[R] Plot in drc package

Hi all, I have the following data and I fit a log logistic model using the drm function in DRC package. I saved the fitted model in an object called "mod". (See below) I understand that we can use the plot function to plot the regression curve with the original data points using the code "plot

Re: [R] question with drm function in "drc package"

Thanks. I see what went wrong. 2015-12-07 16:33 GMT-05:00 Jeff Newmiller : > The fine manual for the drm function mentions a parameter "logDose" ... I > expect that since you did not specify it that the drm function is helpfully > attempting to take the log of your data for you. > > I highly rec

Re: [R] question with drm function in "drc package"

The fine manual for the drm function mentions a parameter "logDose" ... I expect that since you did not specify it that the drm function is helpfully attempting to take the log of your data for you. I highly recommend reading up on making reproducible examples so your helpers can experiment wi

Re: [R] ChAMP: champ.runCombat error with methylation 450k data

Champ is a BioConductor package. You should post to the Bioconductor Help, not here. Cheers, Bert Bert Gunter "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." -- Clifford Stoll On Mon, Dec 7, 2015 at 12:34 PM, Brian Smith wrote: > Hi, > > I w

[R] ChAMP: champ.runCombat error with methylation 450k data

Hi, I was trying to run COMBAT on methylation data, but keep on getting an error: Error in while (change > conv) { : missing value where TRUE/FALSE needed The error occurs irrespective of whether I give the entire or reduced (variation filter keeps only about 140k CpGs) datasets. Is there any o

[R] question with drm function in "drc package"

Hi all, I am trying to use the drm function in drc package to fit a 4 PL or 3PL curve for an assay response. Please see the listed data below. When I do the curve fitting, it returns the following error message. Anyone who familiar with this have any input on what went wrong? Thanks so much in

Re: [R] Simple DLNM in R

Oops, perhaps I should have said “a representative sample of the data” but it looks like it has arrived safely. Let me tell you about head() someday. I am not sure of the data.frame names since the original code has some sub-setting at the beginning. At the moment I am calling the first data se

Re: [R] Spatial Panel Model by Maximum Likelihood: error message

Thank you but no! I have tried that as well and I get: "Error in mat2listw(e) : (list) object cannot be coerced to type 'double'" > From: holterm...@hwwi.org > To: roypete...@hotmail.com; r-help@r-project.org > Subject: AW: [R] Spatial Panel Model by Maximum Likelihood: error message > Date: Mon

[R] [R-pkgs] WriteXLS Version 4.0.0 Released

Hi all, WriteXLS version 4.0.0 has been released. It should start appearing in source tarballs and binaries in due course on CRAN mirrors. The primary changes in this new version are: 1. The new ability to specify either a single data frame object or a list object that contains one or more dat

Re: [R] ggplot2: remove axis ticks

Change the order of adding the themes from theme(axis.ticks=element_blank()) + theme_bw() to theme_bw() + theme(axis.ticks=element_blank()) because theme_bw() adds axis.ticks = element_line(colour = "black"). Bill Dunlap TIBCO Software wdunlap tibco.com On Mon, Dec 7, 2015 at 7:10 AM, Brian

[R] ggplot2: remove axis ticks

Hi, I was trying to remove the axis tick marks and their values using theme() but haven't had much success. Here is sample code: rx <- sample(1:100,10) ry <- sample(1:100,10) rz <- sample(letters[1:3],10,replace=T) rdf <- data.frame(rx,ry,rz) p <- ggplot(rdf,aes(x=rx,y=ry)) p1 <- p + geom_point(

Re: [R] Spatial Panel Model by Maximum Likelihood: error message

Maybe "e" has the wrong class. Probably it is a matrix. Try listw = mat2listw(e) Mit freundlichen Grüßen Linus Holtermann Hamburgisches WeltWirtschaftsInstitut gemeinnützige GmbH (HWWI) Heimhuder Straße 71 20148 Hamburg Tel +49-(0)40-340576-336 Fax+49-(0)40-340576-776 Internet: www.hwwi.org Ema

Re: [R] Ordering Filenames stored in list or vector

Thanks a lot for the clarifying code Mark! Actually, I took a lazy option and after some digging around I found out the package called "naturalsort" which provides a pretty compact solution! As a rookie, I have another question. My main interest in R is that I hope to integrate in a scripting f

Re: [R] Simple DLNM in R

Welcome to the list. You have provided a nic clear question but I think the one thing missing in dealing with it is some sample data. Have a look at ?dput or see the dput() discussions in one of these links : http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-examp

Re: [R] Dense time series

Please have a look at http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example and/or http://adv-r.had.co.nz/Reproducibility.html Probably the image and your code did not come through because R-help is very picky about what types of files it allows as a security mesu

Re: [R] metafor package

The code you posted is totally mangled up, but it's just what can be found here: http://www.metafor-project.org/doku.php/plots:forest_plot_with_subgroups If you don't want an overall estimate, just pass the estimates and corresponding sampling variances to the forest() function (and not the mode

Re: [R] choropleth packages (US)

ggplot2 also can do this with fortify geom_polygon Von meinem iPad gesendet > Am 06.12.2015 um 21:03 schrieb Benjamin Tyner : > > Hi > > I wish to draw a basic choropleth (US, by state) and am wondering if anyone > has any recommendations? I've tried the following thus far: > > 1. choroplethr

[R] [R-pkgs] LW1949 – new package for evaluating dose-effect experiments

LW1949 1.0.0 is now available on CRAN. LW1949 automates the steps taken in Litchfield and Wilcoxon’s (1949) manual approach to evaluating dose-effect experiments. Letting the computer do the work saves time and yields the best fit possible using the Litchfield Wilcoxon approach (by minimizing th