Merge pull request #14 from pdimens/dev

merge dev into release

Project.toml

@@ -1,7 +1,7 @@
 name = "PopGenSims"
 uuid = "e670a858-c023-4621-870e-30d0f49b8322"
 authors = ["Pavel Dimens <[email protected]> and contributors"]
-version = "0.0.2"
+version = "0.0.3"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
@@ -12,11 +12,11 @@ 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"
-StaticArrays = "0.12"
+StaticArrays = "0.12, 1.0"
+PopGen = "0.0.3, 0.1, 0.4"
 StatsBase = "0.33"
 julia = "1.4"
 

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)

src/PopGenSims.jl

@@ -9,7 +9,6 @@ using PopGen:
     get_genotypes,
     read_from,
     write_to,
-    nancycats, 
     sort
 
 include("Cross.jl")
@@ -18,4 +17,3 @@ include("Sibship.jl")
 include("Utils.jl")
 
 end
-