Actually, you'll need to identify the values of the foreach loop in the for
loop for it to work...
require(doParallel)
require(foreach)
set.seed(666)
xyz<-as.data.frame(cbind(x=rep(rpois(5,10),2)+1,
y=rep(rpois(5,10),2)+1,z=round(runif(10, min=-3, max=40),2)))
xyz$mins<-rep(NA, nrow(
On Mon, 8 Aug 2016, Ellis, Alicia M wrote:
I have a large dataset with ~500,000 columns and 1264 rows. Each column
represents the percent methylation at a given location in the genome.
I need to run 500,000 linear models for each of 4 predictors of interest
in the form of:
Methylation.stie
Hi Loris,
If I understand what you want, it seems to be a combination of a Gantt
chart and a sizetree. The Gantt chart provides the horizontal extent
of the rectangles and the sizetree the vertical extent by assigning
relative heights to the initial rectangles and dividing these into
subsets as tim
Hi Loris,
This looks a lot like a Gantt chart with variable bar widths. I'll
check it when I have a bit of time and repost.
JIm
On Mon, Aug 8, 2016 at 6:12 PM, Loris Bennett
wrote:
> Hi,
>
> I want to visualise temporal events as rectangles, one side of the
> rectangle being the length of the e
Don't run 500K separate models. Use the limma package to fit one model that
can learn the variance parameters jointly. Run it on your laptop. And don't
use %methylation as your Y variable, use logit(percent), i.e. the Beta
value.
-Aaron
On Mon, Aug 8, 2016 at 2:49 PM, Ellis, Alicia M
wrote:
> I
> On Aug 8, 2016, at 12:48 AM, Mohsen Sharafatmandrad
> wrote:
>
> I want to change x and y ranges in a PCA plot created by library(labdsv).
> When I run "plot(o.pca, xlim=c(-2, 3), ylim=c(-2, 4))", nothing will
> change. Script is as fallow:
>
>
>
> raw<- matrix(c(1,2,2.5,2.5,1,0.5,0,1,2,4,
I have a large dataset with ~500,000 columns and 1264 rows. Each column
represents the percent methylation at a given location in the genome. I need
to run 500,000 linear models for each of 4 predictors of interest in the form
of:
Methylation.stie1 ~ predictor1 + covariate1+ covariate2 + ... c
Ok - got it, I can handle that. Thank you Luke!
Jacob L Strunk
___
From: luke-tier...@uiowa.edu [luke-tier...@uiowa.edu]
Sent: Monday, August 08, 2016 12:17 PM
To: Strunk, Jacob (DNR)
Cc: r-help@r-project.org
Subject: Re: [R] interaction between clusterMap(), r
Since 2008, Microsoft (formerly Revolution Analytics) staff and guests have
written about R every weekday at the
Revolutions blog: http://blog.revolutionanalytics.com
and every month I post a summary of articles from the previous month of
particular interest to readers of r-help.
And in case you
Getting the dates of the departments CC, DD, FF can be done with
subset(df, deps %in% c("CC", "DD", "FF"))
I am not sure how you intend to match these identified dates with other
departments? From your example you sometimes replace earlier dates,
sometimes later dates.
HTH
Ulrik
On Mon, 8 Aug 2
try is working fine. The problem is that your remote function is
returning the try-error result, which the parallel infrastructure is
interpreting as an error on the remote node, since the remote calling
infrastructure is using try as well. This could be implemented more
robustly, but it would pro
Hi there,
I have a data set like below and wanted to create a new date variable by
extracting the dates for specific departments.I want to extract the dates for
departments CC, DD, FF, put it in a new column and repeat it for other unique
IDs.
Subject<- c("2", "2", "2", "3", "3", "3", "4", "4"
Hello I am attempting to process a list of csv files in parallel, some of which
may be empty and fail with read.csv. I tend to use clusterMap as my go-to
parallel function but have run into an interesting behavior. The behavior is
that try(read.csv(x)) does not catch read errors resulting from h
Greetings, R users!
I am pleased to announce the release of my first CRAN package: ggghost.
https://cran.r-project.org/web/packages/ggghost
https://github.com/jonocarroll/ggghost
Features:
- Minimal user-space overhead for implementation; p %g<% ggplot(dat,
aes(x,y))
- ggplot2 components adde
I want to change x and y ranges in a PCA plot created by library(labdsv).
When I run "plot(o.pca, xlim=c(-2, 3), ylim=c(-2, 4))", nothing will
change. Script is as fallow:
raw<- matrix(c(1,2,2.5,2.5,1,0.5,0,1,2,4,3,1),nrow=6)
colnames(raw)<- c("s1","s2")
rownames(raw)<- c("r1","r2","r3","r4","
Assuming that within each ID the data is sorted by increasing TIME, and
that LABEL==1 occours only once within each ID. Then I would try something
like this.
Suppose that your data is in a data frame named "df".
df.keep <- logical()
for (id in unique(df$ID)) {
df.tmp <- subset(df, df$ID==id)
Hi everyone,
I have three ordered regression models where the ordered dependent variable
ranges from 0 to 2. What I want to do is create marginal effects tables (not a
plot) at each level (0, 1, and 2) for all three models. So, three tables with
each showing the marginal effects at level 0, 1,
xtractomatic is an R package developed to subset and extract satellite and
other oceanographic related data from a remote server. The program can extract
data for a moving point in time along a user-supplied set of longitude,
latitude and time points; in a 3D bounding box; or within a polygon (t
Your code runs without errors so there is no issue with R. The function you are
using is for [Partial] [Constrained] Correspondence Analysis. You have not
defined 3-way correspondence analysis, but my understanding is that it involves
correspondence analysis of a 3-way crosstabulation array. You
Martin Maechler writes:
>> Loris Bennett
>> on Mon, 8 Aug 2016 14:12:47 +0200 writes:
>
> > Loris Bennett writes:
> >> Thanks for the link, John. However, there is a hyphen missing. It
> >> should be:
> >>
> >>
> http://www.dummies.com/how-to/content/how-to-r
> Loris Bennett
> on Mon, 8 Aug 2016 14:12:47 +0200 writes:
> Loris Bennett writes:
>> Thanks for the link, John. However, there is a hyphen missing. It
>> should be:
>>
>>
http://www.dummies.com/how-to/content/how-to-read-errors-and-warnings-in-r.html
>>
Loris Bennett writes:
> Thanks for the link, John. However, there is a hyphen missing. It
> should be:
>
>
> http://www.dummies.com/how-to/content/how-to-read-errors-and-warnings-in-r.html
>
> Appropriately, with the correct URL we find the too often forgotten
> pearl of wisdom:
>
> "Chance
Dear Carlos
If you use functions from a contributed package it is best to tell us
which package. There are nearly 9000 of them.
On 07/08/2016 17:13, Carlos Javier Rincon Rodriguez wrote:
hi,
i am using the funtion metaprop but when i try to save the proportion
estimation by subgrup using the
Thanks for the link, John. However, there is a hyphen missing. It
should be:
http://www.dummies.com/how-to/content/how-to-read-errors-and-warnings-in-r.html
Appropriately, with the correct URL we find the too often forgotten
pearl of wisdom:
"Chances are, you just typed something wrong the
http://www.dummies.com/how-to/content/how-to-read-errors and-warnings-in-r.html
If something goes wrong with your code, R tells you. We have to admit it: These
error messages can range from mildly confusing to completely incomprehensible
if you’re not used to them.
fortune(350) regarding the on
Hi,
I was probably misled by the, to my mind, esoteric error message into
thinking the error was more subtle. Something like "unmatched quotes"
might have helped me recognise that I was just being dopey.
Thanks to John and Rui.
Loris
writes:
> Hello,
>
> You're missing a double quotes. Right
Hello,
You're missing a double quotes. Right after format=
Hope this helps,
Rui Barradas
Citando Loris Bennett :
> Hi,
>
> When I try
>
> d <- as.difftime("6-08:18:33",format=%d-%H:%M:%S")
>
> I get:
>
> Error: unexpected SPECIAL in "as.difftime("6-08:18:33",format=%d-%"
>
> Am I correct in
Try
d <- as.difftime("6-08:18:33","%d-%H:%M:%S")
John Kane
Kingston ON Canada
> -Original Message-
> From: loris.benn...@fu-berlin.de
> Sent: Mon, 8 Aug 2016 11:37:33 +0200
> To: r-h...@stat.math.ethz.ch
> Subject: [R] No "number of days" format for 'difftime'?
>
> Hi,
>
> When I try
Hi,
When I try
d <- as.difftime("6-08:18:33",format=%d-%H:%M:%S")
I get:
Error: unexpected SPECIAL in "as.difftime("6-08:18:33",format=%d-%"
Am I correct in thinking that it is not possible to do something like
this, because there is no character string for the format which
corresponds to
Hi,
I want to visualise temporal events as rectangles, one side of the
rectangle being the length of the event, the other being the size of an
integer variable. The position of the rectangle along the time axis
would be determined by the time of the even, the position on the other
axis is essenti
Dear R-users,
I want to reproduce "a dynamic panel data model, autoregressive of order 1,
with fixed effects" that was originally estimated with 2-step GMM in STATA.
Reproducing the model in R shouldn't be a big deal, however, unfortunately I
don't have the original STATA code and the lagged de
Hi Jennifer,
A very pedestrian method, but I think it does what you want.
remove_rows_after_1<-function(x) {
nrows<-dim(x)[1]
rtr<-NA
rtrcount<-1
got1<-FALSE
thisID<-x$ID[1]
for(i in 1:nrows) {
if(x$ID[i] == thisID && got1) {
rtr[rtrcount]<-i
rtrcount<-rtrcount+1
}
if(x$ID[i] !=
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