Re: [R] calling in inverted commas
Hi
Sigh I'm getting a headache seeing ugly formatted R code. Arun, your code is
almost unreadable. Have a look at e.g.
http://yihui.name/en/2010/04/formatr-farewell-to-ugly-r-code/
Now to the substantial. Why not use the sprintf() function for formatting the
url instead of the more involved approach using several gsub and regular
expressions that not many people (including myself) easily understand.
## here is a small example using sprintf(), see ?sprintf
## %s is format specifier for string
exampleStr - west=%snorth=%seast=%ssouth=%s
sprintf(exampleStr, 1, 2, 3, 4)
## [1] west=1north=2east=3south=4
## since % is used in format specification then if a literal % is needed in the
string as here
## where you have e.g. %2F01% then escape those % with a %, i.e. % becomes %%
in the string
## I have done that in urlPattern:
urlPattern -
http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%sparams=0|3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7prod_id=3B42_dailyaction=ASCII+Output
## some coordinates
df2 - data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75,
25.25, 25.75))
fileDestination - c(C:/Temp)
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2])
download.file(queryUrl, files[i])
}
## import data in first file
precip - read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
sep = , check.names = FALSE, stringsAsFactors = FALSE)
head(precip)
Here is another way using the url() function instead of download.file()
## Escaping the trouble with saving and reading files one can also do it this
way
## having the dataframes in a named list
precipList - vector(list, nrow(df2))
names(precipList) - fileNames
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2])
u - url(queryUrl, open = r)
precipList[[i]] - read.table(u, skip = 4, header = TRUE, na.strings =
-.9,
sep = , check.names = FALSE, stringsAsFactors = FALSE)
close(u)
}
str(precipList)
Have a nice day.
Yours sincerely / Med venlig hilsen
Frede Aakmann Tøgersen
Specialist, M.Sc., Ph.D.
Plant Performance Modeling
Technology Service Solutions
T +45 9730 5135
M +45 2547 6050
fr...@vestas.com
http://www.vestas.com
Company reg. name: Vestas Wind Systems A/S
This e-mail is subject to our e-mail disclaimer statement.
Please refer to www.vestas.com/legal/notice
If you have received this e-mail in error please contact the sender.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of arun
Sent: 12. april 2014 07:16
To: r-help@r-project.org
Subject: Re: [R] calling in inverted commas
Hi,
I noticed some special characters after sending.
It should be:
toreplace - gsub(.*\\.pl\\?(west\\=.*south=.*)\\params.*,\\1,Url1)
end - gsub(.*south=.*(\\params.*),\\1,Url1)
A.K.
On Saturday, April 12, 2014 1:06 AM, arun smartpink...@yahoo.com
wrote:
HI,
Not sure if this helps:
df2 - data.frame(Col1=c(68.25, 68.75, 69.25), Col2=c(24.75, 25.25, 25.75))
Url1 - http://disc2.nascom.nasa.gov/daac-
bin/Giovanni/tovas/Giovanni_cgi.pl?west=68.25north=24.75east=68.25s
outh=24.75¶ms=0%7C3B42_V7plot_type=Time+Plotbyr=1998bmo=01
bdy=1eyr=2007emo=12edy=31begin_date=1998%2F01%2F01end_da
te=2014%2F01%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax
=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRM
M_V7∏_id=3B42_dailyaction=ASCII+Output
toreplace - gsub(.*\\.pl\\?(west\\=.*south=.*)\\¶ms.*,\\1,Url1)
begin - gsub((.*\\.pl\\?).*,\\1,Url1)
end - gsub(.*south=.*(\\¶ms.*),\\1,Url1)
vec2 - strsplit(toreplace,)[[1]]
##replace .csv with .txt and use write.table() if you need as text files.
lapply(seq_len(nrow(df2)),function(i) { val1 -
as.vector(rep(unlist(df2[i,]),2));replaced -
do.call(paste,list(lapply(seq_along(vec2),function(i) gsub([-
+]?(\\d*[.])?\\d+,val1[i],vec2[i])),collapse=)); UrlNew -
paste0(begin,replaced,end); res -
read.csv(UrlNew,header=TRUE,stringsAsFactors=FALSE,skip=4,sep=,check.
names=FALSE);
write.csv(res,file=paste0(file_,paste(val1[1:2],collapse=_),.csv),row.na
mes=FALSE,quote=FALSE)})
sapply(list.files(pattern=file_),function(x) {x1 -
read.csv(x,header=TRUE,stringsAsFactors=FALSE,check.names=FALSE);
dim(x1)[1]})
#file_68.25_24.75.csv file_68.75_25.25.csv file_69.25_25.75.csv
# 3652 3652 3652
### reading the downloaded file
lapply(list.files(pattern=file_),function(x) {x1 -
Re: [R] Save file as Fixed Width using sprintf()
Hi
Have a look at the write.fwf ( fixed width format) in gdata package.
### load package
library(gdata)
### Create a sample data matrix
set.seed(4324)
myMat - matrix(rnorm(9), 3,3)
### cannot get it tp work with matrix so cast to dataframe
write.fwf(as.data.frame(myMat), file = , sep = , colnames = FALSE)
-0.6464857-0.6289709-0.3129283
1.4342941-0.6378252-1.6057577
0.6456513 0.2481384-1.1617556
### same as before
write.fwf(as.data.frame(myMat), file = , width = c(10,10,10), sep = ,
colnames = FALSE)
-0.6464857-0.6289709-0.3129283
1.4342941-0.6378252-1.6057577
0.6456513 0.2481384-1.1617556
### rounding
write.fwf(as.data.frame(round(myMat, 6)), file = , width = rep(9,
ncol(myMat)), sep = , colnames = FALSE)
-0.646486-0.628971-0.312928
1.434294-0.637825-1.605758
0.645651 0.248138-1.161756
With this approach I don't think you can get rid of the space between positive
numbers because there should be place for a minus sign for negative values. If
that's what you want
Yours sincerely / Med venlig hilsen
Frede Aakmann Tøgersen
Specialist, M.Sc., Ph.D.
Plant Performance Modeling
Technology Service Solutions
T +45 9730 5135
M +45 2547 6050
fr...@vestas.com
http://www.vestas.com
Company reg. name: Vestas Wind Systems A/S
This e-mail is subject to our e-mail disclaimer statement.
Please refer to www.vestas.com/legal/notice
If you have received this e-mail in error please contact the sender.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of jim holtman
Sent: 11. april 2014 22:39
To: Doran, Harold
Cc: r-help@r-project.org
Subject: Re: [R] Save file as Fixed Width using sprintf()
Try this. It creates a 'list' that are the parameters for sprintf. It
writes out the file that I attach as the dump:
### Create a sample data matrix
myMat - matrix(rnorm(9), 3,3)
# create the format required -- make sure it is wide enough
# for 'fixed' width
xx - paste(rep(%8.2f, ncol(myMat)), collapse = '')
# create a list for 'do.call(sprintf'
callList - vector('list', ncol(myMat) + 1)
callList[[1]] - xx # store in the format
# add the columns to the list
for (i in seq(ncol(myMat))) callList[[i + 1L]] - myMat[, i]
callList # print it out
result - do.call(sprintf, callList)
# write out the data to a file
writeLines(result, '/temp/file.txt')
Here is what is in the file:
-0.390.45 -0.44
-0.82 -0.68 -0.43
2.05 -0.850.61
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.
On Fri, Apr 11, 2014 at 2:48 PM, Doran, Harold hdo...@air.org wrote:
I have working code to write a file out as fwf as shown below. I have one
question to try and automate this I cannot get to work.
I am generating thousands of data files for a simulation to be run outside
of R and each file varies in its dimensions. So I am trying to write code
that can write the fwf based on the dimensions of each file generated as
shown below. I have commented this code with an example to show
where I am
stuck.
### Create a sample data matrix
myMat - matrix(rnorm(9), 3,3)
### Create the vector of format strings to be equal to the length of the
columns in myMat
aa - rep('%4f', ncol(myMat))
xx - paste(aa, sep='', collapse='')
### Now I could just do this below and it works
(out - sprintf(xx, myMat[, 1], myMat[, 2], myMat[, 3]) )
out - as.matrix(out) # convert to a character matrix
dimnames(out) - list(rep('', nrow(out)), '') # blank row and column names
noquote(out) ## sink this file to a directory
But, the fact that the dimensions of my matrix vary at each iteration
means I need to automate this part in the sprint().
myMat[, 1], myMat[, 2], myMat[, 3])
I think that's needed because something like the following does not work
(out - sprintf(xx, myMat[, 1:3]) )
So, I thought about trying smoething like this
cols - paste(paste('myMat[, ', 1:ncol(myMat), sep=''), ']', sep='')
cols - paste(cols, collapse=', ')
But, this is a string with quotation marks, so I thought using cat() might
work, but it does not
(out - sprintf(xx, cat(cols) ) )
Anyone have a suggestion for the right way to do this, this is getting
messy.
Thank
Harold
[[alternative HTML version deleted]]
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide
Re: [R] invalid multibyte string at 'b0C'
Le vendredi 11 avril 2014 à 16:02 -0700, Fisher Dennis a écrit : R 3.0.2 OS X Mavericks Colleagues I have a file that I converted from SAS (sas7bdat) to CSV (filename: ORIGINAL.csv). I try to read it with read.csv and I receive the error message: Error in type.convert(data[[i]], as.is = as.is[i], dec = dec, na.strings = character(0L)) : invalid multibyte string at 'b0C’ The problem resolves if I delete a single character from each of lines 2 and 4 of the file (filename: FIXED.csv) readLines can read both files without problem and displays the offending character as: \xb0 which appears to be a degree sign. I also tried: read.csv(textConnection(readLines(“ORIGINAL.csv”))) and encountered the same error message. In the past, I have encountered the same problem with Greek symbols (e.g., mu) and other special characters. Short of editing the input file, is there a simple solution within R so that I can read the input data into a dataframe? One possible (but ugly) solution would be: TEMP- readLines(FILENAME) TEMP- gsub(offendingcharacter, replacementcharacter, TEMP) However, this would require that I find all possible offending characters and the corresponding replacements. Well, if the conversion too did its job correctly, you should be able to find out what's the encoding used by the file and import these characters correctly instead of removing them. b0 would be the correct degree character in ISO-8859-1. So try read.csv(file, fileEncoding=ISO-8859-1) The files are available for inspection at: http://www.plessthan.com/FILES/ARCHIVE.zip The link does not appear to work here. Regards __ R-help@r-project.org mailing list 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] operating website through R
This looks not so elegant, while normally data provider must have a nice accessing API, anyway, for example you can do this: myAdd - 'http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=60north=50east=70south=-50params=0|3B42_V7plot_type=Area+Plotbyr=2014bmo=01bdy=31eyr=2014emo=01edy=31begin_date=1998%2F01%2F01end_date=2014%2F01%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7prod_id=3B42_dailyaction=ASCII+Output' myData - read.table(myAdd, skip=5, header=T) Will give you this: str(myData) 'data.frame':16441 obs. of 3 variables: $ Latitude : num -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 ... $ Longitude: num 60 60.2 60.5 60.8 61 ... $ AccRain : num 0 0.42 0.39 0.42 0.66 1.23 2.31 2.37 3.72 3.63 ... For choosing different parameters, for example in case of coordinates, you just need to change the values in 'myAdd' parameters after Giovanni_cgi.pl?, west, north, east, south. But you must be sure that there is a data available with those parameters, no magical error control here. On 11 April 2014 17:45, eliza botto eliza_bo...@hotmail.com wrote: Dear Suzen, I couldn't understand. Could you please elaborate it with a small example? :( Thanks in advance. Eliza Date: Fri, 11 Apr 2014 17:31:18 +0200 Subject: Re: [R] operating website through R From: msu...@gmail.com To: eliza_bo...@hotmail.com CC: r-help@r-project.org You just need to pass the parameters on Giovanni_cgi.pl with action=ASCII+Output On 11 April 2014 17:19, eliza botto eliza_bo...@hotmail.com wrote: Dear Users of R, I wanted to operate certain slots of this website (http://disc2.nascom.nasa.gov/Giovanni/tovas/TRMM_V7.3B42_daily.2.shtml) through R. I wanted to operate Latitude, longitude section, plot type, begin and end year and ASCII Output Resolution. The filling of these slot will produce and output file with I want to D/L at a certain location in my PC. I have a matrix of 2 columns and 3000 rows which contain Latitude and Longitude information which i want to upload automatically in the slots of website. I tried to use certain web scarping techniques in R but to no use. Is there a way of doing it in R. thank you very much in advance, Eliza [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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 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] calling in inverted commas
HI,
Thanks for the link.
I should have used ?sprintf(). BTW, I am not able to reproduce your results.
urlPattern -
http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%params=0|3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7∏_id=3B42_dailyaction=ASCII+Output
##
## some coordinates
df2 - data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75,
25.25, 25.75))
fileDestination - getwd()
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i,
2]) download.file(queryUrl, files[i])
}
precip - read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
+ sep = , check.names = FALSE, stringsAsFactors = FALSE)
Error in read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
:
more columns than column names
So, I checked the file precip_68.25_24.75.txt
Giovanni Error Message
Giovanni Error Message Page
Error: instance configuration file is not found.
Error: product configuration file is not found.
Please send email to Help Desk: h...@daac.gs
fc.nasa.gov
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
A.K.
On Saturday, April 12, 2014 3:24 AM, Frede Aakmann Tøgersen fr...@vestas.com
wrote:
Hi
Sigh I'm getting a headache seeing ugly formatted R code. Arun, your code is
almost unreadable. Have a look at e.g.
http://yihui.name/en/2010/04/formatr-farewell-to-ugly-r-code/
Now to the substantial. Why not use the sprintf() function for formatting the
url instead of the more involved approach using several gsub and regular
expressions that not many people (including myself) easily understand.
## here is a small example using sprintf(), see ?sprintf
## %s is format specifier for string
exampleStr - west=%snorth=%seast=%ssouth=%s
sprintf(exampleStr, 1, 2, 3, 4)
## [1] west=1north=2east=3south=4
## since % is used in format specification then if a literal % is needed in the
string as here
## where you have e.g. %2F01% then escape those % with a %, i.e. % becomes %%
in the string
## I have done that in urlPattern:
urlPattern -
http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%sparams=0|3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7∏_id=3B42_dailyaction=ASCII+Output
## some coordinates
df2 - data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75,
25.25, 25.75))
fileDestination - c(C:/Temp)
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2])
download.file(queryUrl, files[i])
}
## import data in first file
precip - read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
sep = , check.names = FALSE, stringsAsFactors = FALSE)
head(precip)
Here is another way using the url() function instead of download.file()
## Escaping the trouble with saving and reading files one can also do it this
way
## having the dataframes in a named list
precipList - vector(list, nrow(df2))
names(precipList) - fileNames
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2])
u - url(queryUrl, open = r)
precipList[[i]] - read.table(u, skip = 4, header = TRUE, na.strings =
-.9,
sep = , check.names = FALSE, stringsAsFactors = FALSE)
close(u)
}
str(precipList)
Have a nice day.
Yours sincerely / Med venlig hilsen
Frede Aakmann Tøgersen
Specialist, M.Sc., Ph.D.
Plant Performance Modeling
Technology Service Solutions
T +45 9730 5135
M +45 2547 6050
fr...@vestas.com
http://www.vestas.com
Company reg. name: Vestas Wind Systems A/S
This e-mail is subject to our e-mail disclaimer statement.
Please refer to www.vestas.com/legal/notice
If you have received this e-mail in error please contact the sender.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of arun
Sent: 12. april 2014 07:16
To: r-help@r-project.org
Subject: Re: [R] calling in inverted commas
Hi,
I noticed some special characters after sending.
It should be:
toreplace - gsub(.*\\.pl\\?(west\\=.*south=.*)\\params.*,\\1,Url1)
end - gsub(.*south=.*(\\params.*),\\1,Url1)
A.K.
On Saturday, April 12, 2014 1:06 AM,
Re: [R] calling in inverted commas
HI,
Please ignore the previous message. I copied your codes directly from the
email. For some reason, the urlPattern - ... showed some special characters.
I manually fixed it and now it is working.
urlPattern1-(http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%sparams=0%%7C3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7prod_id=3B42_dailyaction=ASCII+Output;)
fileDestination - getwd()
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern1, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2])
download.file(queryUrl, files[i])
}
## import data in first file
precip - read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
sep = , check.names = FALSE, stringsAsFactors = FALSE)
head(precip,2)
# Time(year:month:day) AccRain
#1 1998:01:01 0
#2 1998:01:02 0
A.K.
On , arun smartpink...@yahoo.com wrote:
HI,
Thanks for the link.
I should have used ?sprintf(). BTW, I am not able to reproduce your results.
urlPattern -
http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%params=0|3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7∏_id=3B42_dailyaction=ASCII+Output
##
## some coordinates
df2 - data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75,
25.25, 25.75))
fileDestination - getwd()
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i,
2]) download.file(queryUrl, files[i])
}
precip - read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
+ sep = , check.names = FALSE, stringsAsFactors = FALSE)
Error in read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
:
more columns than column names
So, I checked the file precip_68.25_24.75.txt
Giovanni Error Message
Giovanni Error Message Page
Error: instance configuration file is not found.
Error: product configuration file is not found.
Please send email to Help Desk: h...@daac.gs
fc.nasa.gov
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
A.K.
On Saturday, April 12, 2014 3:24 AM, Frede Aakmann Tøgersen fr...@vestas.com
wrote:
Hi
Sigh I'm getting a headache seeing ugly formatted R code. Arun, your code is
almost unreadable. Have a look at e.g.
http://yihui.name/en/2010/04/formatr-farewell-to-ugly-r-code/
Now to the substantial. Why not use the sprintf() function for formatting the
url instead of the more involved approach using several gsub and regular
expressions that not many people (including myself) easily understand.
## here is a small example using sprintf(), see ?sprintf
## %s is format specifier for string
exampleStr - west=%snorth=%seast=%ssouth=%s
sprintf(exampleStr, 1, 2, 3, 4)
## [1] west=1north=2east=3south=4
## since % is used in format specification then if a literal % is needed in the
string as here
## where you have e.g. %2F01% then escape those % with a %, i.e. % becomes %%
in the string
## I have done that in urlPattern:
urlPattern -
http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%sparams=0|3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7∏_id=3B42_dailyaction=ASCII+Output
## some coordinates
df2 - data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75,
25.25, 25.75))
fileDestination - c(C:/Temp)
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2])
download.file(queryUrl, files[i])
}
## import data in first file
precip - read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
sep = , check.names = FALSE, stringsAsFactors = FALSE)
head(precip)
Here is another way using the url() function instead of download.file()
## Escaping the trouble with saving and reading files one can also do it this
way
## having the dataframes in a named list
precipList - vector(list, nrow(df2))
Re: [R] calling in inverted commas
Hi Arun
It seems to be an error on the server side and not on the client.
The error on the server results in the client receiving a string giving the
type of error on the server. And this doesn't work with read.table of course.
So if one wants to query for thousands of point one really needs to do error
catching using try () or tryCatching ().
I shall check when I get close to my R.
Actually, if the thousands of points is on regular grid ( 0.25 degree
resolution) within a confined region then one could just query for that region
instead of doing the loop. Eliza should know.
Br. Frede
Sendt fra Samsung mobil
Oprindelig meddelelse
Fra: arun
Dato:12/04/2014 12.31 (GMT+01:00)
Til: Frede Aakmann Tøgersen
Cc: Eliza Botto ,R. Help
Emne: Re: [R] calling in inverted commas
HI,
Thanks for the link.
I should have used ?sprintf(). BTW, I am not able to reproduce your results.
urlPattern -
http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%params=0|3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7â_id=3B42_dailyaction=ASCII+Output
##
## some coordinates
df2 - data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75,
25.25, 25.75))
fileDestination - getwd()
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i,
2]) download.file(queryUrl, files[i])
}
precip - read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
+ sep = , check.names = FALSE, stringsAsFactors = FALSE)
Error in read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
:
more columns than column names
So, I checked the file precip_68.25_24.75.txt
Giovanni Error Message
Giovanni Error Message Page
Error: instance configuration file is not found.
Error: product configuration file is not found.
Please send email to Help Desk: h...@daac.gs
fc.nasa.gov
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
A.K.
On Saturday, April 12, 2014 3:24 AM, Frede Aakmann Tøgersen fr...@vestas.com
wrote:
Hi
Sigh I'm getting a headache seeing ugly formatted R code. Arun, your code is
almost unreadable. Have a look at e.g.
http://yihui.name/en/2010/04/formatr-farewell-to-ugly-r-code/
Now to the substantial. Why not use the sprintf() function for formatting the
url instead of the more involved approach using several gsub and regular
expressions that not many people (including myself) easily understand.
## here is a small example using sprintf(), see ?sprintf
## %s is format specifier for string
exampleStr - west=%snorth=%seast=%ssouth=%s
sprintf(exampleStr, 1, 2, 3, 4)
## [1] west=1north=2east=3south=4
## since % is used in format specification then if a literal % is needed in the
string as here
## where you have e.g. %2F01% then escape those % with a %, i.e. % becomes %%
in the string
## I have done that in urlPattern:
urlPattern -
http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%sparams=0|3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7â_id=3B42_dailyaction=ASCII+Output
## some coordinates
df2 - data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75,
25.25, 25.75))
fileDestination - c(C:/Temp)
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2])
download.file(queryUrl, files[i])
}
## import data in first file
precip - read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
sep = , check.names = FALSE, stringsAsFactors = FALSE)
head(precip)
Here is another way using the url() function instead of download.file()
## Escaping the trouble with saving and reading files one can also do it this
way
## having the dataframes in a named list
precipList - vector(list, nrow(df2))
names(precipList) - fileNames
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2])
u - url(queryUrl, open = r)
precipList[[i]] - read.table(u, skip = 4, header = TRUE, na.strings =
-.9,
sep = , check.names = FALSE, stringsAsFactors = FALSE)
close(u)
}
str(precipList)
Have a nice day.
Yours sincerely / Med venlig hilsen
Frede Aakmann Tøgersen
Specialist, M.Sc., Ph.D.
Plant
Re: [R] calling in inverted commas
Oh, I see.
Actually I forgot to check whether if could be an advantage to use the
URLencoding () function on queryUrl. I'll check later.
Br. Frede
Sendt fra Samsung mobil
Oprindelig meddelelse
Fra: arun
Dato:12/04/2014 12.45 (GMT+01:00)
Til: Frede Aakmann Tøgersen
Cc: Eliza Botto ,R. Help
Emne: Re: [R] calling in inverted commas
HI,
Please ignore the previous message. I copied your codes directly from the
email. For some reason, the urlPattern - ... showed some special characters.
I manually fixed it and now it is working.
urlPattern1-(http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%sparams=0%%7C3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7prod_id=3B42_dailyaction=ASCII+Output;)
fileDestination - getwd()
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern1, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2])
download.file(queryUrl, files[i])
}
## import data in first file
precip - read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
sep = , check.names = FALSE, stringsAsFactors = FALSE)
head(precip,2)
# Time(year:month:day) AccRain
#1 1998:01:01 0
#2 1998:01:02 0
A.K.
On , arun smartpink...@yahoo.com wrote:
HI,
Thanks for the link.
I should have used ?sprintf(). BTW, I am not able to reproduce your results.
urlPattern -
http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%params=0|3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7â_id=3B42_dailyaction=ASCII+Output
##
## some coordinates
df2 - data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75,
25.25, 25.75))
fileDestination - getwd()
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i,
2]) download.file(queryUrl, files[i])
}
precip - read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
+ sep = , check.names = FALSE, stringsAsFactors = FALSE)
Error in read.table(files[1], skip = 4, header = TRUE, na.strings = -.9,
:
more columns than column names
So, I checked the file precip_68.25_24.75.txt
Giovanni Error Message
Giovanni Error Message Page
Error: instance configuration file is not found.
Error: product configuration file is not found.
Please send email to Help Desk: h...@daac.gs
fc.nasa.gov
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
A.K.
On Saturday, April 12, 2014 3:24 AM, Frede Aakmann Tøgersen fr...@vestas.com
wrote:
Hi
Sigh I'm getting a headache seeing ugly formatted R code. Arun, your code is
almost unreadable. Have a look at e.g.
http://yihui.name/en/2010/04/formatr-farewell-to-ugly-r-code/
Now to the substantial. Why not use the sprintf() function for formatting the
url instead of the more involved approach using several gsub and regular
expressions that not many people (including myself) easily understand.
## here is a small example using sprintf(), see ?sprintf
## %s is format specifier for string
exampleStr - west=%snorth=%seast=%ssouth=%s
sprintf(exampleStr, 1, 2, 3, 4)
## [1] west=1north=2east=3south=4
## since % is used in format specification then if a literal % is needed in the
string as here
## where you have e.g. %2F01% then escape those % with a %, i.e. % becomes %%
in the string
## I have done that in urlPattern:
urlPattern -
http://disc2.nascom.nasa.gov/daac-bin/Giovanni/tovas/Giovanni_cgi.pl?west=%snorth=%seast=%ssouth=%sparams=0|3B42_V7plot_type=Time+Plotbyr=1998bmo=01bdy=1eyr=2007emo=12edy=31begin_date=1998%%2F01%%2F01end_date=2014%%2F01%%2F31cbar=cdyncmin=cmax=yaxis=ydynymin=ymax=yint=ascres=0.25x0.25global_cfg=tovas.global.cfg.plinstance_id=TRMM_V7â_id=3B42_dailyaction=ASCII+Output
## some coordinates
df2 - data.frame(Longitude = c(68.25, 68.75, 69.25), Latitude = c(24.75,
25.25, 25.75))
fileDestination - c(C:/Temp)
fileNames - paste(precip, df2[,1], df2[,2], sep = _)
fileNames - paste(fileNames, txt, sep = .)
files - file.path(fileDestination, fileNames)
for (i in 1:nrow(df2)){
queryUrl - sprintf(urlPattern, df2[i, 1], df2[i, 2], df2[i, 1], df2[i, 2])
download.file(queryUrl, files[i])
}
## import data in first file
precip - read.table(files[1], skip = 4, header = TRUE, na.strings
[R] Selecting rows from a DF where the value in a selected column matches any element of a vector.
Dear Folks-- I have a file with 3 million-odd rows of data from the 2007 U.S. Economic Census. I am trying to pare it down to a subset of rows that both (1) has any one of a vector of NAICS economic sector codes, and (2) also has any one of a vector of geographic ID codes. Here is the code I am trying to use. ECwork - EC07_A1[ any(GEO_ID == c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) any(SECTOR == c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] I get back the following error: Warning message: In EC07_A1$SECTOR == c(32, 33, 42, 44, 45, 51, 54, : longer object length is not a multiple of shorter object length I see what R is doing. Instead of comparing each element of the column SECTOR to the row vector of codes, and returning a logical vector of the length of SECTOR with rows marked as TRUE that match any of the codes, it is lining my code list up with SECTOR as a column vector and doing element-by-element testing, and then recycling the code list over three million rows. But I am not sure how to make it do what I want -- test the sector code in each row against the vector of code I am looking for. I would be grateful if anyone could suggest an alternative that would achieve my ends. Oh, and I would add, if there is a way of correctly using doing this with the extract function [], I would like to know what it is. If not, I guess I'd like to know that too. Sincerely, Andrew Hoerner -- J. Andrew Hoerner Director, Sustainable Economics Program Redefining Progress (510) 507-4820 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Selecting rows from a DF where the value in a selected column matches any element of a vector.
You need %in% instead. This is untested, but something like this should work: ECwork - EC07_A1[ EC07_A1$GEO_ID %in% c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) EC07_A1$SECTOR %in% c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] (Note that your original code snippet had a shortage of ) and didn't specify the data frame from which to take the columns.) Sarah On Sat, Apr 12, 2014 at 8:36 AM, Andrew Hoerner ahoer...@rprogress.org wrote: Dear Folks-- I have a file with 3 million-odd rows of data from the 2007 U.S. Economic Census. I am trying to pare it down to a subset of rows that both (1) has any one of a vector of NAICS economic sector codes, and (2) also has any one of a vector of geographic ID codes. Here is the code I am trying to use. ECwork - EC07_A1[ any(GEO_ID == c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) any(SECTOR == c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] I get back the following error: Warning message: In EC07_A1$SECTOR == c(32, 33, 42, 44, 45, 51, 54, : longer object length is not a multiple of shorter object length I see what R is doing. Instead of comparing each element of the column SECTOR to the row vector of codes, and returning a logical vector of the length of SECTOR with rows marked as TRUE that match any of the codes, it is lining my code list up with SECTOR as a column vector and doing element-by-element testing, and then recycling the code list over three million rows. But I am not sure how to make it do what I want -- test the sector code in each row against the vector of code I am looking for. I would be grateful if anyone could suggest an alternative that would achieve my ends. Oh, and I would add, if there is a way of correctly using doing this with the extract function [], I would like to know what it is. If not, I guess I'd like to know that too. Sincerely, Andrew Hoerner -- J. Andrew Hoerner Director, Sustainable Economics Program Redefining Progress (510) 507-4820 -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list 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] R, RStudio, and a server for my iPad.
Running rstudio (server) on an ipad. I do'nt have an ipad anymore, but some years ago I noticed that rstudio (server) worked fine on an ipad of you have a separate keyboard. It does not work with the virtual keyboard. The same is true with android tablets. Frans 2014-04-12 3:38 GMT+02:00 Roy Mendelssohn roy.mendelss...@noaa.gov: GIYF - Google VPN and iPad. -Roy On Apr 11, 2014, at 6:34 PM, John Sorkin jsor...@grecc.umaryland.edu wrote: David, Thank you for your assistance. I have, in fact been able to get things to work, at least when my iPad is on my local network. I had to do the following: (1) install Linux (I used linux Mint) on a computer on my LAN (2) install R on the linux box (accomplished using the Mint package manager) (3) install Rstudio and RStudio server on the linux box (accomplished using the Mint package manager) (4) obtain the linux computer's internal IP address (obtained using ifconfig command entered at a terminal). The internal IP address was 192.168.0.101 (5) use a browser on my iPad (I used google chrome, I believe firefox would also work) to connect to the linux box, requesting a connection using port 8787 In the brower I entered http://192.168.0.101:8787 This works like a charm; I can now control RStudio, which runs on the Linux box, by typing on my iPad. I thus gain access to RStudio on my iPad, RStudio works exactly as if it were running directly on my iPad, hooray! My remaining problem is to determine how I can gain access to the linux box from outside my LAN. I know the IP address of my cable router xx.xx.xx.xx (forgive me I am not listing my external IP address for security reasons), but I don't know how I can address the linux box from outside my LAN. Clearly I can't use 192.168.0.101 as it is an internal IP address, and I can't use the external IP address, xx.xx.xx.xx as it is the address of my cable box, not the address of the Linux box behind the cable modem. If I can figure how to address the linux box from outside my LAN my problem will be solved! If anyone can help me with this last problem I would be grateful. I know it is not strictly an R question, but in my case it is related to running R, at least on my iPad. John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) David Winsemius dwinsem...@comcast.net 4/11/2014 9:06 PM On Apr 11, 2014, at 2:00 PM, John Sorkin wrote: I bemoan the fact that I can not run R or Rstudio on my iPad. A possible work around would be to set up a server (probably under Linux), and get the server to present a web page that to would allow me to run R on the server. I fear that the response so far has been focussing on RStudio when the desire at its minimum was to run interactive R session on an iPad. Why not use an SSH client to connect to a machine that recognizes the security keys? https://itunes.apple.com/us/app/server-auditor-ssh-client/id549039908?mt=8 I think RServe could be the server end, but I do not know how graphics devices would be handled. Maybe just create pdfs on the server? Is there a sendfile function that an SSH client could receive and allow the iPad user to open? I think the stats-rosuda-devel mailing list might be the place to find experienced users of such techniques. -- David. I have searched the web for a clear, simple answer on how to do this but can not find one. There are answers, but not for someone who has not built a Linux server. Can someone provide either a reference to, or a short explanation of how I can build the server, get R or RStudio to run on it, and get the server and its R or RStudio program available to me on my iPad? I can probably find guidance on how to build an Apache server under Linux. Thank you, John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) Confidentiality Statement: This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. __ R-help@r-project.org mailing list
[R] Change position in package rgl
Dear all,
I am using package rgl and I want to change the position where I stand.
Maybe a small example might clarify what I am looking for:
# Begininng of explanatory example
library(rgl)
data(volcano)
# the example ?rgl.surface
y - 2 * volcano
x - 10 * (1:nrow(y))
z - 10 * (1:ncol(y))
ylim - range(y)
ylen - ylim[2] - ylim[1] + 1
colorlut - terrain.colors(ylen)
col - colorlut[ y-ylim[1]+1 ]
rgl.open()
rgl.surface(x, z, y, color=col, back=lines)
## now I have the nice volcano surface
## with rgl.viewpoint I can change the elevation
## and the angle from where I look at the rgl.surface
# example of ?rgl.viewpoint
start - proc.time()[3]
while ((i - 36*(proc.time()[3]-start)) 360) {
rgl.viewpoint(i,i/4);
}
# End of explanatory example
What I am looking for (in this example) would be a way for me to stand
on the crater of the volcano, looking in a specific direction. Is there
something like a function where I can specify my coordinates (x,y,z) and
angle and a zoom factor?
Thank you,
Roland
--
This mail has been sent through the MPI for Demographic ...{{dropped:2}}
__
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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] Change position in package rgl
On 12/04/2014, 11:19 AM, Roland Rau wrote:
Dear all,
I am using package rgl and I want to change the position where I stand.
Maybe a small example might clarify what I am looking for:
# Begininng of explanatory example
library(rgl)
data(volcano)
# the example ?rgl.surface
y - 2 * volcano
x - 10 * (1:nrow(y))
z - 10 * (1:ncol(y))
ylim - range(y)
ylen - ylim[2] - ylim[1] + 1
colorlut - terrain.colors(ylen)
col - colorlut[ y-ylim[1]+1 ]
rgl.open()
rgl.surface(x, z, y, color=col, back=lines)
## now I have the nice volcano surface
## with rgl.viewpoint I can change the elevation
## and the angle from where I look at the rgl.surface
# example of ?rgl.viewpoint
start - proc.time()[3]
while ((i - 36*(proc.time()[3]-start)) 360) {
rgl.viewpoint(i,i/4);
}
# End of explanatory example
What I am looking for (in this example) would be a way for me to stand
on the crater of the volcano, looking in a specific direction. Is there
something like a function where I can specify my coordinates (x,y,z) and
angle and a zoom factor?
I think you could hack something like that (see the description in
?par3d of how rendering is accomplished), but there's currently no
support for it, and it wouldn't be easy, as currently P and M in that
description are read-only quantities computed indirectly. So you'd have
to essentially trick rgl into producing the P matrix corresponding to
the viewing position you want.
I am currently working on some changes that might make this easier, but
they likely aren't going to be released for several months.
Duncan Murdoch
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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] R, RStudio, and a server for my iPad.
Grand, Thank you. I have been able to use my iPad to connect to a server running RStudio server as described in an earlier email and can use the virtual keyboard, which works but is not convenient as one needs to go from keyboard screen to another. My current problem is that while I can get everything to work when my iPad is on my local network, I don't know how to access my server from outside my LAN. I know my server's private IP address I know my cable modem's external IP address, but I have no idea what IP address to enter in my iPad, when my iPad is outside my LAN trying to access my server. John On Apr 12, 2014, at 11:46 AM, Frans Marcelissen fransiepansiekever...@gmail.com fransiepansiekever...@gmail.com wrote: Running rstudio (server) on an ipad. I do'nt have an ipad anymore, but some years ago I noticed that rstudio (server) worked fine on an ipad of you have a separate keyboard. It does not work with the virtual keyboard. The same is true with android tablets. Frans 2014-04-12 3:38 GMT+02:00 Roy Mendelssohn roy.mendelss...@noaa.gov: GIYF - Google VPN and iPad. -Roy On Apr 11, 2014, at 6:34 PM, John Sorkin jsor...@grecc.umaryland.edu wrote: David, Thank you for your assistance. I have, in fact been able to get things to work, at least when my iPad is on my local network. I had to do the following: (1) install Linux (I used linux Mint) on a computer on my LAN (2) install R on the linux box (accomplished using the Mint package manager) (3) install Rstudio and RStudio server on the linux box (accomplished using the Mint package manager) (4) obtain the linux computer's internal IP address (obtained using ifconfig command entered at a terminal). The internal IP address was 192.168.0.101 (5) use a browser on my iPad (I used google chrome, I believe firefox would also work) to connect to the linux box, requesting a connection using port 8787 In the brower I entered http://192.168.0.101:8787 This works like a charm; I can now control RStudio, which runs on the Linux box, by typing on my iPad. I thus gain access to RStudio on my iPad, RStudio works exactly as if it were running directly on my iPad, hooray! My remaining problem is to determine how I can gain access to the linux box from outside my LAN. I know the IP address of my cable router xx.xx.xx.xx (forgive me I am not listing my external IP address for security reasons), but I don't know how I can address the linux box from outside my LAN. Clearly I can't use 192.168.0.101 as it is an internal IP address, and I can't use the external IP address, xx.xx.xx.xx as it is the address of my cable box, not the address of the Linux box behind the cable modem. If I can figure how to address the linux box from outside my LAN my problem will be solved! If anyone can help me with this last problem I would be grateful. I know it is not strictly an R question, but in my case it is related to running R, at least on my iPad. John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) David Winsemius dwinsem...@comcast.net 4/11/2014 9:06 PM On Apr 11, 2014, at 2:00 PM, John Sorkin wrote: I bemoan the fact that I can not run R or Rstudio on my iPad. A possible work around would be to set up a server (probably under Linux), and get the server to present a web page that to would allow me to run R on the server. I fear that the response so far has been focussing on RStudio when the desire at its minimum was to run interactive R session on an iPad. Why not use an SSH client to connect to a machine that recognizes the security keys? https://itunes.apple.com/us/app/server-auditor-ssh-client/id549039908?mt=8 I think RServe could be the server end, but I do not know how graphics devices would be handled. Maybe just create pdfs on the server? Is there a sendfile function that an SSH client could receive and allow the iPad user to open? I think the stats-rosuda-devel mailing list might be the place to find experienced users of such techniques. -- David. I have searched the web for a clear, simple answer on how to do this but can not find one. There are answers, but not for someone who has not built a Linux server. Can someone provide either a reference to, or a short explanation of how I can build the server, get R or RStudio to run on it, and get the server and its R or RStudio program available to me on my iPad? I can probably find guidance on how to build an Apache server under Linux. Thank you, John John David Sorkin M.D., Ph.D.
Re: [R] R, RStudio, and a server for my iPad.
That you cannot reach your home LAN from the Internet without learning something about networking is a good thing, since that offers some hope that the Russian Mafia can't use your computer to launch criminal activities against the rest of us, either. Studying how to set up a VPN on your network router was a good recommendation that you have not acknowledged. However, that subject is networking, not R, and is definitely off topic here. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On April 12, 2014 10:37:46 AM PDT, John Sorkin jsor...@grecc.umaryland.edu wrote: Grand, Thank you. I have been able to use my iPad to connect to a server running RStudio server as described in an earlier email and can use the virtual keyboard, which works but is not convenient as one needs to go from keyboard screen to another. My current problem is that while I can get everything to work when my iPad is on my local network, I don't know how to access my server from outside my LAN. I know my server's private IP address I know my cable modem's external IP address, but I have no idea what IP address to enter in my iPad, when my iPad is outside my LAN trying to access my server. John On Apr 12, 2014, at 11:46 AM, Frans Marcelissen fransiepansiekever...@gmail.com fransiepansiekever...@gmail.com wrote: Running rstudio (server) on an ipad. I do'nt have an ipad anymore, but some years ago I noticed that rstudio (server) worked fine on an ipad of you have a separate keyboard. It does not work with the virtual keyboard. The same is true with android tablets. Frans 2014-04-12 3:38 GMT+02:00 Roy Mendelssohn roy.mendelss...@noaa.gov: GIYF - Google VPN and iPad. -Roy On Apr 11, 2014, at 6:34 PM, John Sorkin jsor...@grecc.umaryland.edu wrote: David, Thank you for your assistance. I have, in fact been able to get things to work, at least when my iPad is on my local network. I had to do the following: (1) install Linux (I used linux Mint) on a computer on my LAN (2) install R on the linux box (accomplished using the Mint package manager) (3) install Rstudio and RStudio server on the linux box (accomplished using the Mint package manager) (4) obtain the linux computer's internal IP address (obtained using ifconfig command entered at a terminal). The internal IP address was 192.168.0.101 (5) use a browser on my iPad (I used google chrome, I believe firefox would also work) to connect to the linux box, requesting a connection using port 8787 In the brower I entered http://192.168.0.101:8787 This works like a charm; I can now control RStudio, which runs on the Linux box, by typing on my iPad. I thus gain access to RStudio on my iPad, RStudio works exactly as if it were running directly on my iPad, hooray! My remaining problem is to determine how I can gain access to the linux box from outside my LAN. I know the IP address of my cable router xx.xx.xx.xx (forgive me I am not listing my external IP address for security reasons), but I don't know how I can address the linux box from outside my LAN. Clearly I can't use 192.168.0.101 as it is an internal IP address, and I can't use the external IP address, xx.xx.xx.xx as it is the address of my cable box, not the address of the Linux box behind the cable modem. If I can figure how to address the linux box from outside my LAN my problem will be solved! If anyone can help me with this last problem I would be grateful. I know it is not strictly an R question, but in my case it is related to running R, at least on my iPad. John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) David Winsemius dwinsem...@comcast.net 4/11/2014 9:06 PM On Apr 11, 2014, at 2:00 PM, John Sorkin wrote: I bemoan the fact that I can not run R or Rstudio on my iPad. A possible work around would be to set up a server (probably under Linux), and get the server to present a web page that to would allow me to run R on the server. I fear that the response so far has been focussing on RStudio when the desire at its minimum was to run interactive R session on an iPad. Why not use an SSH client to connect to a machine that
Re: [R] R, RStudio, and a server for my iPad.
You will have to enter the external IP address and then use port forwarding. Just google for that term (port forwarding) ... For example: http://www.howtogeek.com/66214/how-to-forward-ports-on-your-router/ http://en.wikipedia.org/wiki/Port_forwarding Best, Wolfgang From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of John Sorkin [jsor...@grecc.umaryland.edu] Sent: Saturday, April 12, 2014 7:37 PM To: fransiepansiekever...@gmail.com Cc: r-help@r-project.org Subject: Re: [R] R, RStudio, and a server for my iPad. Grand, Thank you. I have been able to use my iPad to connect to a server running RStudio server as described in an earlier email and can use the virtual keyboard, which works but is not convenient as one needs to go from keyboard screen to another. My current problem is that while I can get everything to work when my iPad is on my local network, I don't know how to access my server from outside my LAN. I know my server's private IP address I know my cable modem's external IP address, but I have no idea what IP address to enter in my iPad, when my iPad is outside my LAN trying to access my server. John __ R-help@r-project.org mailing list 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] Programing routine comp()
Dear R users. I am trying to program the comp() routine in package survMisc. I am reading the data below with d=read.table( C:\\. . .,fill=TRUE,header=TRUE) Then I load the packages 'survival' and 'survMisc', library(survival), library(survMisc) and I run the commands s=survfit(Surv(d[,2], d[,3])~d[,1], data=d) comp(s) and I am getting the error Error in get(t1, loc1) : object 'd[, 2]' not found If instead I use the commands s=survfit(Surv(T, Status)~Group, data=d) comp(s) routine comp() runs perfectly. However when I am programing I can't see a way to know in advance the variable names in order to use them. Can anybody give me a suggestion? Thanks in advance Endy NB. The data must be stacked in three (3) columns before red. They are repeated in nine (9) columns for space saving. Group T Status Group T Status Group T Status 1 2081 0 1 55 1 2 414 1 1 1602 0 1 1 1 2 2204 1 1 1496 0 1 107 1 2 1063 1 1 1462 0 1 110 1 2 481 1 1 1433 0 1 332 1 2 105 1 1 1377 0 2 2569 0 2 641 1 1 1330 0 2 2506 0 2 390 1 1 996 0 2 2409 0 2 288 1 1 226 0 2 2218 0 2 421 1 1 1199 0 2 1857 0 2 79 1 1 0 2 1829 0 2 748 1 1 530 0 2 1562 0 2 486 1 1 1182 0 2 1470 0 2 48 1 1 1167 0 2 1363 0 2 272 1 1 418 1 2 1030 0 2 1074 1 1 383 1 2 860 0 2 381 1 1 276 1 2 1258 0 2 10 1 1 104 1 2 2246 0 2 53 1 1 609 1 2 1870 0 2 80 1 1 172 1 2 1799 0 2 35 1 1 487 1 2 1709 0 2 248 1 1 662 1 2 1674 0 2 704 1 1 194 1 2 1568 0 2 211 1 1 230 1 2 1527 0 2 219 1 1 526 1 2 1324 0 2 606 1 1 122 1 2 957 0 1 129 1 2 932 0 1 74 1 2 847 0 1 122 1 2 848 0 1 86 1 2 1850 0 1 466 1 2 1843 0 1 192 1 2 1535 0 1 109 1 2 1447 0 1 55 1 2 1384 0 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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-pkgs] Rcpp11 3.1.0 is on CRAN.
Hello, R version 3.1.0 was released yesterday, and as always is welcome with great pleasure. One of the features that is of particular interest to me is the support for C++11. I would encourage you to read [Writing R Extensions](http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Using-C_002b_002b11-code) to familiarize yourself with what this supports means and how to take advantage of it. C++11 is a major upgrade of the C++ standard, making C++ more expressive, more efficient, more fun to use and teach. It almost feels like a new language if you embrace it fully. The standards committee has done a great job of maintaining compatibility, which means that code written with older standard will still compile and work. However, with C++11 code you write today and tomorrow will not be the same as code you used to write with C++98. To get the best of what C++11 has to offer, I'm releasing Rcpp11 today. Rcpp11 is a complete redesign of Rcpp, focused on C++11. Rcpp11 is a header only C++ library, distributed as an R package on CRAN, that facilitates embedding C++ code in R packages. I'll try to keep this announcement short. More details will follow on dedicated channels. I will just highlight a few aspects of Rcpp11 that are high level enough for such an annoucement. Header Only === Rcpp11 is header only -- it consists only of a set of `.h` files. Rcpp11 has no `.cpp` files, and no R functions. This eliminates many problems inherent to binary compatibility that Rcpp has been fighting with for years. The recommended way to use Rcpp11 is to have these lines in the `DESCRIPTION` file of your package: ``` LinkingTo: Rcpp11 SystemRequirements: C++11 ``` Modernized code base Many features of the original Rcpp code base are the consequence of my learning C++ and the internal API of R. After a few years of experience, I can now admit that mistakes were made while designing it. Unfortunately for reasons outside of my control, it is not possible to fix these mistakes under the umbrella of the Rcpp package. Things are radically different for Rcpp11, which I will maintain. Over the past few months, I have considered many features of the code base and either decided to abandon them or upgrade them to the level of expectation we should have for a modern R/C++ interface. API --- Most of what is usually called the API has been retained. I do not guarantee low level compatibililty, but there is conceptual compatibility. For example, Rcpp11 contains all the classes we would expect: `NumericVector`, `List`, ... I'm not going into details about what the individual differences are. Instead I will start documenting how to use the API provided by Rcpp11. Attributes -- Attributes is probably the best feature that has ever been contributed to Rcpp. It gives a mechanism for decorating C++ functions, parsing these decorations and generating scaffolding code around them. This feature has not been retained in Rcpp11, but instead has been moved into a new package called [attributes](https://github.com/Rcpp11/attributes), which is being developed and will be released later. It is worth mentioning that code generated by Rcpp's `compileAttributes` function should be compilable against Rcpp11. When attributes becomes available it will provide a more flexible approach, and provide facilities for package authors to implement and use their own attributes. Modules --- Rcpp modules was not retained as part of Rcpp11. This was a hard decision, because I invested a lot of time developing the original code behind Rcpp modules. However modules have significant problems which make them hard to maintain. Modules are also very demanding on the compiler. However, I still believe that the promise of Rcpp modules -- exposing C++ classes at the R level -- is very worthwhile. My plan is to redesign it using a different approach, more oriented towards code generation, à la attributes. Time and Date classes - I decided to abandon the classes responsible to handling dates and times. Better classes might be introduced when I'm comfortable with the design. Design documents and pull requests are welcome. Further discussion == Please consider subscribing to the R and C++ mailing list that was created a few days ago: https://groups.google.com/forum/#!forum/r-and-cpp The scope of the mailing list is broader, the intention is to discuss all things R and C++. Questions about Rcpp11, Rcpp or anything related to using C++ and R are welcome. As of today, 37 participants are registered. Please consider replying to this annoucement email through the mailing list. Rcpp11 is developed through the Rcpp11 organisation on github. Feel free to report issues and submit pull requests. https://github.com/Rcpp11/Rcpp11 Versioning == The pattern that has been decided for versions of Rcpp11 is to use
[R] Fwd: Selecting rows from a DF where the value in a selected column matches any element of a vector.
Thanks Sarah! That worked! And you are quite right about the absence of parentheses and EC07_A1$ 's. I apologize for sending that code snip -- I am not quite sure how I managed to do it, since I had already fixed those problems and changed the code in order to get the error message I posted. Apropos of nothing in particular, before I could successfully impliment your fix, I also had to learn another new thing. When saving a CSV file with write.table, if you use sep=, (that's double-quote comma space double-quote) R puts the space _inside_ the quotation marks around character variables. I'm not sure I would call that a bug, but I bet more people are surprised by it than expect it. Again, many thanks! Andrew On Sat, Apr 12, 2014 at 6:04 AM, Sarah Goslee sarah.gos...@gmail.comwrote: You need %in% instead. This is untested, but something like this should work: ECwork - EC07_A1[ EC07_A1$GEO_ID %in% c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) EC07_A1$SECTOR %in% c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] (Note that your original code snippet had a shortage of ) and didn't specify the data frame from which to take the columns.) Sarah On Sat, Apr 12, 2014 at 8:36 AM, Andrew Hoerner ahoer...@rprogress.org wrote: Dear Folks-- I have a file with 3 million-odd rows of data from the 2007 U.S. Economic Census. I am trying to pare it down to a subset of rows that both (1) has any one of a vector of NAICS economic sector codes, and (2) also has any one of a vector of geographic ID codes. Here is the code I am trying to use. ECwork - EC07_A1[ any(GEO_ID == c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) any(SECTOR == c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] I get back the following error: Warning message: In EC07_A1$SECTOR == c(32, 33, 42, 44, 45, 51, 54, : longer object length is not a multiple of shorter object length I see what R is doing. Instead of comparing each element of the column SECTOR to the row vector of codes, and returning a logical vector of the length of SECTOR with rows marked as TRUE that match any of the codes, it is lining my code list up with SECTOR as a column vector and doing element-by-element testing, and then recycling the code list over three million rows. But I am not sure how to make it do what I want -- test the sector code in each row against the vector of code I am looking for. I would be grateful if anyone could suggest an alternative that would achieve my ends. Oh, and I would add, if there is a way of correctly using doing this with the extract function [], I would like to know what it is. If not, I guess I'd like to know that too. Sincerely, Andrew Hoerner -- J. Andrew Hoerner Director, Sustainable Economics Program Redefining Progress (510) 507-4820 -- Sarah Goslee http://www.functionaldiversity.org -- J. Andrew Hoerner Director, Sustainable Economics Program Redefining Progress (510) 507-4820 -- J. Andrew Hoerner Director, Sustainable Economics Program Redefining Progress (510) 507-4820 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Selecting rows from a DF where the value in a selected column matches any element of a vector.
Hi Andrew, On Apr 12, 2014, at 6:36 PM, Andrew Hoerner ahoer...@rprogress.org wrote: Thanks Sarah! That worked! And you are quite right about the absence of parentheses and EC07_A1$ 's. I apologize for sending that code snip -- I am not quite sure how I managed to do it, since I had already fixed those problems and changed the code in order to get the error message I posted. Apropos of nothing in particular, before I could successfully impliment your fix, I also had to learn another new thing. When saving a CSV file with write.table, if you use sep=, (that's double-quote comma space double-quote) R puts the space _inside_ the quotation marks around character variables. I'm not sure I would call that a bug, but I bet more people are surprised by it than expect it. It shouldn’t; that’s incorrect. Can you provide a reproducible example? When I look at your code my reply, I notice that the quote marks are wrong too; could that be the actual problem? Sarah Again, many thanks! Andrew On Sat, Apr 12, 2014 at 6:04 AM, Sarah Goslee sarah.gos...@gmail.comwrote: You need %in% instead. This is untested, but something like this should work: ECwork - EC07_A1[ EC07_A1$GEO_ID %in% c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) EC07_A1$SECTOR %in% c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] (Note that your original code snippet had a shortage of ) and didn't specify the data frame from which to take the columns.) Sarah On Sat, Apr 12, 2014 at 8:36 AM, Andrew Hoerner ahoer...@rprogress.org wrote: Dear Folks-- I have a file with 3 million-odd rows of data from the 2007 U.S. Economic Census. I am trying to pare it down to a subset of rows that both (1) has any one of a vector of NAICS economic sector codes, and (2) also has any one of a vector of geographic ID codes. Here is the code I am trying to use. ECwork - EC07_A1[ any(GEO_ID == c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) any(SECTOR == c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] I get back the following error: Warning message: In EC07_A1$SECTOR == c(32, 33, 42, 44, 45, 51, 54, : longer object length is not a multiple of shorter object length I see what R is doing. Instead of comparing each element of the column SECTOR to the row vector of codes, and returning a logical vector of the length of SECTOR with rows marked as TRUE that match any of the codes, it is lining my code list up with SECTOR as a column vector and doing element-by-element testing, and then recycling the code list over three million rows. But I am not sure how to make it do what I want -- test the sector code in each row against the vector of code I am looking for. I would be grateful if anyone could suggest an alternative that would achieve my ends. Oh, and I would add, if there is a way of correctly using doing this with the extract function [], I would like to know what it is. If not, I guess I'd like to know that too. Sincerely, Andrew Hoerner -- J. Andrew Hoerner Director, Sustainable Economics Program Redefining Progress (510) 507-4820 -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list 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] Selecting rows from a DF where the value in a selected column matches any element of a vector.
Oops! Spoke too soon. Your fix fixed the problem I was having before, but it turns out the test is now accepting every line. So there is still some problem with the logic or with my implimentation of it. I thought I should produce a reproducible example without 3 million lines of data. I made a version with only the geography information and test. Here is the code I am now using, applied to a file with only the first 8 lines of my geo data in it: First I read the data in and print it out: GEOshort.DF - read.table(C:\\Users\\andrewH\\Documents\\Oakland Tech Project\\GEO_short.csv, header = FALSE, sep = ,, quote = \, dec = ., skip=1, col.names= c(originalRow, GEO_ID, GEOGRAPHY), fill = TRUE, colClasses=character) Which yields: GEOshort.DF originalRowGEO_ID GEOGRAPHY 1 1 01000US United States 23115 04000US01 Alabama 35501 04000US02Alaska 47924 04000US04 Arizona 5 10571 04000US05 Arkansas 6 14342 04000US06California 7 17913 04000US08 Colorado 8 20442 04000US09 Connecticut Then I try to select the rows that match my geo-codes: GEOextract.DF - GEOshort.DF[ any(GEOshort.DF$GEO_ID %in% c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084, 05000US06001, E6000US0600153000)), ] This produces: GEOextract.DF originalRowGEO_ID GEOGRAPHY 1 1 01000US United States 23115 04000US01 Alabama 35501 04000US02Alaska 47924 04000US04 Arizona 5 10571 04000US05 Arkansas 6 14342 04000US06California 7 17913 04000US08 Colorado 8 20442 04000US09 Connecticut This is what I want it to produce: GEOextract.DF originalRowGEO_ID GEOGRAPHY 1 1 01000US United States 2 14342 04000US06California Sorry about the confusion, and thanks again for your kind attention. Peace joy, Andrew ... But pattern-matching doesn't equal comprehension. --Peter Watts On Sat, Apr 12, 2014 at 6:04 AM, Sarah Goslee sarah.gos...@gmail.comwrote: You need %in% instead. This is untested, but something like this should work: ECwork - EC07_A1[ EC07_A1$GEO_ID %in% c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) EC07_A1$SECTOR %in% c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] (Note that your original code snippet had a shortage of ) and didn't specify the data frame from which to take the columns.) Sarah On Sat, Apr 12, 2014 at 8:36 AM, Andrew Hoerner ahoer...@rprogress.org wrote: Dear Folks-- I have a file with 3 million-odd rows of data from the 2007 U.S. Economic Census. I am trying to pare it down to a subset of rows that both (1) has any one of a vector of NAICS economic sector codes, and (2) also has any one of a vector of geographic ID codes. Here is the code I am trying to use. ECwork - EC07_A1[ any(GEO_ID == c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) any(SECTOR == c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] I get back the following error: Warning message: In EC07_A1$SECTOR == c(32, 33, 42, 44, 45, 51, 54, : longer object length is not a multiple of shorter object length I see what R is doing. Instead of comparing each element of the column SECTOR to the row vector of codes, and returning a logical vector of the length of SECTOR with rows marked as TRUE that match any of the codes, it is lining my code list up with SECTOR as a column vector and doing element-by-element testing, and then recycling the code list over three million rows. But I am not sure how to make it do what I want -- test the sector code in each row against the vector of code I am looking for. I would be grateful if anyone could suggest an alternative that would achieve my ends. Oh, and I would add, if there is a way of correctly using doing this with the extract function [], I would like to know what it is. If not, I guess I'd like to know that too. Sincerely, Andrew Hoerner -- J. Andrew Hoerner Director, Sustainable Economics Program Redefining Progress (510) 507-4820 -- Sarah Goslee http://www.functionaldiversity.org -- J. Andrew Hoerner Director, Sustainable Economics Program Redefining Progress (510) 507-4820 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] Pie charts using plotGooglemaps
Hi, I am trying to add some pie charts in a list of coordinates.
Please find attached data I am using
Basically I am using this commands:
data-read.csv(file.choose(),header=T) coordinates(data) = ~ x + y
proj4string(data) = CRS(+proj=longlat +datum=WGS84) # colPalette defines
colors for plot mychart-segmentGoogleMaps(data,
zcol=c('City','Village'),mapTypeId='ROADMAP',
filename='myMap4.htm',colPalette=c('#E41A1C','#377EB8'),
strokeColor='black')
But a map with legends shows up without any points or pie chart
Attached my csv https://www.dropbox.com/s/pkvq6xz0ynwok9r/sample.csv
Regards
--
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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] R 3.0.3, Windows 7: Problem installing XML package
On 12.04.2014 22:39, Alpesh Pandya wrote:
Thank you for response Uwe. I tried multiple times by downloading the zip
file from many sources but still the same error. This is a major road block
for me in using R. Appreciate any help on this.
Please ask your local IT staff.
I get, using the same mirror:
options(repos=c(CRAN=http://watson.nci.nih.gov/cran_mirror;))
install.packages(XML, lib=d:/temp)
trying URL
'http://watson.nci.nih.gov/cran_mirror/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
Content type 'application/zip' length 4288136 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb
package ‘XML’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
d:\temp\RtmpqMqL8L\downloaded_packages
Best,
Uwe Ligges
On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
Works for me.
Best,
Uwe Ligges
On 11.04.2014 17:10, Alpesh Pandya wrote:
Using install.package('XML') command produces this error:
trying URL
'
http://watson.nci.nih.gov/cran_mirror/bin/windows/
contrib/3.0/XML_3.98-1.1.zip
'
Content type 'application/zip' length 4288136 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb
Error in read.dcf(file.path(pkgname, DESCRIPTION), c(Package,
Type)) :
cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = wb, ...) :
downloaded length 4276224 != reported length 4288136
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, DESCRIPTION), c(Package, Type)) :
cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
file or directory'
Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from
cran
site. But this zip file is not a valid archive (cannot open using winzip).
Also trying to install using this downloaded file produces the following
error:
Installing package into 'C:/Users/APandya/Documents/R/win-library/3.0'
(as 'lib' is unspecified)
Warning in install.packages :
error 1 in extracting from zip file
Warning in install.packages :
cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
file or directory'
Error in install.packages : cannot open the connection
I downloaded this zip file from multiple sources and tried to install
with
same result.
__
R-help@r-project.org mailing list
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] Pie charts using plotGooglemaps
On 04/13/2014 09:20 AM, drunkenphd wrote:
Hi, I am trying to add some pie charts in a list of coordinates.
Please find attached data I am using
Basically I am using this commands:
data-read.csv(file.choose(),header=T) coordinates(data) = ~ x + y
proj4string(data) = CRS(+proj=longlat +datum=WGS84) # colPalette defines
colors for plot mychart-segmentGoogleMaps(data,
zcol=c('City','Village'),mapTypeId='ROADMAP',
filename='myMap4.htm',colPalette=c('#E41A1C','#377EB8'),
strokeColor='black')
But a map with legends shows up without any points or pie chart
Attached my csv https://www.dropbox.com/s/pkvq6xz0ynwok9r/sample.csv
Hi drunkenphd,
If you have the coordinates, you can use the floating.pie function in
the plotrix package.
Jim
__
R-help@r-project.org mailing list
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] Pie charts using plotGooglemaps
Jim thx, Can you please provide me an example how to use my csv data with plotrix float.pie??? -- View this message in context: http://r.789695.n4.nabble.com/Pie-charts-using-plotGooglemaps-tp4688678p4688683.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] Selecting rows from a DF where the value in a selected column matches any element of a vector.
See inline. On Apr 12, 2014, at 7:04 PM, Andrew Hoerner ahoer...@rprogress.org wrote: Oops! Spoke too soon. Your fix fixed the problem I was having before, but it turns out the test is now accepting every line. So there is still some problem with the logic or with my implimentation of it. I thought I should produce a reproducible example without 3 million lines of data. I made a version with only the geography information and test. Here is the code I am now using, applied to a file with only the first 8 lines of my geo data in it: Please use dput() to provide data, rather than copy paste, since that’s not reproducible. First I read the data in and print it out: GEOshort.DF - read.table(C:\\Users\\andrewH\\Documents\\Oakland Tech Project\\GEO_short.csv, header = FALSE, sep = ,, quote = \, dec = ., skip=1, col.names= c(originalRow, GEO_ID, GEOGRAPHY), fill = TRUE, colClasses=character) Which yields: GEOshort.DF originalRowGEO_ID GEOGRAPHY 1 1 01000US United States 23115 04000US01 Alabama 35501 04000US02Alaska 47924 04000US04 Arizona 5 10571 04000US05 Arkansas 6 14342 04000US06California 7 17913 04000US08 Colorado 8 20442 04000US09 Connecticut Then I try to select the rows that match my geo-codes: GEOextract.DF - GEOshort.DF[ any(GEOshort.DF$GEO_ID %in% c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084, 05000US06001, E6000US0600153000)), ] But that’s not what I suggested: if you use any(), then if there are any matches it will return TRUE and by expansion you’ll get all the rows. You need: GEOextract.DF - GEOshort.DF[ GEOshort.DF$GEO_ID %in% c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084, 05000US06001, E6000US0600153000), ] You can check this yourself by running just the logical portion: compare any(GEOshort.DF$GEO_ID %in% c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084, 05000US06001, E6000US0600153000)) with GEOshort.DF$GEO_ID %in% c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084, 05000US06001, “E6000US0600153000) ... But pattern-matching doesn't equal comprehension. --Peter Watts Happy to help a Peter Watts fan. Sarah On Sat, Apr 12, 2014 at 6:04 AM, Sarah Goslee sarah.gos...@gmail.com wrote: You need %in% instead. This is untested, but something like this should work: ECwork - EC07_A1[ EC07_A1$GEO_ID %in% c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) EC07_A1$SECTOR %in% c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] (Note that your original code snippet had a shortage of ) and didn't specify the data frame from which to take the columns.) Sarah On Sat, Apr 12, 2014 at 8:36 AM, Andrew Hoerner ahoer...@rprogress.org wrote: Dear Folks-- I have a file with 3 million-odd rows of data from the 2007 U.S. Economic Census. I am trying to pare it down to a subset of rows that both (1) has any one of a vector of NAICS economic sector codes, and (2) also has any one of a vector of geographic ID codes. Here is the code I am trying to use. ECwork - EC07_A1[ any(GEO_ID == c(01000US, 04000US06, 33000US488, 31000US41860, 31400US4186036084 05000US06001, E6000US0600153000) any(SECTOR == c(32, 33, 42, 44, 45, 51, 54, 61, 71, 81), ] I get back the following error: Warning message: In EC07_A1$SECTOR == c(32, 33, 42, 44, 45, 51, 54, : longer object length is not a multiple of shorter object length I see what R is doing. Instead of comparing each element of the column SECTOR to the row vector of codes, and returning a logical vector of the length of SECTOR with rows marked as TRUE that match any of the codes, it is lining my code list up with SECTOR as a column vector and doing element-by-element testing, and then recycling the code list over three million rows. But I am not sure how to make it do what I want -- test the sector code in each row against the vector of code I am looking for. I would be grateful if anyone could suggest an alternative that would achieve my ends. Oh, and I would add, if there is a way of correctly using doing this with the extract function [], I would like to know what it is. If not, I guess I'd like to know that too. Sincerely, Andrew Hoerner -- J. Andrew Hoerner Director, Sustainable Economics Program Redefining Progress (510) 507-4820 -- Sarah Goslee http://www.functionaldiversity.org -- J. Andrew Hoerner Director, Sustainable Economics Program Redefining Progress (510) 507-4820 __ R-help@r-project.org mailing list
[R] Adding Nested Random Effects to MCMCglmm
Dear R Experts, Does anyone have advice for how to nest random effects in the MCMCglmm package? Right now, I am running my models with Individual as a random effect; however, the 25 individuals in my study are birds taken from 13 different nests, so I feel that a more accurate model would nest the variable Individual (called RNR in my code) within the variable Nest ID. I am trying to run both univariate and bivariate mixed models using the MCMCglmm package. (My interest is in calculating repeatability estimates using the univariate models, and in partitioning out the within-individual and between-individual correlations using the bivariate models.) I am also trying to include a fixed effect (SMI) but am not sure that I am doing this correctly for either case. Example Univariate MM: Cort0.mcmc-MCMCglmm(CORT0_LOG10_Z~SMI_CEN, random=~indiv, family=gaussian, data=cort0.data,verbose=FALSE) CORT0_LOG10_Z is the variable of interest (which has been measured repeatedly for each given individual) RNR is individual ID SMI_CEN is a fixed effect that varies both within and between individuals Example piece of data frame: RNR HPA CORT0_LOG10_Z SMI_CEN NEST_ID 1 AR04273 1 -3.29844317 1.236170087 3 2 AR04273 2 -0.51328002 0.122035902 3 3 AR04281 10.83631319 1.212914325 8 Example Bivariate MM: cort0_cort15.bivarC.mcmc-MCMCglmm(cbind(CORT0_std,CORT15_std)~(SMI_cen), random=~us(trait):RNR, rcov=~us(trait):units, family=c(gaussian,gaussian), prior=prior.bivar, nitt=130,thin=1000,burnin=30, data=cort0_cort15,verbose=FALSE) CORT0_std and CORT15_std are the 2 variables of interest RNR is individual ID SMI_cen is a fixed effect that varies both within and between individuals Example piece of data frame: RNR SMI SMI_avg SMI_dev CORT0 CORT15 SMI_cen SMI_avg_cen CORT0_std CORT15_std NEST_ID 1 AR04273 18.03640 17.48987 0.546522102 0.460 4.590 1.236170087 0.73332960 -3.80922656 -3.170123623 3 2 AR04273 16.94335 17.48987 -0.546522102 3.493 13.604 0.122035902 0.73332960 -0.04862913 -0.480133012 3 3 AR04281 15.63367 15.86610 -0.232427804 4.875 13.507 -1.212914325 -1.05393597 0.56974795 -0.497849822 8 I am basing my code off of the code supplied in the 2013 paper by Dingemanse and Dochtermann about applying linear mixed modelling to behavioral ecology. Does anyone have advice for how to nest RNR within Nest ID, as well as insight into whether I have coded the fixed effect SMI correctly? Many thanks, Marian __ R-help@r-project.org mailing list 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 two have two legends on a chart with different groups?
I'm trying to have two legends on a chart, with two sets of data with subgroups. Currently ggplot is are merging the to sets of data together. I would like to have the vertical lines in there own legend and not affect the colour shading or show up in the type legend. How would I go about doing this? df - data.frame(val1=rnorm(300, 75, 10), val2=rnorm(300, 75, 10),type=rep(c(A, B, C),100)) cuts1 - data.frame(Stats=Stat A, vals=c(43, 70, 90)) cuts2 - data.frame(Stats=Stat B, vals=cuts2 - c(46, 79, 86)) cuts - rbind(cuts1,cuts2) ggplot(df, aes(x=val1, y=val2, group=type)) + geom_line(aes(colour=type))+ geom_point(aes(colour=type))+ geom_vline(data=cuts, aes(xintercept=vals, linetype=Stats, colour = Stats), show_guide = TRUE) I got the idea of how to do this from: Add vline to existing plot and have it appear in ggplot2 legend? -- View this message in context: http://r.789695.n4.nabble.com/How-two-have-two-legends-on-a-chart-with-different-groups-tp4688666.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] R 3.0.3, Windows 7: Problem installing XML package
Thank you for response Uwe. I tried multiple times by downloading the zip
file from many sources but still the same error. This is a major road block
for me in using R. Appreciate any help on this.
On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
Works for me.
Best,
Uwe Ligges
On 11.04.2014 17:10, Alpesh Pandya wrote:
Using install.package('XML') command produces this error:
trying URL
'
http://watson.nci.nih.gov/cran_mirror/bin/windows/
contrib/3.0/XML_3.98-1.1.zip
'
Content type 'application/zip' length 4288136 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb
Error in read.dcf(file.path(pkgname, DESCRIPTION), c(Package,
Type)) :
cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = wb, ...) :
downloaded length 4276224 != reported length 4288136
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, DESCRIPTION), c(Package, Type)) :
cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
file or directory'
Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from
cran
site. But this zip file is not a valid archive (cannot open using winzip).
Also trying to install using this downloaded file produces the following
error:
Installing package into 'C:/Users/APandya/Documents/R/win-library/3.0'
(as 'lib' is unspecified)
Warning in install.packages :
error 1 in extracting from zip file
Warning in install.packages :
cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
file or directory'
Error in install.packages : cannot open the connection
I downloaded this zip file from multiple sources and tried to install
with
same result.
--
Thanks and Regards
Alpesh
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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-pkgs] frailtypack package 2.6
Dear R users, the frailtypack package, for the analysis of correlated survival data, has been updated on CRAN. The major changes in version 2.6 are: * Fit now a multivariate gaussian frailty model (two types of recurrent events and a terminal event). For instance here is a model that fits a weibull multivariate gaussian frailty model with different adjustments: * modMultiv.weib - multivPenal(Surv(TIMEGAP,INDICREC)~cluster(PATIENT)+v1+v2+ event2(INDICMETA)+terminal(INDICDEATH),formula.Event2=~v1+v2+v3, formula.terminalEvent=~v1,data=dataMultiv,hazard=Weibull) * * New dynamic tool of prediction probabilities in Cox models, standard shared frailty models or joint frailty models. * Concordance measures for clustered data. * initialization of regression coefficients, variance of the random effects, and alpha now available in joint frailty models. Moreover, with 'Alpha=none', frailtyPenal can fit a joint model with a fixed alpha (=1). * Interval-censored frailty models. Best regards, Virginie Rondeau, Alexandre Laurent [[alternative HTML version deleted]] ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list 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] Reading output of a GLMM run in R
Hi, I am a complete novice and dummy when it comes to statistics so I apologise in advance... I have been asked to report the results of my GLMMs (I ran two) in a table. This table must state: effect, standard error, test statistic, and P value, for all fixed effects. Unfortunately I am struggling to read my output. The out put is as follows, if anyone would be kind enough to help I would be very grateful and will know for future reference which bit equates to what (also I have been told my degrees of freedom are different for both the tests, could someone explain why this is?). GLMM 1-run for predictors of step length. Response variable = step length. fixed effects = depth and direction threshold. random factor = individual Models: m2: step ~ (1 | ind) m1: step ~ Depth * threshold + (1 | ind) Df AIC BIC logLik deviance Chisq Chi Df Pr(Chisq) m2 3 373235 373259 -186615 373229 m1 8 373225 373290 -186605 373209 19.767 5 0.001382 ** --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 GLMM 2 -run to investigate potential predictors of PDBA. response variables = depth and step length. fixed effect = direction threshold. random factor = Individual Models: m3: PDBA ~ Depth + (1 | ind) + thresholdepth m2: PDBA ~ step * threshold + Depth * threshold + (1 | ind) Df AIC BIC logLik deviance Chisq Chi Df Pr(Chisq) m3 6 -48205 -48157 24109 -48217 m2 11 -48430 -48341 24226 -48452 235.1 5 2.2e-16 *** --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Models: m4: PDBA ~ step + (1 | ind) + step:threshold m2: PDBA ~ step * threshold + Depth * threshold + (1 | ind) Df AIC BIC logLik deviance Chisq Chi Df Pr(Chisq) m4 6 -48206 -48158 24109 -48218 m2 11 -48430 -48341 24226 -48452 233.81 5 2.2e-16 *** --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] R 3.0.3, Windows 7: Problem installing XML package
@Uwe I tried the same steps from office as well as home network with same
results. Are you using windows 7 with R 3.0.3?
I have seen same question being asked by others without any resolution. Is
anything special about XML package? I am OK use older version of package
but in archives there are no zip files (only gz files). Is windows platform
not recommended for R?
On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
On 12.04.2014 22:39, Alpesh Pandya wrote:
Thank you for response Uwe. I tried multiple times by downloading the zip
file from many sources but still the same error. This is a major road
block
for me in using R. Appreciate any help on this.
Please ask your local IT staff.
I get, using the same mirror:
options(repos=c(CRAN=http://watson.nci.nih.gov/cran_mirror;))
install.packages(XML, lib=d:/temp)
trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
contrib/3.0/XML_3.98-1.1.zip'
Content type 'application/zip' length 4288136 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb
package 'XML' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
d:\temp\RtmpqMqL8L\downloaded_packages
Best,
Uwe Ligges
On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges
lig...@statistik.tu-dortmund.de
wrote:
Works for me.
Best,
Uwe Ligges
On 11.04.2014 17:10, Alpesh Pandya wrote:
Using install.package('XML') command produces this error:
trying URL
'
http://watson.nci.nih.gov/cran_mirror/bin/windows/
contrib/3.0/XML_3.98-1.1.zip
'
Content type 'application/zip' length 4288136 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb
Error in read.dcf(file.path(pkgname, DESCRIPTION), c(Package,
Type)) :
cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = wb, ...) :
downloaded length 4276224 != reported length 4288136
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, DESCRIPTION), c(Package, Type))
:
cannot open compressed file 'XML/DESCRIPTION', probable reason 'No
such
file or directory'
Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from
cran
site. But this zip file is not a valid archive (cannot open using
winzip).
Also trying to install using this downloaded file produces the following
error:
Installing package into 'C:/Users/APandya/Documents/R/win-library/3.0'
(as 'lib' is unspecified)
Warning in install.packages :
error 1 in extracting from zip file
Warning in install.packages :
cannot open compressed file 'XML/DESCRIPTION', probable reason 'No
such
file or directory'
Error in install.packages : cannot open the connection
I downloaded this zip file from multiple sources and tried to install
with
same result.
--
Thanks and Regards
Alpesh
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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] FW: Reading output of a GLMM run in R
Hi, I am a complete novice and dummy when it comes to statistics so I apologise in advance... I have been asked to report the results of my GLMMs (I ran two) in a table. This table must state: effect, standard error, test statistic, and P value, for all fixed effects. Unfortunately I am struggling to read my output. The out put is as follows, if anyone would be kind enough to help I would be very grateful and will know for future reference which bit equates to what (also I have been told my degrees of freedom are different for both the tests, could someone explain why this is?). GLMM 1-run for predictors of step length. Response variable = step length. fixed effects = depth and direction threshold. random factor = individual Models: m2: step ~ (1 | ind) m1: step ~ Depth * threshold + (1 | ind) Df AIC BIC logLik deviance Chisq Chi Df Pr(Chisq) m2 3 373235 373259 -186615 373229 m1 8 373225 373290 -186605 373209 19.767 5 0.001382 ** --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 GLMM 2 -run to investigate potential predictors of PDBA. response variables = depth and step length. fixed effect = direction threshold. random factor = Individual Models: m3: PDBA ~ Depth + (1 | ind) + thresholdepth m2: PDBA ~ step * threshold + Depth * threshold + (1 | ind) Df AIC BIC logLik deviance Chisq Chi Df Pr(Chisq) m3 6 -48205 -48157 24109 -48217 m2 11 -48430 -48341 24226 -48452 235.1 5 2.2e-16 *** --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Models: m4: PDBA ~ step + (1 | ind) + step:threshold m2: PDBA ~ step * threshold + Depth * threshold + (1 | ind) Df AIC BIC logLik deviance Chisq Chi Df Pr(Chisq) m4 6 -48206 -48158 24109 -48218 m2 11 -48430 -48341 24226 -48452 233.81 5 2.2e-16 *** --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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.
