2454,Line 2455,Line 2456.
  • Bug in "View database": The number of loci compared to stains was following the same order as the individual elements in the database. This is now fixed.
    - Notice: Non-contributors assumes to have all markers (i.e. non-missing loci)
    - Missing markers (or not checked) is given "numeric()" as a substitute of the allele names, giving length=0. This is important for the prepareC function.

Updates in euroformix_0.6.3: (22.10.2016):

  • In PP-plots: 0.05 and 0.05/n coverage envelopes are now superimposed to the PP-points (n is number of points). These are theoretical order-quantiles based on the uniform distribution. See EuroForMix manual v1.8 for more details.
  • If single alleles are missing in a reference data file, the user is notified that there are missing alleles. This happens for some exports where homozygous alleles are only given ones.
  • The kit.txt file has been updated: The kits "Fusion 6C", "PowerPlex16", "24plex", "ESSPlexPlus", "ESSPlexSEPlus", "ESSPlexSEQS", "YfilerPlus" have been added.
  • Bug fixed when devonvolution table tries to show NA (thanks to Lourdes Prieto for pointing out this bug). For instance, this happened for empty evidence markers.
  • Bug fixed when marker names include a space: check.names=FALSE has been added to read.table for preventing colNames changes. For instance, now "Penta D" is not changed to "Penta.D" such that it becomes unrecognizable to markers in "kit.txt".
  • In "All results" (used to generate report):
    -> Bug fixed so that the contributor names become correct (thanks to Federica Alessandrini for pointing out the names become wrong when conditional references are not first in the reference list).
    -> The username ("User:") has been added to the file.
    -> "LR-per-marker" result has been added.
    -> Version name of euroformix R package is added.
    -> "(Based on xx MCMC samples)" is now set equal to the sample size in "Set number of samples" under "Toolbar->MCMC".
    -> Header in "All results" removed the phrase "of the maximum likelihood results"
  • The fitted values of the sum peak height distribution are no longer printed (when clicking "View evidence").

Updates in euroformix_0.6.1: (01.09.2016):

  • EuroForMix has been updated to v1.8 from v1.7.
  • The following variables under "Model options" in "Model specification" has been moved to "File->Settings".
    -> Detection threshold
    -> fst-correction
    -> Probability of drop-in
    -> Drop-in peak height hyperparam (lambda)
    -> Stutter prior function.
  • "Settings" were added to "File" toolbar:
    -> Easy Mode can be selected: Simplifies the MLE analysis by deactivating non-important buttons
    -> Maximum number of loci to visualize (maxloc) can be selected
    -> The setting values are stored and remembered (even when the program is closed).
  • Information when clicking the saving button "All results" has been added: Now includes Version, Timestamp, Data, Model options, Hypotheses and LR values (MLE and 5% quantile from LR-sensitivity). Variables are also renamed.
  • A popup-warning is given to the user when the maximum log-likelihood value is -Inf.
  • Buttons in "Step 3)" under Import data has been rearranged.
  • Removed warning in parallellization.
  • Fixed bug in efm(): gtable does not accept NA values anymore. These are changed to "-".
  • The calculation speed of exactMACdistr is now linear with number of markers.
  • Button "Continuous LR (Bayesian based)" was removed from "MLE fit" tab.
  • Update in contLikMCMC:
    logpX <- logdmvnorm(postth, mean = th0, cholC = chol(Sigma0))
    replaced by
    logpX <- logdmvnorm(postth, mean = th0, cholC = chol(delta*Sigma0))

Updates in euroformix_0.5.0: (14.01.2016)

  • Parallell processing using snow R-package: Considered when number of unknowns are at least 3 (not implemented for non-contributor simulation and database searching yet). Number of processes will be equal number of random startpoints required in the optimization.
  • The drop-out alleles from the references are no longer included when assuming the stutter-model. This implies that the LR results may slightly change for situations where reference alleles has dropped out.
  • Bug found in Database search when 1) replicates are considered 2) locus in the population are not in same order as in the evidence. These are fixed.
  • integrate() replaced by adaptIntegrate(rel.error=0.01) in validMLEmodel to increase robustness of integral calculations.
  • simDOdistr() extended to handle a given drop-out probability for any of the contributors.
  • When multiple evidence are checked:
    -> plotEPG now presents multiple evidence in one figure.
    -> Peak height sum per locus now presents multiple evidence in one figure. The model is now using all replicates simultanously.

Updates in euroformix_0.4.0: (19.10.2015)

  • The marginal posterior probabilities for the top ranked genotype at each marker for each unknown contributors are shown as deconvolution layout "Marginal".
  • Two result layouts are now available for deconvolution, "Joint" and "Marginal".
  • EuroForMix has been updated to v1.7 from v1.6.

Updates in euroformix_0.3.11 (from 0.3.4): (17.10.2015)

  • EuroForMix has been updated to v1.6 from v1.5.
  • The posterior probabilities in the deconvolution are now also printed out per locus with corresponding genotype combinations.
  • Using Bayesian based LR in database searching is now possible.
  • Plotting peak heights with GlobalFiler and similar kits with more than 4 dyes is now possible. PlotEPG now uses the color directly from inst/extdata/kit.txt. Thanks to Inaki Yurrebaso¬†for pointing out the error.
  • Prints out the estimated Bayesian based LR when clicking 'LR Sensitivity' based on the MCMC simualations.
  • The likelihood function (build in C++) does not restrict the mixture proportions of the unknown contributors to be decreasing anymore. The reason is that this restriction sometimes causes problem for the maximum likelihood approach.
  • Replicates are now possible also for Bayesian based LR.
  • Max evaluations in integration possible to adjust:
    -> 'Set maximum number of evaluations' has been added to Integration under the toolbar. By default this is value is unlimited.
  • Improved startpoints used for optimizating the likelihood function found by doing regression on sum of the peak heights per markers.
    -> P.H.expectation, P.H.variability, Degrad.slope
  • The degradation model was added to the genData-function.
  • Symmetry in mixture proportions utilized also for more than 2 contributors:
    => Evaluating integration more accurate for:
    -> 3 contributors with 3 unknowns (1/6-size).
    -> 4 contributors with 4 unknowns (1/12-size).
    -> 4 contributors with 3 unknowns (1/2-size).
    -> 5 contributors with 5 unknowns (1/20-size).
    -> 5 contributors with 4 unknowns (1/3-size).
    -> 5 contributors with 3 unknowns (1/2-size).
    -> 6 contributors with 6 unknowns (1/25-size).
    -> 6 contributors with 5 unknowns (1/4-size).
    -> 6 contributors with 4 unknowns (1/3-size).
    -> 6 contributors with 3 unknowns (1/2-size).
  • Bugs fixed:
    -> Bug in non-contribtor simulation for Bayesian based LR fixed
    -> Bug in deconvolution has been fixed: for the case of only one proposed genotype combination for any marker (typically for locus drop-out).
  • Text-changes:
    "Integration based" -> "Bayesian based"