Hi
see inline
Hello,
I've got a small dataset on box turtle shell measurements that I would
like to perform a detrended correspondence analysis on. I thought that
it
would be interesting to examine the morphometrics for each species in
the
area of overlap and in areas where neither species occurs.
I've taken a look at the dune and dune.env datasets in vegan. Using the
str() command gives me
str(dune)
'data.frame': 20 obs. of 30 variables:
$ Belper: num 3 0 2 0 0 0 0 2 0 0 ...
$ Empnig: num 0 0 0 0 0 0 0 0 0 0 ...
$ Junbuf: num 0 3 0 0 0 0 0 0 0 0 ...
$ Junart: num 0 0 0 3 0 0 4 0 0 3 ...
...
However, when I try looking directly at the data frame using the edit
command I see that there is a column called row.names to the left of
Belper.
Likewise, when I use the str() command on dune.env I get
str(dune.env)
'data.frame': 20 obs. of 5 variables:
$ A1: num 3.5 6 4.2 5.7 4.3 2.8 4.2 6.3 4 11.5 ...
$ Moisture : Ord.factor w/ 4 levels 1245: 1 4 2 4 1 1 4 1 2
4 ...
$ Management: Factor w/ 4 levels BF,HF,NM,..: 1 4 4 4 2 4 2 2 3 3
...
$ Use : Ord.factor w/ 3 levels HayfieldHaypastu..: 2 2 2 3
2
2 3 1 1 2 ...
$ Manure: Ord.factor w/ 5 levels 0123..: 3 4 5 4 3 5 4
3 1 1 ...
but using the edit() command shows a column named row.names.
No. This is not a column but it is what it says row.names
str(rosin)
'data.frame': 10 obs. of 5 variables:
$ pytel: int 1 2 3 4 5 6 7 8 9 10
$ rstr : num 1.022 0.981 0.992 1.01 0.976 ...
$ gama : num 1.4 1.44 1.41 1.43 1.39 ...
$ cas : int 0 3 6 9 12 15 18 21 24 27
$ typ : chr anatas anatas anatas anatas
head(rosin)
pytel rstr gama castyp
1 1 1.0216621 1.397885 0 anatas
2 2 0.9809663 1.442439 3 anatas
3 3 0.9916211 1.411767 6 anatas
^^ these are row names
I assume that the the row.names column is used to link the two files
together.
If you are in doubt, recommended way is to consult documentation.
?row.names
All data frames have a row names attribute, a character vector of length
the number of rows with no duplicates nor missing values.
My turtle data is saved as a *.csv, and I've added a column called
row.names, so that it looks like this
row.names,CL,CCL,CW,CCW,CH,CCH
1,104.4,131.8,89.887,137.4,43.391,89.7
2,108.79,135.9,87.78,118.1,50.72,71.2
3,114.12,126.1,89.33,132.8,142.39,78.3
4,102.87,128.2,84.2,125,45.42,72.4
5,84.6,104.8,72.61,111.8,41.1,57.3
I've called this file turtles_dca.csv. I've also created a file called
turtles_dca_env.csv that looks like this
row.names,Species,Sex,Distribution,Concatenated,Species_overlap
1,Terrapene_ornata,Female,overlap,TO_F_Overlap,TO_Overlap
2,Terrapene_ornata,Female,overlap,TO_F_Overlap,TO_Overlap
3,Terrapene_ornata,Female,overlap,TO_F_Overlap,TO_Overlap
4,Terrapene_ornata,Female,overlap,TO_F_Overlap,TO_Overlap
5,Terrapene_ornata,Female,overlap,TO_F_Overlap,TO_Overlap
However, when I read the data into R using this command
turtles.env = read.csv(turtles_dca_env.csv, header = TRUE)
and then using the str() command I get
str(turtles)
'data.frame': 67 obs. of 7 variables:
$ row.names: int 1 2 3 4 5 6 7 8 9 10 ...
$ CL : num 104.4 108.8 114.1 102.9 84.6 ...
$ CCL : num 132 136 126 128 105 ...
$ CW : num 89.9 87.8 89.3 84.2 72.6 ...
$ CCW : num 137 118 133 125 112 ...
$ CH : num 43.4 50.7 142.4 45.4 41.1 ...
$ CCH : num 89.7 71.2 78.3 72.4 57.3 73.4 67 57 68.8 68 ...
When I run decorana() on this dataset, it appears that the column
row.names is included in the analysis, which isn't what I'm looking
for.
Then why you added this column to your data?
If I go ahead and delete the column row.names from my data frames
(i.e.
removing it from turtles and turtles.env), I don't believe that the
analysis is performed correctly. The two species differ significantly in
most of their measurements, but the ordihull() and ordispider() commands
show them overlapping almost completely.
I think that I'm missing something pretty basic about inputting and
formatting this data for this analysis. Can anyone offer a suggestion on
where I'm going astray? I can send a copy of the data if anyone wants to
look at it.
I am not familiar with functions you use. However you probably want to
link those 2 files together. If they both are in the same order you can
just do
turtles.complet - cbind(turtles, turtles.env)
Or if they are in different order you need to find some common column(s)
and
?merge
those two files.
Regards
Petr
Best wishes,
Chris
University of Central Oklahoma
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