Dear Ian,
it sounds more like an R data manipulation issue (which admittedly can
be a pain) than a morphometric issue.
Basically you want to convert from a "long" format to a "wide" format.
You can read about this in multiple places on the internet, such as
http://www.cookbook-r.com/Manipulating_data/Converting_data_between_wide_and_long_format/
https://www.statmethods.net/management/reshape.html
I have tried my hand on your data, see code below. I'm sure there are
1000 other ways you can do this, including in a more elegant fashion...
But in general what I did is to create some indexing variables for
specimen and landmark and used them to restructure the data.
I hope this helps,
Carmelo
--
==================
Carmelo Fruciano
Institute of Biology
Ecole Normale Superieure - Paris
CNRS
http://www.fruciano.it/research/
##################
##################
data <- read.table("Trial2rawcoords.txt", header=TRUE)
# Import data
landmarks=30
# Number of landmarks
data$specimen=as.factor(unlist(lapply(seq_len(landmarks), function(x)
rep(seq_len(landmarks)[x],30))))
data$landmark=as.factor(rep(1:30,30))
# Create two factors to index the various x,y coordinates
library(reshape)
data_wide=reshape(data,
idvar = "specimen",
timevar = "landmark",
direction = "wide")
# Use reshape to convert from long to wide format
landmarknames=unlist(lapply(seq_len(landmarks), function(x)
c(paste("x.",x,sep=""),paste("y.",x,sep=""))))
# Create ad hoc names to use for indexing
data_wide=cbind(data_wide$specimen,data_wide$genus.1,data_wide[,landmarknames])
# Get only the useful columns
######################
######################
On 09/08/2018 01:53, Ian F wrote:
I figured out what the issue was. thank you for your help. regrettably I
have encountered another issue, any insight would be much appreciated.
I am trying to reformat a spreadsheet so that each individual is a row
and each column represents an x or y coordinate. my data set consists of
30 specimens each with 30 landmarks. I keep getting the error code
Error in `[<-`(`*tmp*`, j, 1, value = sub.data[1, 1]) :
subscript out of bounds.
My data is in the link and my code is as follows.
# reformat data from imageJ into R compatible format.
data <- read.table(Trial2rawcoords.txt, header=TRUE)
len <- length(data$X)
overall.table <- matrix(nrow=len/30, ncol=(30*2)+1)
overall.length <- len/30
for(j in c(1:overall.length)) {
print(j)
sub.data <- as.matrix(data[ (1+30*(j-1)):((1+30*(j-1))+29), 2:4])
overall.table[j,1] <- sub.data[1, 1]
overall.table[j,2:3] <- sub.data[1, 2:3]
overall.table[j,4:5] <- sub.data[2, 2:3]
overall.table[j,6:7] <- sub.data[3, 2:3]
overall.table[j,8:9] <- sub.data[4, 2:3]
overall.table[j,10:11] <- sub.data[5, 2:3]
overall.table[j,12:13] <- sub.data[6, 2:3]
overall.table[j,14:15] <- sub.data[7, 2:3]
overall.table[j,16:17] <- sub.data[8, 2:3]
overall.table[j,18:19] <- sub.data[9, 2:3]
overall.table[j,20:21] <- sub.data[10, 2:3]
overall.table[j,22:23] <- sub.data[11, 2:3]
overall.table[j,24:25] <- sub.data[12, 2:3]
overall.table[j,26:27] <- sub.data[13, 2:3]
overall.table[j,28:29] <- sub.data[14, 2:3]
overall.table[j,30:31] <- sub.data[15, 2:3]
overall.table[j,32:33] <- sub.data[16, 2:3]
overall.table[j,34:35] <- sub.data[17, 2:3]
overall.table[j,36:37] <- sub.data[18, 2:3]
overall.table[j,38:39] <- sub.data[19, 2:3]
overall.table[j,40:41] <- sub.data[20, 2:3]
overall.table[j,42:43] <- sub.data[21, 2:3]
overall.table[j,44:45] <- sub.data[22, 2:3]
overall.table[j,46:47] <- sub.data[23, 2:3]
overall.table[j,48:49] <- sub.data[24, 2:3]
overall.table[j,50:51] <- sub.data[25, 2:3]
overall.table[j,52:53] <- sub.data[26, 2:3]
overall.table[j,54:55] <- sub.data[27, 2:3]
overall.table[j,56:57] <- sub.data[28, 2:3]
overall.table[j,58:59] <- sub.data[29, 2:3]
overall.table[j,60:61] <- sub.data[30, 2:3]
}
# Confirm the above loop worked.
head(overall.table)
tail(overall.table)
# Assign the new table column names and write out the reformatted table
to the working directory.
colnames(overall.table) <- c("number", "genus", "x1", "y1", "x2", "y2",
"x3", "y3", "x4", "y4", "x5", "y5", "x6", "y6", "x7", "y7", "x8", "y8",
"x9", "y9", "x10", "y10", "x11", "y11", "x12", "y12", "x13", "y13",
"x14", "y14", "x15", "y15", "x16", "y16", "x17",
"y17","x18","Y18","X19","Y19","X20","Y20","X21","Y21","X22","Y22","X23","Y23","X24","Y24","X25","Y25","X26","Y26","X27","Y27","X28","Y28","X29","Y29","X30","Y30")
write.table(overall.table, "reformat.txt")
On Thursday, August 2, 2018 at 1:32:02 PM UTC-4, Ian F wrote:
I am trying to do an analysis of three specimens. I am using
semi-landmarks and having trouble. perhaps someone can point out mt
error? these are my results
Generalized Procrustes Analysis
with Partial Procrustes Superimposition
-4 fixed landmarks
12 semilandmarks (sliders)
2-dimensional landmarks
6 GPA iterations to converge
Minimized Bending Energy used
Consensus (mean) Configuration
X Y
[1,] 0.51447153 -0.03794928
[2,] 0.36957021 0.11431610
[3,] -0.11602250 0.19898458
[4,] -0.40489951 0.11095030
[5,] -0.43738229 -0.09965594
[6,] -0.20913543 -0.09698422
[7,] 0.04257626 -0.09131803
[8,] 0.29799009 -0.04811314
it should be three individuals with 4 landmarks and 4 sliders each.
i want to perform PCA on the procrustes coordinates. my code and
data are below. Im new to R and its probably an easy fix im just
really confused. any help is greatly appreciated.
Code: Y <- arrayspecs(coordsrformat, k=2, p= ncol(coordsrformat)/2)
slidermatrix
Y.gpa <- gpagen(Y,curves=slidermatrix)
summary(Y.gpa)
plot(Y.gpa)
Y.gpa <- gpagen(Y,curves=slidermatrix,ProcD=FALSE )
summary(Y.gpa)
plot(Y.gpa)
a<-(Y.gpa$coords)
plotTangentSpace(a)
slider matrix:
before slide after
5 6 7
7 8 1
1 2 3
3 4 5
1 8 7
7 6 5
5 4 3
3 2 1
1 2 3
3 4 5
5 6 7
7 8 1
coordsrformat:
1630 1827 1530 1549 1198
1345 908 1557 833 1840
1027 1895 1223 1907 1417 1887
2767 1081 2633 1581 2139
2047 1693 1753 1535 1159
1841 1067 2151 1009 2437 1071
2956 928 2936 1692 2112
2360 1300 1784 1304 1016
1700 888 2084 832 2480 872
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