[adegenet-forum] Responder: RV: From genotypes to pollution data

Gema Fernández-Avilés Calderón Gema.FAviles at uclm.es
Mon Mar 9 23:59:54 CET 2020 

Hi Thibaut,
Thank you for your mail.

Best,
Gema


[Logotipo UCLM]<http://www.uclm.es/>
Gema Fernández-Avilés Calderón
Profesora Titular de Universidad

Universidad de Castilla-La Mancha
FACULTAD CC. JURÍDICAS Y SOCIALES TO | Cobertizo San Pedro Mártir, SN | 45071 Toledo
Tfno: 925 268 800<tel:+34:925268800> | Ext: 5134<tel:+34:5134> | Gema.FAviles at uclm.es<mailto:Gema.FAviles at uclm.es>
http://www.uclm.es/profesorado/gemafaviles/ | Mensaje Instantáneo<sip:Gema.FAviles at uclm.es>
   [ORCID] <http://orcid.org/0000-0001-5934-1916>    [Google Scholar] <https://scholar.google.es/citations?user=hpRf4eMAAAAJ&hl=es>
[In]<https://www.linkedin.com/company/uclm>  [Twitter] <https://twitter.com/#!/uclm_es>   [Facebook] <https://www.facebook.com/uclm.es>   [YouTube] <https://www.youtube.com/user/UCLMvideos>


De: Thibaut Jombart [mailto:thibautjombart at gmail.com]
Enviado el: lunes, 9 de marzo de 2020 11:52
Para: Gema Fernández-Avilés Calderón <Gema.FAviles at uclm.es>
CC: Fernando Hernández <fernando.hernandez33 at outlook.com>; adegenet-forum at lists.r-forge.r-project.org; jombart at biomserv.univ-lyon1.fr
Asunto: Re: [adegenet-forum] Responder: RV: From genotypes to pollution data

Hi Gema,

sorry, I won't be able to help personally, too many things going on atm. But I suspect you'll find help on the ade4 mailing list, which is much more ecology-focussed:
https://listes.univ-lyon1.fr/sympa/info/adelist

Best
Thibaut
--
Dr Thibaut Jombart
Associate Professor in Outbreak Analytics, London School of Hygiene and Tropical Medicine
Senior Lecturer in Genetic Analysis, Imperial College London
UK Public Health Rapid Support Team
President of RECON: repidemicsconsortium.org<http://repidemicsconsortium.org>
https://thibautjombart.netlify.com
Twitter: @TeebzR


On Mon, 9 Mar 2020 at 10:33, Gema Fernández-Avilés Calderón <Gema.FAviles at uclm.es<mailto:Gema.FAviles at uclm.es>> wrote:
Dear Thibaut,
Thank you for your mail. I have reading about 'multispati', and if I’m not wrong, it does not work with the temporal dimensión. The database “mafragh" contaisn environmental variables in diferent locations but not in a time period.

May I send you and example of my database by email?

Thanks in advance,
Gema





[Logotipo UCLM]<http://www.uclm.es/>
Gema Fernández-Avilés Calderón
Profesora Titular de Universidad

Universidad de Castilla-La Mancha
FACULTAD CC. JURÍDICAS Y SOCIALES TO | Cobertizo San Pedro Mártir, SN | 45071 Toledo
Tfno: 925 268 800<tel:+34:925268800> | Ext: 5134<tel:+34:5134> | Gema.FAviles at uclm.es<mailto:Gema.FAviles at uclm.es>
http://www.uclm.es/profesorado/gemafaviles/ | Mensaje Instantáneo




              [cid:image002.jpg at 01D5F66E.D32ACA50] <http://orcid.org/0000-0001-5934-1916>
[Resultado de imagen de research gate"]<https://www.researchgate.net/profile/Gema_Fernandez-Aviles>   [Resultado de imagen de google SCHOLAR"] <https://scholar.google.es/citations?user=hpRf4eMAAAAJ&hl=es>




De: Thibaut Jombart <thibautjombart at gmail.com<mailto:thibautjombart at gmail.com>>
Enviado el: jueves, 5 de marzo de 2020 19:19
Para: Fernando Hernández <fernando.hernandez33 at outlook.com<mailto:fernando.hernandez33 at outlook.com>>
CC: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>; jombart at biomserv.univ-lyon1.fr<mailto:jombart at biomserv.univ-lyon1.fr>; Gema Fernández-Avilés Calderón <Gema.FAviles at uclm.es<mailto:Gema.FAviles at uclm.es>>
Asunto: Re: [adegenet-forum] Responder: RV: From genotypes to pollution data

Dear Gema,

sorry for the late reply. The analysis you describe does exist. It is called 'multispati', and was originally in ade4, now in adespatial:
https://rdrr.io/cran/adespatial/man/multispati.html

A different problem to LDA / DAPC or variants.

Best
Thibaut

--
Dr Thibaut Jombart
Associate Professor in Outbreak Analytics, London School of Hygiene and Tropical Medicine
Senior Lecturer in Genetic Analysis, Imperial College London
UK Public Health Rapid Support Team
President of RECON: repidemicsconsortium.org<http://repidemicsconsortium.org>
https://thibautjombart.netlify.com
Twitter: @TeebzR


On Thu, 5 Mar 2020 at 18:14, Fernando Hernández <fernando.hernandez33 at outlook.com<mailto:fernando.hernandez33 at outlook.com>> wrote:

Dear Gema,


I recommend you the use of other packages to run principal components or discriminant analyses.


If you are interested in some features of DAPC, a linear discriminant analysis probably is more suitable to you.


Saludos


---- Gema Fernández-Avilés Calderón escribió ----
Dear authors,

I was wandering If you had revived this email.
Thanks in advance,
Gema








Dear friends,
I was wandering If you had revived this email.
Thanks in advance,
Gema

[Logotipo UCLM]<http://www.uclm.es/>
Gema Fernández-Avilés Calderón
Profesora Titular de Universidad

Universidad de Castilla-La Mancha
FACULTAD CC. JURÍDICAS Y SOCIALES TO | Cobertizo San Pedro Mártir, SN | 45071 Toledo
Tfno: 925 268 800<tel:+34:925268800> | Ext: 5134<tel:+34:5134> | Gema.FAviles at uclm.es<mailto:Gema.FAviles at uclm.es>
http://www.uclm.es/profesorado/gemafaviles/ | Mensaje Instantáneo




              [cid:image002.jpg at 01D5F66E.D32ACA50] <http://orcid.org/0000-0001-5934-1916>
[Resultado de imagen de research gate"]<https://www.researchgate.net/profile/Gema_Fernandez-Aviles>   [Resultado de imagen de google SCHOLAR"] <https://scholar.google.es/citations?user=hpRf4eMAAAAJ&hl=es>




De: Gema Fernández-Avilés Calderón
Enviado el: martes, 25 de febrero de 2020 23:16
Para: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>; jombart at biomserv.univ-lyon1.fr<mailto:jombart at biomserv.univ-lyon1.fr>
Asunto: From genotypes to pollution data

Dear all,

I would like to carry out sPCA with pollution data. I mean, I have 10 Monitoring station with x,y coordinates that measure 6 pollutans every day for one year. A matrix (365x6) for 10 monitoring stations.

Can I extrapolate your idea to pollution data?
I don’t know how to run data. I don’t know how to create the object in R.

Do you have some idea? I can sent a dataset similar (I’m constructing actually this dataset)

Best and thanks,
Gema


[Logotipo UCLM]<http://www.uclm.es/>
Gema Fernández-Avilés Calderón
Profesora Titular de Universidad

Universidad de Castilla-La Mancha
FACULTAD CC. JURÍDICAS Y SOCIALES TO | Cobertizo San Pedro Mártir, SN | 45071 Toledo
Tfno: 925 268 800<tel:+34:925268800> | Ext: 5134<tel:+34:5134> | Gema.FAviles at uclm.es<mailto:Gema.FAviles at uclm.es>
http://www.uclm.es/profesorado/gemafaviles/ | Mensaje Instantáneo
   [ORCID] <http://orcid.org/0000-0001-5934-1916>    [Google Scholar] <https://scholar.google.es/citations?user=hpRf4eMAAAAJ&hl=es>
[In]<https://www.linkedin.com/company/uclm>  [Twitter] <https://twitter.com/#!/uclm_es>   [Facebook] <https://www.facebook.com/uclm.es>   [YouTube] <https://www.youtube.com/user/UCLMvideos>


_______________________________________________
adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200309/0fb607ed/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.jpg
Type: image/jpeg
Size: 6003 bytes
Desc: image001.jpg
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200309/0fb607ed/attachment-0007.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.jpg
Type: image/jpeg
Size: 17079 bytes
Desc: image002.jpg
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200309/0fb607ed/attachment-0008.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image003.png
Type: image/png
Size: 354 bytes
Desc: image003.png
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200309/0fb607ed/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image004.jpg
Type: image/jpeg
Size: 798 bytes
Desc: image004.jpg
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200309/0fb607ed/attachment-0009.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image005.jpg
Type: image/jpeg
Size: 789 bytes
Desc: image005.jpg
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200309/0fb607ed/attachment-0010.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image006.jpg
Type: image/jpeg
Size: 784 bytes
Desc: image006.jpg
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200309/0fb607ed/attachment-0011.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image007.png
Type: image/png
Size: 320 bytes
Desc: image007.png
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200309/0fb607ed/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image008.jpg
Type: image/jpeg
Size: 871 bytes
Desc: image008.jpg
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200309/0fb607ed/attachment-0012.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image009.jpg
Type: image/jpeg
Size: 945 bytes
Desc: image009.jpg
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20200309/0fb607ed/attachment-0013.jpg>

More information about the adegenet-forum mailing list