[R] Pattern matching and replacement in matrix
Hello, Is there any function like gsub(), that can match and replace patterns in a matrix or a data frame? Cheers! Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Tlf. +34 93 581 1910 Fax: +34 93 581 1573 __ 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] Fitting a function
Hello, It is a very naive question, but here it is. I have this values: x: 0.5 4 6 8 12 y: 0.021 0.021 0.020 0.018 0.012 I need to fit a function to them. How can I do it with R? Thank you so much! Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Tlf. +34 93 581 1910 Fax: +34 93 581 1573 __ 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] Fitting a logistic regression
Thank you very much, Jun. This is what I was looking for. Best! Dani On Wed, 2009-08-19 at 09:52 -0500, Jun Shen wrote: > I would suggest a model with a baseline level, something like > > nls(AMP~E0+(Emax-E0)*Time**gamma/(EC50**gamma+Time**gamma),data=your > data, > start=list(EC50=50,gamma=2,E0=0.2,Emax=1.2))->mod.test > > AIC(mod.test) does improve. Hope this helps. > > Jun > > On Wed, Aug 19, 2009 at 5:04 AM, Dani Valverde > wrote: > Hello, > I have this data: > Time AMP > 0 0.200 >10 0.1958350 >20 0.2914560 >40 0.6763628 >60 0.8494534 >90 0.9874526 > 120 1.0477692 > > where AMP is the concentration of this metabolite with time. > If you plot > the data, you can see that it could be fitted using a logistic > regression. For this purpose, I used this code: > > AMP.nls <- nls(AMP~SSlogis(Time,Asym, xmid, scal), data = > concentrations,model=T) > > When plotting the fitted function, it seems that it fits quite > well at > the end of the time. However, at the beginning it seems that > the fit is > not so good. How can I achieve a better fit? Forgive me if it > is a > stupid question, but I am just starting with non linear > regression. > Thank you, > > Dani > -- > [?] > > __ > 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. > > > > -- > Jun Shen PhD > PK/PD Scientist > BioPharma Services > Millipore Corporation > 15 Research Park Dr. > St Charles, MO 63304 > Direct: 636-720-1589 > -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Tlf. +34 93 581 1910 Fax: +34 93 581 1573 __ 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] Fitting a logistic regression
Hello, I have this data: Time AMP 0 0.200 10 0.1958350 20 0.2914560 40 0.6763628 60 0.8494534 90 0.9874526 120 1.0477692 where AMP is the concentration of this metabolite with time. If you plot the data, you can see that it could be fitted using a logistic regression. For this purpose, I used this code: AMP.nls <- nls(AMP~SSlogis(Time,Asym, xmid, scal), data = concentrations,model=T) When plotting the fitted function, it seems that it fits quite well at the end of the time. However, at the beginning it seems that the fit is not so good. How can I achieve a better fit? Forgive me if it is a stupid question, but I am just starting with non linear regression. Thank you, Dani -- [?] __ 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] Combination
Hello, I have a sequence of numbers: seq(1:50) and I would like to have all the possible combinations with this numbers without repeating any combination: 11, 12, 13, ... ,22,23,24,... How can I do it? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Fitting a model
Sorry, I had no seen your previous e-mail. Just another question. Is there any way to obtain an R2 to have a numeric idea of how good is the fitting? Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 En/na Eik Vettorazzi ha escrit: Actually "drm" as posted before fits a sigmoid curve (a generalized logistic function with 4 parameters, see ?LL.4), so I didn't get the point of your new question. Dani Valverde schrieb: Thank you all for your answers. If you look at the plot resulting from my data, it seems that it is some kind of sigmoid function, not only polynomial. How could I fit it? Best, Dani Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 En/na Eik Vettorazzi ha escrit: you might use the drc-package (equivalently you could use nls with an appropriate "selfstart" model like SSlogis) library(drc) mm<-drm(delta~ph,fct=LL.4()) plot(mm) From your plot I was assuming that "ph" is the independent variable (as modelled above) - so if you want to predict a ph from delta you will need the "inverse" function of your fitted model - you could toy with ED from the drc package or do a simple grid search with "predict". hth. Dani Valverde schrieb: Hello, This is a very basic question, but I don'y know the answer. I have these data delta <- c(28.6-8.825,28.6-8.828,28.6-8.836,28.6-8.845,28.6-8.897,28.6-8.944,28.6-9.027,28.6-9.091,28.6-9.263,28.6-9.4,28.6-9.7,28.6-9.981, 28.6-10.287,28.6-10.48,28.6-10.684,28.6-10.875) ph <- c(4.4,4.6,4.8,5,5.2,5.4,5.6,5.8,6,6.2,6.4,6.6,6.8,7,7.2,7.4) plot(ph,delta,ylab=c(expression(Delta*delta)),xlab="pH") Which kind of model can I fit on these, so that can I predict for a given delta the pH of my sample? Once the model is fitted, how can I plot it on the graph? Best regards, Dani __ 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] Fitting a model
Thank you all for your answers. If you look at the plot resulting from my data, it seems that it is some kind of sigmoid function, not only polynomial. How could I fit it? Best, Dani Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 En/na Eik Vettorazzi ha escrit: you might use the drc-package (equivalently you could use nls with an appropriate "selfstart" model like SSlogis) library(drc) mm<-drm(delta~ph,fct=LL.4()) plot(mm) From your plot I was assuming that "ph" is the independent variable (as modelled above) - so if you want to predict a ph from delta you will need the "inverse" function of your fitted model - you could toy with ED from the drc package or do a simple grid search with "predict". hth. Dani Valverde schrieb: Hello, This is a very basic question, but I don'y know the answer. I have these data delta <- c(28.6-8.825,28.6-8.828,28.6-8.836,28.6-8.845,28.6-8.897,28.6-8.944,28.6-9.027,28.6-9.091,28.6-9.263,28.6-9.4,28.6-9.7,28.6-9.981, 28.6-10.287,28.6-10.48,28.6-10.684,28.6-10.875) ph <- c(4.4,4.6,4.8,5,5.2,5.4,5.6,5.8,6,6.2,6.4,6.6,6.8,7,7.2,7.4) plot(ph,delta,ylab=c(expression(Delta*delta)),xlab="pH") Which kind of model can I fit on these, so that can I predict for a given delta the pH of my sample? Once the model is fitted, how can I plot it on the graph? Best regards, Dani __ 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] Fitting a model
Hello, This is a very basic question, but I don'y know the answer. I have these data delta <- c(28.6-8.825,28.6-8.828,28.6-8.836,28.6-8.845,28.6-8.897,28.6-8.944,28.6-9.027,28.6-9.091,28.6-9.263,28.6-9.4,28.6-9.7,28.6-9.981, 28.6-10.287,28.6-10.48,28.6-10.684,28.6-10.875) ph <- c(4.4,4.6,4.8,5,5.2,5.4,5.6,5.8,6,6.2,6.4,6.6,6.8,7,7.2,7.4) plot(ph,delta,ylab=c(expression(Delta*delta)),xlab="pH") Which kind of model can I fit on these, so that can I predict for a given delta the pH of my sample? Once the model is fitted, how can I plot it on the graph? Best regards, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Problems with playwith()
Hello,
I am trying to execute an example provided in the help files for the
playwith() function. I try to execute the first example:
library(playwith)
if (interactive()) {
options(device.ask.default = FALSE)
## Scatterplot (Lattice graphics).
## Labels are taken from rownames of data.
## Just click on the plot to identify points.
playwith(xyplot(Income ~ log(Population / Area),
data = data.frame(state.x77), groups = state.region,
type = c("p", "smooth"), span = 1, auto.key = TRUE,
ylab = "Income per capita, 1974"))
}
I get many errors regarded with GLib, and finally it says that the
runtime environment asks to close the application in an appropiate way.
Any idea on how to solve thi? I have all packages installed. I use R
2.7.2 and GTK+ 2.12.9. I have all the required packages installed.
Best,
Dani
--
Daniel Valverde Saubí
Grup de Biologia Molecular de Llevats
Facultat de Veterinària de la Universitat Autònoma de Barcelona
Edifici V, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
Centro de Investigación Biomédica en Red
en Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN)
Grup d'Aplicacions Biomèdiques de la RMN
Facultat de Biociències
Universitat Autònoma de Barcelona
Edifici Cs, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
+34 93 5814126
__
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] Text
I've thought about it, but the position should be always the same,
locator() should return me the same value.
Daniel Valverde Saubí
Grup de Biologia Molecular de Llevats
Facultat de Veterinària de la Universitat Autònoma de Barcelona
Edifici V, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
Centro de Investigación Biomédica en Red
en Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN)
Grup d'Aplicacions Biomèdiques de la RMN
Facultat de Biociències
Universitat Autònoma de Barcelona
Edifici Cs, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
+34 93 5814126
En/na Peter Dalgaard ha escrit:
Dani Valverde wrote:
Hello,
I would like to place some text that should appear in the same
position of the graphic device, preferably outside the plotting area,
regardless the x and y axes limits. How can I do this?
I think you can use title() with an adj= argument.
Otherwise, try mtext(), using par("usr") and par("pin") to calculate the
at= argument.
Best,
Dani
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Text
Hello, I would like to place some text that should appear in the same position of the graphic device, preferably outside the plotting area, regardless the x and y axes limits. How can I do this? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Read a file
Hello, I have a text file with this structure: # File created = Thursday, August 28, 2008 3:33:02 PM GMT # Data set = 373 2 1 C:\Bruker\TOPSPIN GABRMN # Spectral Region: # LEFT = 4.5 ppm. RIGHT = 0.5 ppm. # # SIZE = 13111 ( = number of points) # # In the following ordering is from the 'left' to the 'right' limits! # Lines beginning with '#' must be considered as comment lines. # 1628.40625 1628.40625 1964.40625 2242.0625 2533.5 2937.90625 3448.0 3923.96875 Is it possible to read it with R, something like scan() but keeping the structure? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Combine x-axis labels size
Hello, I would like to combine different label sizes in the same x-axis, for example 1 2 3 4 5 6 7 8 9 How can I do it? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Closest value
Hello, I have this command: x.axis <- seq(from=0.5, to=4.5, length.out=13112) How can I which of the x.axis components is the closest to a given value, for example 3.2? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Anova
Hello, I am trying to perform an ANOVA on a dataframe like this: ID Grup ML PC mI Gly Glx X373.txt 11 0.004685889 0.05994939 0.004589104 0.007144027 0.02042549 X373bis.txt 21 0.004685889 0.0599494 0.004589104 0.007144028 0.0204255 X376.txt 31 0.007604898 0.07600049 0.019352470.01678972 0.03363403 X392.txt 41 0.004982747 0.02760991 0.018555960.01413439 0.02013267 X483.txt 51 0.009131522 0.02636227 0.024852320.01493074 0.02532194 X520.txt 61 0.008553895 0.06304886 0.024902610.01907819 0.03356447 X671.txt 71 0.008004383 0.05243909 0.0229447 0.024266 0.03553224 X673A.txt81 0.01306893 0.02799318 0.01155338 0.007668364 0.02123958 X673B.txt91 0.006099385 0.0516078 0.030993240.02664487 0.03766267 X674.txt101 0.005476397 0.04945545 0.014797420.01084873 0.02307815 X681.txt111 0.009807893 0.01680487 0.004524913 0.004705414 0.008969453 X725.txt121 0.01018343 0.0119391 0.007911063 0.008005791 0.01014625 X746.txt131 0.008864319 0.02484126 0.011980480.01276371 0.01042683 X772.txt141 0.005966057 0.07398342 0.02103990.01606057 0.02932874 X814.txt151 0.01350947 0.0317243 0.003234958 0.002958675 0.005194511 X835.txt161 0.005509359 0.02670237 0.074253230.04095533 0.031017 X847.txt171 0.004784228 0.05349206 0.011836790.01230316 0.03073348 X851.txt181 0.004395889 0.03812635 0.019986530.02165763 0.02074277 X865.txt191 0.001514055 0.07128447 0.01068870.00802192 0.01478855 X878.txt201 0.003693918 0.03864821 0.015717970.01972568 0.022711 et2029.txt 211 0.05204285 0.03769878 0.031687990.03631842 0.02732589 et2348.txt 221 0.01407517 0.01679014 0.004900163 0.004243802 0.01052361 The table is truncated because it's very big, but it has 3 different groups (Grup variable) and it's called GBM. I try to use the command: aov(GBM$Grup~GBM$ML,data=GBM) But I get this error: /Error in storage.mode(y) <- "double" : invalid to change the storage mode of a factor In addition: Warning message: In model.response(mf, "numeric") : using type="numeric" with a factor response will be ignored/ How can I solve this? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Expression in axis
Hello, I am creating a plot and I would like to know how to put this expression to the y axis µmol/10^6 cells I've tried some combinations using the expression() function, but none of them worked. Any idea? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] ANOVA error
Hello, I have a dataframe named myMatrix with the structure TreatmentTimeCrmIb ... Being the treatment and time the predictors and Cr, mIb and so on the response variables. When I call Cr.aov <- aov(Cr~Treatment, data=myMatrix) I got this error: Error in storage.mode(y) <- "double" : invalid to change the storage mode of a factor In addition: Warning message: In model.response(mf, "numeric") : using type="numeric" with a factor response will be ignored Can anyone help me? I take the chance to ask another question. I would like to perform an ANOVA on different variables. Is the call aov(Cr+mIb+...~Treatment, data=myMatrix) o correct way of doing it? What I would like to have is a p value for the variance for each response variable. Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] fit.contrast error
Hello, I am trying to perform a fit.contrast() on a lme object with this code: attach(error_DB) model_temperature <- lme(Error ~ Temperature, data = error_DB,random=~1|ID) summary(model_temperature) fit.contrast(model_temperature, "Temperature", c(-1,1), conf.int=0.95 ) detach(error_DB) but I got this error Error in `contrasts<-`(`*tmp*`, value = c(-0.5, 0.5)) : contrasts apply only to factors My database is a dataframe, very similar to that of the Orthodont. Could anyone give me some advise on how to solve the problem? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] lsmeans
Hello, I have the next function call: lme(fixed=Error ~ Temperature * Tumour ,random = ~1|ID, data=error_DB) which returns an lme object. I am interested on carrying out some kind of lsmeans on the data returned, but I cannot find any function to do this in R. I'have seen the effect() function, but it does not work with lme objects. Any idea? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] LDA and centroids
Hello, I have carried out an lda analysis using the lda function of MASS package. I have plotted the LD1xLD2 to represent the data. Now I would like to get the centroids for each group of data and plot it on the LD1xLD2 graph. How can I get the centroid value from the lda object? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Problems with lme
Hello, I want to perform an lme on a database with this structure: ID Sequence Temperature TumourError 15 0 1 8.721872e-08 15 0 2 8.695348e-08 15 0 3 2.019604e-13 15 37 1 2.746476e-01 15 37 2 1.580415e-02 15 37 3 1.586857e-01 12 0 1 8.721872e-08 12 0 2 8.695348e-08 12 0 3 2.019604e-13 12 37 12.746476e-01 I try to perform an lme with the lme() function of the lme package (first I attach the data frame with attach()). This is the code: lme(Error ~ ID + Sequence + Temperature + Tumour) If I use this code, I get the following error: Error in getGroups.data.frame(dataMix, groups) : Invalid formula for groups Can anyone help me? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Clustering large data matrix
Hello, I have a large data matrix (68x13112), each row corresponding to one observation (patients) and each column corresponding to the variables (points within an NMR spectrum). I would like to carry out some kind of clustering on these data to see how many clusters are there. I have tried the function clara() from the package cluster. If I use the matrix as is, I can perform the clara analysis but when I call clusplot() I get this error: Error in princomp.default(x, scores = TRUE, cor = ncol(x) != 2) : 'princomp' can only be used with more units than variables Then, I reduce the dimensionality by using the function prcomp(). Then I take the 13 first principal components (80%< variability) and I carry out the clara() analysis again. Then, I call the clusplot() function again and voilà!, it works. The problem is that clusplot() only represents the two first components of my prcomp() analysis, which represents only 15% of the variability. So, my questions are 1) is clara() a proper way to analyze such a large data set? and 2) Is there an appropiate method for graphic plotting of my data, that takes into account the whole variability if my data, not just two principal components? Many thanks. Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] GLM
Hello, I am trying to perform a glm analysis on a 68x13113 matrix (named data.spect). The first column corresponds to the predictor (data.spect[,1]) and the rest to the response variables (data.spect[,2:13113]). When I try this code glmObject <- glm(data.spect[,2:13113]~data.spect[,1]) I get the following error: Error: (subscript) logical subscript too long Could anyone help me on solving this problem? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] insert() function
Great! Now it works. Many thanks.
Dani
Daniel Valverde Saubí
Grup de Biologia Molecular de Llevats
Facultat de Veterinària de la Universitat Autònoma de Barcelona
Edifici V, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
Centro de Investigación Biomédica en Red
en Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN)
Grup d'Aplicacions Biomèdiques de la RMN
Facultat de Biociències
Universitat Autònoma de Barcelona
Edifici Cs, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
+34 93 5814126
En/na Henrik Bengtsson ha escrit:
>> spect2 <- insert(spect1, ats=pos, values=as.list(intensities))
>> str(spect2)
>>
> num [1:13112] -0.457 -0.457 0.300 1.781 -0.381 ...
>
> /Henrik
>
> On Thu, Feb 21, 2008 at 9:26 AM, Henrik Bengtsson <[EMAIL PROTECTED]> wrote:
>
>> On Thu, Feb 21, 2008 at 4:30 AM, Dani Valverde <[EMAIL PROTECTED]> wrote:
>> > Hello,
>>
>>
>>> I still having problems with insert() from R.utils package. I provide a
>>>
>> > code with no error:
>> >
>> > x <- seq(1:10909)
>> > x1 <- c(13112-10909)
>> > spect1 <- rnorm(10909)
>> >
>> > interpol <- approx(x,spect1,xout=c(seq(from=1, by=((10909 - 1)/(x1 -1)),
>> > length.out=x1)))
>> > pos <- round(interpol$x,0)
>> > intensities <- interpol$y
>> >
>> > str(spect1)
>> > str(pos)
>> > str(intensities)
>>
>> So what does these output? They are the ones that will give you a
>> lead to solving your problem, which I think is unrelated to insert().
>>
>> /Henrik
>>
>>
>>
>> >
>> > Then, when I call:
>> > library(R.utils)
>> >
>> > spect2 <- insert(spect1,ats=pos,values=intensities)
>> >
>> > I have this error:
>> >
>> >
>> > Error in list("insert(spect1, ats = pos, values = intensities)" =
>> > , :
>> >
>> > [2008-02-21 13:27:49] Exception: Argument 'ats' and argument 'values'
>> >
>> > has different lengths: 2203 != 1
>> > at throw(Exception(...))
>> > at throw.default("Argument 'ats' and argument 'values' has different
>> > lengths: ", length(ats), " != ", length(values))
>> > at throw("Argument 'ats' and argument 'values' has different lengths:
>> > ", length(ats), " != ", length(values))
>> > at insert.default(spect1, ats = pos, values = intensities)
>> > at insert(spect1, ats = pos, values = intensities)
>> >
>> > You see that I still having the error, even calling the str() function
>> > before insert().
>> > Here there is my sessionInfo():
>> >
>> > R version 2.6.2 (2008-02-08)
>> > i386-pc-mingw32
>> >
>> > locale:
>> >
>> LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252
>> >
>> > attached base packages:
>> > [1] datasets stats graphics grDevices tcltk utils
>> > methods base
>> >
>> > other attached packages:
>> > [1] R.utils_0.9.8R.oo_1.4.1 R.methodsS3_1.0.0
>> > Hmisc_3.4-3 MASS_7.2-40 scatterplot3d_0.3-25
>> > NMRTools_1.0.2
>> > [8] svSocket_0.9-5 svIO_0.9-5 R2HTML_1.58
>> > svMisc_0.9-5 svIDE_0.9-5
>> >
>> > loaded via a namespace (and not attached):
>> > [1] cluster_1.11.9 grid_2.6.2 lattice_0.17-6 tools_2.6.2
>> >
>> > Can you help?
>> >
>> > Best,
>> >
>> > Dani
>> >
>> > Daniel Valverde Saubí
>> >
>> > Grup de Biologia Molecular de Llevats
>> > Facultat de Veterinària de la Universitat Autònoma de Barcelona
>> > Edifici V, Campus UAB
>> > 08193 Cerdanyola del Vallès- SPAIN
>> >
>> > Centro de Investigación Biomédica en Red
>> > en Bioingeniería, Biomateriales y
>> > Nanomedicina (CIBER-BBN)
>> >
>> > Grup d'Aplicacions Biomèdiques de la RMN
>> > Facultat de Biociències
>> > Universitat Autònoma de Barcelona
>> > Edifici Cs, Campus UAB
>> > 08193 Cerdanyola del Vallès- SPAIN
>> > +34 93 5814126
>> >
>> >
>> >
>> > En/na Henrik Bengtsson ha escr
Re: [R] insert() function
Hello,
I still having problems with insert() from R.utils package. I provide a
code with no error:
x <- seq(1:10909)
x1 <- c(13112-10909)
spect1 <- rnorm(10909)
interpol <- approx(x,spect1,xout=c(seq(from=1, by=((10909 - 1)/(x1 -1)),
length.out=x1)))
pos <- round(interpol$x,0)
intensities <- interpol$y
str(spect1)
str(pos)
str(intensities)
Then, when I call:
library(R.utils)
spect2 <- insert(spect1,ats=pos,values=intensities)
I have this error:
Error in list("insert(spect1, ats = pos, values = intensities)" =
, :
[2008-02-21 13:27:49] Exception: Argument 'ats' and argument 'values'
has different lengths: 2203 != 1
at throw(Exception(...))
at throw.default("Argument 'ats' and argument 'values' has different
lengths: ", length(ats), " != ", length(values))
at throw("Argument 'ats' and argument 'values' has different lengths:
", length(ats), " != ", length(values))
at insert.default(spect1, ats = pos, values = intensities)
at insert(spect1, ats = pos, values = intensities)
You see that I still having the error, even calling the str() function
before insert().
Here there is my sessionInfo():
R version 2.6.2 (2008-02-08)
i386-pc-mingw32
locale:
LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252
attached base packages:
[1] datasets stats graphics grDevices tcltk utils
methods base
other attached packages:
[1] R.utils_0.9.8R.oo_1.4.1 R.methodsS3_1.0.0
Hmisc_3.4-3 MASS_7.2-40 scatterplot3d_0.3-25
NMRTools_1.0.2
[8] svSocket_0.9-5 svIO_0.9-5 R2HTML_1.58
svMisc_0.9-5 svIDE_0.9-5
loaded via a namespace (and not attached):
[1] cluster_1.11.9 grid_2.6.2 lattice_0.17-6 tools_2.6.2
Can you help?
Best,
Dani
Daniel Valverde Saubí
Grup de Biologia Molecular de Llevats
Facultat de Veterinària de la Universitat Autònoma de Barcelona
Edifici V, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
Centro de Investigación Biomédica en Red
en Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN)
Grup d'Aplicacions Biomèdiques de la RMN
Facultat de Biociències
Universitat Autònoma de Barcelona
Edifici Cs, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
+34 93 5814126
En/na Henrik Bengtsson ha escrit:
> Hi.
>
> On Feb 20, 2008 2:38 AM, Dani Valverde <[EMAIL PROTECTED]> wrote:
>
>> Hello,
>> I am trying to insert a certain number of points into a certain position
>> of a vector with this code:
>> x <- seq(1:10909)
>> x1 <- c(13112-10909)
>> spect1 <- rnorm(13112)
>> interpol <- approx(x,spect1,xout=c(seq(from=1, by=((10909 - 1)/(x1 -
>> 1)), length.out=x1)))
>> pos <- round(interpol$x,0)
>> intensities <- interpol$y
>>
>
> Please provide reproducible code that does not give an error.
>
>
>> spect2 <- insert(spect1,ats=pos,values=intensities)
>>
>
> Is this the famous insert() in R.utils? Please give your
> sessionInfo() to help others see what you are using. I repeat, please
> provide us with sessionInfo().
>
>
>> "interpol" object is the result of interpoling the missing x values with
>> respect to spect1. "pos" object is a vector with the indexes where the
>> values are to be placed (it is the rounded values of interpol$x) and
>> "intensities" is a vector with the values to be inserted. I try to
>> insert the values of "intensities" into the positions specified by "pos"
>> in the "x" vector using the insert() functions as shown in the code I
>> paste, but I get this error:
>>
>> Error in list("insert(spect1, ats = pos, values = intensities)" =
>> , :
>>
>> [2008-02-20 11:36:28] Exception: Argument 'ats' and argument 'values'
>> has different lengths: 2203 != 1
>> at throw(Exception(...))
>> at throw.default("Argument 'ats' and argument 'values' has different
>> lengths: ", length(ats), " != ", length(values))
>> at throw("Argument 'ats' and argument 'values' has different lengths:
>> ", length(ats), " != ", length(values))
>> at insert.default(spect1, ats = pos, values = intensities)
>> at insert(spect1, ats = pos, values = intensities)
>>
>> Can anyone help me on how can I solve it? I know that "pos" and
>> "intensities" have the same length, so I don't know why I get this
>> error. Any ideas will be welcome.
>>
>
> I challenge that claim, b
Re: [R] Rd to latex
Hello, I've tried with R CMD Rdeconv and it works, but, when I want to paste it into my main latex file, there are lots of undefined environments. I loaded the package Rd.sty in the latex document preface, but it does not seem to work. Any idea? Best, Dani Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 En/na Stefan Grosse ha escrit: > maybe the xtable package? > > > On Wednesday 20 February 2008 05:42:27 pm Dani Valverde wrote: > DV> Hello, > DV> I would like to convert an Rd object to a latex file, so that I can put > DV> it in my thesis. How can I do it? I tryed latex(), but it only works for > DV> code... > DV> Best, > DV> > DV> Dani > DV> > > > > __ 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] Rd to latex
Hello, I would like to convert an Rd object to a latex file, so that I can put it in my thesis. How can I do it? I tryed latex(), but it only works for code... Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] insert() function
Hello,
I am trying to insert a certain number of points into a certain position
of a vector with this code:
x <- seq(1:10909)
x1 <- c(13112-10909)
spect1 <- rnorm(13112)
interpol <- approx(x,spect1,xout=c(seq(from=1, by=((10909 - 1)/(x1 -
1)), length.out=x1)))
pos <- round(interpol$x,0)
intensities <- interpol$y
spect2 <- insert(spect1,ats=pos,values=intensities)
"interpol" object is the result of interpoling the missing x values with
respect to spect1. "pos" object is a vector with the indexes where the
values are to be placed (it is the rounded values of interpol$x) and
"intensities" is a vector with the values to be inserted. I try to
insert the values of "intensities" into the positions specified by "pos"
in the "x" vector using the insert() functions as shown in the code I
paste, but I get this error:
Error in list("insert(spect1, ats = pos, values = intensities)" =
, :
[2008-02-20 11:36:28] Exception: Argument 'ats' and argument 'values'
has different lengths: 2203 != 1
at throw(Exception(...))
at throw.default("Argument 'ats' and argument 'values' has different
lengths: ", length(ats), " != ", length(values))
at throw("Argument 'ats' and argument 'values' has different lengths:
", length(ats), " != ", length(values))
at insert.default(spect1, ats = pos, values = intensities)
at insert(spect1, ats = pos, values = intensities)
Can anyone help me on how can I solve it? I know that "pos" and
"intensities" have the same length, so I don't know why I get this
error. Any ideas will be welcome.
Best,
Dani
--
Daniel Valverde Saubí
Grup de Biologia Molecular de Llevats
Facultat de Veterinària de la Universitat Autònoma de Barcelona
Edifici V, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
Centro de Investigación Biomédica en Red
en Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN)
Grup d'Aplicacions Biomèdiques de la RMN
Facultat de Biociències
Universitat Autònoma de Barcelona
Edifici Cs, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
+34 93 5814126
__
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] Interpolation between 2 vectors
Hello,
I tried the approx() and it worked. Now, I have a list named "interpol"
resulting from the interpolation. I would like to append the values in
interpol$y in the position specified by interpol$x in a existing vector
"spect1". I tried with append() and the following code:
spect1 <- c(1:10909)
for(i in 1:length(interpol$x)){
append(spect1,interpol$y[i],interpol$x[i])
}
but it didn't work. Any idea?
Best,
Dani
Daniel Valverde Saubí
Grup de Biologia Molecular de Llevats
Facultat de Veterinària de la Universitat Autònoma de Barcelona
Edifici V, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
Centro de Investigación Biomédica en Red
en Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN)
Grup d'Aplicacions Biomèdiques de la RMN
Facultat de Biociències
Universitat Autònoma de Barcelona
Edifici Cs, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
+34 93 5814126
En/na jim holtman ha escrit:
> check out the 'approx' function.
>
> On Feb 19, 2008 12:44 PM, Dani Valverde <[EMAIL PROTECTED]> wrote:
>
>> Hello,
>> I have two vectors, one with 13112 points and the other one with 10909.
>> I wonder if there is a way to interpolate the data so the shorter
>> vectors has the same number of points as the longer one.
>> Best,
>> Dani
>>
>> --
>> Daniel Valverde Saubí
>>
>> Grup de Biologia Molecular de Llevats
>> Facultat de Veterinària de la Universitat Autònoma de Barcelona
>> Edifici V, Campus UAB
>> 08193 Cerdanyola del Vallès- SPAIN
>>
>> Centro de Investigación Biomédica en Red
>> en Bioingeniería, Biomateriales y
>> Nanomedicina (CIBER-BBN)
>>
>> Grup d'Aplicacions Biomèdiques de la RMN
>> Facultat de Biociències
>> Universitat Autònoma de Barcelona
>> Edifici Cs, Campus UAB
>> 08193 Cerdanyola del Vallès- SPAIN
>> +34 93 5814126
>>
>> __
>> 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.
[R] Interpolation between 2 vectors
Hello, I have two vectors, one with 13112 points and the other one with 10909. I wonder if there is a way to interpolate the data so the shorter vectors has the same number of points as the longer one. Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Compile Rd file
Hello,
I am trying to compile a file .Rd into .html using R CMD Rdconv -t=html
/file.rd/>/file.html./ It seems that the process works ok but instead of
having for example loo.cv(NMRTools) at the top of the html file I have
loo.cv{unknown}. Any ideas on how to solve this?
Best,
Dani
//
--
Daniel Valverde Saubí
Grup de Biologia Molecular de Llevats
Facultat de Veterinària de la Universitat Autònoma de Barcelona
Edifici V, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
Centro de Investigación Biomédica en Red
en Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN)
Grup d'Aplicacions Biomèdiques de la RMN
Facultat de Biociències
Universitat Autònoma de Barcelona
Edifici Cs, Campus UAB
08193 Cerdanyola del Vallès- SPAIN
+34 93 5814126
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[R] [Fwd: Problems when checking a package]
Forget my last message, it was a really stupid problem. Sorry about the mess. Best, Dani Missatge original Assumpte: Problems when checking a package Data: Tue, 05 Feb 2008 11:20:28 +0100 De: Dani Valverde <[EMAIL PROTECTED]> A: R Help Hello, I am tryining to build a package called NMRTools and when I check it using R CMD check NMRTools I get this error: Functions/methods with usage in documentation object 'lda.bootstrap' but not in code: lda.bootstrap As far as I undestand there is something present in lda.bootstrap.rd but not in lda.bootstrap.r. The problem is that everything appears in both files. Maybe I misundestand the error message. Any idea? Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Problems when checking a package
Hello, I am tryining to build a package called NMRTools and when I check it using R CMD check NMRTools I get this error: Functions/methods with usage in documentation object 'lda.bootstrap' but not in code: lda.bootstrap As far as I undestand there is something present in lda.bootstrap.rd but not in lda.bootstrap.r. The problem is that everything appears in both files. Maybe I misundestand the error message. Any idea? Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Package compilation
Hello, Is there an easy way to compile a package so that it can be installed as a binary file under Windows? Now I have the source code. I am not used in compiling, and the documentation seems too hard for me, so an easy way would be great. Best regards, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Installing packages
Hello, I have a problem when making packages with version 2.6.1. I have a package which I could install in version 2.5.1. I have made some modifications of the package, and I would like to install it to 2.6.1. I check the package with R CMD check, I build it with R CMD build and when I try to install it it gives me an error, it tries to install something like R.css and tells me that cannot open the DESCRIPTION file. Then, I made the same procedure with version 2.5.1 and it worked fine. I am using Windows Vista and I changed the PATH environment variable to version 2.6.1. Any suggestion to solve the problem? Best regards, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Odp: Cutting a vector
Hello, That's very useful. I think the cut() function is the key. However, in my real vector I have 13112 points. I would like the function to cut the vector every certain number of points (ie 4). Is there a way to specify this without the need of writing each cutting point? For example, I do not want to write breaks=c(4,8,12,...,13108, +Inf), but some expresion to avoid writing such a long argument. Best regards, Dani En/na Petr PIKAL ha escrit: > Hi > > you shall be more specific. Do you want to split your vector according > some pionts > > split(x, findInterval(x, c(6,12,16))) > > if you want to make a factor from your x vector, then you can use > findInterval or cut > > cut(x, breaks = c(0,6,12,17, +Inf)) > > Or something else? > Regards > > Petr > [EMAIL PROTECTED] > > [EMAIL PROTECTED] napsal dne 22.11.2007 12:52:38: > > >> Hello, >> I have a vector, lets say >> x <- 1:50 >> I would like it to be cut at certain points, being for example 1:5, >> 6:11, 12:17, ... >> How can I do it? I have tried the cut() function, but I don not know how >> > > >> to place the cutting points properly. >> Best regards, >> >> Dani >> >> -- >> Daniel Valverde Saubí >> >> Grup de Biologia Molecular de Llevats >> Facultat de Veterinària de la Universitat Autònoma de Barcelona >> Edifici V, Campus UAB >> 08193 Cerdanyola del Vallès- SPAIN >> >> Centro de Investigación Biomédica en Red >> en Bioingeniería, Biomateriales y >> Nanomedicina (CIBER-BBN) >> >> Grup d'Aplicacions Biomèdiques de la RMN >> Facultat de Biociències >> Universitat Autònoma de Barcelona >> Edifici Cs, Campus UAB >> 08193 Cerdanyola del Vallès- SPAIN >> +34 93 5814126 >> >> __ >> 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. >> > > > -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] Cutting a vector
Hello, I have a vector, lets say x <- 1:50 I would like it to be cut at certain points, being for example 1:5, 6:11, 12:17, ... How can I do it? I have tried the cut() function, but I don not know how to place the cutting points properly. Best regards, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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.
