From 95a392c4c416485aacba88836217ece916418529 Mon Sep 17 00:00:00 2001 From: Bonifazi Date: Thu, 23 Jan 2025 22:12:33 +0100 Subject: [PATCH] updated README --- README.Rmd | 12 +++++++----- README.md | 32 +++++++++++++++++++++----------- 2 files changed, 28 insertions(+), 16 deletions(-) diff --git a/README.Rmd b/README.Rmd index 1065936..9d63762 100644 --- a/README.Rmd +++ b/README.Rmd @@ -25,7 +25,7 @@ knitr::opts_chunk$set( The goal of the `labradoR` R package is to facilitate the handling and post-processing in R of the output from [`Retriever`](https://genebankdata.cgn.wur.nl/software/software.html) software. -`Retriever` is a software for retrieving information on population structure, inbreeding, and kinship from pedigrees analysis generating many statistics and plots. For more information on `Retriever` please refer to the [official software website](#0){style="font-size: 11pt;"} and it associated [publication](#0){style="font-size: 11pt;"}. +`Retriever` is a software for retrieving information on population structure, inbreeding, and kinship from pedigrees analysis generating many statistics and plots. For more information on `Retriever` please refer to the [official software website](https://genebankdata.cgn.wur.nl/software/software.html) and it associated [publication](https://www.mdpi.com/2076-2615/11/5/1332). `labradoR` help users to import the output generated by `Retriever` into R for further manipulation and downstream analyses. `labradoR` loads the main tabular information into `data.frames` and generates associated `ggplot2` plots objects similar to those of `Retriever`. @@ -52,6 +52,7 @@ str(output, max.levels = 1, give.attr = F) ``` Note: since the logic of `labradoR` is that of "fetching" lines from `Retriever`'s output, if anything changes in the format of the `.out` file, then `labradoR`'s associated code will need to be adapted accordingly. +Currently, `labradoR` has been tested and used with `Retriever v7` (newer versions and sub-populations are not supported yet). ## Example output @@ -66,11 +67,12 @@ If you use the `labradoR` package in your research, please cite it as follows: To cite the software directly, you can use the following format in your work: - *Bonifazi, R. (2025). labradoR: An R package for handling and post-processing Retriever output. Version 1.0.0. Retrieved from .* + * Bonifazi, R. (2025). labradoR: An R package for handling and post-processing Retriever output. Version 1.0.0. Retrieved from .* 2. **Citing the Associated Paper** - A paper is currently in preparation. + A paper is currently in preparation. For now, you can refer to the associated presentation: + * Winding, J. J., Meuwissen, T. H. E., Croiseau, P., Restoux, G., & Bonifazi, R. (2023). Impact of genomic selection on genetic diversity in five European local cattle breeds. Proceedings of the 74th Annual Meeting of the European Federation of Animal Science, Lyon, France (p. 160). ## Contributing @@ -90,8 +92,8 @@ Check out the [NEWS](NEWS.md) file for the latest updates and changes to the pac ## Acknowledgements -- Jack J. Windig for helping with `Retriever` interpretation. +- [Jack J. Windig](https://research.wur.nl/en/persons/jack-windig) for helping with the interpretation of the `Retriever`'s output. - [Julia Höglund]() for helping editing with `labradoR` logo. -- [Tosten Pook]() for helping with the `MoBPS` simulations. +- [Torsten Pook]() for helping with the `MoBPS` simulations. diff --git a/README.md b/README.md index 17788ed..4c9e991 100644 --- a/README.md +++ b/README.md @@ -19,9 +19,9 @@ software. `Retriever` is a software for retrieving information on population structure, inbreeding, and kinship from pedigrees analysis generating many statistics and plots. For more information on `Retriever` please -refer to the -official software website and -it associated publication. +refer to the [official software +website](https://genebankdata.cgn.wur.nl/software/software.html) and it +associated [publication](https://www.mdpi.com/2076-2615/11/5/1332). `labradoR` help users to import the output generated by `Retriever` into R for further manipulation and downstream analyses. `labradoR` loads the @@ -57,7 +57,9 @@ for English and DUT for Dutch). Note: since the logic of `labradoR` is that of “fetching” lines from `Retriever`’s output, if anything changes in the format of the `.out` file, then `labradoR`’s associated code will need to be adapted -accordingly. +accordingly. Currently, `labradoR` has been tested and used with +`Retriever v7` (newer versions and sub-populations are not supported +yet). ## Example output @@ -78,13 +80,20 @@ follows: To cite the software directly, you can use the following format in your work: - *Bonifazi, R. (2025). labradoR: An R package for handling and - post-processing Retriever output. Version 1.0.0. Retrieved from - .* + - Bonifazi, R. (2025). labradoR: An R package for handling and + post-processing Retriever output. Version 1.0.0. Retrieved from + .\* 2. **Citing the Associated Paper** - A paper is currently in preparation. + A paper is currently in preparation. For now, you can refer to the + associated presentation: + + - Winding, J. J., Meuwissen, T. H. E., Croiseau, P., Restoux, G., & + Bonifazi, R. (2023). Impact of genomic selection on genetic + diversity in five European local cattle breeds. Proceedings of the + 74th Annual Meeting of the European Federation of Animal Science, + Lyon, France (p. 160). ## Contributing @@ -109,10 +118,11 @@ the package. ## Acknowledgements -- Jack J. Windig for helping with `Retriever` interpretation. +- [Jack J. Windig](https://research.wur.nl/en/persons/jack-windig) for + helping with the interpretation of the `Retriever`’s output. - [Julia Höglund](https://github.com/juliahoglund) for helping editing with `labradoR` logo. -- [Tosten Pook](https://github.com/tpook92) for helping with the `MoBPS` - simulations. +- [Torsten Pook](https://github.com/tpook92) for helping with the + `MoBPS` simulations.