Dear R-help,
Hope this email finds you well. My name is Ziyan. I am a graduate student in
Zhejiang University. My subject research involves ks.test in stats-package
{stats}. Based on the code, I have two main questions. Could you provide me
some more information?
I download different
resulted from the methods themselves.
Anyway, people interested can use their own data to test and see.
Best,
Jin
On Tue, Oct 24, 2023 at 4:59 AM Ben Bolker wrote:
>For what it's worth it looks like spm2 is specifically for *spatial*
> predictive modeling; presumably its version of CV is
-- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code
Hi Greg,
This can be done by:
spm::pred.acc(testing$case, predict_testing)
It will return both sensitivity and specificity, along with a few other
commonly used measures.
Hope this helps,
Jin
On Tue, Oct 25, 2022 at 6:01 AM Rui Barradas wrote:
> Às 16:50 de 24/10/2022, greg holly escre
Predictive Modeling with R (doi:10.1201/9781003091776), where many
reproducible examples are provided for various predictive methods including
RF, GBM and SVM.
Hope this helps.
Jin
On Tue, Mar 22, 2022 at 11:51 AM Ebert,Timothy Aaron wrote:
> If you are using the program for data analy
in the references
cited in the description of the package.
Cheers,
--
Jin
--
Jin Li, PhD
Founder, Data2action, Australia
https://www.researchgate.net/profile/Jin_Li32
https://scholar.google.com/citations?user=Jeot53EJ=en
[[alternative HTML version deleted
preparation and predictive accuracy assessment.
Any feedback is welcome and appreciated.
--
Jin
--
Jin Li, PhD
Founder, Data2action, Australia
https://www.researchgate.net/profile/Jin_Li32
https://scholar.google.com/citations?user=Jeot53EJ=en
free to contact me if you have any questions regarding the spm
package.
Best regards,
--
Jin
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to contact me if you have any questions regarding the spm
package.
Best regards,
--
Jin
--
Jin Li, PhD
Founder, Data2action, Australia
https://www.researchgate.net/profile/Jin_Li32
https://scholar.google.com/citations?user=Jeot53EJ=en
:
> Thanks a lot Jin..
>
> If my total number of observations are 500,
> n will be 500,
> mu will be average (500)
> s will be sd (500)
> and m will be RMSE value i.e. 4500 in this case?
>
> tovecv(n=500, mu=average (500), s=sd, m=4500, measure="rmse")
>
>
>
to
VEcv using tovecv in spm.
Hope this helps,
Jin
On Fri, Mar 13, 2020 at 8:08 AM Neha gupta wrote:
> Hi
>
> I have a regression based data where I get the RMSE results as:
>
> SVM=3500
> ANN=4600
> R.Forest=2900
>
> I want to know how can I make it so that its val
suggestions, please send me an
email! Thanks in advance!
Kind regards,
Jin Li, PhD | Spatial Modeller / Computational Statistician
National Earth and Marine Observations | Environmental Geoscience Division
t: +61 2 6249 9899www.ga.gov.au<http://www.ga.gov.au/>
Geoscience Australia Disc
sysname release
"Windows" "7 x64"
version
"build 7601, Service Pack 1"
machine
"x86-64"
Have I miss-specified or missed some param
. Revised RFcv etc. to use pred.acc.
6. Removed samples with missing values in data(hard).
6. Updated vignette accordingly.
Comments, suggestions and contributions are welcome and much appreciated!.
Kind regards,
Jin Li, PhD | Spatial Modeller / Computational Statistician
National Earth
nor r2, why not? Then what? PLOS ONE 12 (8): e0183250.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183250.
The package, spm, can be downloaded from CRAN now.
Any feedback and comments are much appreciated!
Kind regards,
Jin
Jin Li, PhD | Spatial Modeller / Computati
_R3.1.0")
for (p in setdiff(packages, installed.packages()[,"Package"]))
install.packages(p)
Hope this helps.
Jin
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Tobias Knuth
Sent: Friday, 1 April 2016 12:05 AM
To: r-help@r-project.org
Su
.
Best regards,
Zhao
2013/11/2 Jim Lemon j...@bitwrit.com.au
On 11/02/2013 10:35 AM, Zhao Jin wrote:
Dear all,
I am trying to make a series of waffle plot-like figures for my data to
visualize the ratios of amino acid residues at each position. For each one
of 37 positions, there may be one
Dear all,
I am trying to make a series of waffle plot-like figures for my data to
visualize the ratios of amino acid residues at each position. For each one
of 37 positions, there may be one to four different amino acid residues. So
the data consist of the positions, what residues are there, and
I am having difficulty finding a solution to devising an R code to do the
following:
I have 5 numerical variables and I would like to create a new variable that
is the sum of those 5 variables. However, there are many NA values
throughout these 5 variables and everytime I run the following code
Dear Jari,
Thanks a lot for your reply.
Let me describe more about my dataset: it consists of count data for samples,
and shows how many copies of a certain bacteria are in a sample. There are 92
samples (rows), and about 3500 kinds of bacteria (columns). Variable 1 (Var1)
is a factor
in the formula.
Here is more info on the R version and the OS:
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Thanks a lot for any help or comment,
Zhao
--
Zhao JIN
Ph.D. Candidate
Ruth Ley Lab
467 Biotech
Field of Microbiology, Cornell University
Lab: 607.255.4954
Cell: 412.889.3675
Hi R users,
I am trying to fit a Mixed Markov Model and ran into trouble with maximizing
the log-likelihood function. I attached my R codes and the problem I have right
now is that the maximization may end in some local maximum by specifying
different start values. I am thinking if we can
Hi R users,
I am trying to figure out if there is a package in R that can maximize
likelihood function with EM algorithm. Right now, I have derived the
log-likelihood function, which is a function of 9 indicator variables with 14
parameters. Is there a package that I can specify the
http://www.physioth.com/mkqrozh/njy
3/13/2013 3:55:55 PM .
Jin Minming
[[alternative HTML version deleted]]
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R
I am trying to figure out how to calculate p-values for the difference in
prevalence of a risk factor between men and women. For example, I find that
277 out of 710 male patients and 125 out of 305 female patients have
obesity, what is the p-value for their difference?
If there is a package that
this for every column that contains
amino acid residues?
Many thanks for any help you could give me on this topic! :)
Regards,
Zhao
--
Zhao JIN
Ph.D. Candidate
Ruth Ley Lab
467 Biotech
Field of Microbiology, Cornell University
Lab: 607.255.4954
Cell: 412.889.3675
do this for every column that
contains
amino acid residues?
Many thanks for any help you could give me on this topic! :)
Regards,
Zhao
--
Zhao JIN
Ph.D. Candidate
Ruth Ley Lab
467 Biotech
Field
could give me on this topic! :)
Regards,
Zhao
--
Zhao JIN
Ph.D. Candidate
Ruth Ley Lab
467 Biotech
Field of Microbiology, Cornell University
Lab: 607.255.4954
Cell: 412.889.3675
[[alternative HTML version deleted]]
__
R-help@r-project.org
. Then I could calculate the prevalence of each risk factor
separately. This approach will take a very long time so I was hoping
to ask if anyone knew of a solution to this issue I am having with
contingency tables...perhaps a useful R package?
Thank you for your help!
Jin Choi
Masters Student
the
desired result?
Thanks in advance,
Jin
Geoscience Australia Disclaimer: This e-mail (and files transmitted with it) is
intended only for the person or entity to which it is addressed. If you are not
the intended recipient, then you have received this e-mail by mistake and any
use, dissemination
Thank you all for providing various alternatives. They are all pretty fast.
Great help! Based on a test of a dataset with 800,000 rows, the time used
varies from 0.04 to 11.56 s. The champion is:
a1$h2 - 0
a1$h2[a1$h1==H] - 1
Regards,
Jin
Geoscience Australia Disclaimer: This e-mail
Thanks for your validation. Yes Peter's solution is the fastest, faster than
the previous one by saving 25% time. It was missed out in my previous testing.
Jin
-Original Message-
From: Pascal Oettli [mailto:kri...@ymail.com]
Sent: Wednesday, 4 July 2012 2:07 PM
To: Li Jin
Cc: r-help@r
variables. I tried searching for
this function in many R packages, but it has proven elusive to me. I
am an R beginner, and I am hoping that I will find a solution!
Thank you very much.
Sincerely,
Jin Choi
MSc Epidemiology student
McGill University, Montreal, Quebec, CANADA
very much to both of you!
Jin
On Mon, May 7, 2012 at 5:14 AM, Viechtbauer Wolfgang (STAT)
wolfgang.viechtba...@maastrichtuniversity.nl wrote:
Michael just provided a good suggestion, using the subset argument to make
sure that you are really using the same data in both analyses.
However, I
function from the meta-regression.
I thought they should have been the same - can I get help to explain
why there are differences? In both cases, I am transforming raw
Pearson coefficients to z-transformed coefficients, then
back-transforming to raw r after pooling.
Thank you very much.
Jin Choi
MSc
Hi all,
So let's say I have a matrix, mdat and I only know the index number. How do
I retrieve the column and row names?
For example,
mdat - matrix(c(1,2,3, 11,12,13), nrow = 2, ncol=3, byrow=TRUE,
dimnames = list(c(row1, row2),
c(C.1, C.2, C.3)))
Dear All,
There are two packages which can be used for sensitivtiy analysis when the
predictor variables are correlated.
a: pcc (partial correlation coefficient) in R sensitivity package
b: varimp in R party package (conditional importance)
Are other R packages available for sensitivity
estimator using boot package
To: r-help@r-project.org
Date: Tuesday, 6 March, 2012, 3:23
Jim if I understand you, you are
using the ordinary bootstrap instead of the
Efron-Gong optimism bootstrap. I don't think the
ordinary bootstrap is
applicable here.
Frank
Jin Minming wrote
Hello
Dear All,
Anyone has some idea how to implement 632 estimator and leave-one out
bootstraping method by using boot package. I know the bootstrap package has
this function, but it sounds not very flexible for my project.
Thanks,
Jim
__
and supplying your own function
which takes the data and returns a bootstrap sample.
Angelo Canty
Jin Minming wrote:
Dear All,
Anyone has some idea how to implement 632 estimator and
leave-one out bootstraping method by using boot
package. I know the bootstrap package has this
function
bootstrap seem to be a
result only of the use of a discontinuous improper scoring
role (proportion
classified correctly). The advantage may vanish when
better scoring rules
are used. Simulations showing this may be found at
http://biostat.mc.vanderbilt.edu/rms
Frank
Jin Minming wrote
Dear all,
The variable selection in regression is usually determined by the training data
using AIC or F value, such as stepAIC. Is there some R package that can
consider both the training and test dataset? For example, I have two separate
training data and test data. Firstly, a regression
:
From: Liaw, Andy andy_l...@merck.com
Subject: RE: [R] Variable selection based on both training and testing data
To: 'Jin Minming' jminm...@yahoo.com, r-help@r-project.org
r-help@r-project.org
Date: Monday, 30 January, 2012, 13:39
Variable section is part of the
training process-- it chooses
...@wayne.edu
Subject: [R] Fw: Variable selection based on both training and testing data
To: r-help@r-project.org r-help@r-project.org
Date: Monday, 30 January, 2012, 14:57
From: SR Millis srmil...@yahoo.com
To: Jin Minming jminm...@yahoo.com
Sent: Monday, January 30, 2012 9:25 AM
Subject
wrote:
From: Uwe Ligges lig...@statistik.tu-dortmund.de
Subject: Re: [R] Error from Brugs 'r for windows gui front-end has stopped
working''
To: Jin Minming jminm...@yahoo.com
Cc: r-help@r-project.org
Date: Saturday, 28 January, 2012, 18:45
On 25.01.2012 18:50, Jin Minming wrote:
Hello
(alpha) # plot the densities,
#samplesBgr(alpha[1:6]) # plot the bgr statistics, and
#samplesAutoC(alpha[1:6], 1)# plot autocorrelations of 1st chain
# force to print the current loop number
flush.console()
print(mn)
}
--- On Tue, 24/1/12, Jin Minming jminm
Subject: Re: [R] Error from Brugs 'r for windows gui front-end has stopped
working''
To: Jin Minming jminm...@yahoo.com
Cc: r-help@r-project.org
Date: Wednesday, 25 January, 2012, 11:09
I just tried all 100 iterations both
under WinXP and Windows Server 2008
of your script under 32-bit R
Dear all,
I just try to run the example in R brugs packages, but not only once. Loop is
added in this example. After several times (7, 11, or other random number),
there is an error message r for windows gui front-end has stopped working.
This happened in two laptops with windows 7 and vista.
Dear all,
I have a general relationship, which can be easily
solved using forward engineering model,
y=f(x1, x2, x3)
Now I know a distribution of y, how can I get the
corresponding distributions for x1, x2, and x3? In another situation, if I know
the distributions of y and x1, how can I
Hi all
I am trying to solve a combinatorial optimization problem. Basically, I can
reduce my problem into the next problem:
1.- Given a NxN grid of points, with some values in each cell
2.- Find the combination of K points on the grid such that, the maximum
mean value is obtained
I took the
Hi guys,
I have a matrix with values varying from approximately -0.7 to 0.33 that I
want to create a heatmap/levelplot with.
When I execute the levelplot function for my matrix, I end up getting colors
that are adjusted to the max and min rather than around 0. In other words,
ideally I would
Hi all,
I copy metafile boxplot from R to Word. Then save as Pdf file. But I found
there are some unexpected black lines in some plots within this PDF file.
Please give me some advice how to get rid of these black lines in PDF files.
Thanks a lot,
Jim
[[alternative HTML version
of metafile plots when converting word to pdf file
To: Jean-Christophe BOUËTTÉ jcboue...@gmail.com
Cc: Jin Minming jminm...@yahoo.com, r-help@r-project.org
Date: Tuesday, 13 September, 2011, 14:02
Jim,
I have seen this outcome as well with graphs from time to time and
agree with Jean-Christophe
Dear R-users
I'm trying to use lasso in lars package for subset regression, I have a
large matrix of size 1000x100 and my aim is to select a subset k of the 100
variables.
Is there any way in lars to fix the number k (i.e. to select the best 10
variables)
library(lars)
?
Thank you very much.
Zhao Jin
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide
Hello Jim,
Thank you so much!!! It is a magic!!! Now I understand the use of
ifelse. Thank you again!!!
Tae-Jin
On Feb 5, 2011, at 12:49 AM, jim holtman wrote:
You should be able to use 'ifelse'
Os.chr4.gene.new$color -
ifelse(Os.chr4.gene.new$if_TE_related == TE_related, black
== orange)}
}
Gene.color - cbind(Gene, D1)
write.table(Gene.color, file=Gene_color1.txt, sep=\t, row.names=F)
}
Genecolor(Gene)
Tae-Jin
Researcher in NC State University
[[alternative HTML version deleted
Sorry. I made a typo. It is the 5th column (not 4th). Thank you.
Tae-Jin
Begin forwarded message:
From: Tae-Jin Lee tj...@ncsu.edu
Date: February 4, 2011 7:09:38 PM EST
To: r-help@R-project.org
Subject: Help!!! from R beginner
Hello,
I'm trying to add a column to the following data
a supervised learning method such as random forest (I am
guessing I need to obtain a feature list but again, how can I get the scores
for the edges)?
Hope I've explain my questions well but do let me know if more clarification is
need.
Thanks in advance
Eu Jin
0
[2,]0 0
[3,]0 0
[4,]0 1
I'll greatly appreciate it if you may help!
JP Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
UNC at Chapel Hill
Chapel Hill, NC
US
[[alternative HTML version deleted
.Treatment vs. Measurement.T2.M6.placebo (I did not include
Treatment as a factor in the query below yet).
Thanks for your help (data was attached)!
Jp Jin
summary(glm(data$Lesion.Size~Time+Measurement+Time*Measurement, data=data))
Call:
glm(formula = data$Lesion.Size ~ Time + Measurement + Time
/monitor/stats/sandbox
Thanks!
Lanna Jin
-
Lanna Jin
lanna...@gmail.com
510-898-8525
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Hi,
When I try to fit a linear fixed-effect model, I was using glm. I found
that there is no option for ml or reml and the default one is reml.
How can I use ml instead?
Of course, it's not necessary to be glm, I am just looking for commands
which allow me to fit a linear model (without any
Hi,
I want to fit a linear model (without any random effect) with method ml. I
tried to use glm I found that there is no option for ml or reml and
the default one is reml. THen I tried to use lme but it requires a
random effect. How can I fix this problem?
Of course, it's not necessary to be
.
On Sun, May 30, 2010 at 8:01 AM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote:
On Sun, 30 May 2010, Achim Zeileis wrote:
On Sun, 30 May 2010, Sherrie Jin wrote:
Hi,
I want to fit a linear model (without any random effect) with method
ml. I
tried to use glm I found that there is no option
When I ran a Gamma regression in SAS, the algorithm converged. When I ran it
in R, it keeps uncoverged even if I used 1 iterations. What was wrong?
I used the following code in R:
glm(y ~ x1 x2 x3, control=glm.control(maxit=1), data,
family=Gamma(link=log))
[[alternative HTML
Try: x[which(is.na(x)),] - 000/000, where is x is your data frame
-
Lanna Jin
lanna...@gmail.com
510-898-8525
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Sent from the R help
Whoops, my bad. Maybe try using gsub
-
Lanna Jin
lanna...@gmail.com
510-898-8525
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Sent from the R help mailing list archive
Hi Everyone,
Does anyone know of any projects for running an interactive R session within
a web browser?
I'm looking for something similar to the one on the Ruby website
(http://tryruby.org), except for R.
Thanks for your responses in advance!
Lanna
-
Lanna Jin
lanna...@gmail.com
510-898
Try, unique(dataset[,1:a]), where a is the number of columns that you have.
1:a would apply the unique to all columns.
-
Lanna Jin
lanna...@gmail.com
510-898-8525
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Sent
Did you try: if x is the data frame, unique(x)?
-
Lanna Jin
lanna...@gmail.com
510-898-8525
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if that doesn't work, maybe also try:
if x is your data frame with length a columns, unique(x[,1:a]).
-
Lanna Jin
lanna...@gmail.com
510-898-8525
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Sent from the R help
names()
-
Lanna Jin
lanna...@gmail.com
510-898-8525
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Sent from the R help mailing list archive at Nabble.com.
__
R-help@r
Weiss ich nicht genau ob es in R gibt, aber versuch mal Processing.org
-
Lanna Jin
lanna...@gmail.com
510-898-8525
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df[1:2]-df[1:2]*-1
-
Lanna Jin
lanna...@gmail.com
510-898-8525
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?
2) Is it possible to plot with only a function?
3) If not, what is wrong in the code above?
Many thank you in advance,
Jin
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Sent from the R help mailing list archive
Hello Dear,
I am trying to plot a function to see a minimum point (actually, using
optim). For example,
1. y=f(x)
2. x has a range
3. plot(x,y) to see a point x minimizing y
I tried plot(x,y), but it made an error. Am I doing a right way?
Thanks,
Jin
--
View this message in context:
http
Hello Dear,
I am trying to generate samples by using Monte Carlo simulation. For
example,
1000 samples, Exponential distribution (f(x), lambda=0.0005, 0=x=360)
Is there any package for Monte Carlo or just use random sample generation
function?
Many thank you for your help in advance,
Jin
help me solve this problem?
Best,
Jin
NREL, Golden CO
(303) 275-4642
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@nrel.gov
Date: Thu, 25 Mar 2010 07:48:40 -0800
From: ml-node+1690861-886360020-66...@n4.nabble.com
To: realst...@hotmail.com
Subject: Re: how to deal with vector[0]?
Jin wrote:
Hi,
I have a vector with 4 elements, e.g., tau_i=c(100,200,300,400), but
potentially tau_i[0]=0. In a for loop
successful in answering my question. As a new user to R and programming
languages, I truly appreciate your help and thank you for your patience.
Thanks in advance for your response,
Lanna Jin
-
Lanna Jin
lanna...@gmail.com
510-898-8525
--
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spec...@stat.berkeley.edu
On Tue, 16 Mar 2010, Lanna Jin wrote:
Hey All,
So, I am confused how exactly to use nesting loop functions in R to spit
out
data frames. I've managed to create a working function for my data set
that
generates a data frame for a given set
, length)
On Thu, Mar 11, 2010 at 10:55 AM, Lanna Jin lanna...@gmail.comwrote:
Hi Jim,
Here's an example of what I mean by a binary matrix ( 1 = species
presence, 0 = species absence, cols = species, rows = location). This is
just a sample of data from the Year 1998
ACMI2
for your suggestions!
--
Lanna Jin
lanna...@gmail.com
510-898-8525
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!
--
Lanna Jin
lanna...@gmail.com
510-898-8525
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide
Hello All!
I am trying to plot the frequency of species coocurrance.
If given a data set similar like this...(V1=species A, V2=species B,
V3=frequency of cooccurance)
data
V1 V2 V3
1 A B 0
2 A C 2
3 A D 5
4 B C 0
5 B D 1
6 C D 0
.
But How can we implement Prentice jacknife variance estimation in R
strictly?
Thanks
2008/6/17 Thomas Lumley [EMAIL PROTECTED]:
On Mon, 16 Jun 2008, Peter Dalgaard wrote:
Jin Wang wrote:
I tried to compare if cch() and coxph() can generate same result for
same case cohort data
Use the standard
Case cohort function cch() is in survival package. In cch(), the prentice
method is implemented like this:
Prentice - function(tenter, texit, cc, id, X, ntot,robust){
eps - 0.0001
cens - as.numeric(cc0) # Censorship indicators
subcoh - as.numeric(cc2) # Subcohort indicators
Now that we have case cohort model , we have 1000 people and 50 cases
Let the first 10 cases occur at the same time
second 10
third 10
fourth 10
fifth10
How easy is it to randomly sample 50
2.571 0.001
stageIV 1.392 4.021 2.670 6.057 0.000
histolUH 1.506 4.507 3.274 6.203 0.000
age 0.043 1.044 0.996 1.095 0.069
2008/6/12, Terry Therneau [EMAIL PROTECTED]:
Jin Wang had an error. My original note specified a variable that was 1 for
subjects NOT in the subcohort, so
I tried your alternative method on the example in cch() description manual.
The example data nwtco has not time-dependent covariates yet. I test cch()
and coxph() on the same data. But the estimation result is different. I
don't know if I did anything wrong.
subcoh - nwtco$in.subcohort
selccoh -
,
+ data=ccoh1.data.fold,subcoh=~subcohort,id=~seqno,cohort.size=19809)
Error in cch(Surv(start, stop, arrest.time) ~ fin + age + race + wexp + :
Multiple records per id not allowed
===
2008/6/12 Jin Wang [EMAIL PROTECTED
or not?
The cch() manual does not say if time dependent covariate is allowed
I know coxph() in Survival package can estimate time dependent covariates.
Thanks
Jin Wang
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))
[,1]
[1,] 0.06929324
# ==
I don't know if I'm simulating correctly the CAR,
any help?
Thanks in advance
2008/2/15, Henrique Dallazuanna [EMAIL PROTECTED]:
See spautolm function in spdep package
On 15/02/2008, Dae-Jin Lee [EMAIL PROTECTED
, but this is not what
I'm looking for
Thanks in advance
Dae-Jin
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Dae-Jin Lee
Office/Despacho: 7.3.J04
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Departamento de Estadística
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Hi all R users !
I'm using gamm function from Simon Wood's mgcv package, to fit a spatial
regression Generalized Additive Mixed Model, as covariates I have the
geographical longitude and latitude locations of indexed data. I include a
random effect for each district (dist) so the code is
fit -
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