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...a scatterplot? Thanks, David ________________________________ De: David Winsemius <dwinsemius at comcast.net> Enviado: lunes, 2 de octubre de 2017 18:18:36 Para: David Cc: R-help Asunto: Re: [R] Help on adding a negative binomial density plot > On Oct 2, 2017, at 2:05 AM, David <dasolexa at hotmail.com> wrote: > > Dear list, > > > I am just starting on analysis of count data in R 3.4.0. My dataset was obtained from counting particles on a surface before andd after a cleaning process. The sampling positions on the surface are pre-defined and are the same before and...

> On Oct 2, 2017, at 2:05 AM, David <dasolexa at hotmail.com> wrote: > > Dear list, > > > I am just starting on analysis of count data in R 3.4.0. My dataset was obtained from counting particles on a surface before andd after a cleaning process. The sampling positions on the surface are pre-defined and are the same before...

Dear list, I am just starting on analysis of count data in R 3.4.0. My dataset was obtained from counting particles on a surface before andd after a cleaning process. The sampling positions on the surface are pre-defined and are the same before and after cleaning. I have ~20% of 0's. I want to know if the cleaning process was useful at reducing the number of particles. I first fit a

Hi, I am trying to run some R commands into my bash scripts and want to use shell variables in the R commands and store the output of R objects into shell variables for further usage in downstream analyses. So far I have managed the first, but how to get values out of R script? I am using "here documents" (as a starter, maybe something else is simpler or better; suggestions greatly

Dear list, I am trying to evaluate how many elements in a vector equal a certain value. The vectors are the columns of a data.frame, read in using read.table(): > dim(data) [1] 2600 742 > data[1:5,1:5] SNP001 SNP002 SNP003 SNP004 SNP005 1 GG AA TT TT GG 2 GG AA TC TT GG 3 GG AC CC TT GG 4 AG AA TT TT GG 5

Hi, I am trying to upgrade my R version but am having some error trying to get the key for automatic upgrading from aptitude (ubuntu 11.04). This is what I did, following instructions from http://cran.r-project.org/bin/linux/ubuntu/ I added the repository address to my software manager. deb http://stats.bris.ac.uk/R/bin/linux/ubuntu natty/ I am trying to get the key from keyserver.ubuntu.com

Hi, I am trying to calculate confidence intervals using ci.numeric from epicalc package. If I generate a normal set of data and find the 99% and 95% CI, they seem too narrow to me. Am I doing something wrong?? The IQR goes from -0.62 to 0.62, so I thought the CI limits should be more extreme than these values. x<- rnorm(200,0,1) ci.numeric(x=mean(x),n=200,sds=sd(x),alpha=0.05) n

Hi list, I have a 1710x244 matrix of numerical values and I would like to calculate the mean of every group of three consecutive values per column to obtain a new matrix of 570x244. I could get it done using a for loop but how can I do that using apply functions? In addition to this, do I have to initizalize a 570x244 matrix with 0's to store the calculated values or can the output matrix be

Dear list, I am calculating the 95th percentile of a set of values with R and with SPSS In R: > normal200<-rnorm(200,0,1) > qnorm(0.95,mean=mean(normal200),sd=sd(normal200),lower.tail =TRUE) [1] 1.84191 In SPSS, if I use the same 200 values and select Analyze -> Descriptive Statistics -> Frequencies and under "Statistics", I type in '95' under Percentiles,

Dear list, I am using a external program that outputs Q1, Q3, median, upper and lower whisker values for various datasets simultaneously in a tab delimited format. After importing this text file into R, I would like to plot a boxplot using these given values and not the original series of data points, i.e. not using something like boxplot(mydata). Is there an easy way for doing this? If I am not

Dear list, this might be a silly question, but I am a bit lost I have bootstrapped the C-index of a logistic regression model, 500 times. > results <- boot(data=data,statistic=cindex,R=500,formula = myformula) When I plot the results I get a histogram of the bootstrapped where the Y axis is density, but it spans from 0 to about 25 > plot(results) Can anyone help me interpret

Hi R-users, can anyone explain me how to play around with the options of the bootstrap calibration curve obtained using the calibrate() function in Design package? I am trying to colour the diagonal, i.e. the ideal curve, in red, and also hide the bias-corrected curve. Thanks, Dave _________________________________________________________________ Show them the way! Add maps and directions to

Dear list, havig the following matrix "Value" "Class" 13.00 1 12.80 1 11.78 1 11.70 2 11.61 2 11.95 2 11.55 2 12.40 3 11.40 1 12.27 1 12.49 3 11.39 4 11.80 4 12.39 3 12.72 3 12.18 3 11.64 3 11.50 4 12.81 4 11.31 4 11.95 2 12.65 2 11.66 2 12.19 3 12.84 1 11.90 1 11.11 4 12.75 4 how can I

Hi R-users! I am trying to learn how to use the glmpath package. I have a dataframe like this > dim(data) [1] 605 109 and selected the following > response <- data[,1] > features<-as.matrix(data[,3:109]) > mymodel <- glmpath(features,response, family = binomial) Error in if (lambda <= min.lambda) { : missing value where TRUE/FALSE expected Reading the glmpath pdf, I

Dear list, I am trying to work out how the improveProb() function works and how to interpret the results, and I have a few questions. I would be grateful if anyone could shed some light on these. in the Net Reclassification Improvement section of the output, is the 2P column the two-sided p-value for the differences in classification? So if a limit is set at 0.05, then lower values indicate

Hi, I am trying to estimate the sample size needed for the comparison of two groups on a certain measurement, given some previous data at hand. I find that the data collected does not follow a normal distribution, so I would like to use a non-parametric option for sample size calculation. I found the pwr package but I don't think it has this option and on the internet found that

Hi, I created a logistic regression model using the glmnet package. This model is of class "glmnet" or "lognet". I wanted to plot a calibration curve for this model using the calibrate() function from rms package, but the objects used are different, rms requires a fit from lrm(). Is there another function for getting the calibration plot for this glmnet object, or can anyone

Dearl list, can anyone point me to a function or library that can create a graph similar to the one in the following powerpoint presentation? http://bmi.osu.edu/~khuang/IBGP705/BMI705-Lecture7.ppt (pages 36-37) In order to try to explain the graph, the way I see it in R terms is something like this: the "p-q" axis is a vector of positions (for example, seq(0,5000000,1)) the