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Removing set/getMisc(), docs, etc. #592

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Dec 16, 2024
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Removing set/getMisc(), docs, etc. #592

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feb1173
Removing set/getMisc() fully #584
gregorgorjanc Dec 14, 2024
c82d1f6
getPooledGeno(): Handle type arg, better default, and pooled example …
gregorgorjanc Dec 15, 2024
969c8bf
caclBeeGRMIbs() can now return centred genotype matrix, frequencies, …
gregorgorjanc Dec 16, 2024
bf61a09
editCsdLocus() works now also with just 2 alleles #591
gregorgorjanc Dec 16, 2024
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -40,3 +40,5 @@ vignettes/*.pdf

# Other
.DS_Store
src/*.o
src/*.so
4 changes: 2 additions & 2 deletions DESCRIPTION
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@@ -1,7 +1,7 @@
Package: SIMplyBee
Type: Package
Title: 'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes
Version: 0.4.1
Version: 0.4.2
Authors@R: c(
person("Jana", "Obšteter", email = "[email protected]",
role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1511-3916")),
Expand All @@ -27,7 +27,7 @@ License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: methods, R6, stats, utils, extraDistr (>= 1.9.1), RANN, Rcpp (>= 0.12.7)
Depends: R (>= 3.3.0), AlphaSimR (>= 1.5.3)
Depends: R (>= 3.3.0), AlphaSimR (>= 1.6.1)
LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH
RoxygenNote: 7.3.2
Suggests:
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2 changes: 0 additions & 2 deletions NAMESPACE
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Expand Up @@ -69,7 +69,6 @@ export(getGv)
export(getIbdHaplo)
export(getId)
export(getLocation)
export(getMisc)
export(getPheno)
export(getPooledGeno)
export(getQtlGeno)
Expand Down Expand Up @@ -192,7 +191,6 @@ export(replaceWorkers)
export(resetEvents)
export(selectColonies)
export(setLocation)
export(setMisc)
export(setQueensYearOfBirth)
export(simulateHoneyBeeGenomes)
export(split)
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26 changes: 23 additions & 3 deletions NEWS.md
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Expand Up @@ -4,6 +4,28 @@ editor_options:
wrap: 72
---

# SIMplyBee version 0.4.2

- 20??-??-??
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## Major changes
- TODO

## New features
- TODO

## Bug fixes
- editCsdLocus() works now also with just 2 alleles #591

## Backgrond/package/etc. work
- calcBeeGRMIbs() can now return centred genotype matrix, allele frequencies,
and scale factor used to calculate the GRM #594
- Improved default for getPooledGeno() (to type="mean"") and added an example
on how to collect pooled workers' genotype accross colonies (but pooling is
done within a colony!) #592
- We now removed setMisc() and getMisc() because we now use the new AlphaSimR
structure of the misc slot that is much easier to use. #584

# SIMplyBee version 0.4.1

- 2024-09-19
Expand All @@ -26,7 +48,7 @@ which caused an error. We now read in the locations from a csv file.
now c(0, 0) PR#500


## New features ##
## New features
- In setLocation(MultiColony) we can set one location (numeric) or
multiple (list or data.frame) PR#500
- getLocation(MultiColony) got the collapse argument
Expand Down Expand Up @@ -57,8 +79,6 @@ which caused an error. We now read in the locations from a csv file.
- Bug fix - get\*Haplo() functions were returning diploid drones when
input was a Pop-class

-

# SIMplyBee version 0.3.0

- 2022-12-05 First public/CRAN version of the package
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