## qtl2 0.36 (2024-05-13)

### Minor changes

- In `scan1snps()`, subset `genoprobs` and `map` to common positions,
  if they have different markers. (Issue #219)

### Bug fixes

- Fixed a problem with `sdp_panel=TRUE` in `plot_snpasso()`. (Issue #232)

- Stop `index_snps()` with an error if physical map has missing
  values. (Issue #218)


## qtl2 0.34 (2023-11-28)

### Major changes

- Changed `read_csv()` to `fread_csv()` to avoid conflict with
  `readr::read_csv()`. (Issue #223)

- Similarly, changed `read_csv_numer()` to `fread_csv_numer()`.

- Added function `fund_dup_markers()`, for identifying subsets of
  markers with identical genotype data. This is a port of
  `qtl::findDupMarkers()`.

### Minor changes

- Have `calc_het()` stop with an error if the genotypes have labels
  that aren't two characters, and add an explanation of this in the
  help info. (Issue #220)

- More fully explain the use of weights in `est_herit()` and
  `scan1()`. (Issue #221)

### Bug fixes

- Deal with new compiler warning on CRAN. (Issue #230)


## qtl2 0.32 (2023-04-21)

### Major changes

- In `create_variant_query_func()`, added new arguments `id_field` and
  `sdp_field`, and in `create_gene_query_func()`, added arguments
  `name_field` and `strand_field` (Issue #215). This gives new
  flexibility, but also adds new requirements (for example, that the
  variant database has a field `"snp_id"`) and so could potentially
  break working code.

### New features

- Added `smooth_gmap()` for smoothing out a genetic map, particularly
  to eliminate intervals with 0 recombination, by using a "mixture" of
  the map and constant recombination. Also added `unsmooth_gmap()`
  which does the reverse.

### Minor changes

- `read_cross2()` now gives a warning if sex isn't provided but is
  needed. Also, if sex is missing we assume all individuals are
  female; previously we assumed they were male. (Issue #214)

- In `plot_genes()`, allow strand to be +/- 1 and not just `"+"` or
  `"-"`. (Issue #216)

- Fixed date in citation, Broman et al. (2019)
  [doi:10.1534/genetics.118.301595](https://doi.org/10.1534/genetics.118.301595)

### Bug fixes

- In `plot_genes()` there was a case where `stop` was used that should
  have been `end`.


## qtl2 0.30 (2022-12-02)

### Major changes

- For DOF1 and HSF1, revised the results of `calc_genoprob()` for the
  X chromosome, so that it just keeps track of the chromosome from the
  DO/HS parent. In males, we are assuming that the DO/HS parent is the
  mother.

### Minor changes

- Added dependency on version of Rcpp (>= 1.0.7)

- Revised `genoprob_to_alleleprob()` to work with DOF1 and
  HSF1. `plot_onegeno()` should also work now in these cases.
  (Issue #140 and Issue #141)

### Bug fixes

- Revised `predict_snpgeno()` to work for DOF1 and HSF1 populations.

- Now give a better error message in `genoprob_to_snpprob()` if `snpinfo`
  is missing the `sdp` column (Issue #207).

- In `read_csv()`, now give warnings if there are duplicate column names
  or duplicate row names in the file.

- In `read_cross2()`, moved the warning regarding the number of alleles
  to before the alleles object gets corrected (Issue #209).

- Now issue a warning message if founder genotypes are included but not
  used (Issue #211).

- The treatment of the male X chromosome in DOF1 and HSF1 was
  incorrect. We're now assuming that the DO or HS parent was the
  mother in the F1 cross, in which case males will be hemizygous for
  one of the DO/HS founder alleles.


## qtl2 0.28 (2021-10-11)

### Major changes

- The default colors for the Collaborative Cross (CC) have been changed to
  a color-blind friendly palette. The original CC colors remain as
  `CCorigcolors`; the previous default is now `CCaltcolors`. The new
  colors are derived from the palette in Wong (2011) Nature
  Methods [doi:10.1038/nmeth.1618](https://doi.org/10.1038/nmeth.1618).

- `plot_coefCC()` was revised to include `col=CCcolors` as an argument.
  The default is the new color-blind friendly CC colors, but one can
  now more easily use `col=CCaltcolors` or `col=CCorigcolors` to get a
  different choice.

- Added `plot_sdp()` to plot the strain distribution patterns of SNPs
  using tracks of tick-marks for each founder strain. (Issue #163)

- Added arguments `sdp_panel` and `strain_labels` to `plot_snpasso()`
  so that you can include the `plot_sdp()` panel with the SNP
  association results and/or the genes.

### Minor changes

- Added `replace_ids()` for a matrix or data frame (using the row
  names as the individual IDs). (Issue #191)

- Have `calc_het()` give an error if the input are for allele dosages.
  (Issue #190)

- Sneaky change in `ind_ids()` makes it apply to `calc_genoprob` and
  `fst_genoprob` objects. I'm not sure how to document this. (Issue #189)

- The output of `est_herit()` now includes the residual SD as an
  attribute, `"resid_sd"`. (Issue #16)

- Implemented a cross type `"hsf1"` that is similar to `"dof1"`, for a
  cross between an 8-way HS individual and a 9th strain. (Issue #149)

### Bug fixes

- `calc_kinship()` died with cryptic error if genotype probabilities
  didn't have a names attribute; now using `seq_len(probs)`.

- Give better error messages in `est_map()`, `viterbi()`, and
  `sim_geno()` if the cross is missing the genetic map.

- Fixed Issue #194: `calc_genoprob()` was taking chromosome names from
  `cross$gmap` which might have been missing; now using
  `names(cross$geno)`.

- Fixed Issue #195: in `create_snpinfo()`, drop markers that are
  non-informative.

- Fixed Issue #196, that `step()` returns `-Inf` rather than `NaN` for
  general AIL. This had to do with the handling of `-Inf` in `addlog()`.

- In `fit1()` and `scan1coef()`, wasn't grabbing the `...` arguments.
  properly.

- Ugly c++ revisions to avoid clang UBsan warnings on CRAN.
  (Issue #169)


## qtl2 0.24 (2020-12-16)

### Major changes

- Revised treatment of X chromosome in "general AIL" cross type, to be
  the same as the autosomes but with 2/3 as many generations for
  recombination. This should provide a better approximation.

### Minor changes

- Revised `reduce_markers()` so that it can handle the case of _many_
  markers, by working with them in smaller batches.

- `fit1()` now returns both fitted values and residuals.

- `fit1()` can be run with genotype probabilities omitted, in which
  case an intercept column of 1's is used (Issue #151).

- Updated mouse gene database with 2020-09-07 data from
  [MGI](http://www.informatics.jax.org/downloads/mgigff3/archive/monthly/).

- Implemented Issue #184, to make `calc_het()` multi-core.

- Make the [vdiffr](https://vdiffr.r-lib.org) package optional: only
  test the plots locally, and only if vdiffr is installed.

- `calc_sdp()` can now take a plain vector (Issue #142).

- Added a `lodcolumn` argument to `maxlod()` (Issue #137).

### Bug fixes

- Fixed [Issue #181](https://github.com/rqtl/qtl2/issues/181), where
  `calc_het()` gave values > 1 when used with
  [R/qtl2fst](https://github.com/rqtl/qtl2fst)-based probabilities.
  Also fixed a similar bug in `calc_geno_freq()`.

- Fixed [Issue #172](https://github.com/rqtl/qtl2/issues/172), where
  `fit1()` gave incorrect fitted values when `kinship` is provided,
  because they weren't "rotated back".

- `fit1()` no longer provides individual LOD scores (`ind_lod`) when
  `kinship` is used, as with the linear mixed model, the LOD score is
  not simply the sum of individual contributions.

- Fixed [Issue #174](https://github.com/rqtl/qtl2/issues/174) re
  `genoprob_to_alleleprob()` for general AIL crosses. We had not
  implemented the `geno2allele_matrix()` function.

- Fixed Issue #164, so `plot_pxg()` can handle a phenotype that is a
  single-column data frame.

- Fixed Issue #135, so `plot_scan1()` can take vector input (which is
  then converted to a single-column matrix).

- Fixed Issue #157, to have `calc_genoprob()` give a better error
  message about missing genetic map.

- Fixed Issue #178, to have `read_cross2()` give a warning not an error
  if incorrect number of alleles.

- Fixed Issue #180 re `scan1()` error if phenotypes' rownames have rownames.

- Fixed Issue #146, revising `predict_snpgeno()` so that it works for
  homozygous populations, like MAGIC lines or the Collaborative Cross.

- Fixed Issue #176, that `guess_phase()` doesn't work with cross type
  `"genail"`. Needed to define `phase_known_crosstype` as `"genailpk"` in
  [`cross_genail.h`](https://github.com/rqtl/qtl2/blob/main/src/cross_genail.h)
  because otherwise `is_phase_known()` will return TRUE.


## qtl2 0.22-11 (2020-07-09)

### Bug fixes

- Small changes in tests to avoid failures on solaris


## qtl2 0.22-10 (2020-06-30)

### Bug fixes

- Fixed compilation error on Solaris on CRAN, due to a log(10) and
  sqrt(10). Solaris refuses to do log(int) or sqrt(int), I guess.

- Fixed some conflicting enum definitions in c++ code


## qtl2 0.22-8 (2020-06-22)

### Minor changes

- Added recognition of the R Core Team as a contributor, as the
  package includes a copy of code for Brent's method for univariate
  function optimization. Also added a Copyright field in the
  DESCRIPTION field, explaining the copyright of that code.

- Sped up some of the examples and tests. Tests no longer use more
  than 2 cores (even those that are only run locally).

- Added `\value{}` sections in the documentation for various
  functions. Added further explanation of `"viterbi"`, `"scan1"`,
  `"scan1perm"`, etc. S3 classes in the documentation.


## qtl2 0.22 (2020-05-21)

### Major changes

- Added some functions for diagnostics: `recode_snps()`,
  `calc_raw_het()`, `calc_raw_geno_freq()`, `calc_raw_maf()`, and
  `calc_raw_founder_maf()`.

- Added argument `blup` to `fit1()`, for getting BLUPs for a single
  fixed QTL position. At present, just gives estimates and
  coefficients by calling `scan1blup()` with a single position.

- `pull_genoprobpos()` can now take either a marker name (as before) or
  a set of map, chromosome, and position (from which it uses
  `find_marker()` to get the marker name).

- Added plot function for the results of `compare_geno()`. (Plots
  histogram of upper triangle.)

- Added functions `n_founders()` and `founders()` for getting the
  number of founders and the founder strain names for a cross2 object.

- `scan1()` now takes an optional `hsq` argument, so that the residual
  heritability may be specified rather than estimated.

### Minor changes

- `write_control_file()` now allows cross info codes with a cross info
  file (previously only allowed with a covariate). `read_cross2()`
  gives a warning if there are cross info conversion codes but more
  than one cross info column.

- Small fix in `read_cross2()` to allow multiple cross info covariates.

- Added a check that the founder genotypes have the same strain IDs on
  each chromosome.

- `convert2cross2()` now includes `alleles` component even if it
  wasn't present as an attribute.

- Added function `sdp2char()` for converting numeric SDP codes to
  character strings like `"ABC|DEFGH"`.

- Updated mouse gene database with 2019-08-12 data from
  [MGI](http://www.informatics.jax.org/downloads/mgigff3/archive/monthly/).

- `get_common_ids()` strips off names from output, just in case.

- Added internal functions `rqtl1_crosstype()` and `rqtl1_chrtype()`.

### Bug fixes

- Fixed typo in help for `scan1()` and related functions.

- `genoprob_to_snpprob()` was giving an error if you gave a cross2
  object in place of a snpinfo table and it had monomorphic markers.

- Fixed problem with weights in `scan1()` and related functions when
  their derived from `table()`. Make sure they're a plain numeric
  vector, not an array.

- Fixed `check_cross2()`: the check for invalid genotypes wasn't
  happening.

- Better error message for the case that there are no markers in
  common between map and genotypes.

- `extract_dim_from_header()`, used by `read_cross2()` and `read_csv()`,
  now just looks for the number part in the rest of the line.

- `maxlod()` now handles missing values (forcing `na.rm=TRUE`). If all
  values are missing it gives a warning and returns `-Inf`.
  [Fixes Issue #134.]

- In `max_scan1()`, treat the case that the input has no column names.
  [Fixes Issue #133.]

- `max_scan1()` was giving a messed up error message if `lodcolumn`
  was out of range. [Fixes Issue #132.]

- Revised the script `inst/scripts/create_ccvariants.R` to capture _all_
  of the consequences and genes for each SNP (rather than just the
  first), and fixing a bug that prevented capture of indels from
  chromosomes 6-X. Consequently, revised the example SQLite database
  `extdata/cc_variants_small.sqlite` and associated tests.


## qtl2 0.20 (2019-06-03)

### Major changes

- `scan1coef()` and `fit1()` now, by default, gives coefficient
  estimates for the QTL effects that sum to 0, with an additional
  coefficient being the intercept. This makes it more like DOQTL (and
  `scan1blup()`). The previous behavior can be obtained with the
  argument `zerosum=FALSE`.

- Added function `create_snpinfo()` for creating a SNP information table
  from a cross2 object, for use with `scan1snps()`.

### Minor changes

- Updated `extdata/mouse_genes_small.sqlite` using updated MGI
  annotations. Some of the field names have changed.

- In `check_cross2()`, added a test for alleles being a vector of
  character strings.

- Fixed some tests for R 3.6, due to change in random number generation.

- Use Markdown for function documentation, throughout

### Bug fixes

- In `genoprob_to_snpprob()` when a cross object is provided, make
  sure the genotype probabilities get subset to the cross markers.

- Fixed bug in `scan1snps()` re `keep_all_snps=FALSE`. It wasn't
  subsetting to the index SNPs properly. Added an internal function
  `reduce_to_index_snps()`.
  (See [Issue #89](https://github.com/rqtl/qtl2/issues/89).)

- Fixed bug in step probabilities for 4-, 8-, and 16-way RIL by selfing.

- Fixed bug in `zip_datafiles()` when the files are in a subdirectory.
  (See [Issue #102](https://github.com/rqtl/qtl2/issues/102).)

- Fixed bug in `plot_peaks()` for the case that the input `peaks`
  object does not contain QTL intervals.
  (See [Issue #107](https://github.com/rqtl/qtl2/issues/107).)

- Fixed inappropriate warning message for check of `cross_info` with
  cross type `risib8`.

- Fixed bugs in `guess_phase()` and `locate_xo()` where we needed an
  `any()` around a comparison of two vectors.


## qtl2 0.18 (2019-02-08)

### New features

- Added `plot_lodpeaks()` for scatterplot of LOD score vs position for
  inferred QTL from `find_peaks()` output.

- Added new cross types `"genril"` and `"genail"`, implemented to
  handle any number of founders; include the number of founders in the
  cross type, for example `"genril38"` or `"genail38"`. The cross
  information has length 1 + number of founders, with first column
  being the number of generations and the remaining columns being
  non-negative integers that indicate the relative frequencies of the
  founders in the initial population (these will be scaled to sum to
  1). `"genril"` assumes the progeny are inbred lines (recombinant
  inbred lines, RIL), while `"genail"` assumes the progeny have two
  random chromosomes (advanced intercross lines, AIL).

- The internal function `batch_vec()` now made user-accessible, and
  takes an additional argument `n_cores`. This splits a vector into
  batches for use in parallel calculations.

- The internal function `cbind_expand()` now made user-accessible.
  It's for combining matrices using row names to align the rows and
  expanding with missing values if there are rows in some matrices but
  not others.

- In `plot_peaks()`, added `lod_labels` argument. If TRUE, include LOD
  scores as text labels in the figure.

- Added function `calc_het()` for calculating estimated
  heterozygosities, by individual or by marker, from genotype
  probabilities derived by `calc_genoprob()`.

### Minor changes

- Small corrections to documentation.

- Revise some tests due to change in Recla and DOex datasets at
  <https://github.com/rqtl/qtl2data>

- Add tests of decomposed kinship matrix (from `decomp_kinship()`)
  with `scan1()`.

- `rbind_scan1()` and `cbind_scan1()` no longer give error if inputs
  don't all have matching attributes.

- Change default gap between chromosomes in `plot_scan1()` (and
  related) to be 1% of the total genome length.

### Bug fixes

- Fixed bug in `subset_kinship()` that prevented `scan1()` from
  working with decomposed "loco" kinship matrices.

- Fixed descriptions in help files for `cbind.calc_genoprob()` and
  `rbind.calc_genoprob()`, for column- and row-binding genotype
  probabilities objects (as output by `calc_genoprob()`. `cbind()` is
  for the same set of individuals but different chromosomes. `rbind()`
  is for the same set of markers and genotypes but different
  individuals. Made similar corrections for the related functions for
  `sim_geno()` and `viterbi()` output.


## qtl2 0.16 (2018-07-23)

### New features

- Added `pull_genoprobint()` for pulling out the genotype
  probabilities for a given genomic interval. Useful, for example, to
  apply `scan1blup()` over a defined interval rather than an entire
  chromosome.

- `scan1()`, `scan1perm()`, `scan1coef()`, `fit1()`, and `scan1snps()`
  can now use weights when `kinship` is provided, for example for the
  case of the analysis of recombinant inbred line (RIL) phenotype
  means with differing numbers of individuals per line. The residual
  variance matrix is like $v[h^2 K + (1-h^2)D]$ where D is diagonal
  {1/w} for weights w.

- Add `weights` argument to `est_herit()`.

- Added `add_threshold()` for adding significance thresholds to a
  genome scan plot.

- Added `predict_snpgeno()` for predicting SNP genotypes in a
  multiparent populations, from inferred genotypes plus the founder
  strains' SNP alleles.

- In `genoprob_to_snpprob()`, the `snpinfo` argument can now be a
  cross object (for a multiparent population with founder genotypes),
  in which case the SNP information for all SNPs with complete founder
  genotype data is calculated and used.

- `max_scan1()` with `lodcolumn=NULL` returns the maximum for all
  lod score columns. If `map` is included, the return value is in the
  form returned by `find_peaks()`, namely with `lodindex` and
  `lodcolumn` arguments added at the beginning.

- Added `replace_ids()` for replacing individual IDs in an object.
  S3 method for `"cross2"` objects and output of `calc_genoprob()`,
  `viterbi()`, `maxmarg()`, and `sim_geno()`.

- Added `clean_scan1()` plus generic function `clean()` that works
  with both this and with `clean_genoprob()`. `clean_scan1()` replaces
  negative values with `NA` and removes rows that have all `NAs`.

### Minor changes

- More informative error message in `est_herit()`, `scan1()`, etc.,
  when covariates and other data are not numeric.

- Fixed `pull_genoprobpos()` so it will work with
  [qtl2feather](https://github.com/byandell/qtl2feather)
  (and [qtl2fst](https://github.com/rqtl/qtl2fst)).

- In `plot_genes()`, if `xlim` is provided as an argument, subset the
  genes to those that will actually appear in the plotting region.

- Revise `find_marker()` so that the input `map` can also be a "snp
  info" table (with columns `"snp_id"`, `"chr"` and `"pos"`).

- Added `find_index_snp()` for identifying the index SNP that
  corresponds to a particular SNP in a snp info table that's been
  indexed with `index_snps()`.

- Add `overwrite` argument (default `FALSE`) to `zip_datafiles()`,
  similar to that for `write_control_file()`.

- `plot_snpasso()` now takes an argument `chr`.

- `max_scan1()` no longer gives a warning if `map` is not provided.

- `insert_pseudomarkers()` will now accept `pseudomarker_map` that
   includes only a portion of the chromosomes.

- In `fit1()`, replaced `tol` and `maxit` and added `...` which takes
  these plus a few additional hidden control parameters.

### Bug fixes

- Fix a bug in `index_snps()`; messed up results when `start` and
  `end` outside the range of the map.

- Fix a bug in `scan1snps()` regarding use of `chr` argument: need to
  force to be unique character strings, and avoid unnecessary warning
  about `start` and `end`.

- Fix a bug in `scan1snps()` where it didn't check that the `genoprobs`
  and `map` conform.

- Revised underlying binary trait regression function to avoid some of
  the tendency towards NAs.


## qtl2 0.14 (2018-03-09)

### New features

- Added function `clean_genoprob()` which cleans genotype
  probabilities by setting small values to 0 and, for genotype columns
  where the maximum value is not large, setting all values to 0. This
  is intended to help with the problem of unstable estimates of
  genotype effects in `scan1coef()` and `fit1()` when there's a
  genotype that is largely absent.

- Added function `compare_maps()` for comparing marker order between
  two marker maps.

- Revised the order of arguments in `reduce_markers()` to match
  `pick_marker_subset()`, because I like the latter better. Removed
  the function `pick_marker_subset()` because it's identical to
  `reduce_markers()`. (Seriously, I implemented the same thing twice.)

### Minor changes

- `plot_coef()` now uses a named `lodcolumn` argument, if provided, to
  subset `scan1_output`, if that's provided.

- In the documentation for `scan1coef()`, `scan1blup()`, and `fit1()`,
  revised the suggested contrasts for getting additive and dominance
  effects in an intercross.


### Bug fixes

- In `plot_coef()` with `scan1_output` provided, `ylim_lod` was being
  ignored.


## qtl2 0.12 (2018-01-19)

### New features

- `find_peaks()` and `max_scan1()` can now take snpinfo tables (as
  produced by `index_snps()` and `scan1snps()`) in place of the map.

### Minor changes

- Sped up a bunch of the examples in the help files (mostly by
  subsetting the example datasets).

### Bug fixes

- Further embarassment: the bug fix in version 0.10 didn't fully fix
  the problem with `find_peaks()`.


## qtl2 0.10 (2018-01-09)

### Bug fixes

- Fixed embarassing bug in `find_peaks()`. (Stopped with error if no
  LOD scores were above the threshold.)


## qtl2 0.8 (2018-01-05)

- First formal release


## qtl2 0.7-6 (2017-12-12)

### New features

- The output of `fit1()` now includes fitted values.

- Added function `pull_genoprobpos()` for pulling out a specific
  position (by name or position) from a set of genotype probabilities.

- The `chr` column in the result of `find_peaks()` is now a factor.
  This makes it possible to sort by chromosome. Also added an argument
  `sort_by` for choosing how to sort the rows in the result (by
  column, genomic position, or LOD score).

- In `max_scan1()`, if `map` is *not* provided, rather than stopping
  with an error, we just issue a warning and return the genome-wide
  maximum LOD score.

- Revised `find_markerpos()` so it can take a map (as a list of
  vectors of marker positions) in place of a `"cross2"` object.

### Minor changes

- Added many more checks of the inputs to various functions.

### Bug fixes

- Fixed a bug in `plot.scan1()`, which failed to pass `lodcolumn` to
  `plot_snpasso()`.


## qtl2 0.7-1 (2017-11-27)

The previously separate packages qtl2geno, qtl2scan, qtl2plot, and
qtl2db have now been combined into one package.
