Dear list,
I am trying to predict species volume from bioclimatic data, I have various
sites and I have a data frame with species volume and
the corresponding bioclimatic data for each site.
I read on a discussion forum that you can use ordination to predict species
abundance (in my case volume) from 'new' climate data for sites where you do
not know the abundance.
Unfortunately I cannot work out how to do this in the r package vegan, in
fact I cannot even get a simple CCA to work; I have attached a sample of my
data (volume and bioclimate data for around 100 of my sites) and the code I
used is below.
Does the output look right? why am I getting a 0 output? Is
there something wrong with my data, data format, r code etc?
All help is greatly appreciated,
Thank you in advance,
Kitty
########################################################
#R code
data<-read.table("y:directory\\sample.data",header=T)
names(data)
attach(data)
library(vegan)
# I multiplied up the volume because I thought that the issue may have been
the fact that I had x.x numbers but I still got the same problem
sumvol<-sum_vol*10000
cca2<-cca(sumvol~bioclim6+bioclim9+bioclim11)
cca2
###### output:
Call: cca(formula = sumvol ~ bioclim6 + bioclim9 + bioclim11)
Inertia Rank
Total 0
Inertia is mean squared contingency coefficient
########################################################
sum_vol bioclim6 bioclim9 bioclim11 bioclim12
bioclim13 bioclim15
0.59 207 262 250 3270 395 32
3.19 204 257 247 3333 365 21
1.39 215 270 262 3134 352 19
1.31 213 266 255 2879 339 19
0.85 192 252 244 2192 308 34
6.85 197 257 249 1947 337 55
7.52 189 250 242 2275 351 41
7.15 198 257 250 1997 332 50
10.57 204 263 255 1816 296 53
0.96 201 260 252 1823 297 53
6.44 208 268 258 1801 314 65
1.77 211 271 261 1782 311 64
5.01 201 260 252 1833 294 50
4.17 201 260 251 1851 314 57
1.75 203 262 254 1860 320 58
0.87 202 261 253 1854 305 52
2.42 214 275 263 1632 322 85
1.41 212 276 262 1646 306 80
0.74 210 268 260 1876 295 52
4.58 210 270 260 1788 296 57
3.48 211 270 261 1796 292 53
0.81 214 276 264 1720 323 73
5.58 201 260 244 1974 412 65
0.74 209 264 257 1866 339 65
5.49 214 274 261 1948 326 58
0.32 215 270 263 1839 320 62
2.38 207 268 254 2096 367 59
5.65 209 271 257 2042 378 59
11.41 217 273 264 1863 285 48
7.77 203 263 250 2177 398 59
1.01 217 276 264 2013 323 47
3.87 216 276 263 2164 409 59
8.81 208 269 254 2276 389 53
1.99 208 269 254 2276 389 53
3.12 208 269 254 2276 389 53
2.57 214 275 261 2229 375 54
1.41 212 273 259 2118 370 57
4.81 217 277 263 2242 389 54
3.09 211 274 257 2040 412 63
1.57 207 270 254 2146 401 57
3.96 208 271 255 2126 403 58
1.25 207 269 252 2012 390 60
3.02 203 268 250 1996 412 63
2.14 207 270 254 2146 401 57
0.68 206 264 248 2122 372 56
2.96 204 264 248 2011 377 60
3.82 214 275 260 2231 385 53
18.43 213 275 259 2196 388 54
19.4645 201 263 250 2919 451 56
3.9238 203 265 251 2908 443 56
4.0787 202 262 249 2951 446 57
1.5395 208 266 252 3124 476 60
0.8704 208 267 253 3314 512 61
1.2534 212 266 251 2456 328 45
33.7226 215 267 252 2434 324 44
2.8521 215 267 252 2434 324 44
2.7095 215 267 252 2434 324 44
26.8579 215 267 252 2434 324 44
31.3444 215 267 252 2434 324 44
20.4718 215 267 252 2434 324 44
19.9616 215 267 252 2434 324 44
12.5338 215 267 252 2434 324 44
6.7382 210 262 247 2430 327 47
1.22 210 264 254 2906 338 19
1.71 215 267 256 2897 326 18
11.49 204 256 249 3471 365 15
4.66 205 258 250 3454 346 13
1.25 207 259 251 3459 353 13
1.33 206 258 250 3455 362 14
6.88 206 258 250 3439 370 16
9.69 206 260 250 3432 370 16
1.93 204 257 249 3465 353 13
0.39 207 262 252 3184 349 17
1.2 207 262 252 3036 347 18
1.38 208 262 252 2928 341 19
3.75 209 265 254 2855 335 20
10.71 204 258 249 3154 342 17
1.51 205 255 251 3067 318 18
1.87 205 257 250 3474 374 20
1.51 205 254 252 3010 311 19
1.48 204 256 251 2686 287 23
1.31 204 256 249 3579 361 15
22.5 205 258 250 3499 345 12
0.64 204 257 249 3403 350 14
0.85 202 255 250 2758 321 24
1.56 203 256 251 2800 322 24
0.56 204 254 251 3337 341 17
0.94 203 255 251 2722 306 24
1.88 209 261 257 2920 348 27
0.88 208 260 256 2908 365 30
1.2 215 270 261 2600 325 22
3.4 217 271 262 2610 316 21
1.01 215 270 261 2675 326 21
7.91 215 269 261 2562 320 23
1.55 214 269 259 2637 317 21
2.09 214 267 259 2569 308 21
0.78 213 268 258 2617 314 21
0.61 216 271 264 2592 349 29
2.14 210 264 256 2806 327 21
1.55 213 267 258 2721 324 20
0.5 214 267 260 2640 321 23
0.81 209 263 255 2818 330 21
1.57 215 270 262 2500 323 30
2.41 218 274 266 2144 303 35
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
