OpenCASA R package for data processing
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Felipe Martínez Pastor
Feb 16, 2026, 5:53:23 AMFeb 16
to OpenCASA Mailing List
Dear all,
I just uploaded a R package for collating and curating OpenCASA result files. The package provides a single function, OpenCASA2Tables(), which explores a directory tree containing the OpenCASA individual and total motility files and outputs data files with identified individual data and summary data.
I hope this is useful for you. Even of you do not routinely used R, you only have to install it, install the package and run it with the correct information.
For installation, just install.packages("devtools") in R, then:
devtools::install_git(url = "https://codeberg.org/fmartinezpastor/OpenCASA2tables/")
and library(OpenCASA2tables) to load.
You can get help by writing ?OpenCASA2tables. Usually, you just need to provide the path to your OpenCASA folders (they can contain results and video files, no problem) and a couple of parameters for your particular sample.
I just uploaded a R package for collating and curating OpenCASA result files. The package provides a single function, OpenCASA2Tables(), which explores a directory tree containing the OpenCASA individual and total motility files and outputs data files with identified individual data and summary data.
I hope this is useful for you. Even of you do not routinely used R, you only have to install it, install the package and run it with the correct information.
For installation, just install.packages("devtools") in R, then:
devtools::install_git(url = "https://codeberg.org/fmartinezpastor/OpenCASA2tables/")
and library(OpenCASA2tables) to load.
You can get help by writing ?OpenCASA2tables. Usually, you just need to provide the path to your OpenCASA folders (they can contain results and video files, no problem) and a couple of parameters for your particular sample.
I hope this is useful for you. This is free software (FOSS), so you're welcome to collaborate and improve. I have hosted it in Codeberg, but I plan to upload to CRAN so you could eventually directly install it in R (and maybe as part of a larger collection of functions for OpenCASA data).
Best regards,
Felipe
jyaniz
Feb 16, 2026, 6:04:18 AMFeb 16
to Felipe Martínez Pastor, OpenCASA Mailing List
Thank you very much Felipe!
El 2026-02-16 11:52, 'Felipe Martínez Pastor' via OpenCASA Mailing List
escribió:
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> [2].
>
>
> Links:
> ------
> [1]
> https://urldefense.com/v3/__https://codeberg.org/fmartinezpastor/OpenCASA2tables/__;!!D9dNQwwGXtA!R97eEaLXVe20cHCFrHwSJ0RdXnrhvQvEogn3u0LNLMqfFNdVn_mzavdpruixF88ZYgRCYECHzNEy9xP1RwQRl_Ub_nHLaYBY$
> [2]
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--
Jesús Yániz Pérez de Albéniz
Catedrático de Universidad (Full Professor in Animal Science)
Dpto. Producción Animal y CC. de los Alimentos
Escuela Politécnica Superior de Huesca
Universidad de Zaragoza
Ctra. Cuarte s/n, 22071, Huesca
email: jya...@unizar.es
Phone: 34 974 239 312
El 2026-02-16 11:52, 'Felipe Martínez Pastor' via OpenCASA Mailing List
escribió:
> Dear all,
> I just uploaded a R package for collating and curating OpenCASA result
> files. The package provides a single function, OpenCASA2Tables(),
> which explores a directory tree containing the OpenCASA individual and
> total motility files and outputs data files with identified individual
> data and summary data.
> I hope this is useful for you. Even of you do not routinely used R,
> you only have to install it, install the package and run it with the
> correct information.
> For installation, just install.packages("devtools") in R, then:
> devtools::install_git(url =
> "https://codeberg.org/fmartinezpastor/OpenCASA2tables/ [1]")
> I just uploaded a R package for collating and curating OpenCASA result
> files. The package provides a single function, OpenCASA2Tables(),
> which explores a directory tree containing the OpenCASA individual and
> total motility files and outputs data files with identified individual
> data and summary data.
> I hope this is useful for you. Even of you do not routinely used R,
> you only have to install it, install the package and run it with the
> correct information.
> For installation, just install.packages("devtools") in R, then:
> devtools::install_git(url =
> and library(OpenCASA2tables) to load.
> You can get help by writing ?OpenCASA2tables. Usually, you just need
> to provide the path to your OpenCASA folders (they can contain results
> and video files, no problem) and a couple of parameters for your
> particular sample.
> I hope this is useful for you. This is free software (FOSS), so you're
> welcome to collaborate and improve. I have hosted it in Codeberg, but
> I plan to upload to CRAN so you could eventually directly install it
> in R (and maybe as part of a larger collection of functions for
> OpenCASA data).
> Best regards,
> Felipe
>
> --
> You can get help by writing ?OpenCASA2tables. Usually, you just need
> to provide the path to your OpenCASA folders (they can contain results
> and video files, no problem) and a couple of parameters for your
> particular sample.
> I hope this is useful for you. This is free software (FOSS), so you're
> welcome to collaborate and improve. I have hosted it in Codeberg, but
> I plan to upload to CRAN so you could eventually directly install it
> in R (and maybe as part of a larger collection of functions for
> OpenCASA data).
> Best regards,
> Felipe
>
> You received this message because you are subscribed to the Google
> Groups "OpenCASA Mailing List" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to opencasa_mailing...@googlegroups.com.
> To view this discussion, visit
> https://groups.google.com/d/msgid/opencasa_mailinglist/CABe25bZwjKc5TKYNZiLWcWk4Z1mGAc%3DBkyn9zaTgdR5mBQHHUw%40mail.gmail.com
> [2].
>
>
> Links:
> ------
> [1]
> https://urldefense.com/v3/__https://codeberg.org/fmartinezpastor/OpenCASA2tables/__;!!D9dNQwwGXtA!R97eEaLXVe20cHCFrHwSJ0RdXnrhvQvEogn3u0LNLMqfFNdVn_mzavdpruixF88ZYgRCYECHzNEy9xP1RwQRl_Ub_nHLaYBY$
> [2]
> https://urldefense.com/v3/__https://groups.google.com/d/msgid/opencasa_mailinglist/CABe25bZwjKc5TKYNZiLWcWk4Z1mGAc*3DBkyn9zaTgdR5mBQHHUw*40mail.gmail.com?utm_medium=email&utm_source=footer__;JSU!!D9dNQwwGXtA!R97eEaLXVe20cHCFrHwSJ0RdXnrhvQvEogn3u0LNLMqfFNdVn_mzavdpruixF88ZYgRCYECHzNEy9xP1RwQRl_Ub_jlOnuNH$
--
Jesús Yániz Pérez de Albéniz
Catedrático de Universidad (Full Professor in Animal Science)
Dpto. Producción Animal y CC. de los Alimentos
Escuela Politécnica Superior de Huesca
Universidad de Zaragoza
Ctra. Cuarte s/n, 22071, Huesca
email: jya...@unizar.es
Phone: 34 974 239 312
rosperez
Feb 16, 2026, 8:23:09 AMFeb 16
to Felipe Martínez Pastor, OpenCASA Mailing List
Thank you very much, Felipe
Best regards,
Rosaura
---
El 2026-02-16 11:52, 'Felipe Martínez Pastor' via OpenCASA Mailing List
escribió:
> [2]
> https://urldefense.com/v3/__https://groups.google.com/d/msgid/opencasa_mailinglist/CABe25bZwjKc5TKYNZiLWcWk4Z1mGAc*3DBkyn9zaTgdR5mBQHHUw*40mail.gmail.com?utm_medium=email&utm_source=footer__;JSU!!D9dNQwwGXtA!T25hj6XydgTVJnN2uqyiDRORM40-xCL7EbQCADDMk2KIMl4NxGO5UbjEu0IOdpBFyKV6T8Czaw-BGdEgSrueERcaRXEXCRs0xg$
Best regards,
Rosaura
---
El 2026-02-16 11:52, 'Felipe Martínez Pastor' via OpenCASA Mailing List
escribió:
> Dear all,
> I just uploaded a R package for collating and curating OpenCASA result
> files. The package provides a single function, OpenCASA2Tables(),
> which explores a directory tree containing the OpenCASA individual and
> total motility files and outputs data files with identified individual
> data and summary data.
> I hope this is useful for you. Even of you do not routinely used R,
> you only have to install it, install the package and run it with the
> correct information.
> For installation, just install.packages("devtools") in R, then:
> devtools::install_git(url =
> "https://codeberg.org/fmartinezpastor/OpenCASA2tables/ [1]")
> I just uploaded a R package for collating and curating OpenCASA result
> files. The package provides a single function, OpenCASA2Tables(),
> which explores a directory tree containing the OpenCASA individual and
> total motility files and outputs data files with identified individual
> data and summary data.
> I hope this is useful for you. Even of you do not routinely used R,
> you only have to install it, install the package and run it with the
> correct information.
> For installation, just install.packages("devtools") in R, then:
> devtools::install_git(url =
> and library(OpenCASA2tables) to load.
> You can get help by writing ?OpenCASA2tables. Usually, you just need
> to provide the path to your OpenCASA folders (they can contain results
> and video files, no problem) and a couple of parameters for your
> particular sample.
> I hope this is useful for you. This is free software (FOSS), so you're
> welcome to collaborate and improve. I have hosted it in Codeberg, but
> I plan to upload to CRAN so you could eventually directly install it
> in R (and maybe as part of a larger collection of functions for
> OpenCASA data).
> Best regards,
> Felipe
>
> You can get help by writing ?OpenCASA2tables. Usually, you just need
> to provide the path to your OpenCASA folders (they can contain results
> and video files, no problem) and a couple of parameters for your
> particular sample.
> I hope this is useful for you. This is free software (FOSS), so you're
> welcome to collaborate and improve. I have hosted it in Codeberg, but
> I plan to upload to CRAN so you could eventually directly install it
> in R (and maybe as part of a larger collection of functions for
> OpenCASA data).
> Best regards,
> Felipe
>
> --
> You received this message because you are subscribed to the Google
> Groups "OpenCASA Mailing List" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to opencasa_mailing...@googlegroups.com.
> To view this discussion, visit
> https://groups.google.com/d/msgid/opencasa_mailinglist/CABe25bZwjKc5TKYNZiLWcWk4Z1mGAc%3DBkyn9zaTgdR5mBQHHUw%40mail.gmail.com
> [2].
>
>
> Links:
> ------
> [1]
> https://urldefense.com/v3/__https://codeberg.org/fmartinezpastor/OpenCASA2tables/__;!!D9dNQwwGXtA!T25hj6XydgTVJnN2uqyiDRORM40-xCL7EbQCADDMk2KIMl4NxGO5UbjEu0IOdpBFyKV6T8Czaw-BGdEgSrueERcaRXEAm5kR-w$
> You received this message because you are subscribed to the Google
> Groups "OpenCASA Mailing List" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to opencasa_mailing...@googlegroups.com.
> To view this discussion, visit
> https://groups.google.com/d/msgid/opencasa_mailinglist/CABe25bZwjKc5TKYNZiLWcWk4Z1mGAc%3DBkyn9zaTgdR5mBQHHUw%40mail.gmail.com
> [2].
>
>
> Links:
> ------
> [1]
> [2]
> https://urldefense.com/v3/__https://groups.google.com/d/msgid/opencasa_mailinglist/CABe25bZwjKc5TKYNZiLWcWk4Z1mGAc*3DBkyn9zaTgdR5mBQHHUw*40mail.gmail.com?utm_medium=email&utm_source=footer__;JSU!!D9dNQwwGXtA!T25hj6XydgTVJnN2uqyiDRORM40-xCL7EbQCADDMk2KIMl4NxGO5UbjEu0IOdpBFyKV6T8Czaw-BGdEgSrueERcaRXEXCRs0xg$
Felipe Martínez Pastor
Mar 3, 2026, 7:45:42 AM (8 days ago) Mar 3
to OpenCASA Mailing List
Hi,
Just an update. I have added two new functions to the package for some
common modifications to the OpenCASA results (at least in my case) and I
have decided changing the package name accordingly.
This is now just OpenCASA. Therefore, for installation (and updating)
you need to use:
devtools::install_git(url =
"https://codeberg.org/fmartinezpastor/OpenCASA/")
You can remove the package OpenCASA2tables from your installation and
load the new one as library(OpenCASA).
The new functions are OpenCASALighten for obtaining a copy of the
directory tree only with the csv files, without AVI (practical for
archiving, avoiding the boring task of manually replicating the
directory structure and copying the results) and OpenCASAComplete, which
completes the results including observations with no motility (and
therefore no videos).
By the way, since this is a free software-open source project, you can
participate, either directly or forking it (no idea how to do that).
Best wishes,
Felipe
El 16/2/26 a las 11:52, Felipe Martínez Pastor escribió:
--
----------------------------oOo----------------------------
Felipe Martínez Pastor
Research in Biology of Reproduction
Biología Celular
Facultad de CC. Biológicas y Ambientales
Universidad de León
Campus de Vegazana
24071-León
Tfno.: +34 987 291 491
Móvil: +34 687 365 362
e-mail: felipe....@unileon.es
web: http://reprobio.unileon.es
profiles:
https://www.researchgate.net/profile/Felipe_Martinez-Pastor
http://orcid.org/0000-0001-9184-8581
http://www.researcherid.com/rid/B-4277-2008
------------------------------------------------------------
Aviso de confidencialidad https://www.unileon.es/mail-disclaimer/20180525
Confidentiality Notice https://www.unileon.es/mail-disclaimer/20180525
Just an update. I have added two new functions to the package for some
common modifications to the OpenCASA results (at least in my case) and I
have decided changing the package name accordingly.
This is now just OpenCASA. Therefore, for installation (and updating)
you need to use:
devtools::install_git(url =
"https://codeberg.org/fmartinezpastor/OpenCASA/")
You can remove the package OpenCASA2tables from your installation and
load the new one as library(OpenCASA).
The new functions are OpenCASALighten for obtaining a copy of the
directory tree only with the csv files, without AVI (practical for
archiving, avoiding the boring task of manually replicating the
directory structure and copying the results) and OpenCASAComplete, which
completes the results including observations with no motility (and
therefore no videos).
By the way, since this is a free software-open source project, you can
participate, either directly or forking it (no idea how to do that).
Best wishes,
Felipe
El 16/2/26 a las 11:52, Felipe Martínez Pastor escribió:
----------------------------oOo----------------------------
Felipe Martínez Pastor
Research in Biology of Reproduction
Biología Celular
Facultad de CC. Biológicas y Ambientales
Universidad de León
Campus de Vegazana
24071-León
Tfno.: +34 987 291 491
Móvil: +34 687 365 362
e-mail: felipe....@unileon.es
web: http://reprobio.unileon.es
profiles:
https://www.researchgate.net/profile/Felipe_Martinez-Pastor
http://orcid.org/0000-0001-9184-8581
http://www.researcherid.com/rid/B-4277-2008
------------------------------------------------------------
Aviso de confidencialidad https://www.unileon.es/mail-disclaimer/20180525
Confidentiality Notice https://www.unileon.es/mail-disclaimer/20180525
rosperez
Mar 3, 2026, 7:58:59 AM (8 days ago) Mar 3
to Felipe Martínez Pastor, OpenCASA Mailing List
Dear Felipe:
Thank you for your updates and for keeping this communication channel alive and active.
Best regards,
Rosaura
Thank you for your updates and for keeping this communication channel alive and active.
Best regards,
Rosaura
---
El 2026-03-03 13:45, 'Felipe Martínez Pastor' via OpenCASA Mailing List escribió:
Hi,
Just an update. I have added two new functions to the package for some common modifications to the OpenCASA results (at least in my case) and I have decided changing the package name accordingly.
This is now just OpenCASA. Therefore, for installation (and updating) you need to use:
You can remove the package OpenCASA2tables from your installation and load the new one as library(OpenCASA).
The new functions are OpenCASALighten for obtaining a copy of the directory tree only with the csv files, without AVI (practical for archiving, avoiding the boring task of manually replicating the directory structure and copying the results) and OpenCASAComplete, which completes the results including observations with no motility (and therefore no videos).
By the way, since this is a free software-open source project, you can participate, either directly or forking it (no idea how to do that).
Best wishes,
Felipe
El 16/2/26 a las 11:52, Felipe Martínez Pastor escribió:
Dear all,
I just uploaded a R package for collating and curating OpenCASA result
files. The package provides a single function, OpenCASA2Tables(), which
explores a directory tree containing the OpenCASA individual and total
motility files and outputs data files with identified individual data and
summary data.
I hope this is useful for you. Even of you do not routinely used R, you
only have to install it, install the package and run it with the correct
information.
For installation, just install.packages("devtools") in R, then:
devtools::install_git(url = "
and library(OpenCASA2tables) to load.
You can get help by writing ?OpenCASA2tables. Usually, you just need to
provide the path to your OpenCASA folders (they can contain results and
video files, no problem) and a couple of parameters for your particular
sample.
I hope this is useful for you. This is free software (FOSS), so you're
welcome to collaborate and improve. I have hosted it in Codeberg, but I
plan to upload to CRAN so you could eventually directly install it in R
(and maybe as part of a larger collection of functions for OpenCASA data).
Best regards,
Felipe
--
----------------------------oOo----------------------------
Felipe Martínez Pastor
Research in Biology of Reproduction
Biología Celular
Facultad de CC. Biológicas y Ambientales
Universidad de León
Campus de Vegazana
24071-León
Tfno.: +34 987 291 491
Móvil: +34 687 365 362
e-mail: felipe....@unileon.es
web: https://urldefense.com/v3/__http://reprobio.unileon.es__;!!D9dNQwwGXtA!QUIBLHrav1p--TVaQNK8R_bF31kbPDKid6PvToBGDQEw0iQzKDpxHsNQxnvvQzkc7pNM8Aley91YqT1klEBP_r7C4rYZbI1N8g$ profiles:
https://urldefense.com/v3/__https://www.researchgate.net/profile/Felipe_Martinez-Pastor__;!!D9dNQwwGXtA!QUIBLHrav1p--TVaQNK8R_bF31kbPDKid6PvToBGDQEw0iQzKDpxHsNQxnvvQzkc7pNM8Aley91YqT1klEBP_r7C4rZy2IXORA$ https://urldefense.com/v3/__http://orcid.org/0000-0001-9184-8581__;!!D9dNQwwGXtA!QUIBLHrav1p--TVaQNK8R_bF31kbPDKid6PvToBGDQEw0iQzKDpxHsNQxnvvQzkc7pNM8Aley91YqT1klEBP_r7C4rYNvx3FWg$ https://urldefense.com/v3/__http://www.researcherid.com/rid/B-4277-2008__;!!D9dNQwwGXtA!QUIBLHrav1p--TVaQNK8R_bF31kbPDKid6PvToBGDQEw0iQzKDpxHsNQxnvvQzkc7pNM8Aley91YqT1klEBP_r7C4rb25ih6ew$ ------------------------------------------------------------
Aviso de confidencialidad https://urldefense.com/v3/__https://www.unileon.es/mail-disclaimer/20180525__;!!D9dNQwwGXtA!QUIBLHrav1p--TVaQNK8R_bF31kbPDKid6PvToBGDQEw0iQzKDpxHsNQxnvvQzkc7pNM8Aley91YqT1klEBP_r7C4rbPbDxwyw$ Confidentiality Notice https://urldefense.com/v3/__https://www.unileon.es/mail-disclaimer/20180525__;!!D9dNQwwGXtA!QUIBLHrav1p--TVaQNK8R_bF31kbPDKid6PvToBGDQEw0iQzKDpxHsNQxnvvQzkc7pNM8Aley91YqT1klEBP_r7C4rbPbDxwyw$
Erick José Ramo Da Silva
Mar 3, 2026, 8:02:05 AM (8 days ago) Mar 3
to rosperez, Felipe Martínez Pastor, OpenCASA Mailing List
Thank you very much, Felipe!
Your efforts are very much appreciated.
Kind regards,
Erick
Erick J. R. Silva, Ph.D.
Associate Professor
Department of Biophysics and Pharmacology
Institute of Biosciences of Botucatu
Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP)
Rua Prof. Dr. Antonio Celso W. Zanin, S/N
Botucatu-SP, Brasil, 18618-689
Researcher ID: D-2976-2009
Scopus ID: 36176142500
CV Lattes: http://lattes.cnpq.br/4726447529800886
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