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Changelog

sequoia 3.0.3

  • numerous updates to Fortran code to improve assignment accuracy, including several bug fixes related to monogamous mating systems
  • fix inconsistency in ageprior matrix and its use for grandparents and avuncular pairs
  • PedCompare: When dummy parent mismatched 1 or more dummy offspring than it had correct genotyped offspring, all genotyped + dummy offspring were set to ‘nomatch’. Now match is kept, and only actual mismatched flagged as such.
  • ComparePairs: New argument ‘Pairs_suffix’, passed to getRelM.
  • getRelM: when only Pairs is provided, default (for unlisted pairs) changed from ‘U’ to ‘X’
  • fix bug in SimGeno, throwing an error when ParMis=c(0, not-zero)
  • CalcPairLL: force to (almost) always calculate LL even when highly unlikely, by fixing MaxMismatch to the total number of SNPs and T_filter to -999.0.
  • CalcParentProbs: new function to calculate assignment probabilities for any pedigree
  • getAssignCat now also considers parents with only dummifiable offspring as dummifiable; option ‘1sib’ is dropped.
  • PedCompare: when an incorrect half-sibling is added to a true singleton-sibship-with-grandparent, this now counts as 1 mismatch; this erroneously was 3 mismatches (entire sibship wrong).
  • in sequoia, the default value for CalcParentLLR is changed from TRUE to FALSE.
  • fix bug which caused no parents to be assigned to individuals produced by selfing
  • add function Err_Allele2Locus

sequoia 2.11.5

  • fix bug in Fortran code which causes some parents to not be assigned during Module='ped'
  • fix ‘Error in par(oldpar): invalid value specified for graphical parameter “plt”’ when very small plotting window in newer versions of Rstudio.

sequoia 2.11.4

  • GenoConvert fake .map output file: change chrom 0 (unmapped) to chrom 1, as SNPs on chromosome 0 get excluded by default by e.g. PLINK & GCTA
  • CalcRped: drop dummy parents of ‘half founders’ from output (1 known + 1 unknown parent not supported by pkg kinship2)
  • fix errors when using data.tables

sequoia 2.11.3

  • make assignment of grandparents to singletons a bit more conservative

sequoia 2.11.2

CRAN release: 2024-05-28

  • minor fixes to pass CRAN checks

sequoia 2.11

  • improved assignment rate when some birth years are unknown
  • improved messages, with {cli} markup
  • new format of runtime messages, using C script
  • a few minor bugfixes in the Fortran code

sequoia 2.9.1

  • upgrade of GenoConvert: new vcf and genlight input, various bugs fixed, behaviour made more consistent and clearer through additional messages.
  • retain SNP names in GenoConvert and SnpStats

sequoia 2.9.0

CRAN release: 2024-03-01

  • fix bug in MkGenoErrors (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 ElE_l were generated, and then (El/2)2(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.
  • adds log to MkGenoErrors
  • SimGeno ParMis default changed from 0.4 to 0
  • default genotyping pattern slightly changed to ensure the probability a homozyogote does not have a genotyping error is identical to a heterozygote (see ErrToM).
  • Beta-version of EstEr (estimation of genotyping errors) removed due to inaccurate estimations and misuse. Will (probably) be re-implemented in a future version.

sequoia 2.8.3

CRAN release: 2023-12-19

  • fixes bugs introduced since version 2.5, plus various other edits in source code to improve assignment rate
  • fix bug in CalcMaxMismatch: OH with both parents counts as 2 mismatches (was 1)

sequoia 2.7.3

  • fix bug causing some negative parental LLRs, and possibly some non-assignments
  • speed increase for lower call rates
  • add OutFormat ‘ped’ to GenoConvert, and fix bug with OutFormat ‘col’

sequoia 2.7.2

CRAN release: 2023-09-06

  • change EstConf example to nSim=1 to ensure runtime < 5 sec to pass CRAN check

sequoia 2.7.1

  • add mtSame: specify if individuals have the same or different mitochondrial haplotype
  • improved parentage assignment performance when there are many genetically similar candidate parents
  • fixes CRAN issue ‘cannot use Fortran’s random number generator’

sequoia 2.6.0

  • add specification of assumed genotyping error rate via length 3 vector: hom|hom, het|hom, hom|het
  • expand CalcPairLL helpfile

sequoia 2.5.6

CRAN release: 2023-04-22

  • fixes CRAN pretest NOTES, including broken links in vignette

sequoia 2.5.4

  • add updated vignettes (main + age); accidentally included old versions in 2.5.3
  • fixed bug in CalcBYprobs, which caused Year.last to be ignored

sequoia 2.5.3

CRAN release: 2023-03-21

  • fixes CRAN error ‘DLL requires the use of native symbols’

sequoia 2.5.1

Bug fixes & minor changes

  • fix error ‘sibship number out of bounds’
  • fix error when LifeHistData$Sex includes NA
  • fix several minor bugs affecting rare cases

sequoia 2.5.0

New features & major changes

  • improved performance when a large proportion of birth years is not exactly known
  • optional column Year.last added to LifeHistData (last possible offspring birth year)
  • New functions GetAncestors and GetDescendants

Bug fixes & minor changes

  • New parameter MinAgeParent for MakeAgePrior()
  • New parameter StrictGenoCheck, Strict for CheckGeno() ; update msgs
  • update CheckLH, now flexible column order in LifeHistData.
  • changed maxmismatch from qntl = 0.999^(1/nrow(GenoM)) to 0.9999^(1/nrow(GenoM)) in all functions calling CalcMaxMismatch

sequoia 2.4.2

Bug fixes & minor changes

  • checks up to 6 generations back when making assignment to avoid individual being its own ancestor (was 5)
  • fix bug in SnpStats() when AF=0 or SNP is missing for all individuals.

sequoia 2.4.1

CRAN release: 2023-01-08

New features & major changes

  • R markdown file to create (or serve as a first draft of) a summary report of input and output, called via 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.

Minor changes

  • switch from library xlsx to openxlsx in writeSeq() (easier to install)
  • adds purl=FALSE to vignette chunks & include SeqOUT_HSg5 for quicker vignette compilation
  • include additional griffin example data: Geno_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)
  • many examples are rewritten, for clarification & to speed up package check
  • the plotting function of SummarySeq() was internal and is now exported (PlotSeqSum())
  • output from sequoia() now includes args.AP.
  • in 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 tests

Bug fixes

  • fixes several memory issues identified by CRAN
  • fixes various bugs in SimGeno() for non-autosomal inheritance; this option is still experimental and non-autosomal SNPs are not supported by the pedigree reconstruction.
  • fixes 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.
  • fixes bug resulting in LL(FA)=777 (‘impossible’) for pairs with all 4 parents unknown. Likely only affected CalcPairLL(), as LL(HS)=LL(GP)=LL(FA) for these pairs. Origin time unknown.
  • fixes bug in GenoConvert() when Informat='single'.

sequoia 2.3.5

CRAN release: 2021-05-22

  • fixes bug: OH count was always zero when there was no co-parent

sequoia 2.3.4

CRAN release: 2021-05-15

  • fixes bug in CalcPairLL() HS likelihood when conditioning on pedigree was incorrect. No/minimal effect on pedigree reconstruction.
  • fixes bug in DuplicateCheck() (always automatically called by sequoia()) that on very rare occasions caused R to crash

sequoia 2.3.3

CRAN release: 2021-05-02

fixes minor bugs identified by CRAN valgrind and gcc-ASAN

sequoia 2.3.2

CRAN release: 2021-04-29

minor edits to vignette to comply with CRAN precheck

sequoia 2.3.1

New features & major changes

  • Hermaphrodites: dummy individuals with offspring as both dam and as sire now have prefix ‘H’; closer links between the two ‘clonal’ sibship parts during pedigree reconstruction for improved performance
  • Assignment of sibship grandparents moved to before check & assignment of additional parents; this proved to increase correct assignments without increasing incorrect assignments.
  • new function CalcBYprobs() to estimate the probability that individual i is born in year y.

Minor changes

  • various edits to Fortran code improving general performance.

Bug fixes

sequoia 2.3.0

Major bug fixes

  • now possible to run with assumed genotyping error rate Err=0
  • further improvements when a large proportion of birth years are missing
  • various bugs related to hermaphrodites

Reduced computational time

  • Sibship clustering etc. now done from oldest to youngest individual instead of in order of occurrence in genotype file, giving quicker convergence to final high likelihood pedigree.

sequoia 2.2.2

New features & major changes

  • hermaphrodites: re-implemented and greatly improved sibship clustering. Specification of hermaphrodite vs diocious is now separate input parameter Herm instead of specified via Complex. New output list element DummyClones
  • improved performance when a large proportion of birth years are missing
  • new function CalcRped() to calculate pedigree relatedness. Uses package kinship2.

Bug fixes

Various smaller bugs have been fixed, some affecting assignment rate

sequoia 2.1.0

New features & major changes

  • parameter ‘maxSibIter’ (-9/-1/0/>0) deprecated and replaced by ‘Module’ (pre/dup/par/ped).
  • sequoia(): Option FindMaybeRel has been deprecated; call GetMaybeRel() directly instead.
  • new function CalcPairLL(), returns likelihoods for each of the 7 considered relationships (PO, FS, HS, GP, FA, HA, U) for each specified pair of individuals
  • new function RelPlot() for Colony-like visualisation of pairwise relationships (automatically called by ComparePairs())

Bug fixes

  • 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'.
  • various functions: fixed error when dummy prefixes have different number of characters (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 dummies
  • GetMaybeRel(): fixed error causing likely GP pairs not to be included output
  • PedCompare(): fixed id.dam.cat and id.sire.cat being ‘NANA’ instead of XD, XG or XX when Symmetrical=TRUE
  • PlotAgePrior(): Avoid using grDevices::hcl.colors() in R versions <3.6, where this function is not yet available
  • ComparePairs(): fixed bug when Pairs2 but not Ped2 is specified
  • MakeAgePrior(): fixed bug when there are no FS pairs in the input pedigree
  • MakeAgePrior(): MaxAgeParent was ignored when a pedigree with overlapping generations was supplied

Minor changes

  • most examples are now set to \donttest instead of \dontrun, so that they can be run using example(). Note that some can be quite time consuming, especially EstConf().
  • new function PlotPedComp() to visualise PedCompare() output
  • SimGeno(): deprecated input parameters (since v 1.3.1) are dropped completely
  • getAssignCat() no longer drops additional columns from input pedigree
  • Speed increase for CalcOHLLR(, CalcLLR = FALSE)
  • More thorough input checks, which are more consistent across different functions
  • PedCompare() output element DummyMatch now also include output class of matched individual’s parents & offspring
  • Duplicate check in sequoia() 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 pedigrees
  • If the plotting window in Rstudio is too small and Plot=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.

sequoia 2.0.7

CRAN release: 2020-05-18

New features

  • The genotyping error matrix (probability of observed genotype conditional on actual) is now fully customisable in all relevant functions, see help file of new function ErrToM. The default has changed very slightly from version 1.3.
  • new function CalcOHLLR() to calculate Mendelian errors and parental log-likelihood ratios for any pedigree
  • new function getAssignable() to flag genotyped and ‘dummifiable’ individuals in any pedigree
  • new function ComparePairs() to compare pairwise relationships between 2 pedigrees; replaces now-deprecated DyadCompare.
  • function PedPolish() is now user available.

Major changes

  • Deprecated option MaxMismatch of function sequoia, now calculated internally by new function CalcMaxMismatch based on number of SNPs, presumed genotyping error rate, and minor allele frequencies
  • function EstConf() now also estimates confidence for parent-pairs; output has changed considerably.
  • rewrote function PedCompare() to increase clarity of code for easier maintenance; changed output format somewhat.
  • Added a vignette about the ageprior, and rewrote sections of the main vignette to incorporate new functions
  • In the Fortran part, re-implemented how (candidate) (grand)parent-pairs are filtered and assigned

Bug fixes

  • 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 number
  • fixed ERROR! ***Invalid ParProb!*** triggered when some SNPs are monomorphic
  • fixed SEGFAULT triggered when some SNPs have very high missingness (>80%); possibly sibship size out of bounds
  • fixed Error arguments imply differing number of rows when there are dummy parents of 1 sex only
  • fixed various mostly minor bugs in the Fortran code
  • fixed bugs regarding ‘link time optimisation’

Minor changes

  • LifeHistData may have 2 additional columns, with minimum and maximum possible birth year
  • second example pedigree (Ped_griffin) to illustrate overlapping generations, used in age vignette
  • SummarySeq(): 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).

Sequoia 1.3.3

CRAN release: 2019-06-20

Bug fixes

  • fixes bug that caused R to crash (Fortran array indexing out-of-bounds)

Sequoia 1.3.1

CRAN release: 2019-06-14

New features

Minor changes

  • extended vignette with function overview & FAQ
  • numerous edits to fortran source code to better handle certain (rarer) types of relatives

Bug fixes

  • various bug fixes in fortran source code

sequoia 1.1.1

CRAN release: 2018-08-13

Major changes

  • possibly.

sequoia 1.0.0

CRAN release: 2018-03-29

New features

  • added functions EstConf, SnpStats

Major changes

  • considerable changes in Fortran code

sequoia 0.9.2

CRAN release: 2017-07-17

New features

  • added functionality for hermaphrodites (in silico cloned into male + female)

sequoia 0.7.2

CRAN release: 2017-02-13

First version on CRAN!