similar to: Need to calculate within- and between- run CV

Displaying 20 results from an estimated 600 matches similar to: "Need to calculate within- and between- run CV"

2010 Apr 29
1
How to estimate the residual SD for each sample separately in mixed-effects model?
Dear R-helpers, I am developing a Mixed-Effects model for a study of immunoassays using 'lme4' library. The study design is as follows: 10 samples were run using 7 different immunoassays, 3 times each, in duplicates. Data attached. I have developed the following model: c.lme <- lmer(Result~SPL + (SPL|Assay/Run) -1, data=data) This model has excellent predictions - the Rsquared of
2011 Mar 23
2
Estimating correlation in multiple measures data
Dear R-helpers, This may sound simple to you, but I'm a beginner in this, so please be forgiving. I have a following problem: two analytes were measured in patient's blood on 4 occasions: ProteinA and ProteinB. How to correctly evaluate correlation between ProteinA and ProteinB? I tried: x <- data.frame(Patient.ID=rep(1:10, each=4), Visit=rep(c(1:4),10), ProteinA=rnorm(m=10,
2010 Mar 30
5
Problem comparing hazard ratios
Dear R-Helpers, I am a novice in survival analysis. I have the following code: for (i in 3:12) print(coxph(Surv(time, status)~a[,i], data=a)) I used it to fit the Cox Proportional Hazard models separately for every available parameter (columns 3:12) in my data set - with intention to compare the Hazard Ratios. However, some of my variables are in range 0.1 to 1.6, others in range 5000 to
2008 Oct 17
2
Beginner's question: number formatting
Hello R-helpers, I have a problem with formatting a single number to show leading zeros. For example, I want "2" displayed as "002". My numbers have 1 to 3 digits and I would like them all to display 3 digits for printing. I know I could use "paste" in a loop with several "if"s, but I was wondering if there is a single function that can do this. I have
2010 May 26
3
Problem with plotting survival predictions from cph model
Dear R-helpers, I am working with 'cph' models from 'rms' library. When I build simple survival models, based on 'Surv(time, event)', everything is fine and I can make nice plots using plot(Predict(f, time=3)). However, recently I tried to be more specific and used 'Surv(start, stop, event)' type model. Using this model 'plot(Predict(f))' works OK, but
2012 May 02
2
Problem with 'nls' fitting logistic model (5PL)
Dear R-Helpers, I'm working with immunoassay data and 5PL logistic model. I wanted to experiment with different forms of weighting and parameter selection, which is not possible in instrument software, so I turned to R. I am using R 2.14.2 under Win7 64bit, and the 'nls' library to fit the model - I started with the same model and weighting type (1/y) as in the instrument to see
2009 Aug 05
1
Starting NONMEM (nmfe6) from R
Hello, I have made an R script that prepares a NONMEM dataset and I would like to start the NONMEM run right after the dataset is ready. I am using windows XP, R 2.9.1 and NONMEM 6. I have prepared a run.bat file that looks like this: ---------------------------------------- call K:\nmvi\NMdirectories.bat call K:\nmvi\nmfe6 "path\control.txt" "path\output.txt"
2008 Jun 10
1
Problem with by(... , median)
Hello everyone, I am new to R, I have been using SAS for a while. Not surprisingly, I find R much better in graphics, which is publication ready right away. Recently, I have been trying to calculate some basic statistics using R. I have a dataset of multiple rows per subject. For example: Subject Date Factor1 Factor2 Factor3 P1 0.5 1 1 3 P1 1 3 2 5 P1 2 3 5 NA ... P2 0.5 1 6 4 P2 1 2 NA 7 P2
2008 Jul 23
1
[Fwd: Re: Coefficients of Logistic Regression from bootstrap - how to get them?]
I think the argument supporting the use of bootstrap to determine coefficients, as opposed to just running linear regression on the whole dataset, is the comparison of Rsq and prediction errors between these two approaches - page 1502. There's a substantial difference in favor of the bootstrap approach. -- Michal J. Figurski Gustaf Rydevik wrote: > The url for the mentioned paper is
2008 Jul 21
5
Coefficients of Logistic Regression from bootstrap - how to get them?
Hello all, I am trying to optimize my logistic regression model by using bootstrap. I was previously using SAS for this kind of tasks, but I am now switching to R. My data frame consists of 5 columns and has 109 rows. Each row is a single record composed of the following values: Subject_name, numeric1, numeric2, numeric3 and outcome (yes or no). All three numerics are used to predict
2010 Oct 21
1
Big data (over 2GB) and lmer
Dear R-helpers I have a data set of roughly 10 million records, 7 columns. It has only about 500MB as a csv, so it fits in the memory. It's painfully slow to do anything with it, but it's possible. I also have another dataset of covariates that I would like to explore - with about 4GB of data... I would like to merge the two datasets and use lmer to build a mixed effects model. Is
2008 Jul 24
1
[Fwd: Re: Coefficients of Logistic Regression from bootstrap - how to get them?]
Thank you Frank and all for your advices. Here I attach the raw data from the Pawinski's paper. I have obtained permission from the corresponding Author to post it here for everyone. The only condition of use is that the Authors retain ownership of the data, and any publication resulting from these data must be managed by them. The dataset is composed as follows: patient number / MMF dose in
2010 Aug 10
3
Plotting confidence bands around regression line
Dear R-helpers and graphics gurus, I have two problems with plotting confidence bands: 1. First is relatively simple. I am using the Passing-Bablok procedure to obtain "unbiased" regression coefficients. This procedure yields the "a" & "b" coefficient values along with their confidence intervals. I then plot the raw data with the regression line, but I would
2010 Jan 15
1
'nlme' library - lme function results
Dear R-helpers I am running a simple mixed effects model using lme(). The call looks like this: fit <- lme(Analyte~Sample, data=Data, random=~1 | Run) I am particularly interested in the estimated random effects. When I print the 'fit' object, it looks something like example below: (...) Random effects: Formula: ~1 | Run (Intercept) Residual StdDev: 3.483794 3.637523
2011 Jul 01
2
Initiating in BNArray
Hi, I'm trying to understand some details about an example maintened in [1]. According that link, I have total.data as a data set (am I right?). But I don't understand how is built that table. I saved the dataset in a file, with dput(), and had something like this: structure(list(df.all = structure(list(V1 = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L,
2012 Apr 10
3
How to get the SS and MS from oneway.test?
Hello everyone: I'm a new member of this group. I have a question about "oneway.test". When I use "anova(lm(....))" to analysis the ANOVA, I can get the information about Sum Sq and Mean Sq. (The R code and the results are as follows.)
2016 Apr 14
0
Bug in by() function which works for some FUN argument and does not work for others
I think you are not using the best function for what your intentions are. Try: > by(data=mtcars, INDICES=list(as.factor(mtcars$am)), FUN=colMeans) : 0 mpg cyl disp hp drat wt qsec vs 17.1473684 6.9473684 290.3789474 160.2631579 3.2863158 3.7688947 18.1831579 0.3684211 am gear carb 0.0000000
2016 Apr 14
4
Bug in by() function which works for some FUN argument and does not work for others
Dear Sirs, I am Professor at Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India. While taking classes, I found the *by() *function producing following error when I use FUN=mean or median and some other functions, however, FUN=summary works. Given below is the output of the example I used on a built-in dataset "mtcars", along with error message reproduced herewith: >
2009 Aug 07
1
ggplot2-ddply question
Hi all: I am trying to use the ddply function to estimate the mean of 'Total','Fry','Smolt' and 'Fry.Eq' columns without success. I have the dput of my dataset below. I wonder if someone can give me a hand with this function. # dput(winter) winter <-structure(list(IDDate = structure(c(37L, 48L, 59L, 62L, 63L, 64L, 65L, 66L, 67L, 38L, 39L, 40L, 41L, 42L, 43L,
2016 Apr 15
0
Bug in by() function which works for some FUN argument and does not work for others
> On Apr 15, 2016, at 1:16 AM, Akhilesh Singh <akhileshsingh.igkv at gmail.com> wrote: > > Dear All, > > Thanks for your help. However, I would like to draw your attention to the > following: > > Actually, I was replicating the Example 2.3, using the dataset > "brainsize.txt" given in Section 2.3.3 ("Summarize by group") at page 55, > of a