Manuel:
I changed your variable names from x to 'long' and y to 'lat' on the 
riqueza_out.csv file.
The code below should do what you want. Also, since the legend title is kind of 
long, I broke it
down into three lines so you can see more plot area. I am cc'ing the other 
groups so more people
use it if needed.

library(rgdal)
library(ggplot2)
library(sp)
library(maptools)
gpclibPermit()
manuel <- readOGR(dsn=".", layer="AI_BIOTICA_010411_CRTM05")
names(manuel);dim(manuel)
  slotNames(manuel) # look at the slot names
# add the 'id' variable to the shapefile and use it to merge both files
  manuel@data$id = rownames(manuel@data)
# convert shapefile to dataframe
  manuel.df <- as.data.frame(manuel)
# fortify to plot with ggplot2
  manuel_fort <- fortify(manuel,region="id")
  head(manuel_fort)
# Merge shapefile and the as.dataframe shapefile
  manuel_merged <- join(manuel_fort,manuel.df, by ="id")
  head(manuel_merged)
# Read in the csv file
manuel_points <- read.csv("riqueza_out.csv")
  head(manuel_points);dim(manuel_points)
# fortify this one too for the points or else an error will ocurr
 manuel_points <- fortify(manuel_points)
 manuel_points
 
# Plot the shapefile and overlayed the points over it
p <- ggplot(manuel_merged, aes(long,lat,group=group)) +
  geom_polygon(aes(data=manuel_merged,fill=Area_Influ)) +
  geom_path(color="white") + theme_bw() # remove this if you don't want black 
and white background
  p + geom_point(data=manuel_points,aes(size=ACE,colour=ACE,group=NULL)) +
  scale_size(name = "Número\nde\nespecies", breaks = c(2, 4, 6, 8, 10, 12, 14, 
16, 18, 20)) +
 scale_colour_gradientn(name = 'Número\nde\nespecies',
 colours = rainbow(6), breaks = c(2, 4, 6, 8, 10, 12, 14, 16, 18, 20))+ 
 xlab("Longitud") + ylab("Latitud") + opts(axis.text.x = theme_text(size = 8, 
vjust = 1)) + 

 opts(axis.text.y = theme_text(size = 8, hjust = 1)) 
  
  
 Felipe D. Carrillo
Supervisory Fishery Biologist
Department of the Interior
US Fish & Wildlife Service
California, USA
http://www.fws.gov/redbluff/rbdd_jsmp.aspx



>
>From: Manuel Spínola <mspinola10@gmail.com>
>To: Felipe Carrillo <mazatlanmexico@yahoo.com>
>Sent: Sat, April 2, 2011 11:22:24 PM
>Subject: Re: another question on shapefiles and geom_point in ggplot2
>
>No problem, thank you very much Felipe.
>
>Best,
>
>Manuel
>
>On 03/04/2011 12:19 a.m., Felipe Carrillo wrote: 
>I meant to send you this one..Let me clean up the code a little bit and 
>>I will send it to you,,,do you mind if I send it to you in the morning?
>> 
>>Felipe D. Carrillo
>>Supervisory Fishery Biologist
>>Department of the Interior
>>US Fish & Wildlife Service
>>California, USA
>>http://www.fws.gov/redbluff/rbdd_jsmp.aspx
>>
>>
>>
>>
>>>
>>>From: Manuel Spínola <mspinola10@gmail.com>
>>>To: Felipe Carrillo <mazatlanmexico@yahoo.com>
>>>Sent: Sat, April 2, 2011 11:15:28 PM
>>>Subject: Re: another question on shapefiles and geom_point in ggplot2
>>>
>>>Yes Felipe.  That is the graph I was looking for.
>>>
>>>I got something closer but no like yours.  How did you do it?
>>>
>>>Manuel
>>>
>>>On 03/04/2011 12:10 a.m., Felipe Carrillo wrote: 
>>>I was able to open them,,I am attaching a picture of the graph I created..It's 
>>>that what
>>>>you had in mind?
>>>> 
>>>>Felipe D. Carrillo
>>>>Supervisory Fishery Biologist
>>>>Department of the Interior
>>>>US Fish & Wildlife Service
>>>>California, USA
>>>>http://www.fws.gov/redbluff/rbdd_jsmp.aspx
>>>>
>>>>
>>>>
>>>>
>>>>>
>>>>>From: Manuel Spínola <mspinola10@gmail.com>
>>>>>To: Felipe Carrillo <mazatlanmexico@yahoo.com>
>>>>>Sent: Sat, April 2, 2011 10:35:51 PM
>>>>>Subject: Re: another question on shapefiles and geom_point in ggplot2
>>>>>
>>>>>It should be.  I am sending them again.
>>>>>
>>>>>Manuel
>>>>>
>>>>>On 02/04/2011 10:23 p.m., Felipe Carrillo wrote: 
>>>>>Manuel:
>>>>>>I can't open the shapefile, is this the original one?
>>>>>>Is the csv file the one that you are trying to overlay on top of the 
>>>>shapefile?
>>>>>> 
>>>>>>Felipe D. Carrillo
>>>>>>Supervisory Fishery Biologist
>>>>>>Department of the Interior
>>>>>>US Fish & Wildlife Service
>>>>>>California, USA
>>>>>>http://www.fws.gov/redbluff/rbdd_jsmp.aspx
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>
>>>>>>>From: Manuel Spínola <mspinola10@gmail.com>
>>>>>>>To: Felipe Carrillo <mazatlanmexico@yahoo.com>
>>>>>>>Sent: Sat, April 2, 2011 6:14:09 PM
>>>>>>>Subject: Re: another question on shapefiles and geom_point in ggplot2
>>>>>>>
>>>>>>>Files attached.
>>>>>>>
>>>>>>>
>>>>>>>On 02/04/2011 07:04 p.m., Felipe Carrillo wrote: 
>>>>>>>If you want individual points overlayed on the shapefile, you need to add 
>>>>>>>another variable to it before you fortify it.
>>>>>>>>After you fortify merge both the fortified dataset and the original shapefile. 
>>>>>>>>Go ahead and post your shapefile to see if
>>>>>>>>I can figure it out. Do you just want the points or want text also?
>>>>>>>> 
>>>>>>>>Felipe D. Carrillo
>>>>>>>>Supervisory Fishery Biologist
>>>>>>>>Department of the Interior
>>>>>>>>US Fish & Wildlife Service
>>>>>>>>California, USA
>>>>>>>>http://www.fws.gov/redbluff/rbdd_jsmp.aspx
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>>From: Manuel Spínola <mspinola10@gmail.com>
>>>>>>>>>To: Felipe Carrillo <mazatlanmexico@yahoo.com>
>>>>>>>>>Sent: Sat, April 2, 2011 5:24:02 PM
>>>>>>>>>Subject: Re: another question on shapefiles and geom_point in ggplot2
>>>>>>>>>
>>>>>>>>>Hi Felipe,
>>>>>>>>>
>>>>>>>>>I did the same thing that I am trying know, attached is how it looks.
>>>>>>>>>
>>>>>>>>>Best,
>>>>>>>>>
>>>>>>>>>Manuel
>>>>>>>>>
>>>>>>>>>On 02/04/2011 06:09 p.m., Felipe Carrillo wrote: 
>>>>>>>>>Manuel:
>>>>>>>>>>I did something similar a few weeks ago,,If you post your shapefile and describe 
>>>>>>>>>>what you are
>>>>>>>>>>expecting I might be able to help..
>>>>>>>>>> 
>>>>>>>>>>Felipe D. Carrillo
>>>>>>>>>>Supervisory Fishery Biologist
>>>>>>>>>>Department of the Interior
>>>>>>>>>>US Fish & Wildlife Service
>>>>>>>>>>California, USA
>>>>>>>>>>http://www.fws.gov/redbluff/rbdd_jsmp.aspx
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>From: Manuel Spínola <mspinola10@gmail.com>
>>>>>>>>>>>To: "ggplot2@googlegroups.com" <ggplot2@googlegroups.com>
>>>>>>>>>>>Sent: Sat, April 2, 2011 12:01:56 PM
>>>>>>>>>>>Subject: another question on shapefiles and geom_point in ggplot2
>>>>>>>>>>>
>>>>>>>>>>>Dear list members,
>>>>>>>>>>>
>>>>>>>>>>>This is a different question from my previous post.
>>>>>>>>>>>I handle to read my shapefile with ggplot2 following 
>>>>>>>>>>>https://github.com/hadley/ggplot2/wiki/plotting-polygon-shapefiles
>>>>>>>>>>>
>>>>>>>>>>>p = ggplot(ai_biotica.df, aes(long,lat,group=group,fill=Area_Influ)) + 
>
>>>>>>>>>>>  geom_polygon() +
>>>>>>>>>>>  geom_path(color="white") +
>>>>>>>>>>>  coord_equal()
>>>>>>>>>>>
>>>>>>>>>>>I got a nice map.
>>>>>>>>>>>
>>>>>>>>>>>Now I want to plot some point with geom_point but I got an error.
>>>>>>>>>>>
>>>>>>>>>>>> p + geom_point(geo, aes(size = ACE, colour = ACE)) + scale_size(name = "Número 
>>>>>>>>>>>>de especies", breaks = c(2, 4, 6, 8, 10, 12, 14, 16, 18, 20)) + 
>>>>>>>>>>>>scale_colour_gradientn(name = 'Número de especies', colours = rainbow(6), breaks 
>>>>>>>>>>>>= c(2, 4, 6, 8, 10, 12, 14, 16, 18, 20))+ xlab("Longitud") + ylab("Latitud") + 
>>>>>>>>>>>>opts(axis.text.x = theme_text(size = 8, vjust = 1)) + opts(axis.text.y = 
>>>>>>>>>>>>theme_text(size = 8, hjust = 1)) 
>>>>>>>>>>>>
>>>>>>>>>>>Error: ggplot2 doesn't know how to deal with data of class uneval
>>>>>>>>>>>
>>>>>>>>>>>Best,
>>>>>>>>>>>
>>>>>>>>>>>Manuel
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>-- 
>>>>>>>>>>>Manuel Spínola, Ph.D. 
>>>>>>>>>>>Instituto Internacional en Conservación y Manejo de Vida Silvestre 
>>>>>>>>>>>Universidad Nacional 
>>>>>>>>>>>Apartado 1350-3000 
>>>>>>>>>>>Heredia 
>>>>>>>>>>>COSTA RICA 
>>>>>>>>>>>mspinola@una.ac.cr 
>>>>>>>>>>>mspinola10@gmail.com 
>>>>>>>>>>>Teléfono: (506) 2277-3598 
>>>>>>>>>>>Fax: (506) 2237-7036 
>>>>>>>>>>>Personal website: Lobito de río 
>>>>>>>>>>>Institutional website: ICOMVIS -- 
>>>>>>>>>>>You received this message because you are subscribed to the ggplot2 mailing 
>>>>>>>>>>>list.
>>>>>>>>>>>Please provide a reproducible example: http://gist.github.com/270442
>>>>>>>>>>> 
>>>>>>>>>>>To post: email ggplot2@googlegroups.com
>>>>>>>>>>>To unsubscribe: email ggplot2+unsubscribe@googlegroups.com
>>>>>>>>>>>More options: http://groups.google.com/group/ggplot2
>>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>-- 
>>>>>>>>Manuel Spínola, Ph.D. 
>>>>>>>>Instituto Internacional en Conservación y Manejo de Vida Silvestre 
>>>>>>>>Universidad Nacional 
>>>>>>>>Apartado 1350-3000 
>>>>>>>>Heredia 
>>>>>>>>COSTA RICA 
>>>>>>>>mspinola@una.ac.cr 
>>>>>>>>mspinola10@gmail.com 
>>>>>>>>Teléfono: (506) 2277-3598 
>>>>>>>>Fax: (506) 2237-7036 
>>>>>>>>Personal website: Lobito de río 
>>>>>>>>Institutional website: ICOMVIS 
>>>>>>
>>>>>>
>>>>>>-- 
>>>>>>Manuel Spínola, Ph.D. 
>>>>>>Instituto Internacional en Conservación y Manejo de Vida Silvestre 
>>>>>>Universidad Nacional 
>>>>>>Apartado 1350-3000 
>>>>>>Heredia 
>>>>>>COSTA RICA 
>>>>>>mspinola@una.ac.cr 
>>>>>>mspinola10@gmail.com 
>>>>>>Teléfono: (506) 2277-3598 
>>>>>>Fax: (506) 2237-7036 
>>>>>>Personal website: Lobito de río 
>>>>>>Institutional website: ICOMVIS 
>>>>
>>>>
>>>>-- 
>>>>Manuel Spínola, Ph.D. 
>>>>Instituto Internacional en Conservación y Manejo de Vida Silvestre 
>>>>Universidad Nacional 
>>>>Apartado 1350-3000 
>>>>Heredia 
>>>>COSTA RICA 
>>>>mspinola@una.ac.cr 
>>>>mspinola10@gmail.com 
>>>>Teléfono: (506) 2277-3598 
>>>>Fax: (506) 2237-7036 
>>>>Personal website: Lobito de río 
>>>>Institutional website: ICOMVIS 
>>
>>
>>-- 
>>Manuel Spínola, Ph.D. 
>>Instituto Internacional en Conservación y Manejo de Vida Silvestre 
>>Universidad Nacional 
>>Apartado 1350-3000 
>>Heredia 
>>COSTA RICA 
>>mspinola@una.ac.cr 
>>mspinola10@gmail.com 
>>Teléfono: (506) 2277-3598 
>>Fax: (506) 2237-7036 
>>Personal website: Lobito de río 
>>Institutional website: ICOMVIS 


-- 
Manuel Spínola, Ph.D. 
Instituto Internacional en Conservación y Manejo de Vida Silvestre 
Universidad Nacional 
Apartado 1350-3000 
Heredia 
COSTA RICA 
mspinola@una.ac.cr 
mspinola10@gmail.com 
Teléfono: (506) 2277-3598 
Fax: (506) 2237-7036 
Personal website: Lobito de río 
Institutional website: ICOMVIS 
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