Re: consolidate three function into one

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Re: consolidate three function into one

Ding, Yuan Chun
HI R users,

I construct dendrogram tree and cut the tree into different clusters, then generate survival curves by the following three functions. All variables are included in an inputfile.

Can you help me to consolidate the following three function into one functions?  I thought about using if  else function, but not sure how to do it.

Thank you,

Ding

# function to generate RFS
RFS2cluster <- function( inputfile ) {
  cluster2<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
                               data = inputfile)
 
  ggsurvplot(cluster2, data = inputfile, risk.table = F,
             palette = c("red", "black"),
             ylim=c(0,1),
             ggtheme = theme_bw(),
             xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",
             pval = TRUE,
             font.x =  16,
             font.y = 16,
             font.tickslab = 14,
             font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = c("Cluster1", "Cluster2"), lty=1, lwd=3)
}

RFS3cluster <- function( inputfile ) {
  cluster3<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
                     data = inputfile)
 
  ggsurvplot(cluster3, data = inputfile, risk.table = F,
             palette = c("red", "black", "green"),
             ylim=c(0,1),
             ggtheme = theme_bw(),
             xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",
             pval = TRUE,
             font.x =  16,
             font.y = 16,
             font.tickslab = 14,
             font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = c("Cluster1", "Cluster2", "Cluster3"), lty=1, lwd=3)
}

RFS4cluster <- function( inputfile ) {
  cluster4<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
                     data = inputfile)
 
  ggsurvplot(cluster4, data = inputfile, risk.table = F,
             palette = c("red", "black", "green", "blue"),
             ylim=c(0,1),
             ggtheme = theme_bw(),
             xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",
             pval = TRUE,
             font.x =  16,
             font.y = 16,
             font.tickslab = 14,
             font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = c("Cluster1", "Cluster2", "Cluster3", "Cluster4"), lty=1, lwd=3)
}

-----Original Message-----
From: R-help [mailto:[hidden email]] On Behalf Of imane hajar
Sent: Friday, January 12, 2018 7:42 AM
To: [hidden email]
Subject: [R] Help with packages (methods, stats, stats4)

[Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.]





hello,
Can you please give me a hand with this problem,well i can't install these
packages:
- stats
- methods
- stats4

when i tried the following command :  *library(help = "stats") * , it gave me this output (*see picture*), so i contacted the Maintainer of the package at (*[hidden email] <[hidden email]>*) but he said that i write to the wrong place.

(i want to install those packages in order to use the "DVstats" package)

(i have the latest version of R (3.4.3 ) and Rstudio(1.2.240) )

thank you
Regards


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Re: consolidate three function into one

Ding, Yuan Chun
Hi Bert,

Thank you, yes, you are right.  I want to consolidate the three functions into one functions by adding more arguments, adding flexibility  to accommodate  the number of clusters or  the number of Kaplan Meier  curves generated in one figure.  So, I just need to define one function.

Thanks,

Ding

From: Bert Gunter [mailto:[hidden email]]
Sent: Sunday, January 14, 2018 9:50 AM
To: Ding, Yuan Chun <[hidden email]>
Subject: Re: [R] consolidate three function into one

I have not looked at your code *at all*, so I am not sure what exactly you mean by "consolidate."
Is this what you are after?

f1 <- function(...) { code 1}
f2 <- function(...) { code 2}
f3 <- function(...) { code 3}
## can be "consolidated as":
f <- function( someargs, ...){
if( expr(someargs)) f1(...)
else if(expr2(someargs)) f2(...)
else f3(...)
}
The "..." argument to f can soak up any named additional arguments you wish to pass to f1, f2, or f3.
My apologies if this is offbase or too vague, and feel free to ignore in that case. I don't have the patience to go trough your code in detail. Others may and give you what you want.
Cheers,
Bert



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 Sun, Jan 14, 2018 at 9:17 AM, Ding, Yuan Chun <[hidden email]<mailto:[hidden email]>> wrote:
HI R users,

I construct dendrogram tree and cut the tree into different clusters, then generate survival curves by the following three functions. All variables are included in an inputfile.

Can you help me to consolidate the following three function into one functions?  I thought about using if  else function, but not sure how to do it.

Thank you,

Ding

# function to generate RFS
RFS2cluster <- function( inputfile ) {
  cluster2<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
                               data = inputfile)

  ggsurvplot(cluster2, data = inputfile, risk.table = F,
             palette = c("red", "black"),
             ylim=c(0,1),
             ggtheme = theme_bw(),
             xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",
             pval = TRUE,
             font.x =  16,
             font.y = 16,
             font.tickslab = 14,
             font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = c("Cluster1", "Cluster2"), lty=1, lwd=3)
}

RFS3cluster <- function( inputfile ) {
  cluster3<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
                     data = inputfile)

  ggsurvplot(cluster3, data = inputfile, risk.table = F,
             palette = c("red", "black", "green"),
             ylim=c(0,1),
             ggtheme = theme_bw(),
             xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",
             pval = TRUE,
             font.x =  16,
             font.y = 16,
             font.tickslab = 14,
             font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = c("Cluster1", "Cluster2", "Cluster3"), lty=1, lwd=3)
}

RFS4cluster <- function( inputfile ) {
  cluster4<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
                     data = inputfile)

  ggsurvplot(cluster4, data = inputfile, risk.table = F,
             palette = c("red", "black", "green", "blue"),
             ylim=c(0,1),
             ggtheme = theme_bw(),
             xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",
             pval = TRUE,
             font.x =  16,
             font.y = 16,
             font.tickslab = 14,
             font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = c("Cluster1", "Cluster2", "Cluster3", "Cluster4"), lty=1, lwd=3)
}

-----Original Message-----
From: R-help [mailto:[hidden email]<mailto:[hidden email]>] On Behalf Of imane hajar
Sent: Friday, January 12, 2018 7:42 AM
To: [hidden email]<mailto:[hidden email]>
Subject: [R] Help with packages (methods, stats, stats4)

[Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.]





hello,
Can you please give me a hand with this problem,well i can't install these
packages:
- stats
- methods
- stats4

when i tried the following command :  *library(help = "stats") * , it gave me this output (*see picture*), so i contacted the Maintainer of the package at (*[hidden email]<mailto:[hidden email]> <[hidden email]<mailto:[hidden email]>>*) but he said that i write to the wrong place.

(i want to install those packages in order to use the "DVstats" package)

(i have the latest version of R (3.4.3 ) and Rstudio(1.2.240) )

thank you
Regards


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 eceive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)
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______________________________________________
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Re: consolidate three function into one

Ding, Yuan Chun
In reply to this post by Ding, Yuan Chun
Hi Bert,

I am sorry to bother you on weekend.

I am still struggling on defining a correct function.

I first defined the function RFS (see below), then run it by provide the two argument.

m52.2cluster <-RFS(inputfile =allinfo_m52, N=2 )

I do not get error message, but no figure displays on screen. I do not know what is going on.

Can you help me a little more on this issue?

Thank you,

Ding

# function to generate RFS
RFS <- function( inputfile, N ) {
  cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
                               data = inputfile)

         if( N==2) {palette <- c("red", "black")
                           legend.labs <- c("Cluster1", "Cluster2")
                            }

  else if(N==3) {palette <- c("red", "black", "green")
                      legend.labs <- c("Cluster1", "Cluster2", "Cluster3")
                            }

                 else {palette <- c("red", "black","green", "blue")
                           legend.labs <- c("Cluster1", "Cluster2", "Cluster3", "Cluster4")
                          }

  ggsurvplot(cluster, data = inputfile, risk.table = F,
             palette = palette,
             ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",pval = TRUE,font.x =  16,font.y = 16,
             font.tickslab = 14,font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = legend.labs,
             lty=1, lwd=3)
                                }

From: Bert Gunter [mailto:[hidden email]]
Sent: Sunday, January 14, 2018 9:50 AM
To: Ding, Yuan Chun <[hidden email]>
Subject: Re: [R] consolidate three function into one

I have not looked at your code *at all*, so I am not sure what exactly you mean by "consolidate."
Is this what you are after?

f1 <- function(...) { code 1}
f2 <- function(...) { code 2}
f3 <- function(...) { code 3}
## can be "consolidated as":
f <- function( someargs, ...){
if( expr(someargs)) f1(...)
else if(expr2(someargs)) f2(...)
else f3(...)
}
The "..." argument to f can soak up any named additional arguments you wish to pass to f1, f2, or f3.
My apologies if this is offbase or too vague, and feel free to ignore in that case. I don't have the patience to go trough your code in detail. Others may and give you what you want.
Cheers,
Bert



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 Sun, Jan 14, 2018 at 9:17 AM, Ding, Yuan Chun <[hidden email]<mailto:[hidden email]>> wrote:
HI R users,

I construct dendrogram tree and cut the tree into different clusters, then generate survival curves by the following three functions. All variables are included in an inputfile.

Can you help me to consolidate the following three function into one functions?  I thought about using if  else function, but not sure how to do it.

Thank you,

Ding

# function to generate RFS
RFS2cluster <- function( inputfile ) {
  cluster2<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
                               data = inputfile)

  ggsurvplot(cluster2, data = inputfile, risk.table = F,
             palette = c("red", "black"),
             ylim=c(0,1),
             ggtheme = theme_bw(),
             xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",
             pval = TRUE,
             font.x =  16,
             font.y = 16,
             font.tickslab = 14,
             font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = c("Cluster1", "Cluster2"), lty=1, lwd=3)
}

RFS3cluster <- function( inputfile ) {
  cluster3<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
                     data = inputfile)

  ggsurvplot(cluster3, data = inputfile, risk.table = F,
             palette = c("red", "black", "green"),
             ylim=c(0,1),
             ggtheme = theme_bw(),
             xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",
             pval = TRUE,
             font.x =  16,
             font.y = 16,
             font.tickslab = 14,
             font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = c("Cluster1", "Cluster2", "Cluster3"), lty=1, lwd=3)
}

RFS4cluster <- function( inputfile ) {
  cluster4<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
                     data = inputfile)

  ggsurvplot(cluster4, data = inputfile, risk.table = F,
             palette = c("red", "black", "green", "blue"),
             ylim=c(0,1),
             ggtheme = theme_bw(),
             xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",
             pval = TRUE,
             font.x =  16,
             font.y = 16,
             font.tickslab = 14,
             font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = c("Cluster1", "Cluster2", "Cluster3", "Cluster4"), lty=1, lwd=3)
}

-----Original Message-----
From: R-help [mailto:[hidden email]<mailto:[hidden email]>] On Behalf Of imane hajar
Sent: Friday, January 12, 2018 7:42 AM
To: [hidden email]<mailto:[hidden email]>
Subject: [R] Help with packages (methods, stats, stats4)

[Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.]





hello,
Can you please give me a hand with this problem,well i can't install these
packages:
- stats
- methods
- stats4

when i tried the following command :  *library(help = "stats") * , it gave me this output (*see picture*), so i contacted the Maintainer of the package at (*[hidden email]<mailto:[hidden email]> <[hidden email]<mailto:[hidden email]>>*) but he said that i write to the wrong place.

(i want to install those packages in order to use the "DVstats" package)

(i have the latest version of R (3.4.3 ) and Rstudio(1.2.240) )

thank you
Regards


---------------------------------------------------------------------
-SECURITY/CONFIDENTIALITY WARNING-
This message (and any attachments) are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to r
 eceive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)
---------------------------------------------------------------------

______________________________________________
[hidden email]<mailto:[hidden email]> 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]]

______________________________________________
[hidden email] 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: consolidate three function into one

Richard M. Heiberger
FAQ 7.22
You must print a ggplot object, for example with
print(m52.2cluster)

For the FAQ, run the line
   system.file("../../doc/FAQ")
in R on your computer.
Open up the resulting filepath in your favorite editor and scroll down to 7.22

On Sun, Jan 14, 2018 at 4:21 PM, Ding, Yuan Chun <[hidden email]> wrote:

> Hi Bert,
>
> I am sorry to bother you on weekend.
>
> I am still struggling on defining a correct function.
>
> I first defined the function RFS (see below), then run it by provide the two argument.
>
> m52.2cluster <-RFS(inputfile =allinfo_m52, N=2 )
>
> I do not get error message, but no figure displays on screen. I do not know what is going on.
>
> Can you help me a little more on this issue?
>
> Thank you,
>
> Ding
>
> # function to generate RFS
> RFS <- function( inputfile, N ) {
>   cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
>                                data = inputfile)
>
>          if( N==2) {palette <- c("red", "black")
>                            legend.labs <- c("Cluster1", "Cluster2")
>                             }
>
>   else if(N==3) {palette <- c("red", "black", "green")
>                       legend.labs <- c("Cluster1", "Cluster2", "Cluster3")
>                             }
>
>                  else {palette <- c("red", "black","green", "blue")
>                            legend.labs <- c("Cluster1", "Cluster2", "Cluster3", "Cluster4")
>                           }
>
>   ggsurvplot(cluster, data = inputfile, risk.table = F,
>              palette = palette,
>              ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",pval = TRUE,font.x =  16,font.y = 16,
>              font.tickslab = 14,font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = legend.labs,
>              lty=1, lwd=3)
>                                 }
>
> From: Bert Gunter [mailto:[hidden email]]
> Sent: Sunday, January 14, 2018 9:50 AM
> To: Ding, Yuan Chun <[hidden email]>
> Subject: Re: [R] consolidate three function into one
>
> I have not looked at your code *at all*, so I am not sure what exactly you mean by "consolidate."
> Is this what you are after?
>
> f1 <- function(...) { code 1}
> f2 <- function(...) { code 2}
> f3 <- function(...) { code 3}
> ## can be "consolidated as":
> f <- function( someargs, ...){
> if( expr(someargs)) f1(...)
> else if(expr2(someargs)) f2(...)
> else f3(...)
> }
> The "..." argument to f can soak up any named additional arguments you wish to pass to f1, f2, or f3.
> My apologies if this is offbase or too vague, and feel free to ignore in that case. I don't have the patience to go trough your code in detail. Others may and give you what you want.
> Cheers,
> Bert
>
>
>
> 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 Sun, Jan 14, 2018 at 9:17 AM, Ding, Yuan Chun <[hidden email]<mailto:[hidden email]>> wrote:
> HI R users,
>
> I construct dendrogram tree and cut the tree into different clusters, then generate survival curves by the following three functions. All variables are included in an inputfile.
>
> Can you help me to consolidate the following three function into one functions?  I thought about using if  else function, but not sure how to do it.
>
> Thank you,
>
> Ding
>
> # function to generate RFS
> RFS2cluster <- function( inputfile ) {
>   cluster2<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
>                                data = inputfile)
>
>   ggsurvplot(cluster2, data = inputfile, risk.table = F,
>              palette = c("red", "black"),
>              ylim=c(0,1),
>              ggtheme = theme_bw(),
>              xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",
>              pval = TRUE,
>              font.x =  16,
>              font.y = 16,
>              font.tickslab = 14,
>              font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = c("Cluster1", "Cluster2"), lty=1, lwd=3)
> }
>
> RFS3cluster <- function( inputfile ) {
>   cluster3<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
>                      data = inputfile)
>
>   ggsurvplot(cluster3, data = inputfile, risk.table = F,
>              palette = c("red", "black", "green"),
>              ylim=c(0,1),
>              ggtheme = theme_bw(),
>              xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",
>              pval = TRUE,
>              font.x =  16,
>              font.y = 16,
>              font.tickslab = 14,
>              font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = c("Cluster1", "Cluster2", "Cluster3"), lty=1, lwd=3)
> }
>
> RFS4cluster <- function( inputfile ) {
>   cluster4<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
>                      data = inputfile)
>
>   ggsurvplot(cluster4, data = inputfile, risk.table = F,
>              palette = c("red", "black", "green", "blue"),
>              ylim=c(0,1),
>              ggtheme = theme_bw(),
>              xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",
>              pval = TRUE,
>              font.x =  16,
>              font.y = 16,
>              font.tickslab = 14,
>              font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = c("Cluster1", "Cluster2", "Cluster3", "Cluster4"), lty=1, lwd=3)
> }
>
> -----Original Message-----
> From: R-help [mailto:[hidden email]<mailto:[hidden email]>] On Behalf Of imane hajar
> Sent: Friday, January 12, 2018 7:42 AM
> To: [hidden email]<mailto:[hidden email]>
> Subject: [R] Help with packages (methods, stats, stats4)
>
> [Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.]
>
>
>
>
>
> hello,
> Can you please give me a hand with this problem,well i can't install these
> packages:
> - stats
> - methods
> - stats4
>
> when i tried the following command :  *library(help = "stats") * , it gave me this output (*see picture*), so i contacted the Maintainer of the package at (*[hidden email]<mailto:[hidden email]> <[hidden email]<mailto:[hidden email]>>*) but he said that i write to the wrong place.
>
> (i want to install those packages in order to use the "DVstats" package)
>
> (i have the latest version of R (3.4.3 ) and Rstudio(1.2.240) )
>
> thank you
> Regards
>
>
> ---------------------------------------------------------------------
> -SECURITY/CONFIDENTIALITY WARNING-
> This message (and any attachments) are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to
  r

>  eceive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)
> ---------------------------------------------------------------------
>
> ______________________________________________
> [hidden email]<mailto:[hidden email]> 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]]
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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
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Re: consolidate three function into one

Ding, Yuan Chun
Hi Richard,

Thank you so much!!  I understand the problem now,  I assign a name to the "ggsurvplot" object and then add print(fig) at bottom of function definition, now figure gets printed on screen.

Ding

# function to generate RFS curves
RFS <- function( inputfile, N ) {
  cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
                    data = inputfile)
  if( N==2) {palette <- c("red", "black")
  legend.labs <- c("Cluster1", "Cluster2")
                     }

  else if(N==3) {palette <- c("red", "black", "green")
  legend.labs <- c("Cluster1", "Cluster2", "Cluster3")
                              }
  else {palette <- c("red", "black","green", "blue")
  legend.labs <- c("Cluster1", "Cluster2", "Cluster3", "Cluster4")
           }
 
 
  fig <-ggsurvplot(cluster, data = inputfile, risk.table = F,
             palette = palette,
             ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",pval = TRUE,font.x =  16,font.y = 16,
             font.tickslab = 14,font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = legend.labs,
             lty=1, lwd=3)
  print(fig)
                                                     }

-----Original Message-----
From: Richard M. Heiberger [mailto:[hidden email]]
Sent: Sunday, January 14, 2018 1:34 PM
To: Ding, Yuan Chun <[hidden email]>
Cc: Bert Gunter <[hidden email]>; [hidden email]
Subject: Re: [R] consolidate three function into one

FAQ 7.22
You must print a ggplot object, for example with
print(m52.2cluster)

For the FAQ, run the line
   system.file("../../doc/FAQ")
in R on your computer.
Open up the resulting filepath in your favorite editor and scroll down to 7.22

On Sun, Jan 14, 2018 at 4:21 PM, Ding, Yuan Chun <[hidden email]> wrote:

> Hi Bert,
>
> I am sorry to bother you on weekend.
>
> I am still struggling on defining a correct function.
>
> I first defined the function RFS (see below), then run it by provide the two argument.
>
> m52.2cluster <-RFS(inputfile =allinfo_m52, N=2 )
>
> I do not get error message, but no figure displays on screen. I do not know what is going on.
>
> Can you help me a little more on this issue?
>
> Thank you,
>
> Ding
>
> # function to generate RFS
> RFS <- function( inputfile, N ) {
>   cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
>                                data = inputfile)
>
>          if( N==2) {palette <- c("red", "black")
>                            legend.labs <- c("Cluster1", "Cluster2")
>                             }
>
>   else if(N==3) {palette <- c("red", "black", "green")
>                       legend.labs <- c("Cluster1", "Cluster2", "Cluster3")
>                             }
>
>                  else {palette <- c("red", "black","green", "blue")
>                            legend.labs <- c("Cluster1", "Cluster2", "Cluster3", "Cluster4")
>                           }
>
>   ggsurvplot(cluster, data = inputfile, risk.table = F,
>              palette = palette,
>              ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",pval = TRUE,font.x =  16,font.y = 16,
>              font.tickslab = 14,font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = legend.labs,
>              lty=1, lwd=3)
>                                 }
>
> From: Bert Gunter [mailto:[hidden email]]
> Sent: Sunday, January 14, 2018 9:50 AM
> To: Ding, Yuan Chun <[hidden email]>
> Subject: Re: [R] consolidate three function into one
>
> I have not looked at your code *at all*, so I am not sure what exactly you mean by "consolidate."
> Is this what you are after?
>
> f1 <- function(...) { code 1}
> f2 <- function(...) { code 2}
> f3 <- function(...) { code 3}
> ## can be "consolidated as":
> f <- function( someargs, ...){
> if( expr(someargs)) f1(...)
> else if(expr2(someargs)) f2(...)
> else f3(...)
> }
> The "..." argument to f can soak up any named additional arguments you wish to pass to f1, f2, or f3.
> My apologies if this is offbase or too vague, and feel free to ignore in that case. I don't have the patience to go trough your code in detail. Others may and give you what you want.
> Cheers,
> Bert
>
>
>
> 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 Sun, Jan 14, 2018 at 9:17 AM, Ding, Yuan Chun <[hidden email]<mailto:[hidden email]>> wrote:
> HI R users,
>
> I construct dendrogram tree and cut the tree into different clusters, then generate survival curves by the following three functions. All variables are included in an inputfile.
>
> Can you help me to consolidate the following three function into one functions?  I thought about using if  else function, but not sure how to do it.
>
> Thank you,
>
> Ding
>
> # function to generate RFS
> RFS2cluster <- function( inputfile ) {
>   cluster2<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
>                                data = inputfile)
>
>   ggsurvplot(cluster2, data = inputfile, risk.table = F,
>              palette = c("red", "black"),
>              ylim=c(0,1),
>              ggtheme = theme_bw(),
>              xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",
>              pval = TRUE,
>              font.x =  16,
>              font.y = 16,
>              font.tickslab = 14,
>              font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = c("Cluster1", "Cluster2"), lty=1, lwd=3) }
>
> RFS3cluster <- function( inputfile ) {
>   cluster3<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
>                      data = inputfile)
>
>   ggsurvplot(cluster3, data = inputfile, risk.table = F,
>              palette = c("red", "black", "green"),
>              ylim=c(0,1),
>              ggtheme = theme_bw(),
>              xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",
>              pval = TRUE,
>              font.x =  16,
>              font.y = 16,
>              font.tickslab = 14,
>              font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = c("Cluster1", "Cluster2", "Cluster3"),
> lty=1, lwd=3) }
>
> RFS4cluster <- function( inputfile ) {
>   cluster4<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
>                      data = inputfile)
>
>   ggsurvplot(cluster4, data = inputfile, risk.table = F,
>              palette = c("red", "black", "green", "blue"),
>              ylim=c(0,1),
>              ggtheme = theme_bw(),
>              xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",
>              pval = TRUE,
>              font.x =  16,
>              font.y = 16,
>              font.tickslab = 14,
>              font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = c("Cluster1", "Cluster2", "Cluster3",
> "Cluster4"), lty=1, lwd=3) }
>
> -----Original Message-----
> From: R-help
> [mailto:[hidden email]<mailto:[hidden email]
> rg>] On Behalf Of imane hajar
> Sent: Friday, January 12, 2018 7:42 AM
> To: [hidden email]<mailto:[hidden email]>
> Subject: [R] Help with packages (methods, stats, stats4)
>
> [Attention: This email came from an external source. Do not open
> attachments or click on links from unknown senders or unexpected
> emails.]
>
>
>
>
>
> hello,
> Can you please give me a hand with this problem,well i can't install
> these
> packages:
> - stats
> - methods
> - stats4
>
> when i tried the following command :  *library(help = "stats") * , it gave me this output (*see picture*), so i contacted the Maintainer of the package at (*[hidden email]<mailto:[hidden email]> <[hidden email]<mailto:[hidden email]>>*) but he said that i write to the wrong place.
>
> (i want to install those packages in order to use the "DVstats"
> package)
>
> (i have the latest version of R (3.4.3 ) and Rstudio(1.2.240) )
>
> thank you
> Regards
>
>
> ---------------------------------------------------------------------
> -SECURITY/CONFIDENTIALITY WARNING-
> This message (and any attachments) are intended solely for the
> individual or entity to which they are addressed. This communication
> may contain information that is privileged, confidential, or exempt
> from disclosure under applicable law (e.g., personal health
> information, research data, financial information). Because this
> e-mail has been sent without encryption, individuals other than the
> intended recipient may be able to view the information, forward it to
> others or tamper with the information without the knowledge or consent
> of the sender. If you are not the intended recipient, or the employee
> or person responsible for delivering the message to the intended
> recipient, any dissemination, distribution or copying of the
> communication is strictly prohibited. If you received the
> communication in error, please notify the sender immediately by
> replying to this message and deleting the message and any accompanying
> files from your system. If, due to the security risks, you do not wish
> to r  eceive further communications via e-mail, please reply to this
> message and inform the sender that you do not wish to receive further
> e-mail from the sender. (LCP301)
> ---------------------------------------------------------------------
>
> ______________________________________________
> [hidden email]<mailto:[hidden email]> 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]]
>
> ______________________________________________
> [hidden email] 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.
______________________________________________
[hidden email] 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: consolidate three function into one

Bert Gunter-2
That is certainly OK, but you can also just use

print(ggsurvplot(...))

as your final statement.

out <- RFS( ...)

would then return the ggsurvplot object *and* graph it.

Any good R tutorial or a web search will provide more details on function
returns, which you might find useful.


Cheers,
Bert



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 Mon, Jan 15, 2018 at 9:57 AM, Ding, Yuan Chun <[hidden email]> wrote:

> Hi Richard,
>
> Thank you so much!!  I understand the problem now,  I assign a name to the
> "ggsurvplot" object and then add print(fig) at bottom of function
> definition, now figure gets printed on screen.
>
> Ding
>
> # function to generate RFS curves
> RFS <- function( inputfile, N ) {
>   cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
>                     data = inputfile)
>   if( N==2) {palette <- c("red", "black")
>   legend.labs <- c("Cluster1", "Cluster2")
>                      }
>
>   else if(N==3) {palette <- c("red", "black", "green")
>   legend.labs <- c("Cluster1", "Cluster2", "Cluster3")
>                               }
>   else {palette <- c("red", "black","green", "blue")
>   legend.labs <- c("Cluster1", "Cluster2", "Cluster3", "Cluster4")
>            }
>
>
>   fig <-ggsurvplot(cluster, data = inputfile, risk.table = F,
>              palette = palette,
>              ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival
> (Days)",
>              main = "Survival curve",pval = TRUE,font.x =  16,font.y = 16,
>              font.tickslab = 14,font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = legend.labs,
>              lty=1, lwd=3)
>   print(fig)
>                                                      }
>
> -----Original Message-----
> From: Richard M. Heiberger [mailto:[hidden email]]
> Sent: Sunday, January 14, 2018 1:34 PM
> To: Ding, Yuan Chun <[hidden email]>
> Cc: Bert Gunter <[hidden email]>; [hidden email]
> Subject: Re: [R] consolidate three function into one
>
> FAQ 7.22
> You must print a ggplot object, for example with
> print(m52.2cluster)
>
> For the FAQ, run the line
>    system.file("../../doc/FAQ")
> in R on your computer.
> Open up the resulting filepath in your favorite editor and scroll down to
> 7.22
>
> On Sun, Jan 14, 2018 at 4:21 PM, Ding, Yuan Chun <[hidden email]> wrote:
> > Hi Bert,
> >
> > I am sorry to bother you on weekend.
> >
> > I am still struggling on defining a correct function.
> >
> > I first defined the function RFS (see below), then run it by provide the
> two argument.
> >
> > m52.2cluster <-RFS(inputfile =allinfo_m52, N=2 )
> >
> > I do not get error message, but no figure displays on screen. I do not
> know what is going on.
> >
> > Can you help me a little more on this issue?
> >
> > Thank you,
> >
> > Ding
> >
> > # function to generate RFS
> > RFS <- function( inputfile, N ) {
> >   cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
> >                                data = inputfile)
> >
> >          if( N==2) {palette <- c("red", "black")
> >                            legend.labs <- c("Cluster1", "Cluster2")
> >                             }
> >
> >   else if(N==3) {palette <- c("red", "black", "green")
> >                       legend.labs <- c("Cluster1", "Cluster2",
> "Cluster3")
> >                             }
> >
> >                  else {palette <- c("red", "black","green", "blue")
> >                            legend.labs <- c("Cluster1", "Cluster2",
> "Cluster3", "Cluster4")
> >                           }
> >
> >   ggsurvplot(cluster, data = inputfile, risk.table = F,
> >              palette = palette,
> >              ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival
> (Days)",
> >              main = "Survival curve",pval = TRUE,font.x =  16,font.y =
> 16,
> >              font.tickslab = 14,font.legend =c(14,"plain","black"),
> >              legend = "bottom",
> >              legend.title = "Tree Cluster",
> >              legend.labs = legend.labs,
> >              lty=1, lwd=3)
> >                                 }
> >
> > From: Bert Gunter [mailto:[hidden email]]
> > Sent: Sunday, January 14, 2018 9:50 AM
> > To: Ding, Yuan Chun <[hidden email]>
> > Subject: Re: [R] consolidate three function into one
> >
> > I have not looked at your code *at all*, so I am not sure what exactly
> you mean by "consolidate."
> > Is this what you are after?
> >
> > f1 <- function(...) { code 1}
> > f2 <- function(...) { code 2}
> > f3 <- function(...) { code 3}
> > ## can be "consolidated as":
> > f <- function( someargs, ...){
> > if( expr(someargs)) f1(...)
> > else if(expr2(someargs)) f2(...)
> > else f3(...)
> > }
> > The "..." argument to f can soak up any named additional arguments you
> wish to pass to f1, f2, or f3.
> > My apologies if this is offbase or too vague, and feel free to ignore in
> that case. I don't have the patience to go trough your code in detail.
> Others may and give you what you want.
> > Cheers,
> > Bert
> >
> >
> >
> > 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 Sun, Jan 14, 2018 at 9:17 AM, Ding, Yuan Chun <[hidden email]<mailto:
> [hidden email]>> wrote:
> > HI R users,
> >
> > I construct dendrogram tree and cut the tree into different clusters,
> then generate survival curves by the following three functions. All
> variables are included in an inputfile.
> >
> > Can you help me to consolidate the following three function into one
> functions?  I thought about using if  else function, but not sure how to do
> it.
> >
> > Thank you,
> >
> > Ding
> >
> > # function to generate RFS
> > RFS2cluster <- function( inputfile ) {
> >   cluster2<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
> >                                data = inputfile)
> >
> >   ggsurvplot(cluster2, data = inputfile, risk.table = F,
> >              palette = c("red", "black"),
> >              ylim=c(0,1),
> >              ggtheme = theme_bw(),
> >              xlab="Relapse Free Suvival (Days)",
> >              main = "Survival curve",
> >              pval = TRUE,
> >              font.x =  16,
> >              font.y = 16,
> >              font.tickslab = 14,
> >              font.legend =c(14,"plain","black"),
> >              legend = "bottom",
> >              legend.title = "Tree Cluster",
> >              legend.labs = c("Cluster1", "Cluster2"), lty=1, lwd=3) }
> >
> > RFS3cluster <- function( inputfile ) {
> >   cluster3<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
> >                      data = inputfile)
> >
> >   ggsurvplot(cluster3, data = inputfile, risk.table = F,
> >              palette = c("red", "black", "green"),
> >              ylim=c(0,1),
> >              ggtheme = theme_bw(),
> >              xlab="Relapse Free Suvival (Days)",
> >              main = "Survival curve",
> >              pval = TRUE,
> >              font.x =  16,
> >              font.y = 16,
> >              font.tickslab = 14,
> >              font.legend =c(14,"plain","black"),
> >              legend = "bottom",
> >              legend.title = "Tree Cluster",
> >              legend.labs = c("Cluster1", "Cluster2", "Cluster3"),
> > lty=1, lwd=3) }
> >
> > RFS4cluster <- function( inputfile ) {
> >   cluster4<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
> >                      data = inputfile)
> >
> >   ggsurvplot(cluster4, data = inputfile, risk.table = F,
> >              palette = c("red", "black", "green", "blue"),
> >              ylim=c(0,1),
> >              ggtheme = theme_bw(),
> >              xlab="Relapse Free Suvival (Days)",
> >              main = "Survival curve",
> >              pval = TRUE,
> >              font.x =  16,
> >              font.y = 16,
> >              font.tickslab = 14,
> >              font.legend =c(14,"plain","black"),
> >              legend = "bottom",
> >              legend.title = "Tree Cluster",
> >              legend.labs = c("Cluster1", "Cluster2", "Cluster3",
> > "Cluster4"), lty=1, lwd=3) }
> >
> > -----Original Message-----
> > From: R-help
> > [mailto:[hidden email]<mailto:[hidden email]
> > rg>] On Behalf Of imane hajar
> > Sent: Friday, January 12, 2018 7:42 AM
> > To: [hidden email]<mailto:[hidden email]>
> > Subject: [R] Help with packages (methods, stats, stats4)
> >
> > [Attention: This email came from an external source. Do not open
> > attachments or click on links from unknown senders or unexpected
> > emails.]
> >
> >
> >
> >
> >
> > hello,
> > Can you please give me a hand with this problem,well i can't install
> > these
> > packages:
> > - stats
> > - methods
> > - stats4
> >
> > when i tried the following command :  *library(help = "stats") * , it
> gave me this output (*see picture*), so i contacted the Maintainer of the
> package at (*[hidden email]<mailto:[hidden email]> <
> [hidden email]<mailto:[hidden email]>>*) but he said that i
> write to the wrong place.
> >
> > (i want to install those packages in order to use the "DVstats"
> > package)
> >
> > (i have the latest version of R (3.4.3 ) and Rstudio(1.2.240) )
> >
> > thank you
> > Regards
> >
> >
> > ---------------------------------------------------------------------
> > -SECURITY/CONFIDENTIALITY WARNING-
> > This message (and any attachments) are intended solely for the
> > individual or entity to which they are addressed. This communication
> > may contain information that is privileged, confidential, or exempt
> > from disclosure under applicable law (e.g., personal health
> > information, research data, financial information). Because this
> > e-mail has been sent without encryption, individuals other than the
> > intended recipient may be able to view the information, forward it to
> > others or tamper with the information without the knowledge or consent
> > of the sender. If you are not the intended recipient, or the employee
> > or person responsible for delivering the message to the intended
> > recipient, any dissemination, distribution or copying of the
> > communication is strictly prohibited. If you received the
> > communication in error, please notify the sender immediately by
> > replying to this message and deleting the message and any accompanying
> > files from your system. If, due to the security risks, you do not wish
> > to r  eceive further communications via e-mail, please reply to this
> > message and inform the sender that you do not wish to receive further
> > e-mail from the sender. (LCP301)
> > ---------------------------------------------------------------------
> >
> > ______________________________________________
> > [hidden email]<mailto:[hidden email]> 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]]
> >
> > ______________________________________________
> > [hidden email] 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]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: consolidate three function into one

Ding, Yuan Chun
Thank you, your suggestion is simpler and logically better.  I had impression that the last object in a function gets returned, so I did not add the print function at the bottom line of the function definition.  Returning an object and graph the object are different process, I am a beginner for writing R function and need to find a good guide source about writing R functions.   If you know a good book or website for guidance of R function, please let me know.

Thanks,

Ding

From: Bert Gunter [mailto:[hidden email]]
Sent: Monday, January 15, 2018 10:11 AM
To: Ding, Yuan Chun <[hidden email]>
Cc: Richard M. Heiberger <[hidden email]>; [hidden email]
Subject: Re: [R] consolidate three function into one

That is certainly OK, but you can also just use
print(ggsurvplot(...))
as your final statement.
out <- RFS( ...)
would then return the ggsurvplot object *and* graph it.

Any good R tutorial or a web search will provide more details on function returns, which you might find useful.


Cheers,
Bert


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 Mon, Jan 15, 2018 at 9:57 AM, Ding, Yuan Chun <[hidden email]<mailto:[hidden email]>> wrote:
Hi Richard,

Thank you so much!!  I understand the problem now,  I assign a name to the "ggsurvplot" object and then add print(fig) at bottom of function definition, now figure gets printed on screen.

Ding

# function to generate RFS curves
RFS <- function( inputfile, N ) {
  cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
                    data = inputfile)
  if( N==2) {palette <- c("red", "black")
  legend.labs <- c("Cluster1", "Cluster2")
                     }

  else if(N==3) {palette <- c("red", "black", "green")
  legend.labs <- c("Cluster1", "Cluster2", "Cluster3")
                              }
  else {palette <- c("red", "black","green", "blue")
  legend.labs <- c("Cluster1", "Cluster2", "Cluster3", "Cluster4")
           }


  fig <-ggsurvplot(cluster, data = inputfile, risk.table = F,
             palette = palette,
             ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival (Days)",
             main = "Survival curve",pval = TRUE,font.x =  16,font.y = 16,
             font.tickslab = 14,font.legend =c(14,"plain","black"),
             legend = "bottom",
             legend.title = "Tree Cluster",
             legend.labs = legend.labs,
             lty=1, lwd=3)
  print(fig)
                                                     }

-----Original Message-----
From: Richard M. Heiberger [mailto:[hidden email]<mailto:[hidden email]>]
Sent: Sunday, January 14, 2018 1:34 PM
To: Ding, Yuan Chun <[hidden email]<mailto:[hidden email]>>
Cc: Bert Gunter <[hidden email]<mailto:[hidden email]>>; [hidden email]<mailto:[hidden email]>
Subject: Re: [R] consolidate three function into one

FAQ 7.22
You must print a ggplot object, for example with
print(m52.2cluster)

For the FAQ, run the line
   system.file("../../doc/FAQ")
in R on your computer.
Open up the resulting filepath in your favorite editor and scroll down to 7.22

On Sun, Jan 14, 2018 at 4:21 PM, Ding, Yuan Chun <[hidden email]<mailto:[hidden email]>> wrote:

> Hi Bert,
>
> I am sorry to bother you on weekend.
>
> I am still struggling on defining a correct function.
>
> I first defined the function RFS (see below), then run it by provide the two argument.
>
> m52.2cluster <-RFS(inputfile =allinfo_m52, N=2 )
>
> I do not get error message, but no figure displays on screen. I do not know what is going on.
>
> Can you help me a little more on this issue?
>
> Thank you,
>
> Ding
>
> # function to generate RFS
> RFS <- function( inputfile, N ) {
>   cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
>                                data = inputfile)
>
>          if( N==2) {palette <- c("red", "black")
>                            legend.labs <- c("Cluster1", "Cluster2")
>                             }
>
>   else if(N==3) {palette <- c("red", "black", "green")
>                       legend.labs <- c("Cluster1", "Cluster2", "Cluster3")
>                             }
>
>                  else {palette <- c("red", "black","green", "blue")
>                            legend.labs <- c("Cluster1", "Cluster2", "Cluster3", "Cluster4")
>                           }
>
>   ggsurvplot(cluster, data = inputfile, risk.table = F,
>              palette = palette,
>              ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",pval = TRUE,font.x =  16,font.y = 16,
>              font.tickslab = 14,font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = legend.labs,
>              lty=1, lwd=3)
>                                 }
>
> From: Bert Gunter [mailto:[hidden email]<mailto:[hidden email]>]
> Sent: Sunday, January 14, 2018 9:50 AM
> To: Ding, Yuan Chun <[hidden email]<mailto:[hidden email]>>
> Subject: Re: [R] consolidate three function into one
>
> I have not looked at your code *at all*, so I am not sure what exactly you mean by "consolidate."
> Is this what you are after?
>
> f1 <- function(...) { code 1}
> f2 <- function(...) { code 2}
> f3 <- function(...) { code 3}
> ## can be "consolidated as":
> f <- function( someargs, ...){
> if( expr(someargs)) f1(...)
> else if(expr2(someargs)) f2(...)
> else f3(...)
> }
> The "..." argument to f can soak up any named additional arguments you wish to pass to f1, f2, or f3.
> My apologies if this is offbase or too vague, and feel free to ignore in that case. I don't have the patience to go trough your code in detail. Others may and give you what you want.
> Cheers,
> Bert
>
>
>
> 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 Sun, Jan 14, 2018 at 9:17 AM, Ding, Yuan Chun <[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
> HI R users,
>
> I construct dendrogram tree and cut the tree into different clusters, then generate survival curves by the following three functions. All variables are included in an inputfile.
>
> Can you help me to consolidate the following three function into one functions?  I thought about using if  else function, but not sure how to do it.
>
> Thank you,
>
> Ding
>
> # function to generate RFS
> RFS2cluster <- function( inputfile ) {
>   cluster2<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
>                                data = inputfile)
>
>   ggsurvplot(cluster2, data = inputfile, risk.table = F,
>              palette = c("red", "black"),
>              ylim=c(0,1),
>              ggtheme = theme_bw(),
>              xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",
>              pval = TRUE,
>              font.x =  16,
>              font.y = 16,
>              font.tickslab = 14,
>              font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = c("Cluster1", "Cluster2"), lty=1, lwd=3) }
>
> RFS3cluster <- function( inputfile ) {
>   cluster3<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
>                      data = inputfile)
>
>   ggsurvplot(cluster3, data = inputfile, risk.table = F,
>              palette = c("red", "black", "green"),
>              ylim=c(0,1),
>              ggtheme = theme_bw(),
>              xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",
>              pval = TRUE,
>              font.x =  16,
>              font.y = 16,
>              font.tickslab = 14,
>              font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = c("Cluster1", "Cluster2", "Cluster3"),
> lty=1, lwd=3) }
>
> RFS4cluster <- function( inputfile ) {
>   cluster4<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
>                      data = inputfile)
>
>   ggsurvplot(cluster4, data = inputfile, risk.table = F,
>              palette = c("red", "black", "green", "blue"),
>              ylim=c(0,1),
>              ggtheme = theme_bw(),
>              xlab="Relapse Free Suvival (Days)",
>              main = "Survival curve",
>              pval = TRUE,
>              font.x =  16,
>              font.y = 16,
>              font.tickslab = 14,
>              font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = c("Cluster1", "Cluster2", "Cluster3",
> "Cluster4"), lty=1, lwd=3) }
>
> -----Original Message-----
> From: R-help
> [mailto:[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>
> rg>] On Behalf Of imane hajar
> Sent: Friday, January 12, 2018 7:42 AM
> To: [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>
> Subject: [R] Help with packages (methods, stats, stats4)
>
> [Attention: This email came from an external source. Do not open
> attachments or click on links from unknown senders or unexpected
> emails.]
>
>
>
>
>
> hello,
> Can you please give me a hand with this problem,well i can't install
> these
> packages:
> - stats
> - methods
> - stats4
>
> when i tried the following command :  *library(help = "stats") * , it gave me this output (*see picture*), so i contacted the Maintainer of the package at (*[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>> <[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>*) but he said that i write to the wrong place.
>
> (i want to install those packages in order to use the "DVstats"
> package)
>
> (i have the latest version of R (3.4.3 ) and Rstudio(1.2.240) )
>
> thank you
> Regards
>
>
> ---------------------------------------------------------------------
> -SECURITY/CONFIDENTIALITY WARNING-
> This message (and any attachments) are intended solely for the
> individual or entity to which they are addressed. This communication
> may contain information that is privileged, confidential, or exempt
> from disclosure under applicable law (e.g., personal health
> information, research data, financial information). Because this
> e-mail has been sent without encryption, individuals other than the
> intended recipient may be able to view the information, forward it to
> others or tamper with the information without the knowledge or consent
> of the sender. If you are not the intended recipient, or the employee
> or person responsible for delivering the message to the intended
> recipient, any dissemination, distribution or copying of the
> communication is strictly prohibited. If you received the
> communication in error, please notify the sender immediately by
> replying to this message and deleting the message and any accompanying
> files from your system. If, due to the security risks, you do not wish
> to r  eceive further communications via e-mail, please reply to this
> message and inform the sender that you do not wish to receive further
> e-mail from the sender. (LCP301)
> ---------------------------------------------------------------------
>
> ______________________________________________
> [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>> 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]]
>
> ______________________________________________
> [hidden email]<mailto:[hidden email]> 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]]

______________________________________________
[hidden email] 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: consolidate three function into one

Bert Gunter-2
"Good" tutorials are a matter of personal taste -- what's good for me may
be terrible for you, and vice-versa.

One set of recommendations is here:

https://www.rstudio.com/online-learning/#R

but you may do even better by web search on "R tutorials" or "Writing R
function tutorials" and the like.

You should certainly have a look at the "Introduction to R" tutorial that
ships with R, since it's immediately available. It's a bit old, however.

Cheers,
Bert



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 Mon, Jan 15, 2018 at 10:21 AM, Ding, Yuan Chun <[hidden email]> wrote:

> Thank you, your suggestion is simpler and logically better.  I had
> impression that the last object in a function gets returned, so I did not
> add the print function at the bottom line of the function definition.
> Returning an object and graph the object are different process, I am a
> beginner for writing R function and need to find a good guide source about
> writing R functions.   If you know a good book or website for guidance of R
> function, please let me know.
>
>
>
> Thanks,
>
>
>
> Ding
>
>
>
> *From:* Bert Gunter [mailto:[hidden email]]
> *Sent:* Monday, January 15, 2018 10:11 AM
> *To:* Ding, Yuan Chun <[hidden email]>
> *Cc:* Richard M. Heiberger <[hidden email]>; [hidden email]
> *Subject:* Re: [R] consolidate three function into one
>
>
>
> That is certainly OK, but you can also just use
>
> print(ggsurvplot(...))
>
> as your final statement.
>
> out <- RFS( ...)
>
> would then return the ggsurvplot object *and* graph it.
>
>
>
> Any good R tutorial or a web search will provide more details on function
> returns, which you might find useful.
>
>
>
>
>
> Cheers,
>
> Bert
>
>
> 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 Mon, Jan 15, 2018 at 9:57 AM, Ding, Yuan Chun <[hidden email]> wrote:
>
> Hi Richard,
>
> Thank you so much!!  I understand the problem now,  I assign a name to the
> "ggsurvplot" object and then add print(fig) at bottom of function
> definition, now figure gets printed on screen.
>
> Ding
>
> # function to generate RFS curves
> RFS <- function( inputfile, N ) {
>   cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
>                     data = inputfile)
>   if( N==2) {palette <- c("red", "black")
>   legend.labs <- c("Cluster1", "Cluster2")
>                      }
>
>   else if(N==3) {palette <- c("red", "black", "green")
>   legend.labs <- c("Cluster1", "Cluster2", "Cluster3")
>                               }
>   else {palette <- c("red", "black","green", "blue")
>   legend.labs <- c("Cluster1", "Cluster2", "Cluster3", "Cluster4")
>            }
>
>
>   fig <-ggsurvplot(cluster, data = inputfile, risk.table = F,
>              palette = palette,
>              ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival
> (Days)",
>              main = "Survival curve",pval = TRUE,font.x =  16,font.y = 16,
>              font.tickslab = 14,font.legend =c(14,"plain","black"),
>              legend = "bottom",
>              legend.title = "Tree Cluster",
>              legend.labs = legend.labs,
>              lty=1, lwd=3)
>   print(fig)
>                                                      }
>
> -----Original Message-----
> From: Richard M. Heiberger [mailto:[hidden email]]
> Sent: Sunday, January 14, 2018 1:34 PM
> To: Ding, Yuan Chun <[hidden email]>
> Cc: Bert Gunter <[hidden email]>; [hidden email]
> Subject: Re: [R] consolidate three function into one
>
> FAQ 7.22
> You must print a ggplot object, for example with
> print(m52.2cluster)
>
> For the FAQ, run the line
>    system.file("../../doc/FAQ")
> in R on your computer.
> Open up the resulting filepath in your favorite editor and scroll down to
> 7.22
>
> On Sun, Jan 14, 2018 at 4:21 PM, Ding, Yuan Chun <[hidden email]> wrote:
> > Hi Bert,
> >
> > I am sorry to bother you on weekend.
> >
> > I am still struggling on defining a correct function.
> >
> > I first defined the function RFS (see below), then run it by provide the
> two argument.
> >
> > m52.2cluster <-RFS(inputfile =allinfo_m52, N=2 )
> >
> > I do not get error message, but no figure displays on screen. I do not
> know what is going on.
> >
> > Can you help me a little more on this issue?
> >
> > Thank you,
> >
> > Ding
> >
> > # function to generate RFS
> > RFS <- function( inputfile, N ) {
> >   cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
> >                                data = inputfile)
> >
> >          if( N==2) {palette <- c("red", "black")
> >                            legend.labs <- c("Cluster1", "Cluster2")
> >                             }
> >
> >   else if(N==3) {palette <- c("red", "black", "green")
> >                       legend.labs <- c("Cluster1", "Cluster2",
> "Cluster3")
> >                             }
> >
> >                  else {palette <- c("red", "black","green", "blue")
> >                            legend.labs <- c("Cluster1", "Cluster2",
> "Cluster3", "Cluster4")
> >                           }
> >
> >   ggsurvplot(cluster, data = inputfile, risk.table = F,
> >              palette = palette,
> >              ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival
> (Days)",
> >              main = "Survival curve",pval = TRUE,font.x =  16,font.y =
> 16,
> >              font.tickslab = 14,font.legend =c(14,"plain","black"),
> >              legend = "bottom",
> >              legend.title = "Tree Cluster",
> >              legend.labs = legend.labs,
> >              lty=1, lwd=3)
> >                                 }
> >
> > From: Bert Gunter [mailto:[hidden email]]
> > Sent: Sunday, January 14, 2018 9:50 AM
> > To: Ding, Yuan Chun <[hidden email]>
> > Subject: Re: [R] consolidate three function into one
> >
> > I have not looked at your code *at all*, so I am not sure what exactly
> you mean by "consolidate."
> > Is this what you are after?
> >
> > f1 <- function(...) { code 1}
> > f2 <- function(...) { code 2}
> > f3 <- function(...) { code 3}
> > ## can be "consolidated as":
> > f <- function( someargs, ...){
> > if( expr(someargs)) f1(...)
> > else if(expr2(someargs)) f2(...)
> > else f3(...)
> > }
> > The "..." argument to f can soak up any named additional arguments you
> wish to pass to f1, f2, or f3.
> > My apologies if this is offbase or too vague, and feel free to ignore in
> that case. I don't have the patience to go trough your code in detail.
> Others may and give you what you want.
> > Cheers,
> > Bert
> >
> >
> >
> > 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 Sun, Jan 14, 2018 at 9:17 AM, Ding, Yuan Chun <[hidden email]<mailto:
> [hidden email]>> wrote:
> > HI R users,
> >
> > I construct dendrogram tree and cut the tree into different clusters,
> then generate survival curves by the following three functions. All
> variables are included in an inputfile.
> >
> > Can you help me to consolidate the following three function into one
> functions?  I thought about using if  else function, but not sure how to do
> it.
> >
> > Thank you,
> >
> > Ding
> >
> > # function to generate RFS
> > RFS2cluster <- function( inputfile ) {
> >   cluster2<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
> >                                data = inputfile)
> >
> >   ggsurvplot(cluster2, data = inputfile, risk.table = F,
> >              palette = c("red", "black"),
> >              ylim=c(0,1),
> >              ggtheme = theme_bw(),
> >              xlab="Relapse Free Suvival (Days)",
> >              main = "Survival curve",
> >              pval = TRUE,
> >              font.x =  16,
> >              font.y = 16,
> >              font.tickslab = 14,
> >              font.legend =c(14,"plain","black"),
> >              legend = "bottom",
> >              legend.title = "Tree Cluster",
> >              legend.labs = c("Cluster1", "Cluster2"), lty=1, lwd=3) }
> >
> > RFS3cluster <- function( inputfile ) {
> >   cluster3<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
> >                      data = inputfile)
> >
> >   ggsurvplot(cluster3, data = inputfile, risk.table = F,
> >              palette = c("red", "black", "green"),
> >              ylim=c(0,1),
> >              ggtheme = theme_bw(),
> >              xlab="Relapse Free Suvival (Days)",
> >              main = "Survival curve",
> >              pval = TRUE,
> >              font.x =  16,
> >              font.y = 16,
> >              font.tickslab = 14,
> >              font.legend =c(14,"plain","black"),
> >              legend = "bottom",
> >              legend.title = "Tree Cluster",
> >              legend.labs = c("Cluster1", "Cluster2", "Cluster3"),
> > lty=1, lwd=3) }
> >
> > RFS4cluster <- function( inputfile ) {
> >   cluster4<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
> >                      data = inputfile)
> >
> >   ggsurvplot(cluster4, data = inputfile, risk.table = F,
> >              palette = c("red", "black", "green", "blue"),
> >              ylim=c(0,1),
> >              ggtheme = theme_bw(),
> >              xlab="Relapse Free Suvival (Days)",
> >              main = "Survival curve",
> >              pval = TRUE,
> >              font.x =  16,
> >              font.y = 16,
> >              font.tickslab = 14,
> >              font.legend =c(14,"plain","black"),
> >              legend = "bottom",
> >              legend.title = "Tree Cluster",
> >              legend.labs = c("Cluster1", "Cluster2", "Cluster3",
> > "Cluster4"), lty=1, lwd=3) }
> >
> > -----Original Message-----
> > From: R-help
> > [mailto:[hidden email]<mailto:[hidden email]
> > rg>] On Behalf Of imane hajar
> > Sent: Friday, January 12, 2018 7:42 AM
> > To: [hidden email]<mailto:[hidden email]>
> > Subject: [R] Help with packages (methods, stats, stats4)
> >
> > [Attention: This email came from an external source. Do not open
> > attachments or click on links from unknown senders or unexpected
> > emails.]
> >
> >
> >
> >
> >
> > hello,
> > Can you please give me a hand with this problem,well i can't install
> > these
> > packages:
> > - stats
> > - methods
> > - stats4
> >
> > when i tried the following command :  *library(help = "stats") * , it
> gave me this output (*see picture*), so i contacted the Maintainer of the
> package at (*[hidden email]<mailto:[hidden email]> <
> [hidden email]<mailto:[hidden email]>>*) but he said that i
> write to the wrong place.
> >
> > (i want to install those packages in order to use the "DVstats"
> > package)
> >
> > (i have the latest version of R (3.4.3 ) and Rstudio(1.2.240) )
> >
> > thank you
> > Regards
> >
> >
> > ---------------------------------------------------------------------
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> > ______________________________________________
> > [hidden email]<mailto:[hidden email]> 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]]
> >
> > ______________________________________________
> > [hidden email] 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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