[R] simulation\bootstrap of list factors
Dear R experts,
I am trying to simulate a list containing data matrices. Unfortunately, I don't
manage to get it to work.
A small example:
n=5
nbootstrap=2
subsets-list()
for (i in 1:n){
subsets[[i]] - rnorm(5, mean=80, sd=1)
for (j in 1:nbootstrap){
test-list()
test[[j]]-subsets[[i]]
}
}
How can I get test to be 2 simulation rounds with each 5 matrices.
Kind regards, Tobias
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[R] reverse sweep operator
Dear R-users, For obtaining a weighted correlation matrix with (some) missing data I use the sweep operator (swp function in the ggm-package) to find the maximum likelihood estimates of the standardized slopes and error variances. In the end I would like to use a reverse sweep operator but unfortunately I cannot find in google nor R-forums how to do this last step. Does anyone know how the function for a reverse sweep is named? Kind regards, Tobias __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] changing y-axis intervals in a boxplot
Dear R-users, I'm a bit of a rooky in R and do not know how to change the y-axis intervals of a boxplot. The y-axis in my boxplot ranges from 0 to 100 which is fine. The problem is the interval level in between. Now it increases with steps of 20 but I'd like to have it changed by steps of 5. Anyone knows how to do this in R? I used the following code for producing this boxplot: boxplot((fitted(finalfit4) *100) ~ instabilitydata2$MRI_Diag_Instab_rev, ylim=c(0,100), xlab=MRA diagnosis, ylab=Predicted probability (%)) Kind regards, Tobias [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] changing y-axis intervals in a boxplot
Thank you Pascal but unfortunelately i still didn't figure out how to change
the numbers presented at the y-axis.
I looked up your suggestions but if I'm right, yaxt can set if the axis is
presented (yaxt=s) or suppressed (yaxt=n) which does not help for changing
the values on the y-axis.
The 'at' argument did solve my problem but in a clumsy way. Although I'm happy
that I managed, does anyone know how to do the same job in a more convenient
way?
This is the 'clumsy' code I used:
boxplot((fitted(finalfit4) *100) ~ instabilitydata2$MRI_Diag_Instab_rev,
ylim=c(0,100), xlab=MRA diagnosis, ylab=Predicted probability (%))
axis(side=2, at=10)
axis(side=2, at=30)
axis(side=2, at=50)
axis(side=2, at=70)
axis(side=2, at=90)
Kind regards,
Tobias
-Oorspronkelijk bericht-
Van: Pascal Oettli [mailto:kri...@ymail.com]
Verzonden: vrijdag 29 maart 2013 8:44
Aan: Berg, Tobias van den
CC: 'r-help@r-project.org'
Onderwerp: Re: [R] changing y-axis intervals in a boxplot
Hello,
?par (particularly the 'yaxt' argument)
?axis ('side' and 'at' arguments)
Hope this help,
Pascal
On 29/03/13 16:37, Berg, Tobias van den wrote:
Dear R-users,
I'm a bit of a rooky in R and do not know how to change the y-axis intervals
of a boxplot.
The y-axis in my boxplot ranges from 0 to 100 which is fine. The problem is
the interval level in between. Now it increases with steps of 20 but I'd like
to have it changed by steps of 5.
Anyone knows how to do this in R?
I used the following code for producing this boxplot:
boxplot((fitted(finalfit4) *100) ~ instabilitydata2$MRI_Diag_Instab_rev,
ylim=c(0,100), xlab=MRA diagnosis, ylab=Predicted probability (%))
Kind regards, Tobias
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] changing y-axis intervals in a boxplot
Thank you all,
Guess you'll learn everyday new stuff, especially in R.
Tobias
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens
Pascal Oettli
Verzonden: vrijdag 29 maart 2013 12:33
CC: 'r-help@r-project.org'
Onderwerp: Re: [R] changing y-axis intervals in a boxplot
Every week, I learn something new with R-help.
Pascal
On 29/03/13 20:23, Jim Lemon wrote:
And if you would like to be able to read the crowded axis:
boxplot(count ~ spray, data = InsectSprays, col = lightgray, yaxt='n')
library(plotrix)
staxlab(2, at=seq(0,25,1),cex=0.8)
Jim
On 03/29/2013 08:36 PM, Pascal Oettli wrote:
Hi,
Example adapted from ?boxplot
par(las=1, mfrow=c(2,1))
boxplot(count ~ spray, data = InsectSprays, col = lightgray, yaxt='n')
axis(2, at=seq(0,25,2.5))
boxplot(count ~ spray, data = InsectSprays, col = lightgray, yaxt='n')
axis(2, at=seq(0,25,1))
HTH,
Pascal
On 29/03/13 18:22, Berg, Tobias van den wrote:
Thank you Pascal but unfortunelately i still didn't figure out how to
change the numbers presented at the y-axis.
I looked up your suggestions but if I'm right, yaxt can set if the
axis is presented (yaxt=s) or suppressed (yaxt=n) which does not
help for changing the values on the y-axis.
The 'at' argument did solve my problem but in a clumsy way. Although
I'm happy that I managed, does anyone know how to do the same job in a
more convenient way?
This is the 'clumsy' code I used:
boxplot((fitted(finalfit4) *100) ~
instabilitydata2$MRI_Diag_Instab_rev, ylim=c(0,100), xlab=MRA
diagnosis, ylab=Predicted probability (%))
axis(side=2, at=10)
axis(side=2, at=30)
axis(side=2, at=50)
axis(side=2, at=70)
axis(side=2, at=90)
Kind regards,
Tobias
-Oorspronkelijk bericht-
Van: Pascal Oettli [mailto:kri...@ymail.com]
Verzonden: vrijdag 29 maart 2013 8:44
Aan: Berg, Tobias van den
CC: 'r-help@r-project.org'
Onderwerp: Re: [R] changing y-axis intervals in a boxplot
Hello,
?par (particularly the 'yaxt' argument)
?axis ('side' and 'at' arguments)
Hope this help,
Pascal
On 29/03/13 16:37, Berg, Tobias van den wrote:
Dear R-users,
I'm a bit of a rooky in R and do not know how to change the y-axis
intervals of a boxplot.
The y-axis in my boxplot ranges from 0 to 100 which is fine. The
problem is the interval level in between. Now it increases with steps
of 20 but I'd like to have it changed by steps of 5.
Anyone knows how to do this in R?
I used the following code for producing this boxplot:
boxplot((fitted(finalfit4) *100) ~
instabilitydata2$MRI_Diag_Instab_rev, ylim=c(0,100), xlab=MRA
diagnosis, ylab=Predicted probability (%))
Kind regards, Tobias
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] error: in catg (xi, name=nam, label=lab): LO2 has 2 category levels
Dear all,
As David mentioned, I used his R-code to try to see the dimension behind the
'LO2' variable. These are the results:
lapply (subsets, function (x) {table(x$LO2)})
[[1]]
nee geen atrofie ja atrofie aanweizg
173 0
[[2]]
nee geen atrofie ja atrofie aanweizg
169 3
[[3]]
nee geen atrofie ja atrofie aanweizg
174 0
[[4]]
nee geen atrofie ja atrofie aanweizg
172 2
[[5]]
nee geen atrofie ja atrofie aanweizg
173 2
[[6]]
nee geen atrofie ja atrofie aanweizg
171 3
[[7]]
nee geen atrofie ja atrofie aanweizg
167 5
[[8]]
nee geen atrofie ja atrofie aanweizg
174 1
[[9]]
nee geen atrofie ja atrofie aanweizg
173 1
[[10]]
nee geen atrofie ja atrofie aanweizg
175 0
I guess that the lrm model doesn't work - as I tried to model each subset
separately, and it didn't work in subsets 1, 3 and 10 - because there are no
persons in one of the two categories. Therefore this LO2 variable seems unable
to be a predictor - let alone a strong predictor. Regardless of this, it seems
strange that with a lot of simulations in which there is always a change that a
specific variable by chance alone will consist of objects with only one
category gives problems with estimating the prediction models. Does anyone have
a suggestion how to deal with that?
Kind regards and thanks for all the help so far,
Tobias
Van: David Winsemius [dwinsem...@comcast.net]
Verzonden: vrijdag 7 september 2012 18:17
Aan: Berg, Tobias van den
CC: PIKAL Petr; r-help
Onderwerp: Re: [R] error: in catg (xi, name=nam, label=lab): LO2 has 2
category levels
On Sep 7, 2012, at 8:03 AM, Berg, Tobias van den wrote:
Dear all,
Probably I made a beginners mistake. While importing a spss file I didn't
specify that missings should be NA (use.missings = TRUE). Thanks to Petr
Pikal and Bert Gunter I now know how to check how many values are known
within a variable.
Although I can fit my logistic model on this dataset, unfortunately, I
experience the same problem after bootstrapping the original dataset at hand.
The R-code so far:
bootstraps-10
subsets-list()
for (i in 1:bootstraps){
subsets[[i]]-as.matrix(sample(1:length(dat$PatID), replace=TRUE))
}
subsets-lapply (subsets, function (x) {subsets - dat[x,]})
fit.subsets -lapply (subsets, function (x) {lrm(MRI_Diag_RC ~ factor(O4_1r)
+ N6_1r + leeftijd + LO1 + LO2, model=T, x=T, y=T, data=x)})
Everything is fine till I run the last line. The following result shows in R:
Error in catg(xi, name = nam, label = lab) : LO2 has 2 category levels
I checked the simulated datasets how many values within LO2 are known, using:
lapply (subsets, function (x) {str(x$LO2)})
Instead do :
apply (subsets, function (x) {table(x$LO2)})
You cannot tell what distribution of values you are getting with str(). Just
because a factor has 2 levels does NOT mean it has two unique values populating
those levels.
--
David.
The result:
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 NA 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 NA 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
[[1]]
NULL
[[2]]
NULL
[[3]]
NULL
[[4]]
NULL
[[5]]
NULL
[[6]]
NULL
[[7]]
NULL
[[8]]
NULL
[[9]]
NULL
[[10]]
NULL
It would be great to receive ideas, comments or questions about my challenge.
Kind regards, Tobias
-Oorspronkelijk bericht-
Van: PIKAL Petr [mailto:petr.pi...@precheza.cz]
Verzonden: vrijdag 7 september 2012 16:22
Aan: Berg, Tobias van den
CC: r-help
Onderwerp: RE: [R] error: in catg (xi, name=nam, label=lab): LO2 has 2
category levels
Hi
It is good to cc to list. Somebody could have better insight.
Dear Petr,
Thank you for responding. It seems right what you say. The funny thing
however is that the 'LO2' variable in SPSS has 2 answer categories. If
I look at the same variable in R, again I see 2 different values.
How do you know? Any command? You shall provide at least
str(LO2)
result as we do not have access to your PC.
I used your sapply code and guess that I retrieved (per variable) the
amount of answer
Re: [R] error: in catg (xi, name=nam, label=lab): LO2 has 2 category levels
Dear all,
Probably I made a beginners mistake. While importing a spss file I didn't
specify that missings should be NA (use.missings = TRUE). Thanks to Petr Pikal
and Bert Gunter I now know how to check how many values are known within a
variable.
Although I can fit my logistic model on this dataset, unfortunately, I
experience the same problem after bootstrapping the original dataset at hand.
The R-code so far:
bootstraps-10
subsets-list()
for (i in 1:bootstraps){
subsets[[i]]-as.matrix(sample(1:length(dat$PatID), replace=TRUE))
}
subsets-lapply (subsets, function (x) {subsets - dat[x,]})
fit.subsets -lapply (subsets, function (x) {lrm(MRI_Diag_RC ~ factor(O4_1r) +
N6_1r + leeftijd + LO1 + LO2, model=T, x=T, y=T, data=x)})
Everything is fine till I run the last line. The following result shows in R:
Error in catg(xi, name = nam, label = lab) : LO2 has 2 category levels
I checked the simulated datasets how many values within LO2 are known, using:
lapply (subsets, function (x) {str(x$LO2)})
The result:
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 NA 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 NA 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
Factor w/ 2 levels nee geen atrofie,..: 1 1 1 1 1 1 1 1 1 1 ...
[[1]]
NULL
[[2]]
NULL
[[3]]
NULL
[[4]]
NULL
[[5]]
NULL
[[6]]
NULL
[[7]]
NULL
[[8]]
NULL
[[9]]
NULL
[[10]]
NULL
It would be great to receive ideas, comments or questions about my challenge.
Kind regards, Tobias
-Oorspronkelijk bericht-
Van: PIKAL Petr [mailto:petr.pi...@precheza.cz]
Verzonden: vrijdag 7 september 2012 16:22
Aan: Berg, Tobias van den
CC: r-help
Onderwerp: RE: [R] error: in catg (xi, name=nam, label=lab): LO2 has 2
category levels
Hi
It is good to cc to list. Somebody could have better insight.
Dear Petr,
Thank you for responding. It seems right what you say. The funny thing
however is that the 'LO2' variable in SPSS has 2 answer categories. If
I look at the same variable in R, again I see 2 different values.
How do you know? Any command? You shall provide at least
str(LO2)
result as we do not have access to your PC.
I used your sapply code and guess that I retrieved (per variable) the
amount of answer categories/possible values. LO2 scores a 3 in the
accompanying results. Do you know how I can change that?
Hm. Result of this depends on what is LO2. If it is numeric, you have 3 unique
values. If it is factor you can have either 3 levels or 2 levels and NA
values(again str result would be helpful and we need not just guess how your
data look like). Well let me guess
levels(dat$LO2) says you have 3 levels 2 meaningful and one comes out probably
as empty string .
It shall be the first level so
levels(dat$LO2)[1] - NA
shall drop this unused and created levels. Or maybe you can get rid of this
unwanted levels by setting na.string to empty string during import, however my
knowledge of SPSS limitedly approaching zero so I could be completely wrong.
If your values are factors, you can change the code to
sapply(sapply(ff, levels), length)
and you will get 0 for numeric variables and number of levels for factor
variables. More complete insight in your data can be also found by
summary(dat)
Regards
Petr
Kind regards, Tobias
-Oorspronkelijk bericht-
Van: PIKAL Petr [mailto:petr.pi...@precheza.cz]
Verzonden: vrijdag 7 september 2012 15:02
Aan: Berg, Tobias van den; r-help@r-project.org
Onderwerp: RE: [R] error: in catg (xi, name=nam, label=lab): LO2 has
2 category levels
Hi
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Tvandenberg
Sent: Friday, September 07, 2012 1:05 PM
To: r-help@r-project.org
Subject: [R] error: in catg (xi, name=nam, label=lab): LO2 has 2
category levels
Dear R-users,
During a fit procedure in a Logistic prediction model I encounter
the
following problem:
error: in catg (xi, name=nam, label=lab: X has 2 category levels
I do not know lrm but the error seems to be explaining itself, some
variable has only one level and shall have 2
sapply(sapply(dat, unique), length)
shall give you for used variables value 2 or more.
Regards
Petr
The following code is used:
fit -lrm(MRI_Diag_RC ~ factor(O4_1r) + N6_1r + leeftijd + LO1 + LO2
+
LO3+
LO4+ LO5+ LO6+ LO7+ LO8+ LO9+ LO10+ LO11+ LO12+ LO13 + LO14+ LO15+
LO16+
LO17+ LO18+ LO19+ LO20+ LO21+ LO22+ LO23+ LO24 + LO26+ LO27 + LO29,
LO17+ LO18+ LO19+ LO20+ LO21
