Re: [R] Plotting Coxph model with an interaction.

[Gerrit Eichner]

Hi, John,

it should work the same way as without interaction (but make sure
to use the fitted object "coxfit", not just "fit" in our call of
survfit, and note that age*rx already expands to age + rx + age:rx
so that age + rx is redundant in your formula):

coxfit <- coxph(Surv(futime, fustat) ~ age+rx+age*rx, data = ovarian)
plot(survfit(coxfit, newdata=data.frame(age=60,rx=2)))

Or do I missunderstand your question?

 Hth  --  Gerrit

-
Dr. Gerrit Eichner   Mathematical Institute, Room 212
gerrit.eich...@math.uni-giessen.de   Justus-Liebig-University Giessen
Tel: +49-(0)641-99-32104  Arndtstr. 2, 35392 Giessen, Germany
http://www.uni-giessen.de/eichner
-

Am 20.05.2021 um 21:15 schrieb Bert Gunter:

Perhaps this might be useful:

https://rpubs.com/tf_peterson/interactionplotDemo

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, May 20, 2021 at 10:29 AM Sorkin, John 
wrote:


Colleagues,

I hope someone can tell me how to plot a cox model that contains an
interaction term.

I know that plot(survfit(. . . . )) can be used to plot a Cox model, i.e..
coxfit <- coxph(Surv(futime, fustat) ~ age+rx, data = ovarian)
plot(survfit(fit, newdata=data.frame(age=60,rx=2)))

but I don't know how to plot a cox model with an interaction, i.e.

coxfit <- coxph(Surv(futime, fustat) ~ age+rx+age*rx, data = ovarian)
plot(survfit(fit, newdata=data.frame(???)))

Thank you,
John

John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and
Geriatric Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)


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Re: [R] Plotting Coxph model with an interaction.

[Bert Gunter]

Perhaps this might be useful:

https://rpubs.com/tf_peterson/interactionplotDemo

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, May 20, 2021 at 10:29 AM Sorkin, John 
wrote:

> Colleagues,
>
> I hope someone can tell me how to plot a cox model that contains an
> interaction term.
>
> I know that plot(survfit(. . . . )) can be used to plot a Cox model, i.e..
> coxfit <- coxph(Surv(futime, fustat) ~ age+rx, data = ovarian)
> plot(survfit(fit, newdata=data.frame(age=60,rx=2)))
>
> but I don't know how to plot a cox model with an interaction, i.e.
>
> coxfit <- coxph(Surv(futime, fustat) ~ age+rx+age*rx, data = ovarian)
> plot(survfit(fit, newdata=data.frame(???)))
>
> Thank you,
> John
>
> John David Sorkin M.D., Ph.D.
> Professor of Medicine
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology and
> Geriatric Medicine
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>
>
> __
> R-help@r-project.org mailing list -- 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.
>

[[alternative HTML version deleted]]

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[R] Plotting Coxph model with an interaction.

[Sorkin, John]

Colleagues,

I hope someone can tell me how to plot a cox model that contains an interaction 
term.

I know that plot(survfit(. . . . )) can be used to plot a Cox model, i.e.. 
coxfit <- coxph(Surv(futime, fustat) ~ age+rx, data = ovarian) 
plot(survfit(fit, newdata=data.frame(age=60,rx=2))) 

but I don't know how to plot a cox model with an interaction, i.e.

coxfit <- coxph(Surv(futime, fustat) ~ age+rx+age*rx, data = ovarian) 
plot(survfit(fit, newdata=data.frame(???))) 

Thank you,
John

John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric 
Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)


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[R] Error in identifying correlated metrics

[Neha gupta]

Hello everyone

While I am working to identify the correlated metrics on my data, I am
getting the following error? My data has no missing or Inf values as all
other operations (model training etc) could be done without any errors.

Error in hclust(as.dist(1 - abs(cor(data, method = cor_method))), method =
clust_method) :
  NA/NaN/Inf in foreign function call (arg 10)

[[alternative HTML version deleted]]

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Re: [R] Incomplete violin chart representation

[Mahmood Naderan-Tahan]

Yes it seems that it need more than 2 points to create the shape.

Thanks


Regards,
Mahmood


From: Kevin Thorpe 
Sent: Thursday, May 20, 2021 1:38:32 PM
To: Mahmood Naderan-Tahan
Cc: R Help Mailing List
Subject: Re: [R] Incomplete violin chart representation

My guess would be there are only 2 observations contributing to that third 
plot, which is probably not enough to show anything else.

--
Kevin E. Thorpe
Head of Biostatistics,  Applied Health Research Centre (AHRC)
Li Ka Shing Knowledge Institute of St. Michael's
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: kevin.tho...@utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On May 20, 2021, at 5:21 AM, Mahmood Naderan-Tahan  
> wrote:
>
> EXTERNAL EMAIL:
>
> Hi
>
> I use the following command to create a violin chart
>
>
> p <- ggplot(mydata, aes(x=BENCH, y=V))
>
> + geom_violin(trim=FALSE)
>
> + geom_dotplot(binaxis='y', stackdir='center', dotsize=0.6)
>
> + scale_y_continuous(trans = scales::pseudo_log_trans(base = exp(1)))
>
>
> However, in the output one of them are shown in dots only which is weird 
> https://pasteboard.co/K2KeMZL.png
>
> Any idea about that?
>
>
>
> Regards,
> Mahmood
>
>[[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- 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.


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Re: [R] Incomplete violin chart representation

[Kevin Thorpe]

My guess would be there are only 2 observations contributing to that third 
plot, which is probably not enough to show anything else.

-- 
Kevin E. Thorpe
Head of Biostatistics,  Applied Health Research Centre (AHRC)
Li Ka Shing Knowledge Institute of St. Michael's
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: kevin.tho...@utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On May 20, 2021, at 5:21 AM, Mahmood Naderan-Tahan  
> wrote:
> 
> EXTERNAL EMAIL:
> 
> Hi
> 
> I use the following command to create a violin chart
> 
> 
> p <- ggplot(mydata, aes(x=BENCH, y=V))
> 
> + geom_violin(trim=FALSE)
> 
> + geom_dotplot(binaxis='y', stackdir='center', dotsize=0.6)
> 
> + scale_y_continuous(trans = scales::pseudo_log_trans(base = exp(1)))
> 
> 
> However, in the output one of them are shown in dots only which is weird 
> https://pasteboard.co/K2KeMZL.png
> 
> Any idea about that?
> 
> 
> 
> Regards,
> Mahmood
> 
>[[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list -- 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.

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[R] Incomplete violin chart representation

[Mahmood Naderan-Tahan]

Hi

I use the following command to create a violin chart


p <- ggplot(mydata, aes(x=BENCH, y=V))

+ geom_violin(trim=FALSE)

+ geom_dotplot(binaxis='y', stackdir='center', dotsize=0.6)

+ scale_y_continuous(trans = scales::pseudo_log_trans(base = exp(1)))


However, in the output one of them are shown in dots only which is weird 
https://pasteboard.co/K2KeMZL.png

Any idea about that?



Regards,
Mahmood

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Re: [R] Help in modifying code to extract data from url

[Jim Lemon]

Hi Bhaskar,
If you are using read.table or similar, see the "fill=" argument.

Jim

On Thu, May 20, 2021 at 9:54 AM Bhaskar Mitra  wrote:
>
> Hello Everyone,
>
> I am trying to extract data from a url. The codes work well when the
> data structure is as follows:
>
> X Y
> 1 2
> 1 5
> 1 6
> 1 7
> 3 4
>
> However, the code fails when the data structure has no number
> under the 2nd column (shown below).I get the following error:
>
> "Error in data.frame(..., check.names = FALSE) :
>   arguments imply differing number of rows: 242, 241"
>
>
> X Y
> 1 2
> 1
> 1
> 1 7
> 3 4
>
> Can anyone please help me in how I can modify the codes ( shown below) to
> adjust for the above mentioned condition
> in the data structure.
>
> library(rjson)
>
> url <- "abcd.com"
> json_data <- fromJSON(file= url)
> d3 <- lapply(json_data[[2]], function(x) c(x["data"]))
> d3 <- do.call(rbind, d3)
> X_Dataframe = as.data.frame(unlist(d3[[1]]))
> b <- do.call("cbind", split(X_Dataframe, rep(c(1, 2), length.out =
> nrow(X_Dataframe
>
>
> regards,
> bhaskar
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- 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.

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Re: [R-es] BioStatFLOSS y EpiLinux

[Juan Abasolo]

Muchas gracias, Miguel Angel;
Por curiosidad lo voy a intentar probar.
Seguramente me venga muy bien para salir del paso cuando no estoy en mi
máquina.
Espero encontrar la manera de incluirlo en mi flujo de trabajo.

Juan

Mezu hau jaso duzu  helbidetik
(2021 mai. 19, az. (14:13)):

> Hola.
>
>
> Retomando este antiguo hilo, os anuncio la reciente publicación de:
>
>
> - BioStatfloss V5.0:
> https://www.sergas.es/Saude-publica/BioStatFLOSS?idioma=es?
>
>
> - EpiLinux v6.0: https://www.sergas.es/Saude-publica/Epilinux?idioma=es
>
>
>
> Notas (un poco al azar):
>
>
> - Obviamente, R es una de las aplicaciones principales (junto con
> RCommander y RStudio como interfaces gráficas) en ambos proyectos.
>
>
> - A los usuarios de Windows (BioStatFLOSS), os recomiendo que le echéis un
> ojo a Radiant (otro GUI de R basado web -con Shiny-) y como proyectos
> derivados de R: JASP y Jamovi.
>
>
> - Todas las aplicaciones de BioStatFLOSS son portables (no necesitan
> instalación) e independientes unas de otras, por lo que se puede copiar la
> carpeta correspondiente y ejecutar por separado desde un pendrive, HD
> externo o en el propio equipo.
>
>
> - La ISO de EpiLinux se puede probar desde una máquina virtual o
> grabándola en un pendrive (con Rufus o Etcher, por ejemplo); en este caso,
> una vez grabado el pendrive o HD externo, hay que indicarle al equipo que
> arranque desde él.
>
>
> - Tanto en BioStatFLOSS como en EpiLinux se incluye Epidat (otro de
> nuestros proyectos de software). Más info:
> https://www.sergas.es/Saude-publica/EPIDAT?idioma=es
>
>
>
> Espero que a alguien el resulte de utilidad.
>
> Un saludo,
>
> -
>
> Miguel Ángel Rodríguez Muíños
>
> Dirección Xeral de Saúde Pública
>
> Consellería de Sanidade
>
> Xunta de Galicia
>
> https://dxsp.sergas.gal/
>
>
>
>
> [R-es] EpiLinux 5
> miguel.angel.rodriguez.muinos en sergas.es miguel.angel.rodriguez.muinos
> en sergas.es ?Subject=Re%3A%20%5BR-es%5D%20EpiLinux%205=%3C1516609305844.55711%
> 40sergas.es%3E>
> Lun Ene 22 09:21:46 CET 2018
>
>
> Hola.
>
>
> Os anuncio la publicación de la versión 5 de EpiLinux.
>
>
> Es una distribución científica de Linux, basada en Ubuntu de 64 bits con
> entorno de escritorio LXDE, que incluye una recopilación de software
> específicamente orientado al análisis de datos, la bioestadística y/o la
> epidemiología.
>
>
> Obviamente, el "núcleo central" de la distro es R (que viene con tres
> entornos gráficos preinstalados: RCommander, RKward y RStudio) aunque la
> selección de software es amplia.
>
>
> Tenéis más información aquí ->
> https://www.sergas.es/Saude-publica/Epilinux?idioma=es
>
>
> Se puede descargar en forma de ISO (4Gb aprox.). Esta ISO se puede montar
> virtualizada o pasarla a un pendrive para convertirla en una distribución
> live -funciona autónomamente desde el propio pendrive-. También se puede
> instalar en el disco duro del ordenador.
>
>
> Espero que os pueda ser útil. Aunque es difícil que alguien de esta lista
> no tenga ya un entorno de trabajo estable y personalizado, este tipo de
> distribuciones "live" son bastante adecuadas para la formación por no ser
> agresivas con el sistema operativo host del ordenador y/o para iniciarse en
> este campo (nota: para este propósito os recomiendo que probéis JASP, a los
> que no lo conocéis)
>
>
> Si tenéis algún ordenador por ahí que ya no puede con las nuevas versiones
> de Windows, podéis probarla también (mejor instalada en el HD porque ese
> tipo de equipos suele tener puertos USB "lentos"), igual os sorprende su
> ligereza.
>
>
> Se agradecen comentarios, sugerencias, ideas, críticas, 
>
>
> Un saludo,
> Miguel.
>
>
>
>
>
>
>
>
>
> 
>
> Nota: A información contida nesta mensaxe e os seus posibles documentos
> adxuntos é privada e confidencial e está dirixida únicamente ó seu
> destinatario/a. Se vostede non é o/a destinatario/a orixinal desta mensaxe,
> por favor elimínea. A distribución ou copia desta mensaxe non está
> autorizada.
>
> Nota: La información contenida en este mensaje y sus posibles documentos
> adjuntos es privada y confidencial y está dirigida únicamente a su
> destinatario/a. Si usted no es el/la destinatario/a original de este
> mensaje, por favor elimínelo. La distribución o copia de este mensaje no
> está autorizada.
>
> See more languages: http://www.sergas.es/aviso-confidencialidad
>
> [[alternative HTML version deleted]]
>
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-- 
Juan Abasolo, PhD

Hizkuntzaren eta Literaturaren Didaktika Saila | EUDIA ikerketa taldea
Bilboko Hezkuntza Fakultatea
Euskal Herriko Unibertsitatea
UPV/EHU

Sarriena auzoa z/g 48940 - Leioa (Bizkaia)

T   : (+34) 94 601 7567
Telegram: @JuanAbasolo
Skype   : abasolo72

Tutoretza ordutegia 

[R] [Rd] R 4.1.0 is released

[Peter Dalgaard]

The build system rolled up R-4.1.0.tar.gz (codename "Camp Pontanezen") this 
morning.

This is a major update, notably containing the new native pipe operator "|>" 
and 
shorthand inline functions "\(x) x+1".

The list below details the changes in this release. 

You can get the source code from

https://cran.r-project.org/src/base/R-4/R-4.1.0.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you.

Binaries for various platforms will appear in due course.


For the R Core Team,

Peter Dalgaard


These are the checksums (md5 and SHA-256) for the freshly created files, in 
case you wish
to check that they are uncorrupted:

MD5 (AUTHORS) = b9c44f9f78cab3184ad9898bebc854b4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 639fbbba9998cae70ef058be42b80a52
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = b02805558a8315f1a93c7f7d7cd879c1
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = a767f7809324c73c49eaff47d14bce81
MD5 (NEWS.3) = e55ed2c8a547b827b46e08eb7137ba23
MD5 (R-latest.tar.gz) = bd80f97d0e46a71408f5bc25652a0203
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = 251d20510bfc3cc93b82c5a99f7efcc6
MD5 (VERSION-INFO.dcf) = 1f3cf39735afb48fea434bca2b7bf483
MD5 (R-4/R-4.1.0.tar.gz) = bd80f97d0e46a71408f5bc25652a0203

2cde824a7b18958e5f06b391c801c8288be0f84fa8934b7ddefef23c67e60c09  AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4  COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3  COPYING.LIB
0dce85f38b9d6351a1b63f057dfbc7f572966245add12946482e57e60d41547c  FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31  INSTALL
20e7185fb5af0f2ac825b27c16afd57ff206726117c6ac5cf7c6f230337af093  NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62  NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01  NEWS.1
ba74618bc3f4c0e336dca13d472402a1863d12ba6f7f91a1782bc469ee986f6d  NEWS.2
1910a2405300b9bc7c76beeb0753a5249cf799afe175ce28f8d782fab723e012  NEWS.3
e8e68959d7282ca147360fc9644ada9bd161bab781bab14d33b8999a95182781  
R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc  README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9  RESOURCES
c9c7cb32308b4e560a22c858819ade9de524a602abd4e92d1c328c89f8037d73  THANKS
2f834a058dcfcdfb7eedf45aa0d897ea1a7c43a9460ffd22f73b60919cb1bf57  
VERSION-INFO.dcf
e8e68959d7282ca147360fc9644ada9bd161bab781bab14d33b8999a95182781  
R-4/R-4.1.0.tar.gz

This is the relevant part of the NEWS file

CHANGES IN R 4.1.0:

  FUTURE DIRECTIONS:

* It is planned that the 4.1.x series will be the last to support
  32-bit Windows, with production of binary packages for that
  series continuing until early 2023.

  SIGNIFICANT USER-VISIBLE CHANGES:

* Data set esoph in package datasets now provides the correct
  numbers of controls; previously it had the numbers of cases added
  to these.  (Reported by Alexander Fowler in PR#17964.)

  NEW FEATURES:

* www.omegahat.net is no longer one of the repositories known by
  default to setRepositories().  (Nowadays it only provides source
  packages and is often unavailable.)

* Function package_dependencies() (in package tools) can now use
  different dependency types for direct and recursive dependencies.

* The checking of the size of tarball in R CMD check --as-cran
   may be tweaked via the new environment variable
  _R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_, as suggested in
  PR#1 by Jan Gorecki.

* Using c() to combine a factor with other factors now gives a
  factor, an ordered factor when combining ordered factors with
  identical levels.

* apply() gains a simplify argument to allow disabling of
  simplification of results.

* The format() method for class "ftable" gets a new option justify.
  (Suggested by Thomas Soeiro.)

* New ...names() utility.  (Proposed by Neal Fultz in PR#17705.)

* type.convert() now warns when its as.is argument is not
  specified, as the help file always said it _should_.  In that
  case, the default is changed to TRUE in line with its change in
  read.table() (related to stringsAsFactor) in R 4.0.0.

* When printing list arrays, classed objects are now shown _via_
  their format() value if this is a short enough character string,
  or by giving the first elements of their class vector and their
  length.

* capabilities() gets new entry "Rprof" which is TRUE when R has
  been configured with the equivalent of --enable-R-profiling (as
  it is by default).  (Related to Michael Orlitzky's report
  PR#17836.)

* str(xS4) now also shows extraneous attributes of an S4 object
  xS4.

* Rudimentary support for vi-style tags in