Archived versions are found below.

Updates in euroformix_1.10.0 (06.02.18)

  • Updated functions: efm,contLikMLE,contLikMLEpara,validMLEmodel
  • Functions added to euroformix R-package: plotTopEPG, freqImport, tableReader
    - The helpfunction tableReader within efm.R was moved and created as a seperate function, see ?tableReader.
    - freqImport requires the R-packages XML and RCurl.
  • Important notes:
    - Don't use "Select STR kit" if it is not defined in the list (i.e. non-STRs).
  • In the GUI (efm):
    • efm changed how frequencies are imported (using the function freqImport).
    • The kit can now be selected regardless of the population frequencies (only overlapping markers will be considered in the model).
    • One of three options (each given as GUI buttons):
      1) Can be given as a single file. The file name will give the population name.
      2) Can be given as a folder with files. The file names will give the population names.
      3) Can be imported directly from the STRidER webpage. The content from the webpage decides the population names.
    • The number of contributors in "Model specification" panel can now also be selected in either a drop-down panel.
    • A restart button "RESTART" has been added to the "Import data" panel. The user can now restart EuroForMix as a clean session.
    • The button-name "All results" is change to "Create report".
    • The R-version, Selected Kit and Selected Population have been added to the report.
    • The button "Model fitted P.H." has been added under "Further Action" in MLE fit panel.
      - This shows the expected peak heights of the top deconvolved genotypes superimposed with the observed peak heights (the function supports multiple evidences).
    • A signif.-level is required to be set from the user when running "Model validation" in "MLE fit".
      - This denotes the significance level used for the envelope-coverage in "Model validation". Default value is 0.01 .
    • Added "Set max number of iterations" in "Optimization"
      - The user can select maximum number of iterations for the optimization. This can reduce the timeusage drastically when the optimization method converges slowly. This changes the variable "iterlim" in nlm. Default is 50.
    • Added "Set likelihood-scaling to avoid zero" in "Integration"
      - The user can select a scaling value of likelihood function used with integration NOTE: scaleINT necessary to tweak to avoid zero-likelihood values for integration. Default value is 700.
  • The function plotTopEGP has been added.
    - This function shows the expected peak heights of the top deconvoluted genotypes. The peak heights for corresponding alleles are superimposed.
    - This function requires an MLE-fitted object.
  • The function freqImport has been added:
    - This function makes importing frequency files easy: Different formats are allowed.
  • In function contLikMLE and contLikMLEpara:
    - The variable "maxIter" has been added an input parameter to the functions contLikMLE and contLikMLEpara:
    - The maximum number of iterations for the optimization nlm (variable of nlm::iterlim=maxIter)
  • In function validMLEmodel:
    - The variable "alpha" has been added as an input parameter to the functions validMLEmodel (the significance level used for the envelope-coverage).
  • Minor changes:
    - The helptexts for the "Import frequency" buttons have changed.

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"

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