[R] Please Help how to execute R via php script
Dear R members, I want to call my R script thorough php but no I am not
getting output
When I call my r script by bat file works fines also when run by Rstudio it
works fines
but when i cant call via php
here is the php code:
?php
exec('C:/Program Files/R/R-3.2.0/bin/i386/Rscript.exe
C:/xampp/htdocs/postam/DrawGraph.R')
echo 'img src=C:/xampp/htdocs/postam/radargplot100.png?t='.time().'
style=height:600px;width:auto; /' ;
?
here is R script
args=(commandArgs(TRUE))
library(ggplot2)
library(readxl)
#library(RMySQL)
#library(readxl,lib.loc =C:\Program Files\R\R-3.2.0\bin\i386)
library(RMySQL,lib.loc =C:/Users/Mbowe/Documents/R/win-library/3.2)
library(arulesViz, quietly=TRUE)
drv_postam = dbDriver(MySQL)
con = dbConnect(drv_postam, user=root,
dbname=evtlogr,host=localhost)
tbl_data2-dbGetQuery(con,select * from `tblsevtlogs` where datetime
BETWEEN '5/20/2015' AND '5/28/2015';)
closeAllConnections()
head( tbl_data2)
tail( tbl_data2)
#summary(data)
w1 =
table(tbl_data2$evtcategory,tbl_data2$evttype,tbl_data2$evt_usr_source)
t1 = as.data.frame(w1)
t1
LogonType-t1$Var1
LogonTypeCount-t1$Freq
Yaxis-paste(paste(Frequency Count))
user_obj-paste(User: ,tbl_data2$evt_usr_source)
myplot - ggplot(t1, aes(y = LogonTypeCount, x = reorder(t1$Var2,
t1$Freq),
group = LogonType, colour = LogonType)) + coord_polar()
+ geom_point(size=3) + geom_path(size=1) +
labs(x = paste(Data Mined From (,user_obj,), Event Logs),y=Yaxis)
ggsave(file=C:/xampp/htdocs/postam/radargplot100.png)
dev.off()
[[alternative HTML version deleted]]
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Re: [R] [FORGED] date format in xyplot
See inline below. On 18/08/15 16:15, Christine Lee via R-help wrote: To whom it may concern, I have tried to plot some numbers against time with the time on the X-axis shown as Jan, Feb, etc. I used the following commands: Raw-structure(list(Date = structure(c(6L, 7L, 2L, 4L, 12L, 9L, 7L, 2L, 4L, 12L), .Label = c(1/10, 1/11, 11/11, 12/11, 13/10, 19/9, 2/10, 2/11, 20/9, 26/11, 29/10, 29/11, 30/11, 31/10, 4/10, 6/10), class = factor), Year = c(2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L ), Station = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), .Label = c(E, F, H, I), class = factor), Abun = c(3.42, 1.33, 3.67, 3.67, 3.92, 2.17, 2.5, 1.67, 6.33, 0.67), Date1 = structure(c(16697, 16710, 16740, 16751, 16768, 16698, 16710, 16740, 16751, 16768 ), class = Date)), .Names = c(Date, Year, Station, Abun, Date1), row.names = c(NA, 10L), class = data.frame) Raw$Date1-as.Date(Raw$Date,%d/%m) What does this accomplish? As far as I can tell Raw$Date1 is the same after doing this replacement as it was before. xyplot(Abun~Date1|as.factor(Year),Raw,type=p,xlab=list(Month,cex=1.5), lab=list(Abundance,cex=1.5),cex=2,pch=c(16,16,21),col=c(Black,Grey,Black), strip=strip.custom(bg='white'),format=%B-%d) The date format shown on X-axis was just 10-1, 10-15 Not what I get. I should be grateful if any one could help indicating what has gone wrong? No idea. When I try your code, the x-axis labels that I get are Oct 01, Oct 15, ..., Dec 01, which looks pretty much as it should. General advice --- when you are getting unexpected results, try the example in a stripped down keep it simple form --- i.e. eliminate most of the bells and whistles in your very complicated call to xyplot(). That might give you a better chance at discerning what is causing things to go wrong for you. cheers, Rolf Turner -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ 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.
[R] 回覆︰ [FORGED] date format in xyplot
Thanks Mr. Turner, This puzzles me. Why do we come out with different axis labels with the same command? Is this because of my R version or my computer? Regards,Christine Rolf Turner r.tur...@auckland.ac.nz 於 2015年08月18日 (週二) 2:02 PM 寫道﹕ See inline below. On 18/08/15 16:15, Christine Lee via R-help wrote: To whom it may concern, I have tried to plot some numbers against time with the time on the X-axis shown as Jan, Feb, etc. I used the following commands: Raw-structure(list(Date = structure(c(6L, 7L, 2L, 4L, 12L, 9L, 7L, 2L, 4L, 12L), .Label = c(1/10, 1/11, 11/11, 12/11, 13/10, 19/9, 2/10, 2/11, 20/9, 26/11, 29/10, 29/11, 30/11, 31/10, 4/10, 6/10), class = factor), Year = c(2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L ), Station = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), .Label = c(E, F, H, I), class = factor), Abun = c(3.42, 1.33, 3.67, 3.67, 3.92, 2.17, 2.5, 1.67, 6.33, 0.67), Date1 = structure(c(16697, 16710, 16740, 16751, 16768, 16698, 16710, 16740, 16751, 16768 ), class = Date)), .Names = c(Date, Year, Station, Abun, Date1), row.names = c(NA, 10L), class = data.frame) Raw$Date1-as.Date(Raw$Date,%d/%m) What does this accomplish? As far as I can tell Raw$Date1 is the same after doing this replacement as it was before. xyplot(Abun~Date1|as.factor(Year),Raw,type=p,xlab=list(Month,cex=1.5), lab=list(Abundance,cex=1.5),cex=2,pch=c(16,16,21),col=c(Black,Grey,Black), strip=strip.custom(bg='white'),format=%B-%d) The date format shown on X-axis was just 10-1, 10-15 Not what I get. I should be grateful if any one could help indicating what has gone wrong? No idea. When I try your code, the x-axis labels that I get are Oct 01, Oct 15, ..., Dec 01, which looks pretty much as it should. General advice --- when you are getting unexpected results, try the example in a stripped down keep it simple form --- i.e. eliminate most of the bells and whistles in your very complicated call to xyplot(). That might give you a better chance at discerning what is causing things to go wrong for you. cheers, Rolf Turner -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 [[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.
Re: [R] date format in xyplot
Hi Christine If somethings go wrong: 1 first check your data str(Raw) 'data.frame': 10 obs. of 5 variables: $ Date : Factor w/ 16 levels 1/10,1/11,..: 6 7 2 4 12 9 7 2 4 12 $ Year : int 2002 2002 2002 2002 2002 2002 2002 2002 2002 2002 $ Station: Factor w/ 4 levels E,F,H,I: 1 1 1 1 1 2 2 2 2 2 $ Abun : num 3.42 1.33 3.67 3.67 3.92 2.17 2.5 1.67 6.33 0.67 $ Date1 : Date, format: 2015-09-19 2015-10-02 2015-11-01 2015-11-12 ... Raw$Date2 - as.character(Raw$Date1) Raw$Date2 [1] 2015-09-19 2015-10-02 2015-11-01 2015-11-12 2015-11-29 2015-09-20 2015-10-02 2015-11-01 2015-11-12 2015-11-29 Raw$Date2 - as.Date(Raw$Date2, %Y-%m-%d) 2 read the help guide again if not done recently ?lattice::xyplot or ?xyplot 3 start with a minimum number of arguments xyplot(Abun~Date2|as.factor(Year), Raw) or xyplot(Abun~Date2, Raw) if you are still having problems Dates are hard work in any language as they are not consistent so: a. use default b. use your own This works xyplot(Abun~Date2|as.factor(Year), Raw, par.settings = list(stripbackground = transparent), # background colour controlled here type=p, scales = list(x = list(at = sort(c(seq(as.Date(Raw$Date2[1]-4), by = months, length = 4), seq(as.Date(Raw$Date2[1]+12), by = months, length = 3))), labels = format(sort(c(seq(as.Date(Raw$Date2[1]-4), by = months, length = 4), seq(as.Date(Raw$Date2[1]+12), by = months, length = 3))), %m-%d) ) ), xlab=list(Month,cex=1.5), ylab=list(Abundance,cex=1.5), cex=2, pch=c(16,16,21), col=c(Black,Grey,Black) ) par.settings is confining the parameters set by trellis.par.set() to the function to get them names(trellis.par.get() ) and going further trellis.par.get()$superpose.symbol will give you the values for superpose.symbol Beware: Do not make the labels etc so big that the axis labels are hard to read. Think of final size Regards Duncan Duncan Mackay Department of Agronomy and Soil Science University of New England Armidale NSW 2351 Email: home: mac...@northnet.com.au -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Christine Lee via R-help Sent: Tuesday, 18 August 2015 14:16 To: r-help@r-project.org Subject: [R] date format in xyplot To whom it may concern, I have tried to plot some numbers against time with the time on the X-axis shown as Jan, Feb, etc. I used the following commands: Raw-structure(list(Date = structure(c(6L, 7L, 2L, 4L, 12L, 9L, 7L, 2L, 4L, 12L), .Label = c(1/10, 1/11, 11/11, 12/11, 13/10, 19/9, 2/10, 2/11, 20/9, 26/11, 29/10, 29/11, 30/11, 31/10, 4/10, 6/10), class = factor), Year = c(2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L ), Station = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), .Label = c(E, F, H, I), class = factor), Abun = c(3.42, 1.33, 3.67, 3.67, 3.92, 2.17, 2.5, 1.67, 6.33, 0.67), Date1 = structure(c(16697, 16710, 16740, 16751, 16768, 16698, 16710, 16740, 16751, 16768 ), class = Date)), .Names = c(Date, Year, Station, Abun, Date1), row.names = c(NA, 10L), class = data.frame) Raw$Date1-as.Date(Raw$Date,%d/%m) xyplot(Abun~Date1|as.factor(Year),Raw,type=p,xlab=list(Month,cex=1.5),yl ab=list(Abundance,cex=1.5),cex=2,pch=c(16,16,21),col=c(Black,Grey,Bla ck),strip=strip.custom(bg='white'),format=%B-%d) The date format shown on X-axis was just 10-1, 10-15 I should be grateful if any one could help indicating what has gone wrong? Regards, Christine __ 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. __ 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.
[R] How are packages installed with install_github() updated in RStudio?
Hallo. I use RStudio. Because of a bug in the latest CRAN version of dplyr, I installed the GitHub version with install_github(). Now I wonder what happens when there is a new version. Does RStudio update the packages installed from GitHub? If so, does it replace it with the new CRAN version, or a new GitHub version? Many thanks for you answer, Michal Kvasnicka [[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.
Re: [R] 回覆︰ [FORGED] date format in xyplot
On 18/08/15 18:15, Christine Lee wrote: Thanks Mr. Turner, Please!!! Either Rolf or (if you insist on formality) *Dr.* Turner. :-) This puzzles me. Why do we come out with different axis labels with the same command? Is this because of my R version or my computer? SNIP It is most likely a *version* issue; in your version the default format is %m-%e whereas in mine it's %b %d. Or something like that. Or it just might be a Windoze thing. (If Micro$oft can find a way to mess things up, they will.) I run *Linux*, as do all right-thinking people. Be that as it may, I have now looked at the help for xyplot() a little more carefully (when in doubt try reading TFM!!!) and saw that format must be supplied as part of the *scales* argument, which is a *list*. So try: xyplot(Abun ~ Date1 | ... etc. etc ..., scales=list(format=%B=%d)) and I think you'll get what you want. cheers, Rolf Turner -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Please Help how to execute R via php script
Joseph Mbowe mbo...@nm-aist.ac.tz writes:
Dear R members, I want to call my R script thorough php but no I am not
getting output
When I call my r script by bat file works fines also when run by Rstudio it
works fines
but when i cant call via php
here is the php code:
?php
exec('C:/Program Files/R/R-3.2.0/bin/i386/Rscript.exe
C:/xampp/htdocs/postam/DrawGraph.R')
echo 'img src=C:/xampp/htdocs/postam/radargplot100.png?t='.time().'
style=height:600px;width:auto; /' ;
?
I know nothing about PHP, but you seem to have a missing double quote in
your call to 'exec'.
Cheers,
Loris
here is R script
args=(commandArgs(TRUE))
library(ggplot2)
library(readxl)
#library(RMySQL)
#library(readxl,lib.loc =C:\Program Files\R\R-3.2.0\bin\i386)
library(RMySQL,lib.loc =C:/Users/Mbowe/Documents/R/win-library/3.2)
library(arulesViz, quietly=TRUE)
drv_postam = dbDriver(MySQL)
con = dbConnect(drv_postam, user=root,
dbname=evtlogr,host=localhost)
tbl_data2-dbGetQuery(con,select * from `tblsevtlogs` where datetime
BETWEEN '5/20/2015' AND '5/28/2015';)
closeAllConnections()
head( tbl_data2)
tail( tbl_data2)
#summary(data)
w1 =
table(tbl_data2$evtcategory,tbl_data2$evttype,tbl_data2$evt_usr_source)
t1 = as.data.frame(w1)
t1
LogonType-t1$Var1
LogonTypeCount-t1$Freq
Yaxis-paste(paste(Frequency Count))
user_obj-paste(User: ,tbl_data2$evt_usr_source)
myplot - ggplot(t1, aes(y = LogonTypeCount, x = reorder(t1$Var2,
t1$Freq),
group = LogonType, colour = LogonType)) + coord_polar()
+ geom_point(size=3) + geom_path(size=1) +
labs(x = paste(Data Mined From (,user_obj,), Event Logs),y=Yaxis)
ggsave(file=C:/xampp/htdocs/postam/radargplot100.png)
dev.off()
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] date format in xyplot
Sorry, quick follow-up: is there any chance you used Date rather than Date1 in the original plot? John Kane Kingston ON Canada -Original Message- From: r-help@r-project.org Sent: Mon, 17 Aug 2015 21:15:39 -0700 To: r-help@r-project.org Subject: [R] date format in xyplot To whom it may concern, I have tried to plot some numbers against time with the time on the X-axis shown as Jan, Feb, etc. I used the following commands: Raw-structure(list(Date = structure(c(6L, 7L, 2L, 4L, 12L, 9L, 7L, 2L, 4L, 12L), .Label = c(1/10, 1/11, 11/11, 12/11, 13/10, 19/9, 2/10, 2/11, 20/9, 26/11, 29/10, 29/11, 30/11, 31/10, 4/10, 6/10), class = factor), Year = c(2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L ), Station = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), .Label = c(E, F, H, I), class = factor), Abun = c(3.42, 1.33, 3.67, 3.67, 3.92, 2.17, 2.5, 1.67, 6.33, 0.67), Date1 = structure(c(16697, 16710, 16740, 16751, 16768, 16698, 16710, 16740, 16751, 16768 ), class = Date)), .Names = c(Date, Year, Station, Abun, Date1), row.names = c(NA, 10L), class = data.frame) Raw$Date1-as.Date(Raw$Date,%d/%m) xyplot(Abun~Date1|as.factor(Year),Raw,type=p,xlab=list(Month,cex=1.5),ylab=list(Abundance,cex=1.5),cex=2,pch=c(16,16,21),col=c(Black,Grey,Black),strip=strip.custom(bg='white'),format=%B-%d) The date format shown on X-axis was just 10-1, 10-15 I should be grateful if any one could help indicating what has gone wrong? Regards, Christine __ 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. FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! __ 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.
Re: [R] How are packages installed with install_github() updated in RStudio?
Hi Michal, Because RStudio seems to use its own method of updating you might be better off asking in their forum. John Kane Kingston ON Canada -Original Message- From: prgo...@gmail.com Sent: Tue, 18 Aug 2015 10:43:20 +0200 To: r-help@r-project.org Subject: [R] How are packages installed with install_github() updated in RStudio? Hallo. I use RStudio. Because of a bug in the latest CRAN version of dplyr, I installed the GitHub version with install_github(). Now I wonder what happens when there is a new version. Does RStudio update the packages installed from GitHub? If so, does it replace it with the new CRAN version, or a new GitHub version? Many thanks for you answer, Michal Kvasnicka [[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. Can't remember your password? Do you need a strong and secure password? Use Password manager! It stores your passwords protects your account. __ 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.
Re: [R] date format in xyplot
Hi Christine, I am afraid I cannot help as it 'appears' fine here I get an x-axis witih Oct 01 Oct 15 Nov 15 Dec 01 I don't normally use lattice but the dates seem reasonable to me Do a str(Raw) and check if Date1 is actually a date in your orginal data. It is one here but who knows with R :) John Kane Kingston ON Canada -Original Message- From: r-help@r-project.org Sent: Mon, 17 Aug 2015 21:15:39 -0700 To: r-help@r-project.org Subject: [R] date format in xyplot To whom it may concern, I have tried to plot some numbers against time with the time on the X-axis shown as Jan, Feb, etc. I used the following commands: Raw-structure(list(Date = structure(c(6L, 7L, 2L, 4L, 12L, 9L, 7L, 2L, 4L, 12L), .Label = c(1/10, 1/11, 11/11, 12/11, 13/10, 19/9, 2/10, 2/11, 20/9, 26/11, 29/10, 29/11, 30/11, 31/10, 4/10, 6/10), class = factor), Year = c(2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L ), Station = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), .Label = c(E, F, H, I), class = factor), Abun = c(3.42, 1.33, 3.67, 3.67, 3.92, 2.17, 2.5, 1.67, 6.33, 0.67), Date1 = structure(c(16697, 16710, 16740, 16751, 16768, 16698, 16710, 16740, 16751, 16768 ), class = Date)), .Names = c(Date, Year, Station, Abun, Date1), row.names = c(NA, 10L), class = data.frame) Raw$Date1-as.Date(Raw$Date,%d/%m) xyplot(Abun~Date1|as.factor(Year),Raw,type=p,xlab=list(Month,cex=1.5),ylab=list(Abundance,cex=1.5),cex=2,pch=c(16,16,21),col=c(Black,Grey,Black),strip=strip.custom(bg='white'),format=%B-%d) The date format shown on X-axis was just 10-1, 10-15 I should be grateful if any one could help indicating what has gone wrong? Regards, Christine __ 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. FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! __ 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.
Re: [R] How are packages installed with install_github() updated in RStudio?
On 18/08/2015 10:01 AM, Hadley Wickham wrote: RStudio just calls the same underlying R functions, so it doesn't make any difference that you're using RStudio. Currently, there's no automatic way to update packages installed from github. And to clarify a bit more: this means if you install a patched version of something from github that is newer than what is on CRAN, then call update.packages(), you'll keep the new one as long as the version number is higher than the one on CRAN. On the other hand, if you run install.packages(foo), then you'll install the CRAN version of foo even if you already have a newer one from github. Duncan Murdoch Hadley On Tue, Aug 18, 2015 at 8:14 AM, John Kane jrkrid...@inbox.com wrote: Hi Michal, Because RStudio seems to use its own method of updating you might be better off asking in their forum. John Kane Kingston ON Canada -Original Message- From: prgo...@gmail.com Sent: Tue, 18 Aug 2015 10:43:20 +0200 To: r-help@r-project.org Subject: [R] How are packages installed with install_github() updated in RStudio? Hallo. I use RStudio. Because of a bug in the latest CRAN version of dplyr, I installed the GitHub version with install_github(). Now I wonder what happens when there is a new version. Does RStudio update the packages installed from GitHub? If so, does it replace it with the new CRAN version, or a new GitHub version? Many thanks for you answer, Michal Kvasnicka [[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. Can't remember your password? Do you need a strong and secure password? Use Password manager! It stores your passwords protects your account. __ 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. __ 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.
[R] data frame formatting
Hello all, I would like to take a data frame such as the following one: df - data.frame(id=c(A,A,B,B),first=c(BX,NA,NA,LF),second=c(NA,TD,BZ,NA),third=c(NA,NA,RB,BT),fourth=c(LG,QR,NA,NA)) df id first second third fourth 1 ABX NA NA LG 2 A NA TD NA QR 3 B NA BZRB NA 4 BLF NABT NA and merge rows based on the id, such that the value in the column will be one of four possibilities: if both values in the original df are NA, the new value should also be NA. If there are two non-NA values, then the new value should read clash. Otherwise, the new value should be whichever value was not NA. An example output from the command would read in df and read out: id first second third fourth 1 ABX TD NA clash 2 BLF BZclash NA I'd be grateful if someone could point me in the right direction. Thanks, Jonathan [[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.
Re: [R] data frame formatting
Here's one way in base R:
df - data.frame(id=c(A,A,B,B),
first=c(BX,NA,NA,LF),
second=c(NA,TD,BZ,NA),
third=c(NA,NA,RB,BT),
fourth=c(LG,QR,NA,NA))
new_df - data.frame(do.call(rbind, by(df, df$id, function(x) {
sapply(x[,-1], function(y) {
if (all(is.na(y))) return(NA)
if (all(!is.na(y))) return(clash)
return(as.character(y[which(!is.na(y))]))
})
})))
new_df$id - rownames(new_df)
rownames(new_df) - NULL
new_df
## first second third fourth id
## 1BX TD NA clash A
## 2LF BZ clash NA B
On Tue, Aug 18, 2015 at 3:06 PM, Jon BR jonsle...@gmail.com wrote:
df -
data.frame(id=c(A,A,B,B),first=c(BX,NA,NA,LF),second=c(NA,TD,BZ,NA),third=c(NA,NA,RB,BT),fourth=c(LG,QR,NA,NA))
df
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Re: [R] How are packages installed with install_github() updated in RStudio?
Thanks Hadley I had some vague impression that RStudio was maintaining a slightly diffferent repository thought I am not sure why I thought that. John Kane Kingston ON Canada -Original Message- From: h.wick...@gmail.com Sent: Tue, 18 Aug 2015 09:01:09 -0500 To: jrkrid...@inbox.com Subject: Re: [R] How are packages installed with install_github() updated in RStudio? RStudio just calls the same underlying R functions, so it doesn't make any difference that you're using RStudio. Currently, there's no automatic way to update packages installed from github. Hadley On Tue, Aug 18, 2015 at 8:14 AM, John Kane jrkrid...@inbox.com wrote: Hi Michal, Because RStudio seems to use its own method of updating you might be better off asking in their forum. John Kane Kingston ON Canada -Original Message- From: prgo...@gmail.com Sent: Tue, 18 Aug 2015 10:43:20 +0200 To: r-help@r-project.org Subject: [R] How are packages installed with install_github() updated in RStudio? Hallo. I use RStudio. Because of a bug in the latest CRAN version of dplyr, I installed the GitHub version with install_github(). Now I wonder what happens when there is a new version. Does RStudio update the packages installed from GitHub? If so, does it replace it with the new CRAN version, or a new GitHub version? Many thanks for you answer, Michal Kvasnicka [[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. Can't remember your password? Do you need a strong and secure password? Use Password manager! It stores your passwords protects your account. __ 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. -- http://had.co.nz/ FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks orcas on your desktop! __ 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.
[R] Unable to get the 64-bit version of R (3.2.1 Terminal or GUI) to start on a Windows 7 machine
I am unable to get the 64-bit version of R (3.2.1 Terminal or GUI) to
start on a Windows 7 machine. I can get the 32-bit to start, just not
the 64-bit.
I am receiving a dialog box box that points me to four files but nothing
seems usable when examining them.
Installed to C:\Dev\R\R-3.2.1. I have set my R_HOME environment
variable to C:\Dev\R\R-3.2.1 and added C:\Dev\R\R-3.2.1\bin\x64 to
my Windows PATH environment variable.
I have also checked the Windows Registry to make sure everything is
pointing to the x64 directory and one example is given below:
Registry Key: “HKEY_CLASSES_ROOT\RWorkspace\shell\open\command”
Registry Key Value:C:\Dev\R\R-3.2.1\bin\x64\RGui.exe %1
I have searched and have tried for some time to resolve this based on
what I have found but am not having any success. Any help you can
provide would be greatly appreciated.
I have embedded three of the four troubleshooting files as text below in
the hope that it might be helpful.
The WER8836.tmp.wmi.txt file looks like Windows is using a 32-Bit
processor but it is a 64-bit install of the OS. I have embedded below:
instance of Win32_Processor
{
Family = 198;
};
instance of Win32_OperatingSystem
{
BuildNumber = 7601;
OSLanguage = 1033;
ProductType = 1;
ServicePackMajorVersion = 1;
ServicePackMinorVersion = 0;
SuiteMask = 272;
Version = 6.1.7601;
};
instance of Win32_ComputerSystem
{
Domain = chkenergy.net;
Manufacturer = Dell Inc.;
Model = Latitude E6420;
Name = CHK4WL6DS1;
PartOfDomain = TRUE;
UserName = CHKENERGY\\bmorris2;
};
The WER8798.tmp.apcompat.txt is another file given for troubleshooting
in the error message. I have embedded it below as well:
?xml version=1.0 encoding=UTF-16?
DATABASE
EXE NAME=Rgui.exe FILTER=CMI_FILTER_PRIVACY
MATCHING_FILE NAME=open.exe SIZE=16384 CHECKSUM=0xB287F521
MODULE_TYPE=WIN32 PE_CHECKSUM=0x6F3E LINKER_VERSION=0x0
LINK_DATE=06/18/2015 17:20:02 UPTO_LINK_DATE=06/18/2015 17:20:02
EXE_WRAPPER=0x0 /
MATCHING_FILE NAME=R.dll SIZE=25820672 CHECKSUM=0x6850795A
BIN_FILE_VERSION=3.21.2995.0 BIN_PRODUCT_VERSION=3.0.0.0
FILE_DESCRIPTION=R for Windows DLL FILE_VERSION=3.2.1 (2015-06-18)
LEGAL_COPYRIGHT=R Core Team 1995-2015 VERDATEHI=0x0 VERDATELO=0x0
VERFILEOS=0x4 VERFILETYPE=0x2 MODULE_TYPE=WIN32
PE_CHECKSUM=0x18A30E0 LINKER_VERSION=0x0
UPTO_BIN_FILE_VERSION=3.21.2995.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0
LINK_DATE=06/18/2015 17:19:42 UPTO_LINK_DATE=06/18/2015 17:19:42
EXPORT_NAME=R.dll VER_LANGUAGE=English (United States) [0x409]
EXE_WRAPPER=0x0 /
MATCHING_FILE NAME=R.exe SIZE=39936 CHECKSUM=0x8919B6FD
BIN_FILE_VERSION=3.21.2995.0 BIN_PRODUCT_VERSION=3.0.0.0
FILE_DESCRIPTION=R for Windows front-end FILE_VERSION=3.2.1
(2015-06-18) LEGAL_COPYRIGHT=R Core Team 1995-2015 VERDATEHI=0x0
VERDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32
PE_CHECKSUM=0x15CE3 LINKER_VERSION=0x0
UPTO_BIN_FILE_VERSION=3.21.2995.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0
LINK_DATE=06/18/2015 17:20:00 UPTO_LINK_DATE=06/18/2015 17:20:00
VER_LANGUAGE=English (United States) [0x409] EXE_WRAPPER=0x0 /
MATCHING_FILE NAME=Rblas.dll SIZE=343623 CHECKSUM=0x3B624D2B
BIN_FILE_VERSION=3.21.2995.0 BIN_PRODUCT_VERSION=3.0.0.0
FILE_DESCRIPTION=R for Windows DLL FILE_VERSION=3.2.1 (2015-06-18)
LEGAL_COPYRIGHT=R Core Team 1995-2015 VERDATEHI=0x0 VERDATELO=0x0
VERFILEOS=0x4 VERFILETYPE=0x2 MODULE_TYPE=WIN32
PE_CHECKSUM=0x5F357 LINKER_VERSION=0x0
UPTO_BIN_FILE_VERSION=3.21.2995.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0
LINK_DATE=06/18/2015 17:19:54 UPTO_LINK_DATE=06/18/2015 17:19:54
EXPORT_NAME=Rblas.dll VER_LANGUAGE=English (United States) [0x409]
EXE_WRAPPER=0x0 /
MATCHING_FILE NAME=Rcmd.exe SIZE=39936 CHECKSUM=0x8F60F12D
BIN_FILE_VERSION=3.21.2995.0 BIN_PRODUCT_VERSION=3.0.0.0
FILE_DESCRIPTION=R for Windows front-end FILE_VERSION=3.2.1
(2015-06-18) LEGAL_COPYRIGHT=R Core Team 1995-2015 VERDATEHI=0x0
VERDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32
PE_CHECKSUM=0x13E5C LINKER_VERSION=0x0
UPTO_BIN_FILE_VERSION=3.21.2995.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0
LINK_DATE=06/18/2015 17:19:59 UPTO_LINK_DATE=06/18/2015 17:19:59
VER_LANGUAGE=English (United States) [0x409] EXE_WRAPPER=0x0 /
MATCHING_FILE NAME=Rfe.exe SIZE=23040 CHECKSUM=0x8D69D4D8
BIN_FILE_VERSION=3.21.2995.0 BIN_PRODUCT_VERSION=3.0.0.0
FILE_DESCRIPTION=R for Windows front-end FILE_VERSION=3.2.1
(2015-06-18) LEGAL_COPYRIGHT=R Core Team 1995-2015 VERDATEHI=0x0
VERDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32
PE_CHECKSUM=0x13155 LINKER_VERSION=0x0
UPTO_BIN_FILE_VERSION=3.21.2995.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0
LINK_DATE=06/18/2015 17:20:03 UPTO_LINK_DATE=06/18/2015 17:20:03
VER_LANGUAGE=English (United States) [0x409] EXE_WRAPPER=0x0 /
MATCHING_FILE NAME=Rgraphapp.dll SIZE=377702
CHECKSUM=0xC8C6CA6E BIN_FILE_VERSION=3.21.2995.0
BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=Graphapp DLL for R
FILE_VERSION=3.2.1 (2015-06-18) LEGAL_COPYRIGHT=R Core Team
1995-2015
Re: [R] Survival Analysis and Predict time-to-death
On 2015-08-18 01:44, David Winsemius wrote: On Aug 17, 2015, at 1:51 PM, David Winsemius wrote: On Aug 17, 2015, at 12:10 PM, survivalUser wrote: Dear All, I would like to build a model, based on survival analysis on some data, that is able to predict the /*expected time until death*/ for a new data instance. Are you sure you want to use life expectancy as the outcome? In order to establish a mathematical expectation you need to have know the risk at all time in the future, which as pointed out in the print.survfit help page is undefined unless the last observation is a death. Very few datasets support such an estimate. If on the other hand you have sufficient events in the future, then you may be able to more readily justify an estimate of a median survival. Dear survivalUser; I've been reminded that you later asked for a parametric model built with survreg. The above commentary applies to the coxph models and objects and not to survreg objects. If you do have a parametric model, even with incomplete observation then calculating life expectancy should be a simple matter of plugging the parameters for the distribution's mean value, since life-expectancy is the statistical mean. So maybe you do want such a modle. The default survreg distribution is weibull so just go to your mathematical statistics text and look up the formula for the mean of a Weibull distribution with the estimated parameters. No need for 'the mathematical statistics text': The necessary information is found on the help page for the Weibull distribution: E(T) = b Gamma(1 + 1/a), where 'b' is scale (really!) and 'a' is shape. You must however take into account the special parametrization that is used by 'survreg'; see its help page for how to do it. Alternatively, use 'aftreg' in the package 'eha' and get the same parametrization as in base R. After getting the baseline expectation by the formula above, simply multiply that value by exp(-lp) to get the expected life for an individual with linear predictor lp. A useful alternative is simulation (use 'rweibull') or numerical integration, especially for estimating remaining expected life 'later in life'. And for other distributions than the Weibull. Göran Broström (author of the eha package) __ 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.
Re: [R] Survival Analysis and Predict time-to-death
It depends on several factors. You need answers to all these questions: How many events occurred, ... and was the period of observation long enough to cover a significant fraction of the life expectancy, …. and is there external evidence or theory that will help establish that this process should follow Weibull statistics? — David. On Aug 17, 2015, at 2:18 PM, survivalUser tufanomich...@hotmail.it wrote: Thank you David for your answer. Some follow-up questions: - So, do you think that try to estimate the life expectancy would be risky and probably not justifiable? Is there some sort of 'confidence' that the model could give me for a prediction? - type=response - I found it here: https://stat.ethz.ch/R-manual/R-devel/library/survival/html/predict.survreg.html I have not tried it yet, but I was planning to use that because it says that predict the original scale of the data. - Yes, I think they are time-varying predictors. Would you suggest other models? (coxph?) Overall, do you think this analysis is feasible/correct? Predicting how much time a new individual (with those covariates) will be alive till death, is a reasonable thing to predict with survival model? Thank you again! -- View this message in context: http://r.789695.n4.nabble.com/Survival-Analysis-and-Predict-time-to-death-tp4711198p4711207.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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.
[R] R: forecasting a binary time series using the VLMC package
I would like to ask some clarifications on the method:
predict.vlmc
My problem is to forecast a binary time series one period ahead. I have a
time series bin2 of length 2000. When using
m2-vlmc(bin2)
fc2-predict(m2)
1. fc2[i] is a prediction for i, not for i+1, is that correct? I am
aware that the documentation stipulates Compute predictions on a fitted
VLMC object for each (but the first) element of another discrete time
series., but am still asking to make it 100% clear.
2.
I guess that the predictions fc2 are based on the full range [1:2000] of
bin2, because I fitted a VLMC to the full timeseries on the first line
above. Therefore, I am actually forecasting each period by already knowing
the future, is that correct?
3.
In order to forecast while not knowing the future, can I do the
following:
for(i in 1000:1999) {
retFull2 - window(retFull, start=1, end=i)
bin2- window(bin, start=1, end=i)
dummy-ts(c(bin2,0)) #Adding a dummy zero at the end of each window
#so that a prediction will be made for i+1 as well
#without using i+1 while fitting the model
m2-vlmc(bin2) # bin2 granges from 1 to i
fct2-predict(m2, dummy)[i+1,1] #forecasting on an
artificially-added i+1 index.}
I am adding a dummy zero at the end of each windowed ts, and
predicting for i+1 as well. Is it relevant at all? Any suggestions? Any
practical suggestions on how to best forecast these binary time series?
Many thanks in advance, cheers
[[alternative HTML version deleted]]
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[R] NB-L Regression
Hi All, I am trying to run Negative Binomial Lindley regression under glm. But NB-L is not defined in the family group. I will perform a simulation. The model has only one covariate generated from uniform distribution, the count response variable follows the NB distribution. the model should be glm(count~x, family=nbl) I would greatly appreciate any help. Serpil [[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.
Re: [R] date format in xyplot
Hi I forgot to change the format and put the panel back in - I was trying to get the data right see ? strptime for a list of all the combinations for dates. Have a look at http://lmdvr.r-forge.r-project.org/figures/figures.html which may give you some ideas. If you want to restrict data to a certain period you will have to put limits on the x axis and you do that in the scales argument ie x =list(limits = c(min date, max date) ) NB date format For one panel it is easy but for 2+ it can be tricky as you will be working with a list. Then the code would be something like xyplot(Abun~Date2|Year, Raw, scales = list(x = list(limits = list(c(min y1, max y1), c(min y2, max y2))) .. ) where y[1...] is the applicable year have a look at aspect which may improve things for the final plot if desired. If you want to space groups of years-- see between Regards Duncan -Original Message- From: Christine Lee [mailto:leptostra...@yahoo.com] Sent: Wednesday, 19 August 2015 00:26 To: R; Duncan Mackay Subject: RE: [R] date format in xyplot Thank you Duncan, I have tried the scales function. It ends up with 2015-09-15, which is acceptable. It is far much better than 09 15 shown on the axis. The problem is the data were obtained in different years. This makes 2015 shown in lattice plots of different years. I have tried to put in the year in the raw data (such as 1/10/2013), but the plot is really bizzard, with the 2002 plots have all the points on the left of the plot whereas 2013 plots have all the data points on the right of the plots because the x-axis shows data from 2001 to 2013. I feel like hopeless to insist to have the axis label shown as Sep 15 because it seems to be the problem of my computer setting. Is there a way to shows graphs in different years, but with the same scale beginning from September to December? Regards, Christine 2015年8月18日 星期二，Duncan Mackay dulca...@bigpond.com 寫道﹕ 主題: RE: [R] date format in xyplot 收件人: R r-help@r-project.org 副本(CC): 'Christine Lee' leptostra...@yahoo.com 日期: 2015年8月18日,星期二,下午4:08 Hi Christine If somethings go wrong: 1 first check your data str(Raw) 'data.frame': 10 obs. of 5 variables: $ Date : Factor w/ 16 levels 1/10,1/11,..: 6 7 2 4 12 9 7 2 4 12 $ Year : int 2002 2002 2002 2002 2002 2002 2002 2002 2002 2002 $ Station: Factor w/ 4 levels E,F,H,I: 1 1 1 1 1 2 2 2 2 2 $ Abun : num 3.42 1.33 3.67 3.67 3.92 2.17 2.5 1.67 6.33 0.67 $ Date1 : Date, format: 2015-09-19 2015-10-02 2015-11-01 2015-11-12 ... Raw$Date2 - as.character(Raw$Date1) Raw$Date2 [1] 2015-09-19 2015-10-02 2015-11-01 2015-11-12 2015-11-29 2015-09-20 2015-10-02 2015-11-01 2015-11-12 2015-11-29 Raw$Date2 - as.Date(Raw$Date2, %Y-%m-%d) 2 read the help guide again if not done recently ?lattice::xyplot or ?xyplot 3 start with a minimum number of arguments xyplot(Abun~Date2|as.factor(Year), Raw) or xyplot(Abun~Date2, Raw) if you are still having problems Dates are hard work in any language as they are not consistent so: a. use default b. use your own This works xyplot(Abun~Date2|as.factor(Year), Raw, par.settings = list(stripbackground = transparent), # background colour controlled here type=p, scales = list(x = list(at = sort(c(seq(as.Date(Raw$Date2[1]-4), by = months, length = 4), seq(as.Date(Raw$Date2[1]+12), by = months, length = 3))), labels = format(sort(c(seq(as.Date(Raw$Date2[1]-4), by = months, length = 4), seq(as.Date(Raw$Date2[1]+12), by = months, length = 3))), %m-%d) ) ), xlab=list(Month,cex=1.5), ylab=list(Abundance,cex=1.5), cex=2, pch=c(16,16,21), col=c(Black,Grey,Black) ) par.settings is confining the parameters set by trellis.par.set() to the function to get them names(trellis.par.get() ) and going further trellis.par.get()$superpose.symbol will give you the values for superpose.symbol Beware: Do not make the labels etc so big that the axis labels are hard to read. Think of final size Regards Duncan Duncan Mackay Department of Agronomy and Soil Science University of New England Armidale NSW 2351 Email: home: mac...@northnet.com.au -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Christine Lee via R-help Sent: Tuesday, 18 August 2015 14:16 To: r-help@r-project.org Subject: [R] date format in xyplot To whom it may concern, I have tried to plot some numbers against time with the time on the X-axis shown as Jan, Feb, etc. I used the following commands: Raw-structure(list(Date = structure(c(6L, 7L, 2L, 4L, 12L, 9L, 7L, 2L, 4L, 12L), .Label = c(1/10, 1/11, 11/11, 12/11, 13/10, 19/9, 2/10, 2/11, 20/9, 26/11, 29/10, 29/11, 30/11, 31/10, 4/10, 6/10), class =
[R] Output In R
Hello All, As i am a newbie in R so most of you would have seen this question zillion times. I searched for the answer on this forum as well on other various forums however could not find the answer i am looking for. I am dplyr package and used a very basic code: select(june,city,state,mod) The data sheet i am using has more than 3 million observations but the console does not print all of them and show only few options and give a message: [ reached getOption(max.print) -- omitted 376341 rows ] What is the option that i need to add to see all values in the output. Similarly once i scroll down and then if i scroll up i am not able to see the values starting from row #1. Please suggest -- View this message in context: http://r.789695.n4.nabble.com/Output-In-R-tp4711227.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] Running R in Server
There is probably nothing that can give you a step by step guide. You are touching on a couple of different subjects. If you just want to run code automatically on a windows server you can use task scheduler to call Rscript filename.R. If you want to create Web application, that's a bit harder. I still use Rpad, which works on windows, but development of it stopped a long time so I wouldn't suggest using it. All the other web application approaches such as RApache only work on Linux. If I understand correctly what you want to do, you might be able to create a HTML report using RMarkdown and host that on the website. If you really need a web app, I suggest looking into Shiny. You can make a shiny app, host it for free on the cloud. You will have a lot to learn, but it will be time well spent. https://www.rstudio.com/ Thanks, Roger *** This message and any attachments are for the intended recipient's use only. This message may contain confidential, proprietary or legally privileged information. No right to confidential or privileged treatment of this message is waived or lost by an error in transmission. If you have received this message in error, please immediately notify the sender by e-mail, delete the message, any attachments and all copies from your system and destroy any hard copies. You must not, directly or indirectly, use, disclose, distribute, print or copy any part of this message or any attachments if you are not the intended recipient. -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Swagato Chatterjee Sent: Sunday, August 16, 2015 4:17 AM To: r-help@r-project.org Subject: [R] Running R in Server Hello, I have written a R script which runs a regression of a dataset and saves the result in a csv file. Now this dataset has to be edited periodically which is done in a server. I need to run the R script in a server so that the results can also be shared in a server and used in a web application. I have coded in R and have used R in windows. I have never used Ubuntu/Linux. Is there a step by step guide on how to run a R code in server? Thanks and Regards, -- Swagato Chatterjee [[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. __ 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.
Re: [R] How are packages installed with install_github() updated in RStudio?
RStudio just calls the same underlying R functions, so it doesn't make any difference that you're using RStudio. Currently, there's no automatic way to update packages installed from github. Hadley On Tue, Aug 18, 2015 at 8:14 AM, John Kane jrkrid...@inbox.com wrote: Hi Michal, Because RStudio seems to use its own method of updating you might be better off asking in their forum. John Kane Kingston ON Canada -Original Message- From: prgo...@gmail.com Sent: Tue, 18 Aug 2015 10:43:20 +0200 To: r-help@r-project.org Subject: [R] How are packages installed with install_github() updated in RStudio? Hallo. I use RStudio. Because of a bug in the latest CRAN version of dplyr, I installed the GitHub version with install_github(). Now I wonder what happens when there is a new version. Does RStudio update the packages installed from GitHub? If so, does it replace it with the new CRAN version, or a new GitHub version? Many thanks for you answer, Michal Kvasnicka [[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. Can't remember your password? Do you need a strong and secure password? Use Password manager! It stores your passwords protects your account. __ 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. -- http://had.co.nz/ __ 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.
Re: [R] Running R in Server
Swagato Chatterjee swagato1...@gmail.com writes: Hello, I have written a R script which runs a regression of a dataset and saves the result in a csv file. Now this dataset has to be edited periodically which is done in a server. I need to run the R script in a server so that the results can also be shared in a server and used in a web application. I have coded in R and have used R in windows. I have never used Ubuntu/Linux. Is there a step by step guide on how to run a R code in server? Thanks and Regards, Swagato If you are lucky, you can just copy your script to the server and call Rscript /path/to/your/r/script on the linux command line. However, you'll probably have to make sure that all the packages you need are installed on the server. HTH Loris -- This signature is currently under construction. __ 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.
Re: [R] Survival analysis and predict time-to-death
I read this list a day late as a digest so my answers are rarely the first. (Which is nice as David W answers most of the survival questions for me!) What you are asking is reasonable, and in fact is common practice in the realm of industrial reliability, e.g., Meeker and Escobar, Statistical Methods for Reliability Analysis. Extrapolation of the survival curve to obtain the mean and percentiles of the lifetime distribution for some device (e.g. a washing machine) is their bread and butter, used for instance to determine the right size for an inventory of spare parts. For most of us on this list who do medical statistics and live in the Kaplan-Meier/ Cox model world the ideas are uncommon. I was lucky enough to sit through one of Bill Meeker's short courses and retain some (minimal) memory of it. 1. You are correct that parametric models are essential. If the extrapolation is substantial (30% or more censored, say), then the choice of distribution can be critical. If failure is due to repeated insult, e.g., the multi-hit model, then Weibull tends to be preferred; if it is from degradation, e.g., flexing of a diaphram, then the log-normal. Beyond this you need more guidance than mine. 2. The survreg routine assumes that log(y) ~ covariates + error. For a log-normal distribion the error is Gaussian and thus the predict(fit, type='response') will be exp(predicted mean of log time), which is not the predicted mean time. For Weibull the error dist is asymmetric so things are more muddy. Each is the MLE prediction for the subject, just not interpretable as a mean. To get the actual mean you need to look up the formulas for Weibull and/or lognormal in a textbook, and map from the survreg parameterization to whatever one the textbook uses. The two parameterizations are never the same. 3. Another option is predicted quantiles. ?predict.survreg shows how to get the entire survival curve. The mean can be obtained as the area under the survival curve. Relevant to your question, the expected time remaining for a subject still alive at time =10, say, is integral(S(t), from 10 to infin) / S(10), where S is the survival curve. You can also read off quantiles of the expected remaining life. Terry Therneau (author of the survival package) On 08/18/2015 05:00 AM, r-help-requ...@r-project.org wrote: Dear All, I would like to build a model, based on survival analysis on some data, that is able to predict the /*expected time until death*/ for a new data instance. Data For each individual in the population I have the, for each unit of time, the status information and several continuous covariates for that particular time. The data is right censored since at the end of the time interval analyzed, instances could be still alive and die later. Model I created the model using R and the survreg function: lfit - survreg(Surv(time, status) ~ X) where: - time is the time vector - status is the status vector (0 alive, 1 death) - X is a bind of multiple vectors of covariates Predict time to death Given a new individual with some covariates values, I would like to predict the estimated time to death. In other words, the number of time units for which the individual will be still alive till his death. I think I can use this: ptime - predict(lfit, newdata=data.frame(X=NEWDATA), type='response') Is that correct? Am I going to get the expected-time-to-death that I would like to have? In theory, I could provide also the time information (the time when the individual has those covariates values), should I simply add that in the newdata: ptime - predict(lfit, newdata=data.frame(time=TIME, X=NEWDATA), type='response') Is that correct? Is this going to improve the prediction? (for my data, the time already passed should be an important variable). Any other suggestions or comments? Thank you! __ 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.
Re: [R] Running R in Server
On Sun, Aug 16, 2015 at 3:27 AM, Swagato Chatterjee swagato1...@gmail.com wrote: Hello, I have written a R script which runs a regression of a dataset and saves the result in a csv file. Now this dataset has to be edited periodically which is done in a server. I need to run the R script in a server so that the results can also be shared in a server and used in a web application. I have coded in R and have used R in windows. I have never used Ubuntu/Linux. Is there a step by step guide on how to run a R code in server? Thanks and Regards, Swagato I was going to answer yesterday, but work went insane. Also, I was hoping someone else had something, because I don't have any step by step instructions. This is a rather complicated question. So I'm going to ask a number of questions and make some statement for you to correct, if necessary. Statement: You have a Windows desktop and have used R on it, so you are familiar with R in a Windows environment. Statement: You are not Linux (Ubuntu) trained. Statement: You wrote an R script on Windows, which works, but you need to run it on Ubuntu. The above is my starting point. Now I have some questions. Can you connect to the Ubuntu server from your Windows desktop? If so, how? If not, I'm confused about how you could get anything to run on the Ubuntu server. Where does this dataset reside? On you desktop? On a Windows shared folder? On the Ubuntu server? Other? Who or what edits the dataset? That is, is it always yourself? Some one in your group? Some other human? Some automated process? Why can't you run the R script as you do now, then deploy the results to the Ubuntu server? Since I don't know the environment that the Ubuntu server runs in, I can't address how to deploy an updated file into it. I assume you have some sort of deployment software. It could be as easy as being able to ftp the results from your desktop to the proper places on the Ubuntu server. === Now, whatever the answers are to the above, you'll likely need some help from your Ubuntu server people. My first approach, given my ignorance, would be that I would have something set up so that you could edit this dataset on your desktop (assuming that's what you do). I would then have you ftp it to a special directory on the Ubuntu server set up especially for this function. Now, what remains would be running the R script, likely in a shell script (like a PowerShell command file), whenever you do the ftp. There is a function in Ubuntu (any Linux) called icrond. This is a daemon (Windows service equivalent) which can monitor a file or directory for changes. When a change is detected it can take an action. In this case it would be to schedule the execution of the previously mentioned shell script. The shell script would then take the actions necessary to do the R script (R CMD script-name parameters ... for instance) and then deploy the results to the web server (however you normally do this). Setting up the icrond environment is going to take some work by your Ubuntu administrator. === I hope this was at least the start of some help to you. -- Schrodinger's backup: The condition of any backup is unknown until a restore is attempted. Yoda of Borg, we are. Futile, resistance is, yes. Assimilated, you will be. He's about as useful as a wax frying pan. 10 to the 12th power microphones = 1 Megaphone Maranatha! John McKown [[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.
Re: [R] date format in xyplot
Thank you Duncan, I have tried the scales function. It ends up with 2015-09-15, which is acceptable. It is far much better than 09 15 shown on the axis. The problem is the data were obtained in different years. This makes 2015 shown in lattice plots of different years. I have tried to put in the year in the raw data (such as 1/10/2013), but the plot is really bizzard, with the 2002 plots have all the points on the left of the plot whereas 2013 plots have all the data points on the right of the plots because the x-axis shows data from 2001 to 2013. I feel like hopeless to insist to have the axis label shown as Sep 15 because it seems to be the problem of my computer setting. Is there a way to shows graphs in different years, but with the same scale beginning from September to December? Regards, Christine 2015年8月18日 星期二，Duncan Mackay dulca...@bigpond.com 寫道﹕ 主題: RE: [R] date format in xyplot 收件人: R r-help@r-project.org 日期: 2015年8月18日,星期二,下午4:08 Hi Christine If somethings go wrong: 1 first check your data str(Raw) 'data.frame': 10 obs. of 5 variables: $ Date : Factor w/ 16 levels 1/10,1/11,..: 6 7 2 4 12 9 7 2 4 12 $ Year : int 2002 2002 2002 2002 2002 2002 2002 2002 2002 2002 $ Station: Factor w/ 4 levels E,F,H,I: 1 1 1 1 1 2 2 2 2 2 $ Abun : num 3.42 1.33 3.67 3.67 3.92 2.17 2.5 1.67 6.33 0.67 $ Date1 : Date, format: 2015-09-19 2015-10-02 2015-11-01 2015-11-12 ... Raw$Date2 - as.character(Raw$Date1) Raw$Date2 [1] 2015-09-19 2015-10-02 2015-11-01 2015-11-12 2015-11-29 2015-09-20 2015-10-02 2015-11-01 2015-11-12 2015-11-29 Raw$Date2 - as.Date(Raw$Date2, %Y-%m-%d) 2 read the help guide again if not done recently ?lattice::xyplot or ?xyplot 3 start with a minimum number of arguments xyplot(Abun~Date2|as.factor(Year), Raw) or xyplot(Abun~Date2, Raw) if you are still having problems Dates are hard work in any language as they are not consistent so: a. use default b. use your own This works xyplot(Abun~Date2|as.factor(Year), Raw, par.settings = list(stripbackground = transparent), # background colour controlled here type=p, scales = list(x = list(at = sort(c(seq(as.Date(Raw$Date2[1]-4), by = months, length = 4), seq(as.Date(Raw$Date2[1]+12), by = months, length = 3))), labels = format(sort(c(seq(as.Date(Raw$Date2[1]-4), by = months, length = 4), seq(as.Date(Raw$Date2[1]+12), by = months, length = 3))), %m-%d) ) ), xlab=list(Month,cex=1.5), ylab=list(Abundance,cex=1.5), cex=2, pch=c(16,16,21), col=c(Black,Grey,Black) ) par.settings is confining the parameters set by trellis.par.set() to the function to get them names(trellis.par.get() ) and going further trellis.par.get()$superpose.symbol will give you the values for superpose.symbol Beware: Do not make the labels etc so big that the axis labels are hard to read. Think of final size Regards Duncan Duncan Mackay Department of Agronomy and Soil Science University of New England Armidale NSW 2351 Email: home: mac...@northnet.com.au -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Christine Lee via R-help Sent: Tuesday, 18 August 2015 14:16 To: r-help@r-project.org Subject: [R] date format in xyplot To whom it may concern, I have tried to plot some numbers against time with the time on the X-axis shown as Jan, Feb, etc. I used the following commands: Raw-structure(list(Date = structure(c(6L, 7L, 2L, 4L, 12L, 9L, 7L, 2L, 4L, 12L), .Label = c(1/10, 1/11, 11/11, 12/11, 13/10, 19/9, 2/10, 2/11, 20/9, 26/11, 29/10, 29/11, 30/11, 31/10, 4/10, 6/10), class = factor), Year = c(2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L, 2002L ), Station = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), .Label = c(E, F, H, I), class = factor), Abun = c(3.42, 1.33, 3.67, 3.67, 3.92, 2.17, 2.5, 1.67, 6.33, 0.67), Date1 = structure(c(16697, 16710, 16740, 16751, 16768, 16698, 16710, 16740, 16751, 16768 ), class = Date)), .Names = c(Date, Year, Station, Abun, Date1), row.names = c(NA, 10L), class = data.frame) Raw$Date1-as.Date(Raw$Date,%d/%m) xyplot(Abun~Date1|as.factor(Year),Raw,type=p,xlab=list(Month,cex=1.5),yl ab=list(Abundance,cex=1.5),cex=2,pch=c(16,16,21),col=c(Black,Grey,Bla ck),strip=strip.custom(bg='white'),format=%B-%d) The date format shown on X-axis was just 10-1, 10-15 I should be grateful if any one could help indicating what has gone wrong? Regards, Christine __ 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
Re: [R] Output In R
I would suggest that instead of trying to view all the results in the console that you save the result into a object then use the View (note the capitol V) function to be able to scroll through the results. The head and tail functions have already been mentioned and I second their use for a quick view. Since you are already using dplyr you should look at the slice (and possibly filter) function for another way to display pieces of the resulting object. On Tue, Aug 18, 2015 at 6:41 AM, Shivi82 shivibha...@ymail.com wrote: Hello All, As i am a newbie in R so most of you would have seen this question zillion times. I searched for the answer on this forum as well on other various forums however could not find the answer i am looking for. I am dplyr package and used a very basic code: select(june,city,state,mod) The data sheet i am using has more than 3 million observations but the console does not print all of them and show only few options and give a message: [ reached getOption(max.print) -- omitted 376341 rows ] What is the option that i need to add to see all values in the output. Similarly once i scroll down and then if i scroll up i am not able to see the values starting from row #1. Please suggest -- View this message in context: http://r.789695.n4.nabble.com/Output-In-R-tp4711227.html Sent from the R help mailing list archive at Nabble.com. __ 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. -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com __ 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.
Re: [R] Output In R
Shivi82 shivibha...@ymail.com writes: Hello All, As i am a newbie in R so most of you would have seen this question zillion times. I searched for the answer on this forum as well on other various forums however could not find the answer i am looking for. I am dplyr package and used a very basic code: select(june,city,state,mod) The data sheet i am using has more than 3 million observations but the console does not print all of them and show only few options and give a message: [ reached getOption(max.print) -- omitted 376341 rows ] What is the option that i need to add to see all values in the output. Similarly once i scroll down and then if i scroll up i am not able to see the values starting from row #1. Please suggest You need to sharpen your searching skills. The first result of looking for r max.print via a well-known search engine is a question on StackOverflow. One of the answers given there is to set the value of max.print in the following manner: options(max.print=99) I'll leave finding the appropriate value as an exercise for the reader. Cheers, Loris -- This signature is currently under construction. __ 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.
Re: [R] Output In R
?write.csv and look at with the editor of choice. On Tue, Aug 18, 2015 at 6:41 AM, Shivi82 shivibha...@ymail.com wrote: Hello All, As i am a newbie in R so most of you would have seen this question zillion times. I searched for the answer on this forum as well on other various forums however could not find the answer i am looking for. I am dplyr package and used a very basic code: select(june,city,state,mod) The data sheet i am using has more than 3 million observations but the console does not print all of them and show only few options and give a message: [ reached getOption(max.print) -- omitted 376341 rows ] What is the option that i need to add to see all values in the output. Similarly once i scroll down and then if i scroll up i am not able to see the values starting from row #1. Please suggest -- View this message in context: http://r.789695.n4.nabble.com/Output-In-R-tp4711227.html Sent from the R help mailing list archive at Nabble.com. __ 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]] __ 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.
[R] Non linear regression - Von Bertalanffy Growth Function - singular gradient matrix at initial parameter estimates
Dear all, I am trying to estimate VBGF parameters K and Linf using non linear regression and nls(). First I used a classic approach where I estimate both parameters together as below with alkdyr being a subset per year of my age-length-key database and running in a loop. vbgf.par - nls(Lgtcm ~ Linf *(1 - exp(-K * (Age - tzero))), start = c(K= 0.07, Linf = 177.1), data=alkdyr) I obtain an estimation of both parameters that are strongly correlated. Indeed after plotting Linf ~ K and fitting a linear regression I obtain a function (Linf = a + b*K) with R2= 0.8 and a = 215, b = -763. In this context, to take into account explicitly correlation between parameters, I decided to fit a new non linear regression derivate from VBGF but where Linf is expressed depending on K (I am most interested in K). To do so, I tried this model: vbgf.par - nls(Lgtcm ~ (a + (b*k)) *(1 - exp(-k * (Age - tzero))), start = c(k= 0.07, a= 215, b=-763), data=alkdyr) Unfortunately at this point I cannot go further as I get the error message singular gradient matrix at initial parameter estimates. I tried to use alg= plinear (which I am not sure I understand properly yet). If I give a starting value for a and b only, I have an error message stating step factor below minFactor (even when minFactor is set to 1000). Any help will be more than welcome as this is quite urgent Best, Xochitl C. -- Xochitl CORMON +33 (0)3 21 99 56 84 Doctorante en écologie marine et science halieutique PhD student in marine ecology and fishery science IFREMER Centre Manche Mer du Nord 150 quai Gambetta 62200 Boulogne-sur-Mer __ 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.
Re: [R] Running R in Server
On Sun, Aug 16, 2015, 2:29 PM Swagato Chatterjee swagato1...@gmail.com wrote: Hello, I have written a R script which runs a regression of a dataset and saves the result in a csv file. Now this dataset has to be edited periodically which is done in a server. I need to run the R script in a server so that the results can also be shared in a server and used in a web application. Have a look at deployR on Revolutioanalytic website. There is a free open-source solution for windows. I have coded in R and have used R in windows. I have never used Ubuntu/Linux. Is there a step by step guide on how to run a R code in server? Thanks and Regards, Swagato [[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. [[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.
Re: [R] Non linear regression - Von Bertalanffy Growth Function - singular gradient matrix at initial parameter estimates
These appear to be primarily statistics/nonlinear optimization issues that are off topic here, which is about R programming. Post on a statistics list like stats.stackexchange.com instead. Cheers, Bert Bert Gunter Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. -- Clifford Stoll On Tue, Aug 18, 2015 at 9:08 AM, Xochitl CORMON xochitl.cor...@ifremer.fr wrote: Dear all, I am trying to estimate VBGF parameters K and Linf using non linear regression and nls(). First I used a classic approach where I estimate both parameters together as below with alkdyr being a subset per year of my age-length-key database and running in a loop. vbgf.par - nls(Lgtcm ~ Linf *(1 - exp(-K * (Age - tzero))), start = c(K= 0.07, Linf = 177.1), data=alkdyr) I obtain an estimation of both parameters that are strongly correlated. Indeed after plotting Linf ~ K and fitting a linear regression I obtain a function (Linf = a + b*K) with R2= 0.8 and a = 215, b = -763. In this context, to take into account explicitly correlation between parameters, I decided to fit a new non linear regression derivate from VBGF but where Linf is expressed depending on K (I am most interested in K). To do so, I tried this model: vbgf.par - nls(Lgtcm ~ (a + (b*k)) *(1 - exp(-k * (Age - tzero))), start = c(k= 0.07, a= 215, b=-763), data=alkdyr) Unfortunately at this point I cannot go further as I get the error message singular gradient matrix at initial parameter estimates. I tried to use alg= plinear (which I am not sure I understand properly yet). If I give a starting value for a and b only, I have an error message stating step factor below minFactor (even when minFactor is set to 1000). Any help will be more than welcome as this is quite urgent Best, Xochitl C. -- Xochitl CORMON +33 (0)3 21 99 56 84 Doctorante en écologie marine et science halieutique PhD student in marine ecology and fishery science IFREMER Centre Manche Mer du Nord 150 quai Gambetta 62200 Boulogne-sur-Mer __ 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. __ 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.
Re: [R] Output In R
That's a very odd request: surely you would not want to visually inspect 3 million rows in the console? Typically one would assign the (large) results of a function to a variable for further processing. If you need to inspect the beginning and end of your dataset, use head() and tail(). Try getOption(max.print) to see what it is set to: it's a large and reasonable value, remember your console uses memory and at some point it needs to truncate the values you store in the console, to stay within its allotted memory. You can change the max.print option, but I can't see how that would be reasonable. Cheers, Boris On Aug 18, 2015, at 8:41 AM, Shivi82 shivibha...@ymail.com wrote: Hello All, As i am a newbie in R so most of you would have seen this question zillion times. I searched for the answer on this forum as well on other various forums however could not find the answer i am looking for. I am dplyr package and used a very basic code: select(june,city,state,mod) The data sheet i am using has more than 3 million observations but the console does not print all of them and show only few options and give a message: [ reached getOption(max.print) -- omitted 376341 rows ] What is the option that i need to add to see all values in the output. Similarly once i scroll down and then if i scroll up i am not able to see the values starting from row #1. Please suggest -- View this message in context: http://r.789695.n4.nabble.com/Output-In-R-tp4711227.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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.
