Hi,
I want to solve the following optimisation problem:
[image: \hat{\beta} = \arg \min_{\beta \geq 0} \| y-A\beta \|_2^2 + \lambda
\|\beta\|_1]
For that, I am using glmnet package (cv.glmnet for finding đ and
lower.limits = 0 to impose non-negativity).
I would like to modify the fdev parameter
Thank you,
both train and test are originated from the same data object.
attached the missing code:
data<-read.csv("old4.csv", header=TRUE)
library(imputeMissings)
data<-impute(data,object = NULL ,method = "median/mode")
for (i in col[13:68]) {
data[i]<-lapply(data[i], factor)
}
for (i in col
On 11/15/19 10:49 AM, Amir Hadanny wrote:
Hi all,
i'm trying to get the prediction probabilities for a survival elastic net.
When i use try to predict using the train model on the test set, it creates
an object with the number rows of the train data (6400 rows) instead of the
test data (2400 ro
Hi all,
i'm trying to get the prediction probabilities for a survival elastic net.
When i use try to predict using the train model on the test set, it creates
an object with the number rows of the train data (6400 rows) instead of the
test data (2400 rows). I really don't understand why, and that d
> On Dec 9, 2016, at 2:45 PM, Hu Xinghai wrote:
>
> I come across the following error training Logistic Regression model using
> cv.glmnet:
>
>> Error in drop(y %*% rep(1, nc)) : error in evaluating the argument 'x' in
>> selecting a method for function 'drop': Error in y %*% rep(1, nc) :
>> no
I come across the following error training Logistic Regression model using
cv.glmnet:
> Error in drop(y %*% rep(1, nc)) : error in evaluating the argument 'x' in
> selecting a method for function 'drop': Error in y %*% rep(1, nc) :
> non-conformable arguments
> error in evaluating the argument 'x'
You seem to be mainly asking for help with statistical methodology,
which is generally off topic for this list, which is about help with R
programming. I suggest you study the references given in the
vignette/package and/or post to a statistical list like
stats.stackexchange.com instead.
Cheers,
B
> Is there a way to extract MSE for a lambda, e.g. lambda.1se?
nevermind this specific question. it's now obvious. However my overall
question stands.
On Fri, Sep 16, 2016 at 10:10 AM, Dominik Schneider <
dominik.schnei...@colorado.edu> wrote:
> I'm doing some linear modeling and am new to the ri
I'm doing some linear modeling and am new to the ridge/lasso/elasticnet
procedures. In my case I have N>>p (p=15 based on variables used in past
literature and some physical reasoning) so my understanding is that I
should be interested in ridge regression to avoid the issue of
multicollinearity of
Hi all,
I'm trying to use glmnet with penalty factors in a multigaussian response
model.
In case of the gaussian response the input for penalty factors is a vector,
but I haven't figured out how can I use penalty factors with a
multigaussian response, and even if it's possible. I've tried to use a
Thanks for your reply Mehmet. I've found that the problem was that I
didn't scale the lambda value. My original example did not follow the
instruction not to give a single lambda value, but that in itself
wasn't the problem. Example shown below.
library(glmnet)
library(MASS)
set.seed(1)
n <- 20
This is interesting, can you post your lm.ridge solution as well? I
suspect in glmnet, you need to use model.matrix with intercept, that
could be the reason.
-m
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/m
Dear R-help,
I'm having trouble understanding how glmnet converts its coefficient
estimates back to the original scale. Here's an example with ridge
regression:
library(glmnet)
set.seed(1)
n <- 20 # sample size
d <- data.
Dear all,
I have a question that hopefully is an R question and does not simply arise
from my lack of understanding of the LASSO.
The code below generates two different sets of relationships between y and X,
one in which both variables matter (coefficients .5 each, line 14) and one in
which on
Hello all,
In glmnet package, cv.glmnet is giving error
>data(iris)
>df<-data.frame(iris$Sepal.Length, iris$Sepal.Width, iris$Petal.Length,
iris$Petal.Width)
>x<- as.matrix(df)
>y<- as.numeric(iris$Species)
>fit = glmnet(x, y, family = "multinomial", type.multinomial = "grouped")
>plot(fit, xvar =
I just started to use the Glmnet function for doing analysis of multinomial
data. See the attached code for the analysis of the Fisher iris data as an
example. My question is. When I want to determine the coefficients for the best
lambda value, it returns more than one set of coefficents.. Which
It means that 10/10 = 1 < 3.
It also means that what you're trying to do (fitting 10 cases to 12000
variables) is ridiculous (assuming I understand your message
correctly).
Cheers,
Bert
On Tue, Nov 12, 2013 at 1:07 PM, Kripa R wrote:
> Hi I'm getting the following warning msg after ?cv.glmnet
Hi I'm getting the following warning msg after ?cv.glmnet and I'm wondering
what it means...
dim(x) 10 12000;
dim(y) 10; #two groups case=1 and control=0
cv.glmnet(x, y)
Warning message:
Option grouped=FALSE enforced in cv.glmnet, since < 3 observations per fold
Thanks,
.kripa
Greetings,
I have recently been exploring the 'glmnet' package and subsequently
cv.glmnet. The basic code as follows:
model <- cv.glmnet(variables, group, family="multinomial", alpha=.5,
standardize=F)
I understand that cv.glmnet does k-fold cross-validation to return a value
of lambda. Howeve
On Aug 9, 2013, at 12:52 PM, kevin.shaney wrote:
> Thanks! I tried doing the type.multinomial="grouped" argument - but it
> didn't work for me. Maybe I did something wrong. I thought I understood why
> it didn't work because of sparse.model.matrix recoding variables (like below
> to V12 & V
Thanks! I tried doing the type.multinomial="grouped" argument - but it didn't
work for me. Maybe I did something wrong. I thought I understood why it
didn't work because of sparse.model.matrix recoding variables (like below to
V12 & V13} makes GLMNET unable to tell that they actually came fro
On Aug 9, 2013, at 6:44 AM, Kevin Shaney wrote:
>
> Hello -
>
> I have been using GLMNET of the following form to predict multinomial
> logistic / class dependent variables:
>
> mglmnet=glmnet(xxb,yb ,alpha=ty,dfmax=dfm,
> family="multinomial",standardize=FALSE)
>
> I am using both continuou
Hi,
On Fri, Aug 9, 2013 at 6:44 AM, Kevin Shaney wrote:
>
> Hello -
>
> I have been using GLMNET of the following form to predict multinomial
> logistic / class dependent variables:
>
> mglmnet=glmnet(xxb,yb ,alpha=ty,dfmax=dfm,
> family="multinomial",standardize=FALSE)
>
> I am using both conti
Hello -
I have been using GLMNET of the following form to predict multinomial logistic
/ class dependent variables:
mglmnet=glmnet(xxb,yb ,alpha=ty,dfmax=dfm,
family="multinomial",standardize=FALSE)
I am using both continuous and categorical variables as predictors, and am
using sparse.model.
On Jul 17, 2013, at 5:26 PM, Axel Urbiz wrote:
Dear List,
I'm running simulations using the glmnet package. I need to use an
'automated' method for model selection at each iteration of the
simulation.
The cv.glmnet function in the same package is handy for that purpose.
However, in my simul
Dear List,
I'm running simulations using the glmnet package. I need to use an
'automated' method for model selection at each iteration of the simulation.
The cv.glmnet function in the same package is handy for that purpose.
However, in my simulation I have p >> N, and in some cases the selected
mo
Hi List,
I have a little confused when to glmnet() vs cv.glmnet().
I know that,
glmnet(): gives the fit
cv.glment(): does the cv after the fit
I just want to get the beta coefficients after the fit, that's it!
But of all the glmnet examples I've seen, the beta coefficient is
obtained ONLY AFTER
Hello -
I am using glmnet to generate a model for multiple cohorts i. For each i, I
run 5 separate models, each with a different x variable. I want to compare
the fit statistic for each i and x combination.
When I use auc, the output is in some cases is < .5 (.49). In addition, if
I compare mean
Dear R users
I used glmnet generating a regression model, now I need to convert it to pmml
format, but I noticed pmml r package doesn't support glmnet object, has anyone
find a way solving this problem? I was thinking convert glmnet object to glm
object, has anyone tried it?
Many thanks
Yan
Dear R users
I generated a model using glmnet, I need to convert it to pmml, but R pmml
package doesn't support glmnet, has anyone come across similar problem? any
idea to solve it?
Many thanks
YAn
--
View this message in context:
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I'm using glmnet for logistic regression, I got a fairly sparse dataset,
20,000 samples(very imbalanced too, 5% from one group), 1500 variables,.
the code have beed running for 2 hours, still waiting for result, I am doing
lasso here(alpha=1), my computer is core 2 due CPU @3Ghz, 4GB ram, why it's
I'm running into an unexpected error using the glmnet and Matrix packages.
I have a matrix that is 8 million rows by 100 columns with 75% of the
entries being zero. When I run a vanilla glmnet logistic model on my server
with 300 GB of RAM, the task completes in 20 minutes:
> x # 8 million x 100
Hi Juliet,
First of all, cv.glmnet is used to estimate lambda based on
cross-validation. To get a glmnet prediction, you should use glmnet
function which uses all data in the training set. Second, you
constructed testX using a different data set (data.test.std) from one
for glmnet predict (data.te
Oops. Coefficients are returned on the scale of the original data.
testX <- cbind(1,data.test)
yhat2 <- testX %*% beta
# works
plot(yhat2,yhat_enet)
On Wed, Mar 21, 2012 at 2:35 PM, Juliet Hannah wrote:
> All,
>
> For my understanding, I wanted to see if I can get glmnet predictions
> using
All,
For my understanding, I wanted to see if I can get glmnet predictions
using both the predict function and also by multiplying coefficients
by the variable matrix. This is not worked out. Could anyone suggest
where I am going wrong?
I understand that I may not have the mean/intercept correct,
On 03/21/2012 06:30 AM, Vito Muggeo (UniPa) wrote:
It appears that glmnet(), when "selecting" the covariates entering the
model, skips from K covariates, say, to K+2 or K+3. Thus 2 or 3
variables are "added" at the same time and it is not possible to obtain
a ranking of the covariates according t
dear all,
It appears that glmnet(), when "selecting" the covariates entering the
model, skips from K covariates, say, to K+2 or K+3. Thus 2 or 3
variables are "added" at the same time and it is not possible to obtain
a ranking of the covariates according to their importance in the model.
On t
On 11-10-25 01:35 PM, julien giami wrote:
> The reason i use glmnet is that it makes the handling of 400,000
> observations easier to handle in terms of memory,
>
> I am looking on sparse matrices but i dont understand how to build
> interacting using sparse matrices
>
If you're not familiar w
The reason i use glmnet is that it makes the handling of 400,000
observations easier to handle in terms of memory,
I am looking on sparse matrices but i dont understand how to build
interacting using sparse matrices
On Tue, Oct 25, 2011 at 12:34 PM, Marc Schwartz wrote:
>
> On Oct 25, 2011, at
On Oct 25, 2011, at 11:16 AM, Ben Bolker wrote:
> Bert Gunter gene.com> writes:
>
>>
>> If I understand you correctly, it sounds like you need to do some reading.
>>
>> ?lm and ?formula tell you how to specify linear models for glm or glmnet.
>> However, if you do not have sufficient statisti
Bert Gunter gene.com> writes:
>
> If I understand you correctly, it sounds like you need to do some reading.
>
> ?lm and ?formula tell you how to specify linear models for glm or glmnet.
> However, if you do not have sufficient statistical background, It probably
> will be incomprehensible, in
If I understand you correctly, it sounds like you need to do some reading.
?lm and ?formula tell you how to specify linear models for glm or glmnet.
However, if you do not have sufficient statistical background, It probably
will be incomprehensible, in which case you should consult your local
stat
We are workin on building a logistic regression using
1. We are doing a logistic regression with binary outcome variable
using a set of predictors that include 8 continuous and 8 category
predictors
2. We are trying to implement interaction between two variables
(continuous and category or just c
Hi Bert,
You are correct. I checked the data and did find some empty values in the X
matrix.
Thanks for your kindly help!
Noah
--
View this message in context:
http://r.789695.n4.nabble.com/glmnet-for-Binary-trait-analysis-tp3828547p3830581.html
Sent from the R help mailing list archive at Na
... another possibiity, probably more likely since you read your files in
from disk, is that there is a stray character of some sort (e.g. extra
comma, quotation mark, period) in your data that is causing what should be
numeric data to be read in as character. Check your data after you've read
them
The man page tells you that y must be a factor. Is it?
-- Bert
On Tue, Sep 20, 2011 at 5:25 PM, Noah wrote:
> Hello,
>
> I got an error message saying
>
> Error in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
> NA/NaN/Inf in foreign function call (arg 5)
>
> when I try to an
Hello,
I got an error message saying
Error in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
NA/NaN/Inf in foreign function call (arg 5)
when I try to analysis a binary trait using glmnet(R) by running the
following code
library(glmnet)
Xori <- read.table("c:\\SNP.txt", s
n
To: r-help@r-project.org
Sent: Tuesday, August 23, 2011 10:45 AM
Subject: [R] Glmnet lambda value choice
Hi,
When using the glmnet() function of the package glmnet, A series of
coefficients is returned for a list of descending lambda values.
I am unable to locate anything in the documentation
Hi,
When using the glmnet() function of the package glmnet, A series of
coefficients is returned for a list of descending lambda values.
I am unable to locate anything in the documentation that explains HOW this
choice of lambda series is made. (There is documentation about how to choose
my o
On 08/10/2011 03:00 AM, Nick Sabbe wrote:
Finally, to avoid downward bias, you could run a normal glm with only the
variables selected in the previous step.
At the cost, of course, of introducing upward bias
--
Patrick Breheny
Assistant Professor
Department of Biostatistics
Department of S
ilto:r-help-bounces@r-
> project.org] On Behalf Of Andra Isan
> Sent: woensdag 10 augustus 2011 5:59
> To: r-help@r-project.org
> Subject: [R] glmnet
>
> Hi All,
> I have been trying to use glmnet package to do LASSO linear regression.
> my x data is a matrix n_row by n_col and y
Hi All,Â
I have been trying to use glmnet package to do LASSO linear regression. my x
data is a matrix n_row by n_col and y is a vector of size n_row corresponding
to the vector data. The number of n_col is much more larger than the number of
n_row. I do the following:
fits = glmnet(x, y, family
Hi All,
I am looking for some help figuring out what is causing an error in my
attempt to fit a regularized logistic regression (specifically finding the
optimal lambda value using cv.glmnet).
Running the following command:
RegLR_CV<-cv.glmnet(x=train.sub.clean[,-c(431)],y=as.factor(train.sub$fi
On 07/23/2011 11:43 AM, fongchun wrote:
I was also thinking of a bootstrapping approach where I would actually run
cv.glmnet say 100 times and then take the mean/median lambda across all the
cv.glmnet runs. This way I generate a confidence interval for my optimal
lambda I woud use in the end.
10 fold cv has high variation compared to other methods. Use repeated cv or the
bootstrap instead (both of which can be used with glmnet by way of the train()
function on the caret package).
Max
On Jul 23, 2011, at 11:43 AM, fongchun wrote:
> Hi Patrick,
>
> Thanks for the reply. I am ref
Hi Patrick,
Thanks for the reply. I am referring to using the cv.glmnet() function with
10-fold cross validation and letting glmnet determine the lambda sequence.
The optimal lambda that it is returning fluctuates between different runs of
cv.glmnet. Sometimes the model that is return deviates
On 07/22/2011 07:51 PM, fongchun wrote:
I am using the glmnet R package to run LASSO with binary logistic
regression.
...
What I am finding is that this optimal lambda value fluctuates
everytime I run glmnet with LASSO.
> ...
Does anyone know why there is such a fluctuation in the
generation o
Hi all,
I am using the glmnet R package to run LASSO with binary logistic
regression. I have over 290 samples with outcome data (0 for alive, 1 for
dead) and over 230 predictor variables. I currently using LASSO to reduce
the number of predictor variables.
I am using the cv.glmnet function to d
Hi all,Â
I have two questions about variables in glmnet:
Â
1. We are doing a logistic regression with binary outcome variable using a
set of predictors that include continuous and binary predictors(coded 0 and
1). Â If the latter are centered and standardized, they will be transformed
into negative
oject.org
Subject: [R] glmnet package: penalty.factor option
Anyone have experience specifying the "penalty.factor" option in the
"glmnet" command?
I have 3 variables (out of a million genotype variables) that I want to
force into the model (i.e., set penalty factor to 0), but I ca
Anyone have experience specifying the "penalty.factor" option in the
"glmnet" command?
I have 3 variables (out of a million genotype variables) that I want to
force into the model (i.e., set penalty factor to 0), but I can't figure out
how to do that.
[[alternative HTML version deleted]]
Am 13.04.2011 16:58, schrieb Janina Hemmersbach:
Hello,
I´m trying to in install the package 'glmnet' but I get always the error massage "package âMatrixâ is
not available". I search on you site, but I coundn´t find the package there either. Is their still a
package called "Matrix"? Or how can
Janina Hemmersbach scai.fraunhofer.de> writes:
>
> Hello,
> I´m trying to in install the package 'glmnet'
> but I get always the error massage "package âMatrixâ is
> not available". I search on you site, but I coundn´t
> find the package there either. Is their still a
> package called "Matrix"?
Hello,
I´m trying to in install the package 'glmnet' but I get always the error
massage "package âMatrixâ is not available". I search on you site, but I
coundn´t find the package there either. Is their still a package called
"Matrix"? Or how can I use "glmnet"?
Thank You in advance.
Kind regard
ent.be
wink: A1.056, Coupure Links 653, 9000 Gent
ring: 09/264.59.36
-- Do Not Disapprove
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of sambit rath
Sent: donderdag 3 februari 2011 10:58
To: r-help@r-project.org
Subject: [
Hi Everybody!
I must start with a declaration that I am a sparse user of R. I am
creating a credit scorecard using a dataset which has a variable
depicting actual credit history (good/bad) and 41 other variables of
yes/no type. The procedure I am asked to follow is to use a penalized
logistic proc
Hi Brian,
On Wed, Jul 7, 2010 at 10:54 PM, Brian Tsai wrote:
> Hi,
>
> I am trying to use the glmnet package to do some simple feature selection.
> Â However, Â I would ideally like to be able to specify the number of features
> to return (the glmnet package, as far as I can tell, only allows
> spe
Hi,
I am trying to use the glmnet package to do some simple feature selection.
However, I would ideally like to be able to specify the number of features
to return (the glmnet package, as far as I can tell, only allows
specification of a regularization parameter, lambda, that in turn returns a
m
I think I have figured out the problem. The response variable has one level
with only one observation -- hence when that one observation was in the test
set the training data did not contain any observations from that level and
so did not fit a logistic model for that level causing the somewhat cr
Could you give us the traceback? (In case you don't know, just type
traceback() right after you got the error message.) I can't reproduce the
error, so it gets a bit difficult to solve without having the real data.
Cheers
Joris
On Wed, Jun 2, 2010 at 6:51 PM, Dave_F wrote:
>
> Hello fellow R us
Hello fellow R users,
I have been getting a strange error message when using the cv.glmnet
function in the glmnet package. I am attempting to fit a multinomial
regression using the lasso. covars is a matrix with 80 rows and roughly 4000
columns, all the covariates are binary. resp is an eight lev
Dear all,
I want to train my model with LASSO using caret package
(glmnet). So, in glmnet, there are two parameters, alpha and lambda. How can
I fix my alpha=1 to get a lasso model?
con<-trainControl(method="cv",number=10)
model <- train(X, y, "glmnet", metric="RMSE",tuneLength =
Dear Hao,
It works for me. Here is my sessionInfo():
> sessionInfo()
R version 2.8.0 Patched (2008-11-08 r46864)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
Could any one help ? I start to learn the glmnet package. I tried with
the example in the manual.
x=matrix(rnorm(100*20),100,20)
y=rnorm(100)
fit1=glmnet(x,y)
When I tried to fit the model, I received the error message:
Error in validObject(.Object) :
invalid class "dgCMatrix" object: row in
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