Displaying 20 results from an estimated 900 matches similar to: "Help: PLSR"
2020 Oct 23
2
How to shade area between lines in ggplot2
also from this site: https://plotly.com/ggplot2/geom_ribbon/
I get the answer is geom_ribbon but I am still missing something
```
#! plot
p = ggplot(data = trainset, aes(x=x, y=y, color=z)) +
geom_point() + scale_color_manual(values = c("red", "blue"))
# show support vectors
df_sv = trainset[svm_model$index, ]
p = p + geom_point(data = df_sv, aes(x=x, y=y),
2020 Oct 23
0
How to shade area between lines in ggplot2
Hi
Did you try google? I got several answers using your question
e.g.
https://stackoverflow.com/questions/54687321/fill-area-between-lines-using-g
gplot-in-r
Cheers
Petr
> -----Original Message-----
> From: R-help <r-help-bounces at r-project.org> On Behalf Of Luigi Marongiu
> Sent: Friday, October 23, 2020 9:59 AM
> To: r-help <r-help at r-project.org>
> Subject:
2011 Jan 24
5
Train error:: subscript out of bonds
Hi,
I am trying to construct a svmpoly model using the "caret" package (please
see code below). Using the same data, without changing any setting, I am
just changing the seed value. Sometimes it constructs the model
successfully, and sometimes I get an ?Error in indexes[[j]] : subscript out
of bounds?.
For example when I set seed to 357 following code produced result only for 8
2012 Nov 29
1
Help with this error "kernlab class probability calculations failed; returning NAs"
I have never been able to get class probabilities to work and I am relatively new to using these tools, and I am looking for some insight as to what may be wrong.
I am using caret with kernlab/ksvm. I will simplify my problem to a basic data set which produces the same problem. I have read the caret vignettes as well as documentation for ?train. I appreciate any direction you can give. I
2005 May 12
1
pls -- crossval vs plsr(..., CV=TRUE)
Hi,
Newbie question about the pls package.
Setup:
Mac OS 10.3.9
R: Aqua GUI 1.01, v 2.0.1
I want to get R^2 and Q^2 (LOO and Leave-10-Out) values for each
component for my model.
I was running into a few problems so I played with the example a little
and the results do not match up with the comments
in the help pages.
$ library(pls)
$ data(NIR)
$ testing.plsNOCV <- plsr(y ~ X, 6, data =
2013 Jul 06
1
problem with BootCV for coxph in pec after feature selection with glmnet (lasso)
Hi,
I am attempting to evaluate the prediction error of a coxph model that was
built after feature selection with glmnet.
In the preprocessing stage I used na.omit (dataset) to remove NAs.
I reconstructed all my factor variables into binary variables with dummies
(using model.matrix)
I then used glmnet lasso to fit a cox model and select the best performing
features.
Then I fit a coxph model
2020 Oct 23
5
How to shade area between lines in ggplot2
Hello,
I am running SVM and showing the results with ggplot2. The results
include the decision boundaries, which are two dashed lines parallel
to a solid line. I would like to remove the dashed lines and use a
shaded area instead. How can I do that?
Here is the code I wrote..
```
library(e1071)
library(ggplot2)
set.seed(100)
x1 = rnorm(100, mean = 0.2, sd = 0.1)
y1 = rnorm(100, mean = 0.7, sd =
2020 Oct 23
0
How to shade area between lines in ggplot2
Hi
What about something like
p+geom_ribbon(aes(ymin = slope_1*x + intercept_1 - 1/w[2],
ymax = slope_1*x + intercept_1 + 1/w[2], fill = "grey70", alpha=0.1))
Cheers
Petr
> -----Original Message-----
> From: Luigi Marongiu <marongiu.luigi at gmail.com>
> Sent: Friday, October 23, 2020 11:11 AM
> To: PIKAL Petr <petr.pikal at precheza.cz>
> Cc: r-help
2020 Oct 23
2
How to shade area between lines in ggplot2
Thank you, but this split the area into two and distorts the shape of
the plot. (compared to
```
p + geom_abline(slope = slope_1, intercept = intercept_1 - 1/w[2],
linetype = "dashed", col = "royalblue") +
geom_abline(slope = slope_1, intercept = intercept_1 + 1/w[2],
linetype = "dashed", col = "royalblue")
```
Why there
2012 Dec 02
2
How to re-combine values based on an index?
I am able to split my df into two like so:
dataset <- trainset
index <- 1:nrow(dataset)
testindex <- sample(index, trunc(length(index)*30/100))
trainset <- dataset[-testindex,]
testset <- dataset[testindex,-1]
So I have the index information, how could I re-combine the data using that back into a single df?
I tried what I thought might work, but failed with:
2020 Oct 26
0
How to shade area between lines in ggplot2
Hi
Put fill outside aes
p+geom_ribbon(aes(ymin = slope_1*x + intercept_1 - 1/w[2],
ymax = slope_1*x + intercept_1 + 1/w[2]), fill = "blue", alpha=0.1)
The "hole" is because you have two levels of data (red and blue). To get rid
of this you should put new data in ribbon call.
Something like
newdat <- trainset
newdat$z <- factor(0)
p+geom_ribbon(data=newdat, aes(ymin =
2011 May 12
1
Fw: Help with PLSR
Hi
I am attempting to use plsr which is part of the pls package in r. I
amconducting analysis on datasets to identify which proteins/peptides are
responsible for the variance between sample groups (Biomarker Spoting) in a
multivariate fashion.
I have a dataset in R called "FullDataListTrans". as you can see below the
structure of the data is 40 different rows representing a
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 <-
2009 May 07
1
I need your help about plsr
Hi, I need your help, so I send letter to you.
I have a problem about plsr in pls package. I want to show how classfied or
related each ohter samples, so I tried to use plsr and biplot.
But, I failed. Because, I had to change data type of my sample.
Unfortunately, I didn't know how change data type.
I want you to help me about that.
please, help me.
I show you my sample data , my scripts
2007 May 25
2
R-About PLSR
hi R help group,
I have installed PLS package in R and use it for princomp & prcomp
commands for calculating PCA using its example file(USArrests example).
But How I can use PLS for Partial least square, R square, mvrCv one more
think how i can import external file in R. When I use plsr, R2, RMSEP it
show error could not find function plsr, RMSEP etc.
How I can calculate PLS, R2, RMSEP, PCR,
2007 Oct 16
1
data structure for plsr
All,
I am working with NIR spectral data and it was great to find that the example in ?plsr also used spectral data. Unfortunately, I am having difficulty figuring out how the "yarn" dataset is structured to allow for the plsr model to read:
library(pls)
data(yard)
yarn.oscorespls <- mvr(density ~ NIR, 6, data = yarn, validation = "CV", method = "oscorespls")
2005 Sep 26
2
Help: x11 position in the Unix environment
Hello,
In the Unix environment, I open a window by x11(). May I specify the
position of this window by specifying the position of the top left of
the window as in Windows environment? Or some other parameters can be
used to do that?
Thank you,
Shengzhe
2010 Nov 23
5
cross validation using e1071:SVM
Hi everyone
I am trying to do cross validation (10 fold CV) by using e1071:svm method. I
know that there is an option (?cross?) for cross validation but still I
wanted to make a function to Generate cross-validation indices using pls:
cvsegments method.
#####################################################################
Code (at the end) Is working fine but sometime caret:confusionMatrix
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)
2013 Jan 15
1
Random Forest Error for Factor to Character column
Hi,
Can someone please offer me some guidance?
I imported some data. One of the columns called "JOBTITLE" when imported was imported as a factor column with 416 levels.
I subset the data in such a way that only 4 levels have data in "JOBTITLE" and tried running randomForest but it complained about "JOBTITLE" having more than 32 categories. I know that is the limit