estimated in emmeans? I was led to believe that components="response" ,
type = "response" would do that but that does not seem to be the case.
Thank you
Brian
Brian S. Cade, PhD
U. S. Geological Survey (emeritus)
Fort Collins Science Center
2150 Centre Ave., Bldg. C
Fort Colli
ents and
p-values for the 5 baseline variables, so I assumed
that it was due to the small number of levels (in fact, too few ). However,
when computing anova(model.rand, model.fix),
the output indicates a p-value < 0.001 in favour of the "model.rand". What's
happ
CRAN as in cranberry.
Just my minor thought.
Brian
Brian S. Cade, PhD
U. S. Geological Survey
Fort Collins Science Center
2150 Centre Ave., Bldg. C
Fort Collins, CO 80526-8818
email: ca...@usgs.gov<mailto:brian_c...@usgs.gov>
tel: 970 226-9326
From:
-08 57084544 16741008.5984.31
252 10-Aug-08 57084544 16841002.8 1008.5 10
253 22-Oct-08 57084544 1757 977.6 1002.8 73
254 2-Dec-08 57084544 17981000.6977.6 41
Brian
Brian S. Cade, PhD
U
Country <- c('Angola', 'Angola','Botswana',
'Botswana','Zimbabwe','Zimbabwe')
year <- c('2006', '2007', '2008', '2009', '2010', '2006')
bank_ratio <- c(24,25,38,34,42,49)
Reserve_ratio <- c(77,59,64,65,57,86)
broad_money <- c(163,188,317,361,150,288)
id <- (c(1,1,2,2,3,3))
df <- data.frame(Country
All the xYplot() functions using Cbind() or cbind() does just exactly what I
want (Cbind provides aplot of 3 summary statistics and cbind provides the raw
values). I just cannot find anyway to overlay them.
Brian
Brian S. Cade, PhD
U. S. Geological Survey
Fort Collins Science Center
2150
separately, but I would
really like to have them overlayed on each other. I've tried various
approaches with add=T, new=T, etc and none of those seem to work with xYplot().
Any pointers?
Brian
Brian S. Cade, PhD
U. S. Geological Survey
Fort Collins Science Center
2150 Centre Ave., Bl
Chris, thank you so much for your answer!!
Best,
Frank S.
De: Andrews, Chris
Enviado: martes, 3 de septiembre de 2019 14:14
Para: Frank S.
Cc: r-help@r-project.org
Asunto: Re: [R] Efficient way to update a survival model
library("survival")
set
Charles, thank you for your suggestion!
Frank S.
De: Berry, Charles
Enviado: s�bado, 31 de agosto de 2019 19:21
Para: Frank S.
Cc: Andrews, Chris ; r-help@r-project.org
Asunto: Re: Efficient way to update a survival model
The i^th model is included in the Cox
that, when computing Cox[[1]], the term
Cox[[k -1]]
does not exist. Is it possible to perform some "trick" (e.g. re-indexing) in
order to achieve this?
Best,
Frank
De: Andrews, Chris
Enviado: viernes, 30 de agosto de 2019 15:08
Para: Frank S. ; Vito
date(Cox0, substitute(. ~ . + Z[, 1:k]), data = pbc)
attr(Cox[[k]]$coefficients, "names")[2:(k+1)] <- paste0("sin(", 1:k, "* v)")
}
Cox
Best,
Frank
De: Frank S.
Enviado: jueves, 29 de agosto de 2019 12:38
Para: Vito Michele Rosa
hat OK?
Additionally, in my original question I wondered about the possibility of
reducing the
10 lines of code to one general expression or some loop. Is it possible?
Best,
Frank
De: Vito Michele Rosario Muggeo
Enviado: jueves, 29 de agosto de 2019 8:54
Para: Frank S.
Hello everybody, I come with a question which I do not know how to conduct in
an efficient way. In order to
provide a toy example, consider the dataset "pbc" from the package "survival".
First, I fit the Cox model "Cox0":
library("survival")
set.seed(1)
v <- runif(nrow(pbc), min = 0, max = 2)
Co
How many data points do you have in each group?
- How much do the two groups overlap?
If the answers are 'not many' or 'lots' (in that order), and especially if both
apply, you can't expect a significant test result.
S Ellison
*
> tb2a$TID2 <- gsub(tb2a$TID, pattern="-[0-0]{0,7}", replacement = "")
Just to add something on why this didn't work ...
It looks like you were trying to match a hyphen followed by a number up to
seven digits. by mistake(?) you gave the digit range as [0-0] so it would
repmatch a hyphen followe
> I am having an issue with creating a code in which i can hold information such
> as the author of a paper, the year of publication, and the title.
This doesn't really tell me what the trouble is. But ...
> Also would like
> to add into this data frame a logical variable which would show some
>
Not really my field, but would you not approach this using FFT on selected
regions?
I think IMageJ has some capability in that area; see example at
https://imagej.nih.gov/ij/docs/examples/tem/.
Steve Ellison
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On
> Limited water resources need to be apportioned among various competing
> users
> (e.g,, agriculture, fish and wildlife, Tribes, potable human water
> supplies).
Water management is definitely not my field, but for interest - and maybe to
help other folk respond - can I ask what the loss functio
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Michael
> Friendly
> Check out the `matlib` package on CRAN and devel on github:
Very nice! Thanks for the pointer.
Steve E
***
This
You can drop the quote marks by calling print() explicitly with quote=FALSE, by
using as.data.frame round your cbind, or - perhaps best - by constructing your
output matrix as a data frame in the first place. (print.data.frame defaults
to quote=FALSE). And if you suppress name checking in a dat
)
which uses default colours. Once you have an aes mapping you can change the
scale, so
( p + scale_colour_manual(values = c("red", "blue", "green")) )
gives you the colour ordering you want.
( p + scale_colour_manual(values = c("red", "blue", "gr
subset(t1, apply(t1, 1, function(x) !all(is.na(x
(or the equivalent '[' usage)
and, as an aside, using '==' for floating point numbers is not generally safe;
for example
> sqrt(2)^2 == 2.0
[1] FALSE
See R FAQ 7.31 for details of why '==' is bad for floating poin
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Jose
> Claudio Faria
>
> The Tinn-R project has a new web page:
> http://nbcgib.uesc.br/tinnr/en/index.php
>
Thanks for this - and thanks, also, for maintaining Tinn-R and keeping it
available as free software. The effort is muc
install.packages :
package ‘xyplot’ is not available (for R version 3.5.2)
Do you know how I can solve that?
--
S. M. Nasrollahi
Postdoctoral Researcher
French National Institute for Agricultural Research
Unite´ Mixte de Recherches sur les Herbivores,
63122 St Gene`s Champanelle, France
sayyed
Pointers inline below:
> > Since I'm a newbie on R, I was wondering if you could help me to achieve a
> > small project that I think it's possible with this project (I cant seem to
> > find a similar tool)
> >
> > I have a data file with about 2000 value lines, organized like this:
> >
> > x;y;z;j
> With your code you just remove diagonal elements from your matrix.
Worse; it removed _all_ elements from the matrix that match _anything_ in the
diagonal!
Which, in that example, was everything ...
***
This email and any attach
i) Your code creates w2 but references w1 to create aa.
So you needed
aa <- matrix(rep(c(0.4, 0.1, 0.2), 3), 3,3)
for a working example.
ii) This
> matrix(as.numeric(aa)[!as.numeric(aa) %in% diag(aa)],2,3)
removes any value that is present in the diagonal of aa. Look up ?"%in%" to see
what that
You might take a look at the reshape package, which switches from 'long' to
'wide' formats and vice versa in a fairly flexible way.
S Ellison
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of lily li
> Sent: 13 Novemb
Dear R experts --
I never needed to add a dummy column and always query statistical results
by querying summary(model) for GLMER. However, I was recently asked to add
a dummy column for interaction variables when performing GLMER. Could
anyone tell me if it's necessary to add a dummy column for GL
tions are not currently implemented there."
>
>
> https://www.rdocumentation.org/packages/utils/versions/3.5.1/topics/savehistory
> or
> ?savehistory
>
> If my wild guess is wrong, then you'll need, at a minimum, to provide the
> output of
> sessionInfo()
> for anyone to be able
Hi,
I just start to learn R, but I have problem to use "savehistory()"
When I run, it pops out "Error in .External2(C_savehistory, file) :
'savehistory' is not currently implemented". I searched a little bit
online, but I still cannot figure out how to fix that.
thanks,
Suy
[[alterna
You could look at combning a number of palettes from the RColorBrewer package
to get the palette length you want.
S Ellison
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Federico
> Calboli
> Sent: 11 September 2018 08:35
&g
> This package uses a modified version of aov() function, which uses
> Permutation Tests
>
> I obtain different p-values for each run!
Could that be because you are defaulting to perm="Prob"?
I am not familiar with the package, but the manual is informative.
You may have missed something when r
x likelihood, maybe nlme in the nlme package.
For other ideas, look up 'non-linear fitting with R' on any search engine, or
check the R Task Views
S Ellison
***
This email and any attachments are confidential. Any use, copyi
> If I install R on my work network computer, will the data ever leave our
> network?
As far as I know, if you run R locally (and not, say, on an amazon EC2
instance) your data - indeed anything about you or your machine - will only
leave your desktop if you download and run an R package that tr
> Most of my methods, are not exported to the namespace using the
> @examples
> options.
Joanna,
You normally need to export _all_ the objects/functions that you expect users
to be able to run.
And if you are giving an example of a function, it seems likely that you expect
users to use it, so it
> > Eric Bergeron Wed, 8 Aug 2018 12:53:32 +0300 writes:
>
> > You only need one "for loop"
> > for(i in 2:nrow(myMatrix)) {
> >myMatrix[i-1,i-1] = -1
> >myMatrix[i-1,i] = 1
> > }
Or none, with matrix-based array indexing and explicit control of the indices
to prevent overrun i
Another possible approach, using the transformation returned by persp() to
locate axes explicitly and using base graphics to place labels etc, is given at
http://entrenchant.blogspot.com/2014/03/custom-tick-labels-in-r-perspective.html
> -Original Message-
> From: R-help [mailto:r-help-
g your business.
S Ellison
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you have received this message in error, please notify the
> Given that clarification, I'd just generate the full set and remove
> the ones you aren't interested in, as in:
I'd agree; that is probably the most efficient thing to do with only half a
dozen binary variables and a single condition.
A way of going about it for a more complex case might be to
Suggest you take a look at the R website at www.r-project.org; the most
important answers are evident there.
If you 'require' more authoritative answers within a particular timescale, I
suggest you engage an R consultant and pay for them. This is a voluntary list.
S Ellison
>
> On Thu, Aug 2, 2018 at 11:20 AM, R Stafford
> wrote:
> > But I have the extra condition that if E is true, then F must be false, and
> > vice versa,
Question: Does 'vice versa' mean
a) "if E is False, F must be True"
or
b) "if F is True, E must be False"?
... which are not the same.
b) (and
xpected results.
S Ellison
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Naresh
> Gurbuxani
> Sent: 25 July 2018 07:17
> To: R-help@r-project.org
> Subject: [R] Using apply function to merge list of data frames
>
> I have
> #I need to get this final result
> r<-data.frame(i=c(1,1,1,2,2,3), s=c(97, 98, 99, 103, 105, 118))
Nothing magic to suggest.
But maybe:
list.s <- strsplit(d$s,",")
r <- data.frame(i=rep(d$i, times=sapply(list.s, length)), s=unlist(list.s),
stringsAsF
", not the
menu function or the package installation function "install.packages"
The latter needs a list of packages to install. The former tells you what is
already installed.
S Ellison
***
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levels=c("name_b", "name_c", "name_a"))
#or, for a more obviously likely example
lmh <- factor(sample(c("High", "Medium", "Low"), 30, replace=T),
levels=c("Low&qu
need_ the enclosiong {}, though;
> expression(NO[3]^'-'~(mg/L))
works as you intended
S Ellison
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ats[3,], names, pos=1) #labels just below
the medians
#And for placing means on the plot:
RTFmeans <- with(AmbientTr, tapply(RTF, batch, mean))
points(1:length(RTFmeans), RTFmeans, pch=19)
text(1:length(RTFmeans), RTFmeans, paste(round(RTFmeans,0)), pos=
> I am traying to create a a column in my data frame filled down with a
> number.
>
> > df$newcolumn <- number
>
> How can I do it? I am considering use rep() but in this case it is
> necessary know the number of rows in each data base that I have and I would
> like to do it in a faster ( and m
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of JEFFERY
> REICHMAN
> # Standard deviations and correlation
> sig_x <- 1
> sig_y <- 1
> rho_xy <- 0.0
>
> # Covariance between X and Y
> sig_xy <- rho_xy * sig_x *sig_y
>
> # Covariance matrix
> Sig
rn tells me
that you have not constructed your data frame correctly. I can't tell you what
you did wrong there.
- As another poster has said, data.frame is the name of a function - one that
construicts a data frame. R can often tell which you want, but it is never safe
to use the na
he differential function from your function for
y; see ?D
S Ellison
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R-help@r-project.org mailing list --
Hi,
I want to access the R code for UnivRNG but unable to load the files. I am new
to R platform.
The link is https://cran.r-project.org/web/packages/UnivRNG/
Regards,
Gagandeep
[[alternative HTML version deleted]]
__
R-help@r-project.org
> Following the given codes below, I generated a plot that has 6 regions around
> a
> center point (IL), with 5 regions containing
>
> a point (L1, L2 to L5) and sixth vacant region. I want background of all the
> filled
> regions turned "green", while "red" for the
>
> vacant region. Can it be
t?
See ?summary.lm
For a linear model L
summary(L)$r.squared
gives R^2
and the adjusted R^2 is
summary(L)$adj.r.squared
S Ellison
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, "P3", "P4"}}
Note the double parentheses ... this is still a set of sets with one member,
not a set of character strings with four members.
Hope that helps ...
S Ellison
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Neha
ors constructed from allele data, you will usually get
complete nonsense in genetic terms.
You should probably look at something like dist.gene in the ape package: see
https://www.rdocumentation.org/packages/ape/versions/5.0/
Hi All,
I am trying to convert random forest model developed into a pmml file.
randomForest package was used to build the model. The input to the model is
in the form of a matrix (term frequency matrix used for text analytics).
While i try to convert the model into a pmml file an error pops.
Err
ps something that picks the minimum
year for a subject or other relevant group might work? For example
paste("survey", ave(year, studyno, FUN=min), sep="_")
S Ellison
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Kevin
>
> > From: Leif Ruckman [mailto:leif.ruck...@kau.se]
> > Sent: Friday, February 16, 2018 3:27 PM
> > To: PIKAL Petr
> > Subject: RE: stem - strange leaves
> >
> > Thank you, I also found that solution but I think it is strange that
> > this happens at all. I have tried different data and sometimes
Hi Lauren,
Did you ever receive an answer on this? I’ve been having the same errors, and
am stumped, so I’d love to hear how you sorted this out with your models.
Thanks for your help!
Cheers,
Rachel
--
Rachel Smith
PhD Candidate
Odum School of Ecology
University of Georgia
Athens, GA 30602
Hi all
I am hoping to use the SamplingStrata R package for a dataset describing a
population of businesses wherein I have information on the type of
business, as well as, for designated employment number bands, number of
employees and business turnover information. So ideally the stratification
wi
Hi,
I'm using a Cox-Regression to estimate hazard rates on prepayments.
I'm using the "pspline" function to face non-linearity, but I have no clue
how to interpret the result.
Unfortunately I did not find enough information on the "pspline" function
wether in the survival package nor using google
nd is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
> On Tue, Oct 31, 2017 at 4:43 AM, Chris S wrote:
>
>> Hi all
>>
>> I am hoping to use the SamplingStrata R pac
Hi all
I am hoping to use the SamplingStrata R package for a dataset describing a
population of businesses wherein I have information on the type of
business, as well as, for designated employment number bands, number of
employees and business turnover information. So in this context the
employmen
Dear All,
I am unable to complete the R code for deleting nodes in a binary search
tree.
Have provided the code snippet below for an usecase where the node to be
deleted would have a leftnode and no rightnode. I am stuck up at how to
release the node pertaining to the key value given by the funct
standard errors.
So this particular example is apparently version-specific.
S Ellison
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R-help@r-project.o
e thing.
So there's probably more than one reason // was added to C. That and better
editors.
S Ellison
***
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___
Mathias,
If it's any comfort, I appreciated the example; 'expected' behaviour maybe, but
a very nice example for staff/student training!
S Ellison
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Matthias
> Gondan
> Se
> >Is it possible to download and run R on Asus ZenFone, if yes, which
> >version
Try Googling 'R on Android'
The top link is
https://www.r-bloggers.com/install-r-in-android-via-gnuroot-no-root-required/
***
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anova is defaulting to anova.lm, and that doesn't expect a mixed effects model.
Switch them round to put model2 first:
anova (model2, model1)
S Ellison
***
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that there is a difference across three types,
is there a reason not to use something like Levene's test to confirm that the
variances differ by more than chance?
S Ellison
***
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ify Upper limit and Lower limit,
though I've not tried omitting them.
S Ellison
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disclosure other than by the intended recipient is unauthorised. If
you have
istician and explain what you are
trying to achieve. They should be able to tell you either how to get there or,
perhaps, why it's not sensible to start and what to do instead.
Sorry I can't help further
S.
***
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> However, my variable is simulated from the cumulative distribution function
> of the Poisson distribution.
Then I am afraid I don't know what you're trying to achieve.
Or why.
However, the principle holds; write a function that maps [0,1] to the 'pattern'
you want, do that and apply it to the
ke a list of either subpopulations or sets
of population parameters, lapply your simulation generator over the list and
(assuming the output from each of those is a vector) use c(that.list,
recursive=TRUE) to concatenate the resulting list of
> How can I draw a Hypercube sample for the variable mortality_probability so
> that this variable exhibits the same pattern as the observed distribution?
One simple way is to use the uniform random output of randomLHS as input to the
quantile function for your desired distribution(s)
> use
>
> par(mfrow=c(2,2), cex = 1)
This does work as written. But when I first checked single-call setting, an
mfrow change to cex in the same call superseded cex=1; hence my suggestion to
use separate calls to par().
Further checking confirms that the result of a call to par is dependent on
Checking ?par,
" In a layout with exactly two rows and columns the base value
of '"cex"' is reduced by a factor of 0.83: if there are three
or more of either rows or columns, the reduction factor is
0.66."
You should be able to simply set cex to 1/0.83 for a 2x2 layout and by 1/0.66
for
> I'm having trouble with a simple application with metRology.
Well, what you probably need is to contact the maintainer of the metRology
package.
Fortunately that's me.
An immediate problem that I have is that I don't quite understand what you're
doing (in the measurement), so I may need to
I'm looking for a histogram variant in which data points are plotted as
labelled rectangles 'piled up' to form a histogram. I've posted an example at
https://www.dropbox.com/s/ozi8bhdn5kqaufm/labelled_histogram.png?dl=0
It seems to have a long pedigree, as I see it (as
I'm trying to use the following command.
arima (x, order = c(p,d,q), seasonal =list(order=c(P,D,Q), period=s)
How can I write an estimated seasonal ARIMA model from the outputs. To be
specifically, which sign to use? I know R uses a different signs from S plus.
Is it correct that the mod
u run the product on the command line, either inside I() or not, what's the
class of the result?
If that is order-dependent for the object types you're combining, while I don't
know why that might be it would go some way to explaining
appear.
>
> How can I do this?
Use unique() on each row and pad with NA?
Example:
uniq10 <- function(x, L=10) {
u <- unique(x)
c(u, rep(NA, L-length(u)) )
}
as.data.frame( t( apply(tmp, 1, uniq10) ) )
assuming tmp is
atrix with the available
flow data
dT.m[as.matrix(dataTrade.ag[1:2]) ] <- dataTrade.ag$Flow
#This relies on a default conversion from data frame factors to a
character matrix, together
#with R's facility for matrix indexing by 2-column matrix
#Then
dataTrade.ag[1:10
very, very circumspect about presuming to know better than
> SQL
It's a choice. I understand and respect R's. But I can also understand why
someone might have expected something different.
S
***
This email
]
#Which returns
#
# FALSE
which - particularly since it appears without warning - is not an obviously
sensible outcome.
I am not suggesting a change to R's logical operations, which have clearly been
thought through (that is evident from NA&FALSE == FALSE&NA == FALSE). But
I'm using R 3.4.0.
-- Forwarded message --
From: Yves S. Garret
Date: Sun, May 14, 2017 at 2:35 PM
Subject: Cannot generate a *.docx file
To: r-help
Hello,
I have the following code example:
library(ReporteRs)
# Create a word document to contain R outputs
doc &l
Hello,
I have the following code example:
library(ReporteRs)
# Create a word document to contain R outputs
doc <- docx()
# Add a title to the document
doc <- addTitle(doc, "Simple Word document", level = 1)
# Add a paragraph of text into the Word document
cat("Output 1\n")
doc <- addParagraph(
Maybe a daft question arising from lack of reproducible example, but have you
run ls() manually to make sure there are objects that _exactly_ match "_Figs_" ?
The simplest explanation for a loop doing nothing is that there are no cases.
S Ellison
> The following function is suppo
radians=azimuth
)
arrows(x, y, x+cos(az.rad)*size, y+sin(az.rad)*size, ...)
}
plot(0:6, 0:6, type="n")
arrows.az(x, y, Azimuth, Length)
"..." means you can pass all the other options to arrows()
S Ellison
>
>
> Thanks,
>
> Julio
>
>
<- switch(units,
degrees=azimuth*pi/180,
radians=azimuth
)
arrows(x, y, x+cos(az.rad)*length, y+sin(az.rad)*length, ...)
}
plot(0:6, 0:6, type="n")
arrows.az(x, y, Azimuth, Length)
"..." means you can pass all the
recommend you avoid using common function names as variable names)
If you do need to test elements for zeroes, though, note that '==' and '!=' are
not usually recommended for comparisons with zero owing to finite numerical
representation. So that may well be unwise. See the N
b="")
barplot(height = df$Percent[df$Sex == "Males"], add = TRUE, axes = F,
col="#f8bb85", ylab="",
names.arg=c("18-29", "30-44", "45-59", "60+"))
axis(side=2, at = seq(-35,35,by=5),
labels=format(abs(seq
Folks,
The following function works like a charm!
> #Amortization for multiple rows
> createAmorts<-function(ams, numPer, term) {
> fctrs<-rep(1:term, each = numPer)
>
> oneRow<-function(am, fac){
> tdf<-data.frame(ams = c(am), yrs=fac)
> agg<-aggregate(ams ~ yrs, data
Hi,
I raised this question @ stack overflow and got below partial answer. Hope this
mailing list can help on rest to complete.
library(dplyr)
library(tidyr)
input <- "1.8 - versicolor"
temp <- data.frame(input = input) %>%
tidyr::separate(input, c("Petal.Width", "Species"),sep = " -
format.Date
# weekday is the (numerica) day of the week to be used to place the
week
# in a specific month. The default, 4, takes the Thursday.
#Get the year as a character vector
Y <- format(as.Date(yw, yearformat), "%Y&
Apologies for posting a possibly package-specific question, but I'm not sure
whether this is an R or rstan ussue.
Running rstan under R 3.1.1 in windows 10 I get the well-known error
"Compilation ERROR, function(s)/method(s) not created!
C:/Rtools/mingw_64/bin/g++: not found"
ot factors. You will
then get a numerical gradient for each factor instead of a single offset for
each upper level. That isn't really what Placket and Burman had in mind, so I
would not normally start with a P-B design if I wanted to do that. Consider a
response surface model instead.
S
NA)
>
plabor
A slightly more compact variant that avoids the intermediate 'vals' variable is
to apply an anonymous function that does the check internally:
plabor$colD <- apply(plabor, 1, function(x) if(all(is.na(x))) NA else prod(x,
na.rm=TRUE))
S Ellison
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