If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
-<one line to give the program's name and a brief idea of what it does.>
-Copyright (C) <year> <name of author>
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.<one line to give the program's name and a brief idea of what it does.>
+Copyright (C) <year> <name of author>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
-<program> Copyright (C) <year> <name of author>
-This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
-This is free software, and you are welcome to redistribute it
-under certain conditions; type 'show c' for details.<program> Copyright (C) <year> <name of author>
+This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type 'show c' for details.The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/docs/articles/index.html b/docs/articles/index.html index 6b26181..8f83411 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html index 73d1bb2..cff55b4 100644 --- a/docs/articles/introduction.html +++ b/docs/articles/introduction.html @@ -40,7 +40,7 @@ @@ -298,7 +298,7 @@library(future)
availableCores()
#> system
-#> 8
+#> 16
plan(multisession, workers = 2)
Let’s simulate some data at equilibrium to demonstrate our methods:
diff --git a/docs/authors.html b/docs/authors.html index 592d08d..1bd8420 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ @@ -75,30 +75,33 @@Gerard D (2022). +
Gerard D (2023). “Double reduction estimation and equilibrium tests in natural autopolyploid populations.” -Biometrics, In press. +Biometrics, 79(3), 2143–2156. doi:10.1111/biom.13722.
@Article{,
title = {Double reduction estimation and equilibrium tests in natural autopolyploid populations},
author = {David Gerard},
journal = {Biometrics},
- year = {2022},
+ year = {2023},
doi = {10.1111/biom.13722},
- volume = {In press},
+ volume = {79},
+ number = {3},
+ pages = {2143--2156},
}
- Gerard D (2022). +
Gerard D (2023). “Bayesian Tests for Random Mating in Polyploids.” -bioRxiv. -doi:10.1101/2022.08.11.503635. +Molecular Ecology Resources, In press. +doi:10.1111/1755-0998.13856.
@Article{,
title = {Bayesian Tests for Random Mating in Polyploids},
author = {David Gerard},
- journal = {bioRxiv},
- year = {2022},
- doi = {10.1101/2022.08.11.503635},
+ journal = {Molecular Ecology Resources},
+ year = {2023},
+ doi = {10.1111/1755-0998.13856},
+ volume = {In press},
}
diff --git a/docs/index.html b/docs/index.html
index df18507..1589cc3 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -31,8 +31,8 @@
findings, and conclusions or recommendations expressed are those of
the author and do not necessarily reflect the views of the National
Science Foundation. For details of these methods, see
- Gerard (2022a) <doi:10.1111/biom.13722> and
- Gerard (2022b) <doi:10.1101/2022.08.11.503635>.">
+ Gerard (2023a) <doi:10.1111/biom.13722> and
+ Gerard (2023b) <doi:10.1111/1755-0998.13856>.">
-Inference concerning equilibrium and random mating in autopolyploids. Methods are available to test for equilibrium and random mating at any even ploidy level (>2) in the presence of double reduction at biallelic loci. For autopolyploid populations in equilibrium, methods are available to estimate the degree of double reduction. We also provide functions to calculate genotype frequencies at equilibrium, or after one or several rounds of random mating, given rates of double reduction. For details of these methods, see Gerard (2022a) <doi:10.1111/biom.13722> and Gerard (2022b) <doi:10.1101/2022.08.11.503635>.
+Inference concerning equilibrium and random mating in autopolyploids. Methods are available to test for equilibrium and random mating at any even ploidy level (>2) in the presence of double reduction at biallelic loci. For autopolyploid populations in equilibrium, methods are available to estimate the degree of double reduction. We also provide functions to calculate genotype frequencies at equilibrium, or after one or several rounds of random mating, given rates of double reduction. For details of these methods, see Gerard (2023a) <doi:10.1111/biom.13722> and Gerard (2023b) <doi:10.1111/1755-0998.13856>.
The main functions for inference are:
hwefit(): Fit either hwelike(),rmlike(), hweustat(), hwenodr(), or hweboot() across many loci. Parallelization is supported through the future package.
To cite hwep in publications use:
-Gerard D (2022). “Double reduction estimation and equilibrium tests in natural autopolyploid populations.” Biometrics In press. doi:10.1111/biom.13722.
+Gerard D (2023). “Double reduction estimation and equilibrium tests in natural autopolyploid populations.” Biometrics, 79(3), 2143–2156. doi:10.1111/biom.13722.
A BibTeX entry for LaTeX users is
-@Article{,
- title = {Double reduction estimation and equilibrium tests in natural autopolyploid populations},
- author = {David Gerard},
- journal = {Biometrics},
- year = {2022},
- doi = {10.1111/biom.13722},
- volume = {In press},
-}@Article{,
+ title = {Double reduction estimation and equilibrium tests in natural autopolyploid populations},
+ author = {David Gerard},
+ journal = {Biometrics},
+ year = {2023},
+ doi = {10.1111/biom.13722},
+ volume = {79},
+ number = {3},
+ pages = {2143--2156},
+}If you use rmbayes(), rmbayesgl(), or menbayeslg(), then please also cite
-Gerard D (2022). “Bayesian tests for random mating in polyploids.” bioRxiv. doi:10.1101/2022.08.11.503635.
+Gerard D (2023). “Bayesian tests for random mating in polyploids.” Molecular Ecology Resources, In press. doi:10.1111/1755-0998.13856.
A BibTeX entry for LaTeX users is
-@article{,
- author = {Gerard, David},
- title = {Bayesian Tests for Random Mating in Polyploids},
- year = {2022},
- doi = {10.1101/2022.08.11.503635},
- publisher = {Cold Spring Harbor Laboratory},
- journal = {bioRxiv}
-}@Article{,
+ title = {Bayesian Tests for Random Mating in Polyploids},
+ author = {David Gerard},
+ journal = {Molecular Ecology Resources},
+ year = {2023},
+ doi = {10.1111/1755-0998.13856},
+ volume = {In press},
+}NEWS.md
+ simgl() to increase the flexibility of the simulations.