Displaying 20 results from an estimated 600 matches similar to: "data structure for plsr"
2007 Nov 26
1
mvr error in PLS package
All,
I have been using a data set to build pls models for three different soil properties. Two of the three models run fine; however I receive the following error for the final model.
> libs.IC.cal <- mvr(libs.IC.fmla, data = libsdata.cond.cal, ncomp=20,validation = "LOO", method = "oscorespls")
Error in colMeans(x, n, prod(dn), na.rm) :
'x' must
2007 Jul 26
1
princomp error
I am attempting to run principal components analysis on a dataset of
spectral reflectance (6 decimal places). I imported the data using
read.table and there are both column and row headers. When I run
princomp I receive the following error:
Error in cov.wt(z) : 'x' must contain finite values only
Where am I going wrong?
Ross
2007 Sep 13
1
grouping data by a portion of the row name
I am attempting to write a routine where I can run PAM (partition around mediods) on a dataset containing multiple soil cores and PCA spectral data from several depths per core. I want to run PAM on each individual core, so I need to group the data by core to run the analysis. Below is an example of my data structure:
Lab.id PC1 PC2 PC3
MAT057.2.5 2.438454966 -1.011182986 -3.040881377
2008 Dec 10
1
Error: protect () : protection stack overflow
I am attempting to create a formula using as.formula for a PLS analysis. I have used the code below successfully, but in a previous R version and with many fewer predictors. Any help getting all of these predictors into one formula would be greatly appreciated.
TC.fmla <- as.formula(paste("TC ~ ", paste(vars, collapse= "+")))
As I mentioned, this code worked fine in a
2013 Jul 13
1
Alternative to eval(cl, parent.frame()) ?
Dear developeRs,
I maintain a package 'pls', which has a main fit function mvr(), and
functions plsr() and pcr() which are meant to take the same arguments as
mvr() and do exactly the same, but have different default values for the
'method' argument. The three functions are all exported from the name
space.
In the 'pre namespace' era, I took inspiration from lm() and
2011 May 13
1
PLSR error
Hi,
this is my R-Script
library(pls)
file <- "C:\\TXT\\brix.txt"
d <- as.matrix(read.table(file, header=T, sep=",", row.names = NULL))
plsdata <- data.frame(NIR=c(1:nrow(X)))
plsdata$NIR <- I(d[,3:603])
plsdata$Brix <- d[,2]
results <- plsr(Brix ~ NIR, data=plsdata)
after the last string i have this error
> results <- plsr(Brix ~ NIR, data=plsdata)
2011 May 17
1
Help with PLSR with jack knife
Hi
I am analysing a dataset of 40 samples each with 90,000 intensity measures for
various peptides. I am trying to identify the Biomarkers (i.e. most significant
peptides). I beleive that PLS with jack knifing, or alternativeley
CMV(cross-model-validation) are multivariateThe 40 samples belong to four
different groups.
I have managed to conduct the plsr using the commands:
BHPLS1 <-
2007 Jun 04
3
Mandriva Spring 2007 and R
I am new to Linux (not to R) and recently installed Mandriva Spring 2007 on my partitioned hard drive. My next objective is to install R in the Linux environment, unfortunately Mandriva is not one of the Linux distributions available for download... Could someone please let me know which distribution I should use?
Thanks.
Jonathan
---------------------------------
Boardwalk for $500?
2009 Jun 30
1
please help me about data format.
Hi~ helpers.
I was surprised by R data type.
I use to data type like table.
I don't know R allow several data type such as list, number, matrix in the
same matrix.
I want to use plsr in pls package to anlaysis data.
So, I read R help and example of plsr.
that example show me that data as yarn has three colname as NIR, density and
train.
the NIR was 268(No. of col) X 71(No. of row)
2012 Oct 04
1
data structure for plsr
I am having a similar problem understanding the data structure of the
"yarn" dataset described in the "[R] data structure for plsr" posts. I have
spectroscopic data I'd like to run through a PLSR and have read the
tutorial series, but still do not understand the data format required for
the code to process my data. My current data structure consists of a .csv
file read into
2010 Mar 12
2
Data frame question
Hi,
I have the following question about creating data frames. I want to
create a data frame with 2 components: a vector and a matrix.
Let me use a simple example:
y <- rnorm(10)
x <- matrix(rnorm(150), nrow=10)
Now if I do
dd <- data.frame(x=x, y=y)
I get a data frame with 16 colums, but if, according to the documentation,
I do
dd <- data.frame(x=I(x), y=y)
then str(dd)
2011 May 18
1
Help with Memory Problems (cannot allocate vector of size)
While doing pls I found the following problem
> BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = 10, data = PLSdata, jackknife =
>FALSE, validation = "LOO")
when not enabling jackknife the command works fine, but when trying to enable
jackknife i get the following error.
>BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = 10, data = PLSdata, jackknife =
>TRUE,
2013 Mar 02
2
caret pls model statistics
Greetings,
I have been exploring the use of the caret package to conduct some plsda
modeling. Previously, I have come across methods that result in a R2 and
Q2 for the model. Using the 'iris' data set, I wanted to see if I could
accomplish this with the caret package. I use the following code:
library(caret)
data(iris)
#needed to convert to numeric in order to do regression
#I
2007 Jul 06
1
about R, RMSEP, R2, PCR
Hi,
I want to calculate PLS package in R. Now I want to calculate R, MSEP,
RMSEP and R2 of PLSR and PCR using this.
I also add this in library of R. How I can calculate R, MSEP, RMSEP and R2
of PLSR and PCR in R.
I s any other method then please also suggest me. Simply I want to
calculate these value.
Thanking you.
--
Nitish Kumar Mishra
Junior Research Fellow
BIC, IMTECH, Chandigarh, India
2010 Jul 08
4
Column header strategy
Hopefully simple question: What is the best way to name, and treat factor
columns for data that has lots of columns?
This is my column list:
id pID50 D.1 D.2 D.3 D.4 D.5 , etc. all the way to D.185
I was under the impression from several R examples in pls that if you name
your columns like above, you should be able to simply call all the D factors
with "D", instead of going in and
2007 Feb 27
1
compiling issues with Mandriva Linux 2007 Discovery
All,
I am a new user to Linux but I am familiar with R. I have previously
used and installed R on a Windows platform without problems. I recently
set up a dual boot system (XP_64, Mandriva) to run R on a Linux platform
in order to more efficiently handle large datasets. I have not done
compiling before, but read the R instructions and followed to my best
ability. I downloaded the most recent
2009 May 08
1
What package I use to draw 3D plot after plsda?
Hi.
I was used to draw 2D plot to show distribution of my samples. It was very
powerful in small samples.
Recently , I handle a lot of type of samples as more 15.
so, I want to use more dimention.
I was used that I conduct plsda function and draw biplot, such as,
p1=plsda(mw, sp)
biplot(p1)
How can I draw 3D graph with my data??
I don't know exactly numerical value each spot.
please,
2012 Oct 07
3
what exactly is the dim of data set yarn in package "pls"?
Hi list,
I am looking at the data yarn in package, I don't understand what is
dimension of this data set.
I did the following:
> library(pls)
> data(yarn)
> dim(yarn)
[1] 28 3
> head(yarn)
NIR.1 NIR.2 NIR.3 NIR.4 NIR.5 NIR.6 NIR.7 NIR.8 NIR.9
NIR.10 NIR.11
1 3.06630 3.08610 3.10790 3.09720 2.99790 2.82730 2.62330 2.40390 2.19310
2.00580 1.83790
2
2008 Oct 20
1
Calculate SPE in PLS package
Dear list,
I want to calculate SPE (squared prediction error) in x-space, can
someone help?
Here are my codes:
fit.pls<-
plsr(Y~X,data=DAT,ncomp=3,scale=T,method='oscorespls',validation="CV",x=
T)
actual<-fit.pls$model$X
pred<-fit.pls$scores %*% t(fit.pls$loadings)
SPE.x<-rowSums((actual-pred)^2)
Am I missing something here?
Thanks in advance.
Stella Sim
2007 Mar 01
1
repost-configure error on Mandriva 2007
All,
Apparently the attachment did not make it through the list serve.
I am having difficulty installing R-2.4.1 on Mandriva Linux 2007
Discovery. Thanks to the help of Doug Bates I got further along the
path (Thanks Doug!!). I now cannot figure out which line of code needs
modified in order for configure to complete. Please see below for the
last several lines of output.
checking whether