From 399771d9e6f407f484d8e5b7a28aaf2650e587b3 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat, 14 Nov 2020 00:06:54 +0000 Subject: [PATCH 1/8] CompatHelper: bump compat for "PopGen" to "0.1" --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 0689744..d0035d7 100644 --- a/Project.toml +++ b/Project.toml @@ -15,7 +15,7 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" DataFrames = "0.21" InvertedIndices = "1.0" PooledArrays = "0.5" -PopGen = "0.0.3" +PopGen = "0.0.3, 0.1" StaticArrays = "0.12" StatsBase = "0.33" julia = "1.4" From 8f7534b5dac6f8a5f93408caa6b6fcbbc00348fe Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 16 Nov 2020 00:07:33 +0000 Subject: [PATCH 2/8] CompatHelper: bump compat for "DataFrames" to "0.22" --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index d0035d7..d0aa863 100644 --- a/Project.toml +++ b/Project.toml @@ -12,7 +12,7 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" [compat] -DataFrames = "0.21" +DataFrames = "0.21, 0.22" InvertedIndices = "1.0" PooledArrays = "0.5" PopGen = "0.0.3, 0.1" From 88f70ebfae6164634b08ff56f6c6f38fb403f103 Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" Date: Thu, 19 Nov 2020 10:45:00 -0600 Subject: [PATCH 3/8] Update README.md --- README.md | 55 +++---------------------------------------------------- 1 file changed, 3 insertions(+), 52 deletions(-) diff --git a/README.md b/README.md index 76ebc3b..0c391ea 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,10 @@ ![logo](PopGenSims.png) +[![alt text](https://img.shields.io/badge/docs-stable-informational?style=for-the-badge&logo=Read%20The%20Docs&logoColor=white)](https://pdimens.github.io/PopGen.jl/docs/simulations/simulate_samples) ## Create population genetics simulations This package builds off of [PopGen.jl](http://github.com/pdimens/PopGen.jl) and -simulates offspring that would be generated under certain conditions. With this package you can simulate the offspring of specific individuals, simulate full-sibs, half-sibs, unrelated individuals, and parent-offspring pairs for use with PopGen.jl. +simulates offspring that would be generated under certain conditions. With this package you can simulate the offspring of specific individuals, simulate full-sibs, half-sibs, unrelated individuals, and parent-offspring pairs for use with PopGen.jl. You can also randomly generate samples given population-specific allele frequencies. ### Installation ```julia @@ -13,54 +14,4 @@ pkg(v1.5)> add "http://github.com/pdimens/PopGenSims.jl" ``` ### Usage -#### Import the package -``` -julia> using PopGenSims -``` - -#### Import the data -``` -# to use included dataset -julia> cats = nancycats() - -# to use your own data -julia> data = read_from("path/to/filename.ext", kwargs...); -``` - -#### Perform a cross -The `cross` function for a simple parental cross from individuals in the same `PopData` object follows the syntax -``` -cross(::PopData, parent1::String, parent2::String; n::Int) -``` -where `parent1` and `parent2` are strings of the names of the parents in the PopData, and the keyword `n` specifies the number of offspring you would like to simulate. - -##### example -``` -julia> f1 = cross(data, "sample1", "sample2", n = 100000) ; -``` - -#### Perform a backcross -This syntax uses the `Pair` notation of `PopData => Parent` to specify inputs. -``` -cross(PopData => "Parent1Name", PopData => "Parent2Name", n::Int, generation::String) -``` -where again `n` is a keyword argument for the number of offspring to produce, and `generation` is a keyword argument for the `population` identity to the assign the offspring. - -##### example -``` -julia> f2_backcross = cross(data => "sample1", f1 => "offspring_99", n = 100000, generation = "F2") ; - -# merge PopData objects -crossed_sims = append(data, f1) -``` - -Currently, `PopGenSims` can create crosses for: -- haploids (ploidy = 1) -- diploids (ploidy = 2) -- tetraploids (ploidy = 4) -- hexaploids (ploidy = 6) -- octaploids (ploidy = 8) - -To learn more about reading in data, see the docstring `?read_from` or read the [PopGen.jl docs section](https://pdimens.github.io/PopGen.jl/docs/io/file_import) on it. - -To learn more about crossing see their docstrings with `?cross` +Documentation for PopGenSims.jl has been integrated into [the PopGen.jl docs](https://pdimens.github.io/PopGen.jl/docs/simulations/simulate_samples) From ac77e4da7b22f7882db8d0feefef34c547544b98 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun, 22 Nov 2020 00:09:34 +0000 Subject: [PATCH 4/8] CompatHelper: bump compat for "PopGen" to "0.4" --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index d0aa863..3f5bdb5 100644 --- a/Project.toml +++ b/Project.toml @@ -15,7 +15,7 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" DataFrames = "0.21, 0.22" InvertedIndices = "1.0" PooledArrays = "0.5" -PopGen = "0.0.3, 0.1" +PopGen = "0.0.3, 0.1, 0.4" StaticArrays = "0.12" StatsBase = "0.33" julia = "1.4" From 207d3f473bb73ded8b0df02641ec256653ca67cf Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat, 28 Nov 2020 00:08:09 +0000 Subject: [PATCH 5/8] CompatHelper: bump compat for "StaticArrays" to "1.0" --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index d0aa863..afc49cf 100644 --- a/Project.toml +++ b/Project.toml @@ -16,7 +16,7 @@ DataFrames = "0.21, 0.22" InvertedIndices = "1.0" PooledArrays = "0.5" PopGen = "0.0.3, 0.1" -StaticArrays = "0.12" +StaticArrays = "0.12, 1.0" StatsBase = "0.33" julia = "1.4" From dfa29abdf181418d78ebbe7bfe18609fcaf32ddc Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" Date: Tue, 5 Jan 2021 11:41:30 -0500 Subject: [PATCH 6/8] Update PopGenSims.jl --- src/PopGenSims.jl | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/PopGenSims.jl b/src/PopGenSims.jl index 8a3d69b..9ef542d 100644 --- a/src/PopGenSims.jl +++ b/src/PopGenSims.jl @@ -9,7 +9,7 @@ using PopGen: get_genotypes, read_from, write_to, - nancycats, + @nancycats, sort include("Cross.jl") @@ -18,4 +18,3 @@ include("Sibship.jl") include("Utils.jl") end - From 7ff175a7fc61ec0b05530a92172b091477c7adba Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" Date: Tue, 5 Jan 2021 11:42:09 -0500 Subject: [PATCH 7/8] Update Project.toml --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 642b92e..adff472 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "PopGenSims" uuid = "e670a858-c023-4621-870e-30d0f49b8322" authors = ["Pavel Dimens and contributors"] -version = "0.0.2" +version = "0.0.3" [deps] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" From 5a83d6c9f9b103ce230a813fcb143615301925bf Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" Date: Thu, 7 Jan 2021 10:36:25 -0500 Subject: [PATCH 8/8] Update PopGenSims.jl --- src/PopGenSims.jl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/PopGenSims.jl b/src/PopGenSims.jl index 9ef542d..cc466a0 100644 --- a/src/PopGenSims.jl +++ b/src/PopGenSims.jl @@ -9,7 +9,6 @@ using PopGen: get_genotypes, read_from, write_to, - @nancycats, sort include("Cross.jl")