updated README

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 <https://github.com/bonifazi/labradoR>.*
+    * Bonifazi, R. (2025). labradoR: An R package for handling and post-processing Retriever output. Version 1.0.0. Retrieved from <https://github.com/bonifazi/labradoR>.*
 
 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](<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.

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
-<a href="#0" style="font-size: 11pt;">official software website</a> and
-it associated <a href="#0" style="font-size: 11pt;">publication</a>.
+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
-    <https://github.com/bonifazi/labradoR>.*
+    - Bonifazi, R. (2025). labradoR: An R package for handling and
+      post-processing Retriever output. Version 1.0.0. Retrieved from
+      <https://github.com/bonifazi/labradoR>.\*
 
 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.