Displaying 4 results from an estimated 4 matches for "cca1".
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cca
2017 Jul 19
0
Redundancy canonical analysis plot problem in 3D using VEGAN, RGL, SCATTERPLOT3D and SFSMISC
...quot;, sheetName ="strain", header = T, row.names = 1)
str(strain.data) # lists 9 columns at the end with all NAs
strain.data1 <- (strain.data, sqrt.dist = TRUE) # this is not a valid R line. I get
Error: unexpected ',' in "strain.data1 <- (strain.data,"
strain.cca1 <- cca(log1p(strain.data) ~ Ph + TotalN + Organicmatter + Ca + K + Na + P + Cu + Mn, env.data) # More errors resulting from all the NA values
Error in Math.data.frame(strain.data) :
non-numeric variable in data frame: NA..1NA..2NA..3NA..4NA..5NA..6NA..7NA..8NA..9
You have only 6 observation...
2017 Jul 18
3
Redundancy canonical analysis plot problem in 3D using VEGAN, RGL, SCATTERPLOT3D and SFSMISC
...Inertia Proportion Rank
Total 5 1
Constrained 5 1 5
Unconstrained 0 0 0
Inertia is mean squared contingency coefficient
Some constraints were aliased because they were collinear (redundant)
Eigenvalues for constrained axes:
CCA1 CCA2 CCA3 CCA4 CCA5
1 1 1 1 1
> plot(strain.cca)
> summary (strain.cca)
Call:
cca(formula = strain.data ~ Ph + TotalN + Organicmatter + Ca + K + Na + P + Cu + Mn, data = env.data)
Partitioning of mean squared contingency coefficient:
Inertia Propor...
2009 Feb 08
0
library vegan - cca - versus CANOCO
...mental variables and my community data matrix where,
following bibliography, I have eliminated rare species.
All variables were log-transformed (x+1) befor the analysis was carried out
since they did not fit a normal distribution and to improve linearity.
I performed cca analysis as follows in R:
CCA1<-cca(spp.data~VAR1+VAR2+VAR3+VAR4, data=DATA)
and I used anova(CCA1, perm.max=499) to test the significance by means of
Monte Carlo permutations under full model.
The model was p<0.05 and the result of the plot was "good for my eyes",
however, when I did summary(CCA1), the first t...
2012 Nov 09
1
CCA with Vegan - Plot problem
...ot;Species_2" "Species_3" etc
Sample_1 0 0.12432 0.3456
etc
and is in a .csv file
My environment data (.csv again) looks like this:
Temp Water etc
18 33.3
etc
I can get vegan to run the CCA with no problems but when I enter
>cca1.plot <- plot(cca.1,choices=c(1,2))
I get the following error message:
Error in function (formula, data = NULL, subset = NULL, na.action = na.fail,
:
invalid type (list) for variable 'org'
('org' is the name of my organism file once attached).
I'd appreciate some help....