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GenoConvert: new vcf and genlight input, various bugs fixed, behaviour made more consistent and clearer through additional messages.GenoConvert and SnpStatsMkGenoErrors (used by SimGeno) causing about 3x too many hom|hom errors when SnpError is a single value: first beta-distributed per-SNP genotyping error rates \(E_l\) were generated, and then \((E_l/2)^2\) calculated. Now the single value is by default first morphed into a length 3 vector (hom|hom, het|hom, hom|het), and three beta distributions are generated.MkGenoErrorsSimGeno ParMis default changed from 0.4 to 0ErrToM).EstEr (estimation of genotyping errors) removed due to inaccurate estimations and misuse. Will (probably) be re-implemented in a future version.CalcMaxMismatch: OH with both parents counts as 2 mismatches (was 1)GenoConvert, and fix bug with OutFormat ‘col’EstConf example to nSim=1 to ensure runtime < 5 sec to pass CRAN checkmtSame: specify if individuals have the same or different mitochondrial haplotypeCalcPairLL helpfileCalcBYprobs, which caused Year.last to be ignoredLifeHistData$Sex includes NAYear.last added to LifeHistData (last possible offspring birth year)GetAncestors and GetDescendantsMinAgeParent for MakeAgePrior()StrictGenoCheck, Strict for CheckGeno() ; update msgsCheckLH, now flexible column order in LifeHistData.qntl = 0.999^(1/nrow(GenoM)) to 0.9999^(1/nrow(GenoM)) in all functions calling CalcMaxMismatchSnpStats() when AF=0 or SNP is missing for all individuals.sequoia_report()PedCompare() parameter minSibSize (minimum sibship size for which the non-genotyped parent is considered ‘dummyfiable’) changed default value from 2sib (2 genotyped siblings) to 1sib1GP. This reflects the increased success of reconstructing grandoffspring-grandparent pairs in newest version, which make the output of PedCompare(,minSibSize='2sib') confusing. This also affects EstConf().GetRelM() now allows input of Pedigree AND Pairs. This a.o. allows PlotRelPairs() with both inferred pedigree plus GetMaybeRel() output.writeSeq() (easier to install)SeqOUT_HSg5 for quicker vignette compilationGeno_griffin, Conf_griffin (output from EstConf()) and MaybeRel_griffin (output from GetMaybeRel()), as well as the script used to create these (mk_griffin_data.R)SummarySeq() was internal and is now exported (PlotSeqSum())sequoia() now includes args.AP.SummarySeq(), if Pedigree is provided rather than SeqList and SNPd=NULL, all individuals are categorised as Observed (was: Genotyped).PedPolish() now has arguments to specify whether to drop extra columns (besides id-dam-sire) and whether to keep rows with non-unique or NA ids.SnpStats() now includes HWE testsSimGeno() for non-autosomal inheritance; this option is still experimental and non-autosomal SNPs are not supported by the pedigree reconstruction.cannot allocate vector of size ... issue in GetRelM() with very large pedigrees, which affected MakeAgePrior() and thereby sequoia().EstConf() $ConfProb used the wrong denominator, namely the number of parents in the reference pedigree rather than in the inferred pedigree.CalcPairLL(), as LL(HS)=LL(GP)=LL(FA) for these pairs. Origin time unknown.GenoConvert() when Informat='single'.CalcPairLL() HS likelihood when conditioning on pedigree was incorrect. No/minimal effect on pedigree reconstruction.DuplicateCheck() (always automatically called by sequoia()) that on very rare occasions caused R to crashfixes minor bugs identified by CRAN valgrind and gcc-ASAN
minor edits to vignette to comply with CRAN precheck
CalcBYprobs() to estimate the probability that individual i is born in year y.EstConf() outputGenoConvert() regarding InData vs InFileErr=0Herm instead of specified via Complex. New output list element DummyClonesCalcRped() to calculate pedigree relatedness. Uses package kinship2.Various smaller bugs have been fixed, some affecting assignment rate
sequoia(): Option FindMaybeRel has been deprecated; call GetMaybeRel() directly instead.CalcPairLL(), returns likelihoods for each of the 7 considered relationships (PO, FS, HS, GP, FA, HA, U) for each specified pair of individualsRelPlot() for Colony-like visualisation of pairwise relationships (automatically called by ComparePairs())sequoia(): fixed error object 'ErrM' not found when re-using output from a previous sequoia run. Circumvent this bug in version 2.0.7 by fooling the program to think it’s output from an older version: names(ParOUT$Specs)[match("MaxMismatchOH", names(ParOUT$Specs))] <- "foo".sequoia(): fixed bug causing genotyped parents to not always be monogamous when Complx='mono'.Error in data.frame(id = c(dID[s(nd[1]), 1], dID[s(nd[2]), 2]), VtoM(TMP$dumparrf, : arguments imply differing number of rows) )GetMaybeRel(): fixed error (subscript) logical subscript too long when input pedigree contains dummiesGetMaybeRel(): fixed error causing likely GP pairs not to be included outputPedCompare(): fixed id.dam.cat and id.sire.cat being ‘NANA’ instead of XD, XG or XX when Symmetrical=TRUEPlotAgePrior(): Avoid using grDevices::hcl.colors() in R versions <3.6, where this function is not yet availableComparePairs(): fixed bug when Pairs2 but not Ped2 is specifiedMakeAgePrior(): fixed bug when there are no FS pairs in the input pedigreeMakeAgePrior(): MaxAgeParent was ignored when a pedigree with overlapping generations was supplied\donttest instead of \dontrun, so that they can be run using example(). Note that some can be quite time consuming, especially EstConf().PlotPedComp() to visualise PedCompare() outputSimGeno(): deprecated input parameters (since v 1.3.1) are dropped completelygetAssignCat() no longer drops additional columns from input pedigreeCalcOHLLR(, CalcLLR = FALSE)PedCompare() output element DummyMatch now also include output class of matched individual’s parents & offspringsequoia() now only returns pairs for which LL_duplicate - max(LL_{not duplicate}) > T_filter; when call rates are low this may be a substantially shorter list than in previous versions, where all pairs with fewer than MaxMismatchDUP differences were listed.ComparePairs() can now be called for a single pedigree, as well as to compare two pedigreesPlot=TRUE, all functions will print a message and return results as usual, instead of throwing an error and not returning results.MakeAgePrior(): more consistent implementation; is now called by sequoia() with only lifehistory data of genotyped individuals.EstConf() now also returns the full Counts table from PedCompare(); $RunParams now holds the evaluated input paramters, instead of e.g. V[i] when called from inside a loop.ErrToM. The default has changed very slightly from version 1.3.CalcOHLLR() to calculate Mendelian errors and parental log-likelihood ratios for any pedigreegetAssignable() to flag genotyped and ‘dummifiable’ individuals in any pedigreeComparePairs() to compare pairwise relationships between 2 pedigrees; replaces now-deprecated DyadCompare.PedPolish() is now user available.MaxMismatch of function sequoia, now calculated internally by new function CalcMaxMismatch based on number of SNPs, presumed genotyping error rate, and minor allele frequenciesEstConf() now also estimates confidence for parent-pairs; output has changed considerably.PedCompare() to increase clarity of code for easier maintenance; changed output format somewhat.GenoConvert() skipped first individual when reading .raw file. Circumvent this bug in earlier versions by using option header=FALSE (then header row is removed only once…)ConfProb() expected input parameter nSim to be strictly integer, now relaxed to any value convertible to a whole numberERROR! ***Invalid ParProb!*** triggered when some SNPs are monomorphicSEGFAULT triggered when some SNPs have very high missingness (>80%); possibly sibship size out of boundsError arguments imply differing number of rows when there are dummy parents of 1 sex onlyLifeHistData may have 2 additional columns, with minimum and maximum possible birth yearPed_griffin) to illustrate overlapping generations, used in age vignetteSummarySeq(): added a pedigree summary table identical to a subset of the table returned by R package pedantics’ pedStatSummary; that package has been archived on CRAN. Added option Panels to only plot (a) specific panel(s).CheckGeno(), MkGenoErrors(), GetMaybeRel(), GetRelCat()PlotAgePrior() and SummarySeq()SimGeno() input parameters have changed, old ones will be deprecatedEstConf, SnpStatsFirst version on CRAN!
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