GLMM with spatial coordinates

My example matrix was wrong! I attacher another more simple!

Plot    Block    Cod     Lat                            Long                     Elev     Baresoil       Litter       Vneo        Cova     Aren...
1             1       S8360   Gg?mm'ss.s" S     Gg?mm'ss.s" W       8           0                      0         0.20          0.69      0.05...
2             1       C8360   Gg?mm'ss.s" S     Gg?mm'ss.s" W       8           0.35              0.20         0            0.20      0.50...
.               .             .                 .                               .                       .              .                        .           .               .             .
.               .             .                 .                               .                       .              .                        .           .               .             .
.               .             .                 .                               .                        .             .                         .          .               .             .
Thank you all!

Jhonny
Capichoni Massante
Universidade
Federal Fluminense - UFF

From: jcmassante at hotmail.com
To: r-sig-ecology-bounces at r-project.org
CC: r-sig-ecology at r-project.org
Date: Thu, 10 Mar 2016 19:29:08 +0300
Subject: [R-sig-eco] GLMM with spatial coordinates

Dear all,
 
My name is Jhonny and I'm finishing my master with plant ecology.
I need some help with my data because I want to analysis with GLMM and to include spatial coordinates, but I don't know to do it! Someone help me?
I have a data.frame with 200 obs. of 45 variables. This data.frame is in block as example below:
 
 
 
 
 
 
 
 
 
 
 
  Plot
  Bock
  Cod
  Lat
  Long
  Area
  Elev (m)
  Baresoil
 
  Litter
 
  Vneo
  Cova
  Aren
  Mfum...
 
 
  1             
 
  1             
 
  M8400
  Gg?mm'ss.s" s
  Gg?mm'ss.s" w
  2.47275
        8
   0         
 
  0            
 
  0.2         
 
  0.69          
 
  0.05         
 
  0.02         
 
 
 
  2             
 
  1             
 
  C8400
  Gg?mm'ss.s" s
  Gg?mm'ss.s" w
  1
        8
  0.35      
 
  0.2         
 
  0           
 
  0.1           
 
     0.2          
 
  0.05         
 
 
 
  3             
 
  2             
 
  M8340
  Gg?mm'ss.s" s
  Gg?mm'ss.s" w
  2.190386
         9
  0.03      
 
  0.13       
 
  0           
 
      0            
 
   0           
 
  0           
 
 
 
  4             
 
  2             
 
  C8340
  Gg?mm'ss.s" s
  Gg?mm'ss.s" w
  1
         9
  0.7        
 
  0.01       
 
  0           
 
  0            
 
  0           
 
  0.15       
 
 
 
 
  .
.
.

From Vneo (in blue) are my plant species with its cover (from 0.00 to 1.00) and between Lat and Litter are my predictor variables. Before Lat are plot number, block (paired) number and plot code.

I want to know if predictor variables (or its interactions) explain the co-ocurrence of plants at scrub vegetation surrounding by baresoil and to know if is there spatial autocorrelation. The lat and long are position of plots and they make up a gradient of distance from a source of stress (hypersaline coastal lagoon).
 
How can I begin this analisys? 
 
Thank you so much!
Best wishes!!!
 
 Jhonny
Capichoni Massante
Universidade
Federal Fluminense - UFF
 
 
 		 	   		  
 

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Hi Jhonny,

As you can see below, posting in HTML means that your message becomes
impossible to read. Your second example matrix is at least readable,
but not really helpful Using dput() is much better for providing R
data.

It looks like the spaMM package provides spatial GLMM. Have you looked
into that yet? This list really isn't equipped to assist you with
basic statistical questions, but we can help with specific ecological
R questions.

Sarah



On Thu, Mar 10, 2016 at 11:29 AM, Jhonny Capichoni Massante

Dear all,

My name is Jhonny and I'm finishing my master with plant ecology.
I need some help with my data because I want to analysis with GLMM and to include spatial coordinates, but I don't know to do it! Someone help me?
I have a data.frame with 200 obs. of 45 variables. This data.frame is in block as example below:











  Plot
  Bock
  Cod
  Lat
  Long
  Area
  Elev (m)
  Baresoil

  Litter

  Vneo
  Cova
  Aren
  Mfum...


  1

  1

  M8400
  Gg?mm'ss.s" s
  Gg?mm'ss.s" w
  2.47275
        8
   0

  0

  0.2

  0.69

  0.05

  0.02



  2

  1

  C8400
  Gg?mm'ss.s" s
  Gg?mm'ss.s" w
  1
        8
  0.35

  0.2

  0

  0.1

     0.2

  0.05



  3

  2

  M8340
  Gg?mm'ss.s" s
  Gg?mm'ss.s" w
  2.190386
         9
  0.03

  0.13

  0

      0

   0

  0



  4

  2

  C8340
  Gg?mm'ss.s" s
  Gg?mm'ss.s" w
  1
         9
  0.7

  0.01

  0

  0

  0

  0.15




  .
.
.

From Vneo (in blue) are my plant species with its cover (from 0.00 to 1.00) and between Lat and Litter are my predictor variables. Before Lat are plot number, block (paired) number and plot code.

I want to know if predictor variables (or its interactions) explain the co-ocurrence of plants at scrub vegetation surrounding by baresoil and to know if is there spatial autocorrelation. The lat and long are position of plots and they make up a gradient of distance from a source of stress (hypersaline coastal lagoon).

How can I begin this analisys?

Thank you so much!
Best wishes!!!

 Jhonny
Capichoni Massante
Universidade
Federal Fluminense - UFF



        [[alternative HTML version deleted]]

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R-sig-ecology mailing list
R-sig-ecology at r-project.org
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Sarah Goslee
http://www.functionaldiversity.org