Dear Ashim,
If you really want to use lynx, then you need to open up a new terminal to make
this work. For example, this will do:
browseURL("http://www.r-project.org","xterm -e lynx")
But this will open up a new terminal for each call to browseURL().
Best,
Wolfgang
>-Original Message-
Tobit models. Just explore these
packages to see what they can do.
Best,
Wolfgang
>-Original Message-
>From: Chris Evans [mailto:chrish...@psyctc.org]
>Sent: Tuesday, 21 December, 2021 12:56
>To: Viechtbauer, Wolfgang (SP)
>Cc: r-help@r-project.org
>Subject: Re: Creat
Hi Chris,
The survival package provides machinery for handling censored observations.
Whether time is censored or some other type of variable (e.g., viral load due
to some lower detection limit) does not make a fundamental difference. In fact,
the type of model you are thinking of with 2) is a
Hello all,
Say I would like to change the outcome in a formula to a variable not part of
the original dataset. This works just fine:
res <- lm(mpg ~ wt + cyl, data=mtcars)
res
y <- rnorm(nobs(x))
update(x, formula = y ~ .)
But not when doing so within a function:
rm(y)
f <- function(x) {
y
>-Original Message-
>From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
>Sent: Monday, 12 April, 2021 1:58
>To: Viechtbauer, Wolfgang (SP); R-help
>Subject: Re: [R] evil attributes
>
>On 11/04/2021 2:46 p.m., Viechtbauer, Wolfgang (SP) wrote:
>> The is.vector
The is.vector() thing has also bitten me in the behind on a few occasions. When
I want to check if something is a vector, allow for it to possibly have some
additional attributes (besides names) that would make is.vector() evaluate to
FALSE, but evaluate to FALSE for lists (since is.vector(list(
Dear Roger,
The problem is this. qss() looks like this:
if (is.matrix(x)) {
[...]
}
if (is.vector(x)) {
[...]
}
qss
Now let's check these if() statements:
is.vector(B$x) # TRUE
is.vector(D$x) # FALSE
is.matrix(B$x) # FALSE
is.matrix(D$x) # FALSE
is.vector(D$x) being FALSE may be surprisin
Dear Usmle Ck,
This is what the 'slab' argument is for (for adding 'study labels'). For an
example, see:
https://www.metafor-project.org/doku.php/plots:forest_plot
Best,
Wolfgang
>-Original Message-
>From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Usmle Ck
>Sent: Monday
.]
Warning message:
In wilcox.test.default(c(1, 3, 2, 2, 4), exact = TRUE) :
cannot compute exact p-value with ties
Best,
Wolfgang
>-Original Message-
>From: Jiefei Wang [mailto:szwj...@gmail.com]
>Sent: Friday, 19 March, 2021 16:32
>To: Viechtbauer, Wolfgang (SP)
>Cc: r-help
&g
Dear Jiefei,
This behavior is documented. From help(wilcox.test):
"By default (if exact is not specified), an exact p-value is computed if the
samples contain less than 50 finite values and there are no ties. Otherwise, a
normal approximation is used."
Best,
Wolfgang
>-Original Message---
/DejaVuSansMono.ttf
Substitute your favorite (ttf/otf) monospaced font above.
Best,
Wolfgang
>-Original Message-
>From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Viechtbauer,
>Wolfgang (SP)
>Sent: Wednesday, 20 January, 2021 10:10
>To: Paul Mu
>From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Viechtbauer,
>Wolfgang (SP)
>Sent: Wednesday, 20 January, 2021 9:44
>To: Paul Murrell; r-help@r-project.org
>Subject: Re: [R] Monospaced font not shown correctly (Xubuntu 20.04)
>
>Dear Paul,
>
>Thanks for t
-*-*-%d-*-*-*-*-*-*-*")
X11(family="mono")
plot(1)
Best,
Wolfgang
>-Original Message-
>From: Paul Murrell [mailto:p...@stat.auckland.ac.nz]
>Sent: Wednesday, 20 January, 2021 0:37
>To: Viechtbauer, Wolfgang (SP); r-help@r-project.org
>Subject: Re: [R] Monos
Hi all,
On my system (Xubuntu 20.04), using par(family="mono") is not rendered
correctly. The same issue was raised here:
https://stackoverflow.com/questions/64207220/rendering-plot-in-r-with-mono-spaced-family-font-does-not-display-characters-any
Using par(family="monospace") does work:
par(m
Dear Sigbert,
The mathjaxr package provides this:
https://cran.r-project.org/package=mathjaxr
https://github.com/wviechtb/mathjaxr
Best,
Wolfgang
>-Original Message-
>From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Sigbert
>Klinke
>Sent: Tuesday, 12 January, 2021 9:14
>T
ailto:amoatwi...@gmail.com]
>Sent: Tuesday, 23 June, 2020 16:37
>To: Viechtbauer, Wolfgang (SP)
>Cc: r-help@r-project.org
>Subject: Re: [R] Error message in meta-analysis package Metafor-weights =""
>
>Dear Wolfgang,
>I have posted the requested information you as
Dear Kobby,
Please post the output of sessionInfo() and class(result.md).
Best,
Wolfgang
>-Original Message-
>From: K Amoatwi [mailto:amoatwi...@gmail.com]
>Sent: Monday, 22 June, 2020 22:30
>To: Viechtbauer, Wolfgang (SP)
>Cc: r-help@r-project.org
>Subject: Re: [R
Dear Amoatwi,
This way of using the escalc() function has been deprecated. It might be added
back once there is actually any benefit from having this functionality, but for
years it just meant that I had to maintain two different ways of doing the
exact same thing without any additional benefit
Dear All,
I would like to announce the release of the 'mathjaxr' package:
https://cran.r-project.org/package=mathjaxr
The package provides MathJax and a handful of macros to enable its use within
Rd files for rendering equations in the HTML help files.
Package authors wanting to make use of t
Dear John,
The linearHypothesis() function from the 'car' package does this.
>From the help file: "The value of the linear hypothesis and its covariance
>matrix are returned respectively as "value" and "vcov" attributes of the
>object (but not printed)." For a single linear combination, vcov w
Dear Heather,
You can do this with clogit() from the 'survival' package, using strata(). See:
http://www.metafor-project.org/doku.php/tips:clogit_paired_binary_data
You can also use lme4::glmer(), glmmML::glmmML(), or metafor::rma.glmm() for
that. [1]
[1] Rerunning this example, I noticed a sl
Gunter [mailto:bgunter.4...@gmail.com]
Sent: Tuesday, 26 March, 2019 17:43
To: Viechtbauer, Wolfgang (SP)
Cc: r-help mailing list
Subject: Re: [R] Substitution in expressions
Perhaps something like this (apologies if beating a dead horse):
plot(NA,NA, xlim = c(-1,5),ylim = c(-1,5), xlab = "&q
Hi Bert,
I am indeed creating a mathematical expression, but ?plotmath doesn't cover how
to do such a vectorized substitution.
Best,
Wolfgang
-Original Message-
From: Bert Gunter [mailto:bgunter.4...@gmail.com]
Sent: Tuesday, 26 March, 2019 15:52
To: Viechtbauer, Wolfgang (SP)
Ok, thanks. Happy to stick with mapply() then.
Best,
Wolfgang
-Original Message-
From: peter dalgaard [mailto:pda...@gmail.com]
Sent: Tuesday, 26 March, 2019 15:40
To: Viechtbauer, Wolfgang (SP)
Cc: r-help mailing list
Subject: Re: [R] Substitution in expressions
I think mapply() is
, 2019 14:42
To: Viechtbauer, Wolfgang (SP)
Cc: r-help mailing list
Subject: Re: [R] Substitution in expressions
Er, I'm confused.
You post some code, the code does something. In which sense is this not what
you want?
This is slightly more direct:
> mapply(function(x,y) as.expression(bq
Hi All,
I am trying to create a vector of expressions, where the elements in the
expressions are contained in other vectors (i.e., they should be substituted).
I made some attempts with substitute() and bquote(), but couldn't get this to
work. My solution so far is:
base <- 1:5
expo <- c(2,2,3
ata=a, method="REML", slab=paste(a$study), digits=3)
Best,
Wolfgang
-Original Message-
From: greg holly [mailto:mak.hho...@gmail.com]
Sent: Monday, 25 February, 2019 21:20
To: Viechtbauer, Wolfgang (SP)
Subject: Re: [R] differences between meat and metafor packages
Hi Wolfg
The second argument (called 'vi') in rma() is for the variances. If you have
SEs, then use the 'sei' argument:
res <- rma(HR, sei=SE, data=a)
Best,
Wolfgang
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of greg holly
Sent: Monday, 25 February, 2019 18:4
Dear Petr,
Sorry, no experience with the FTH, but related to this, has anybody gotten R to
interface nicely with the Retro Encabulator, providing live read outs of the
synchronizing cardinal grammeters?
(my apologies, I just couldn't resist)
Best,
Wolfgang
>-Original Message-
>From: R
Dear Greg,
I am not sure if I understand your question. If you are asking how to do this
in R, then one could use the metafor or meta package for this. The specificity
and sensitivity values are proportions, so one would usually meta-analyze them
after a logit transformation. But all of the spe
g
>-Original Message-
>From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
>Sent: Tuesday, 03 July, 2018 17:48
>To: r-help@r-project.org; Viechtbauer, Wolfgang (SP); r-help@r-
>project.org
>Subject: Re: [R] Combine by columns a vector with another vector that is
Hi All,
I have one vector that I want to combine with another vector and that other
vector should be the same for every row in the combined matrix. This obviously
does not work:
vec <- c(2,4,3)
cbind(1:5, vec)
This does, but requires me to specify the correct value for 'n' in replicate():
cbi
This aside, there is the R-sig-meta-analysis mailing list where this probably
belongs:
https://stat.ethz.ch/mailman/listinfo/r-sig-meta-analysis
Best,
Wolfgang
>-Original Message-
>From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Bert
>Gunter
>Sent: Thursday, 15 February,
Hi All,
It seems to me that xyTable() gets thrown off by NAs:
x <- c(1, 1, 2, 2, 2, 3)
y <- c(1, 2, 1, 3, NA, 3)
table(x, y, useNA="always")
xyTable(x, y)
Is this intended behavior?
Best,
Wolfgang
__
R-help@r-project.org mailing list -- To UNSUBSCRI
The code in your mail in a mangled mess, since you posted in HTML. Please
configure your email client to send emails in plain text.
Could you explain what exactly you mean by "Currently it is using a mixed
effects model. Is it possible to change the code so a random effects model is
used?"
Be
I would suggest to post this to the (recently created) R-sig-meta-analysis
mailing list. See:
https://stat.ethz.ch/mailman/listinfo/r-sig-meta-analysis
Best,
Wolfgang
>-Original Message-
>From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Naike Wang
>Sent: Monday, June 26,
You could use an offset term. An example:
n <- 100
x1 <- rnorm(n)
x2 <- rnorm(n)
x3 <- rnorm(n)
y <- 0 + .2 * x1 - .5 * x2 + .3 * x3 + rnorm(n)
res1 <- lm(y ~ x1 + x2)
summary(res1)
res2 <- lm(y ~ 1 + offset(coef(res1)[2] * x1 + coef(res1)[3] * x2))
summary(res2) ### identical intercept as in res1
Sort of an obvious approach, but after every upgrade (regardless if it is
major/minor), I just delete my entire personal library and reinstall everything
from scratch. For this, I have a script that includes just a bunch of
install.packages() calls. Like:
install.packages(c("lme4", "glmmML", "M
You are not conducting a proper test of the moderator. When you use 'mods =
~factor(sample_data$Participants) - 1', the model does not include an intercept
term but dummy variables corresponding to all levels of the moderator. The
omnibus test you are getting therefore tests the null hypothesis
Very difficult to diagnose what is going on without actually seeing the data.
But as I said on CV: Depending on the data, the variance components may not be
estimated precisely, so negative values for those kinds of pseudo-R^2
statistics are quite possible. In fact, if a particular moderator is
Hi Laura,
As far as I am concerned, you account for multiple effects sizes from the same
study by setting up and fitting an appropriate model, not by fiddling with the
weights. Several examples are described here:
http://www.metafor-project.org/doku.php/analyses#multivariate_multilevel_meta-ana
Dr. Harrell,
Thanks for your patient replies. I've two more questions:
1) Is your book appropriate for beginners or is it more for advanced users?
2) f <- ols(y ~ rcs(x,3), data=mydata)
Function(f)
does not produce anything for me (i.e.) it's empty.
Sincerely,
sp
--- On Tue, 12
t the regression curve differs from the actual
points by as high as 10^5 with 3 knots and roughly -10^5 with 4 knots as I make
y=x^2, y=x^3
If this is NOT a good way to test fitting, could you pls tell me a better way?
Respectfully,
sp
--- On Tue, 12/23/08, Frank E Harrell Jr wrote:
> Fr
tercept 5.90958 0.0672612 87.860
x1 0.03679 0.0002259 162.880
x1' -0.01529 0.0002800 -54.600
Residual standard error: 0.76 on 997 degrees of freedom
Adjusted R-Squared: 0.9897
"
I appreciate any and all help!
Sincerely,
sp
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