Hi All,
This may be too long of an explanation, if so I am very sorry!
I am trying to create an ordination that shows one dot for every avian species and a vector for each vegetation character ( I have 32). Basically I want to view which species are most impacted by each veg characteristic as well as view which veg characters are most correlated ( I know I can do this in a simple correlation test but its more about the end product graph)
I believe I need to use an NMDS and the Vegan package to put my species in an ordination space and then later use a permutation test for the veg characters (I have not even gotten to the point of attempting this yet so explanation would be appreciated).
This is the code I have run on my species data
library(vegan)
SpeciesData <- Analyzable_veg_and_Bird_Abundance[2:26]
Species.mds <- metaMDS(SpeciesData, distance = "bray", autotransform = FALSE)
and I am getting this error. Do I need to get rid of the 197 rows in which no birds were counted? I hope not because my other analysis will be presence/absence .
Error in distfun(comm, method = distance, ...) :
missing values are not allowed with argument 'na.rm = FALSE'
I have attached a piece of my data, not all because it goes on for over 1000 rows. Any help at all would be appreciated. I need to know why I'm getting this error and if I am even headed in the right direction to get an ordination from this data. My problem is I am new enough to R that I can not figure out how to include all that my data encompasses in one ordination.
| Point ID |
BEVI |
BEWR |
BGGN |
BHCO |
BLGR |
CACH |
CASP |
CARW |
DICK |
EAME |
FISP |
GRSP |
INBU |
LASP |
MODO |
NOBO |
NOCA |
NOMO |
PABU |
RCSP |
STFL |
TUTI |
WEME |
WEVI |
YBCU |
Max % Grass DF |
Max % Forb DF |
Max % Bare DF |
Max % Litter DF |
Max % Woody DF |
Average % Grass DF |
Average % Forb DF |
Average % Bare DF |
Average % Litter DF |
Average % Woody DF |
Max Height Grass DF |
Max Height Forb DF |
Max Height Litter DF |
Max Height Woody DF |
Avg Height Grass DF |
Avg Height Forb DF |
Avg Height Litter DF |
Avg Height Woody DF |
Avg Concealment Cover |
Max Concealment Cover |
Avg % Bare LI |
Avg % Herb LI |
Avg % Litter LI |
Avg % Shrub LI |
Max % Bare LI |
Max % Herb LI |
Max % Litter LI |
Max % Shrub LI |
% Canopy Cover |
Average Extimated Height |
Max Estimated Height |
Average Shrubs per Hectare |
| 18BR3015 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
63 |
85 |
3 |
63 |
0 |
21 |
50.25 |
0.75 |
27 |
0 |
0.48 |
0.83 |
0.39 |
0 |
0.335 |
0.7475 |
0.18 |
0 |
7 |
9 |
0 |
19.5 |
0 |
0.1 |
0 |
20 |
0 |
1 |
0.16 |
0.625 |
0.75 |
277.7777778 |
| 18BR3019 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
38 |
63 |
15 |
85 |
3 |
11 |
44.75 |
8.25 |
40.75 |
0.75 |
1 |
1 |
0.5 |
0.33 |
0.4725 |
0.775 |
0.2975 |
0.0825 |
8.75 |
11 |
0 |
13.45 |
0.9 |
1.13 |
0 |
14.8 |
1.1 |
7.2 |
0.16 |
0.875 |
1 |
17777.77778 |
| 18BR3043 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
38 |
63 |
85 |
15 |
0 |
14.75 |
29.75 |
27.25 |
12 |
0 |
0.5 |
0.52 |
0.01 |
0 |
0.305 |
0.37 |
0.0025 |
0 |
1.75 |
4 |
0 |
20 |
0 |
0 |
0 |
20 |
0 |
0 |
0.16 |
1.4375 |
2 |
3.844675125 |
| 18BR3051 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
63 |
63 |
38 |
15 |
0 |
29.75 |
56.75 |
20.75 |
5.25 |
0 |
0.36 |
0.61 |
0.16 |
0 |
0.295 |
0.5475 |
0.0575 |
0 |
4.25 |
8 |
1.35 |
16.55 |
0.65 |
0.29 |
1.6 |
17 |
1.3 |
1.5 |
0.16 |
0.6875 |
1 |
625 |
| 18BR3070 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
98 |
3 |
0 |
0 |
0 |
98 |
1.5 |
0 |
0 |
0 |
0.72 |
0.72 |
0 |
0 |
0.5425 |
0.18 |
0 |
0 |
3.25 |
4 |
0 |
20 |
0 |
0 |
0 |
20 |
0 |
0 |
0.16 |
1.75 |
3 |
22.67573696 |
Thank You!
Jennifer