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

Mon Mar 9 11:51:43 CET 2020

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
https://thibautjombart.netlify.com
Twitter: @TeebzR

On Mon, 9 Mar 2020 at 10:33, Gema Fernández-Avilés Calderón <
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
>
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> [image: 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 <+34:925268800> | Ext: 5134 <+34:5134> |
> Gema.FAviles at uclm.es
> http://www.uclm.es/profesorado/gemafaviles/ | Mensaje Instantáneo
>
>
>
>
>
>
>
>
>
>               <http://orcid.org/0000-0001-5934-1916>
>
> [image: Resultado de imagen de research gate"]
> <https://www.researchgate.net/profile/Gema_Fernandez-Aviles>   [image:
> Resultado de imagen de google SCHOLAR"]
> <https://scholar.google.es/citations?user=hpRf4eMAAAAJ&hl=es>
>
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> *De:* Thibaut Jombart <thibautjombart at gmail.com>
> *Enviado el:* jueves, 5 de marzo de 2020 19:19
> *Para:* Fernando Hernández <fernando.hernandez33 at outlook.com>
> *CC:* adegenet-forum at lists.r-forge.r-project.org;
> jombart at biomserv.univ-lyon1.fr; Gema Fernández-Avilés Calderón <
> 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
>
> https://thibautjombart.netlify.com
>
> Twitter: @TeebzR
>
>
>
>
>
> On Thu, 5 Mar 2020 at 18:14, Fernando Hernández <
> 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
>
>
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>
>
> Dear friends,
>
> I was wandering If you had revived this email.
>
> Thanks in advance,
>
> Gema
>
>
>
> [image: 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 <+34:925268800> | Ext: 5134 <+34:5134> |
> Gema.FAviles at uclm.es
> http://www.uclm.es/profesorado/gemafaviles/ | Mensaje Instantáneo
>
>
>
>
>
>
>
>
>
>               <http://orcid.org/0000-0001-5934-1916>
>
> [image: Resultado de imagen de research gate"]
> <https://www.researchgate.net/profile/Gema_Fernandez-Aviles>   [image:
> 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;
> 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
>
>
>
>
>
> [image: 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 <+34:925268800> | Ext: 5134 <+34:5134> |
> Gema.FAviles at uclm.es
> http://www.uclm.es/profesorado/gemafaviles/ | Mensaje Instantáneo
>
>    [image: ORCID] <http://orcid.org/0000-0001-5934-1916>   [image: Google
> Scholar] <https://scholar.google.es/citations?user=hpRf4eMAAAAJ&hl=es>
> [image: In] <https://www.linkedin.com/company/uclm>  [image: Twitter]
> <https://twitter.com/#!/uclm_es>  [image: Facebook]
> <https://www.facebook.com/uclm.es>  [image: YouTube]
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