Hello everyone,
I?m currently working with package geomorph in R to generate a PCA plot. Now I
want to add confidence ellipses to my plot. I couldn?t find any command
integrated in package geomorph for doing this.
So I tried package vegan for adding confidence ellipses but the command does not
work with geomorph as my data is a 3D-array (for the PCA) and vegan needs a
2D-array for creating confidence ellipses. Changing the data from 3D to 2D
doesn?t work either as in this case I can?t plot the PCA at all.
Does anyone know a command in geomorph for confidence ellipses or a package
compatible with geomorph for adding confidence ellipses?
Technical details: I am currently working with RStudio Version 0.99.484
My code so far:
library(rgl)
library(ape)
library(geomorph)
morpho<-readland.tps(file,specID="ID") #adding my data#
classifiers<-read.table(file,header=T) #adding the classifiers#
attach(classifiers)
morpho.gpa<-gpagen(morpho, pointscale=1,ShowPlot=T) #doing the Procrustes
Fit#
plotTangentSpace(morpho,axis1=2,axis2=3,label=T,group=classifiers$Stretch)
#plotting the PCA with Stretch as group, there are 4 different levels in group#
Now I want to add confidence ellipses. As I know no command in geomorph, I used
vegan:
library(lattice)
library(permute)
library(vegan)
ordiellipse(morpho,classifiers$Stretch,kind="sd",conf=0.95)
This gives me the following error message:
Error in ordiellipse(morpho, classifiers$Stretch, kind = "sd", conf =
0.95) :
ordiellipse needs two dimensions
My data for the PCA is a 3D-array:
dim(morpho) #asking if data is 3D or 2D, as my command returns 3 values, the
data is in the form of a 3D-array#
[1] 16 2 88
Changing my data into a 2D-array does not solve the problem, because then I am
unable to plot the PCA at all:
morpho2D<-two.d.array(morpho.gpa$coords)
plotTangentSpace(morpho2D,axis1=2,axis2=3,label=T,group=classifiers$Stretch)
Error in plotTangentSpace(morpho2D, axis1 = 2, axis2 = 3, label = T, group =
classifiers$Stretch) :
Data matrix not a 3D array (see 'arrayspecs').
I am grateful for any help on this topic!
Kind regards,
Tatze
This is what my data looks like:
morpho[,,1] #I have 16 landmarks per fish, in total 87 fish; each of the 16
landmarks is given as coordinates#
[,1] [,2]
[1,] 3.632444 4.795980
[2,] 4.767132 4.726264
[3,] 5.428232 4.735880
[4,] 8.721712 3.935348
[5,] 9.810724 3.899288
[6,] 9.844380 2.704500
[7,] 8.361112 2.716520
[8,] 5.750368 2.646804
[9,] 3.240592 2.488140
[10,] 3.440124 3.074716
[11,] 3.663696 4.344028
[12,] 2.995384 4.358452
[13,] 1.382300 4.211808
[14,] 0.613020 3.673312
[15,] 1.447208 3.137220
[16,] 2.055420 2.853548
head(classifiers)
ID Nr TotalLength Weight Sex Stretch riverbank centroid
1 0 L010 11.5 15.0 1 Kel Kel_l 12.180512
2 1 L094 8.0 7.4 1 Reg Reg_r 8.459462
3 2 L033 9.6 12.6 1 Vils Vils_r 10.262179
Look at scatter3d() in the car package. It has an option to add a confidence
ellipsoid to an interactive 3d plot.
-------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of taze4 at
web.de
Sent: Tuesday, December 22, 2015 1:58 AM
To: R Help
Subject: [R] geomorph: adding confidence ellipses
Hello everyone,
I?m currently working with package geomorph in R to generate a PCA plot. Now I
want to add confidence ellipses to my plot. I couldn?t find any command
integrated in package geomorph for doing this.
So I tried package vegan for adding confidence ellipses but the command does not
work with geomorph as my data is a 3D-array (for the PCA) and vegan needs a
2D-array for creating confidence ellipses. Changing the data from 3D to 2D
doesn?t work either as in this case I can?t plot the PCA at all.
Does anyone know a command in geomorph for confidence ellipses or a package
compatible with geomorph for adding confidence ellipses?
Technical details: I am currently working with RStudio Version 0.99.484
My code so far:
library(rgl)
library(ape)
library(geomorph)
morpho<-readland.tps(file,specID="ID") #adding my data#
classifiers<-read.table(file,header=T) #adding the classifiers#
attach(classifiers)
morpho.gpa<-gpagen(morpho, pointscale=1,ShowPlot=T) #doing the Procrustes
Fit#
plotTangentSpace(morpho,axis1=2,axis2=3,label=T,group=classifiers$Stretch)
#plotting the PCA with Stretch as group, there are 4 different levels in group#
Now I want to add confidence ellipses. As I know no command in geomorph, I used
vegan:
library(lattice)
library(permute)
library(vegan)
ordiellipse(morpho,classifiers$Stretch,kind="sd",conf=0.95)
This gives me the following error message:
Error in ordiellipse(morpho, classifiers$Stretch, kind = "sd", conf =
0.95) :
ordiellipse needs two dimensions
My data for the PCA is a 3D-array:
dim(morpho) #asking if data is 3D or 2D, as my command returns 3 values, the
data is in the form of a 3D-array#
[1] 16 2 88
Changing my data into a 2D-array does not solve the problem, because then I am
unable to plot the PCA at all:
morpho2D<-two.d.array(morpho.gpa$coords)
plotTangentSpace(morpho2D,axis1=2,axis2=3,label=T,group=classifiers$Stretch)
Error in plotTangentSpace(morpho2D, axis1 = 2, axis2 = 3, label = T, group =
classifiers$Stretch) :
Data matrix not a 3D array (see 'arrayspecs').
I am grateful for any help on this topic!
Kind regards,
Tatze
This is what my data looks like:
morpho[,,1] #I have 16 landmarks per fish, in total 87 fish; each of the 16
landmarks is given as coordinates#
[,1] [,2]
[1,] 3.632444 4.795980
[2,] 4.767132 4.726264
[3,] 5.428232 4.735880
[4,] 8.721712 3.935348
[5,] 9.810724 3.899288
[6,] 9.844380 2.704500
[7,] 8.361112 2.716520
[8,] 5.750368 2.646804
[9,] 3.240592 2.488140
[10,] 3.440124 3.074716
[11,] 3.663696 4.344028
[12,] 2.995384 4.358452
[13,] 1.382300 4.211808
[14,] 0.613020 3.673312
[15,] 1.447208 3.137220
[16,] 2.055420 2.853548
head(classifiers)
ID Nr TotalLength Weight Sex Stretch riverbank centroid
1 0 L010 11.5 15.0 1 Kel Kel_l 12.180512
2 1 L094 8.0 7.4 1 Reg Reg_r 8.459462
3 2 L033 9.6 12.6 1 Vils Vils_r 10.262179
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Ridge
2015-Dec-22 16:32 UTC
[R] mice error: data<simpleError in cor(xobs[, keep, drop = FALSE], use = "all.obs"): 'x' is empty>
Hi All,
I used mice to impute NA values in a data frame like this:
envdata = complete(mice(envdata,m=1,maxit=1)).
It seems that the mice function can only works well with 1st and 2nd envdata.
When enter the 3rd data, it triggers an error: data<simpleError in cor(xobs[,
keep, drop = FALSE], use = "all.obs"): 'x' is empty>.
iter imp variable
1 1 data data10 data25 data50
iter imp variable
1 1 data data10 data25 data50
iter imp variable
1 1 data<simpleError in cor(xobs[, keep, drop = FALSE], use =
"all.obs"): 'x' is empty>
So what should I do to fix it?
appreciate for any help.
Ridge
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