Re: [R] Change database in SQL Server using RODBC
Thanks for everyone’s help.
I followed the instruction given on a variety of web pages in order to
set up the connection. The problem is trying to use the first connection
for a second database and doing so from within R.
It seems to me that an easy workaround is to simply set up another
connection and use a second database as the default.
In Windows 7 the basic strategy is do the following:
Control Panel
Administrative Tools
Data Sources (ODBC)
In the ODBC Data Source Administrator pop up select SQL 2012 and then
click on Add.
Since I do not have to work with a large number of databases, I consider
this to be a satisfactory work around.
On 6/30/2014 8:17 AM, Frede Aakmann Tøgersen wrote:
Hi
I can see that you do have troubles understanding how all this works
using the RODBC package. Peter wasn't really being helpful to you.
This is something that is quite difficult to help with not sitting
beside you. Do you not having some local help from e.g. the IT department?
However for a start please let me know how you managed to get
con = odbcConnect("SQLServer2012")
to work.
It seems like that some DSN was set up.
From there we can probably find a solution.
Br. Frede
Sendt fra Samsung mobil
Oprindelig meddelelse
Fra: Ira Sharenow
Dato:30/06/2014 16.42 (GMT+01:00)
Til: Peter Crowther ,R list
Emne: Re: [R] Change database in SQL Server using RODBC
Thanks for everyone’s feedback.
library(RODBC)
con = odbcConnect("SQLServer2012")
orders1 = sqlFetch(con,"dbo.orders")
odbcClose(con)
Allowed me to close the connection properly. Thanks.
However, I still cannot figure out how to connect to the second database
and table.
library(RODBC)
>con2 = odbcConnect("[sportsDB].dbo.sports")
Warning messages:
1: In odbcDriverConnect("DSN=[sportsDB].dbo.sports") :
[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver
Manager] Data source name not found and no default driver specified
2: In odbcDriverConnect("DSN=[sportsDB].dbo.sports") :
ODBC connection failed
>con2 = odbcConnect("[sportsDB].[dbo].sports")
Warning messages:
1: In odbcDriverConnect("DSN=[sportsDB].[dbo].sports") :
[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver
Manager] Data source name not found and no default driver specified
2: In odbcDriverConnect("DSN=[sportsDB].[dbo].sports") :
ODBC connection failed
>con2 = odbcConnect("[sportsDB].[dbo].[sports]")
Warning messages:
1: In odbcDriverConnect("DSN=[sportsDB].[dbo].[sports]") :
[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver
Manager] Data source name not found and no default driver specified
2: In odbcDriverConnect("DSN=[sportsDB].[dbo].[sports]") :
ODBC connection failed
>con3 = odbcConnect("SQLServer2012")
>orders3 = sqlFetch(con3, "sportsDB.dbo.sports")
Error in odbcTableExists(channel, sqtable) :
‘sportsDB.dbo.sports’: table not found on channel
On 6/30/2014 1:34 AM, Peter Crowther wrote:
> On 30 June 2014 02:44, Ira Sharenow wrote:
>> I wish to query tables that are NOT in the default SQL Server 2012
database.
>> Now for the problem. I also want to read in the table dbo.sports. That
>> table is in the database sportsDB. I did not see any way to do so from
>> within R.
> Can you not use sportsDB.dbo.sports to reference the table?
>
> In general, table reference syntax is [ [ [ serverName '.' ]
> databaseName '.' ] [schema ] '.' ] tableName, where the names need
> only be surrounded by [...] if they are not valid SQL Server
> identifiers. Many people may suggest you reference
> [sportsDB].[dbo].[sports]; this is unnecessary verbiage.
>
> Cheers,
>
> - Peter
>
[[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] 1-dinemsional point process
Hi, As a new user, is it possible to look at clustering/dispersion processes of a 1D point process (i.e. points along a transect)? My limited understanding is that spatstat is for 2&3D point patterns. Thanks -- View this message in context: http://r.789695.n4.nabble.com/1-dinemsional-point-process-tp4693315.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.
[R] What are the other Options for hiddenActFunc in the RSNNS r package?
I am trying to figure out the options for hiddenActFunc..any help would be great!! -- View this message in context: http://r.789695.n4.nabble.com/What-are-the-other-Options-for-hiddenActFunc-in-the-RSNNS-r-package-tp4693313.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.
[R] New editions of R Books from Chapman & Hall/CRC
Take advantage of a 20% discount on new editions of the most recent R books from Chapman & Hall/CRC! June and July will be very busy for us, with new editions of some of our most popular R books publishing. We are pleased to offer a 20% discount on these titles through our website. To take advantage of this offer, simply visit www.crcpress.com, choose your titles, and insert code AJL01 in the Promotion Code field at checkout. Standard Shipping is always FREE on all orders from CRCPress.com! *** Linear Models with R, Second Edition Julian Faraway ISBN: 978-1-4398-8733-2 Publication Date: July 17, 2014 Number of pages: 286 New to the Second Edition * Reorganized material on interpreting linear models, which distinguishes the main applications of prediction and explanation and introduces elementary notions of causality * Additional topics, including QR decomposition, splines, additive models, Lasso, multiple imputation, and false discovery rates * Extensive use of the ggplot2 graphics package in addition to base graphics List Price: $89.95 / £57.99 For more details and to order: http://www.crcpress.com/product/isbn/9781439887332 *** Using R for Introductory Statistics, Second Edition John Verzani ISBN: 978-1-4665-9073-1 Publication Date: June 26, 2014 Number of pages: 518 New to the Second Edition: * Increased emphasis on more idiomatic R provides a grounding in the functionality of base R * Discussions of the use of RStudio helps new R users avoid as many pitfalls as possible * Use of knitr package makes code easier to read and therefore easier to reason about * Additional information on computer-intensive approaches motivates the traditional approach * Updated examples and data make the information current and topical List Price: $59.95 / £38.99 For more details and to order: http://www.crcpress.com/product/isbn/9781466590731 *** A Handbook of Statistical Analyses using R, Third Edition Torsten Hothorn & Brian S. Everitt ISBN: 978-1-4822-0458-2 Publication Date: June 25, 2014 Number of pages: 448 Pages New to the Third Edition: * Three new chapters on quantile regression, missing values, and Bayesian inference * Extra material in the logistic regression chapter that describes a regression model for ordered categorical response variables * Additional exercises * More detailed explanations of R code * New section in each chapter summarizing the results of the analyses * Updated version of the HSAUR package (HSAUR3), which includes some slides that can be used in introductory statistics courses List Price: $64.95 / £39.99 For more details and to order: http://www.crcpress.com/product/isbn/9781482204582 *** SAS and R: Data Management, Statistical Analysis, and Graphics, Second Edition Ken Kleinman & Nicholas J. Horton ISBN: 978-1-4665-8449-5 Publication Date: July 9, 2014 Number of pages: 468 New to the Second Edition: This edition now covers RStudio, a powerful and easy-to-use interface for R. It incorporates a number of additional topics, including using application program interfaces (APIs), accessing data through database management systems, using reproducible analysis tools, and statistical analysis with Markov chain Monte Carlo (MCMC) methods and finite mixture models. It also includes extended examples of simulations and many new examples. List Price: $79.95 / £49.99 For more details and to order: http://www.crcpress.com/product/isbn/9781466584495 *** Introduction to Scientific Programming and Simulation Using R, Second Edition Owen Jones, Robert Maillardet, Andrew Robinson ISBN: 978-1-4665-6999-7 Publication Date: June 12, 2014 Number of pages: 600 New to the Second Edition: In a new chapter on systems of ordinary differential equations (ODEs), the authors cover the Euler, midpoint, and fourth-order Runge-Kutta (RK4) schemes for solving systems of first-order ODEs. They compare the numerical efficiency of the different schemes experimentally and show how to improve the RK4 scheme by using an adaptive step size. There is also a new chapter focuses on both discrete- and continuous-time Markov chains. It describes transition and rate matrices, classification of states, limiting behaviour, Kolmogorov forward and backward equations, finite absorbing chains, and expected hitting times. It also presents methods for simulating discrete- and continuous-time chains as well as techniques for defining the state space, including lumping states and supplementary variables. List Price: $79.95 / £49.99 For more details and to order: http://www.crcpress.com/product/isbn/9781466569997 *** Linear Mixed Models: A Practical Guide Using Statistical Software, Second Edition Brady T. West, Kathleen B. Welch, Andrzej T Galecki ISBN: 978-1-4665-6099-4 Publication Date: July 24, 2014 Number of pages: 440 New to the Second Edition * A new chapter on models with crossed random effects that uses a case study to illustrate software procedures capable of fi
Re: [R] From long to wide format
HI Jorge,
I was able to reproduce the error. The link below provides a way to adjust the
stack. I didn't test it.
http://stackoverflow.com/questions/14719349/error-c-stack-usage-is-too-close-to-the-limit
Also check this link
http://stackoverflow.com/questions/13245019/how-to-change-the-stack-size-using-ulimit-or-per-process-on-mac-os-x-for-a-c-or
A.K.
On Monday, June 30, 2014 10:08 PM, Jorge I Velez
wrote:
Hi Arun,
Thank you very much for your suggestion.
While running some tests, I came across the following:
# sample data
n <- 2000
p <- 1000
x2 <- data.frame(variable = rep(paste0('x', 1:p), each = n), id =
rep(paste0('p', 1:p), n), outcome = sample(0:2, n*p, TRUE), rate = runif(n*p,
0.5, 1))
str(x2)
library(dplyr)
library(tidyr)
# Arun's suggestion
system.time({wide1 <- x2%>%
select(-rate) %>%
mutate(variable=factor(variable, levels=unique(variable)),id=factor(id,
levels=unique(id))) %>%
spread(variable,outcome)
colnames(wide1)[-1] <- paste("outcome",colnames(wide1)[-1],sep=".")
})
# Error: C stack usage 18920219 is too close to the limit
# Timing stopped at: 13.833 0.251 14.085
Do you happen to know what can be done to avoid this?
Thank you.
Best,
Jorge.-
On Mon, Jun 30, 2014 at 6:51 PM, arun wrote:
>
>Hi Jorge,
>
>You may try:
>library(dplyr)
>library(tidyr)
>
>#Looks like this is faster than the other methods.
>system.time({wide1 <- x2%>%
> select(-rate) %>%
> mutate(variable=factor(variable,
>levels=unique(variable)),id=factor(id, levels=unique(id))) %>%
> spread(variable,outcome)
>colnames(wide1)[-1] <- paste("outcome",colnames(wide1)[-1],sep=".")
>})
>
> #user system elapsed
> # 0.006 0.00 0.006
>
>
>
>system.time(wide <- reshape(x2[, -4], v.names = "outcome", idvar = "id",
> timevar = "variable", direction = "wide"))
> #user system elapsed
> # 0.169 0.000 0.169
>
>
>
>system.time({
>sel <- unique(x2$variable)
>id <- unique(x2$id)
>
>X <- matrix(NA, ncol = length(sel) + 1, nrow = length(id))
>X[, 1] <- id
>colnames(X) <- c('id', sel)
>r <- mclapply(seq_along(sel), function(i){
> out <- x2[x2$variable == sel[i], ][, 3]
> }, mc.cores = 4)
>X[, -1] <- do.call(rbind, r)
>X
>})
>
># user system elapsed
># 0.125 0.011 0.074
>
>
> wide2 <- wide1
>wide2$id <- as.character(wide2$id)
> wide$id <- as.character(wide$id)
>all.equal(wide, wide2, check.attributes=F)
>#[1] TRUE
>
>A.K.
>
>
>
>
>On Sunday, June 29, 2014 11:48 PM, Jorge I Velez
>wrote:
>Dear R-help,
>
>I am working with some data stored as "filename.txt.gz" in my working
>directory.
>After reading the data in using read.table(), I can see that each of them
>has four columns (variable, id, outcome, and rate) and the following
>structure:
>
># sample data
>x2 <- data.frame(variable = rep(paste0('x', 1:100), each = 100), id =
>rep(paste0('p', 1:100), 100), outcome = sample(0:2, 1, TRUE), rate =
>runif(1, 0.5, 1))
>str(x2)
>
>Each variable, i.e., x1, x2,..., x100 is repeated as many times as the
>number of unique IDs (100 in this example). What I would like to do is to
>transform the data above
>in a long format. I can do this by using
>
># reshape
>wide <- reshape(x2[, -4], v.names = "outcome", idvar = "id",
> timevar = "variable", direction = "wide")
>str(wide)
>
># or a "hack" with mclapply:
>
>require(parallel)
>sel <- as.character(unique(x2$variable))
>id <- as.character(unique(x2$id))
>X <- matrix(NA, ncol = length(sel) + 1, nrow = length(id))
>X[, 1] <- id
>colnames(X) <- c('id', sel)
>r <- mclapply(seq_along(sel), function(i){
> out <- x2[x2$variable == sel[i], ][, 3]
> }, mc.cores = 4)
>X[, -1] <- do.call(rbind, r)
>X
>
>However, I was wondering if it is possible to come up with another solution
>, hopefully faster than these
>. Unfortunately, either one of these takes a very long time to process,
>specially when the number of variables is very large
>(> 250,000) and the number of ids is ~2000.
>
>I would very much appreciate your suggestions. At the end of this message
>is my sessionInfo().
>
>Thank you very much in advance.
>
>Best regards,
>Jorge Velez.-
>
>
>R> sessionInfo()
>
>R version 3.0.2 Patched (2013-12-11 r64449)
>Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
>locale:
>[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
>attached base packages:
>[1] graphics grDevices utils datasets parallel compiler stats
>[8] methods base
>
>other attached packages:
>[1] knitr_1.6.3 ggplot2_1.0.0 slidifyLibraries_0.3.1
>[4] slidify_0.3.52
>
>loaded via a namespace (and not attached):
>[1] colorspace_1.2-4 digest_0.6.4 evaluate_0.5.5 formatR_0.10
>[5] grid_3.0.2 gtable_0.1.2 markdown_0.7.1 MASS_7.3-33
>[9] munsell_0.4.2 plyr_1.8.1 proto_0.3-10 Rcpp_0.11.2
>[13] reshape2_1.4 scales_0.2.4
Re: [R] matrix
Hi Izhak, If the position of the elements to be replaced follow the pattern below: seq(1,length(t), by=7) #[1] 1 8 15 t[seq(1,length(t), by=7)] <- c(50,90,100) A.K. On Monday, June 30, 2014 4:19 PM, "Adams, Jean" wrote: t[1, 1] <- 50 t[3, 2] <- 90 t[5, 3] <- 100 Jean On Mon, Jun 30, 2014 at 10:27 AM, IZHAK shabsogh wrote: > > > kindly guide me on how i can delete and replace an element from a matrix t > below > > for example delete first element in column one and replace it with 50, > third element in column 2 by 90 and fifth element in column 3 by 100 > > > t1<-c(1,2,3,4,5) > t2<-c(6,7,8,9,10) > t3<-c(11,12,13,14,15) > t<-cbind(t1,t2,t3) > > > thanks > [[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. > [[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] R Console Output
Thank you for your response. I would like to produce Flash animation with
code such as what is below.
saveSWF({
}, img.name = "file",swf.name = "file2.swf" , single.opts = "'utf8':
false", autoplay = FALSE ,
interval = 0.1, imgdir = "directory", htmlfile = "random.html", ani.height
= 500,
ani.width = 500, title = "groups",
description = c("group1", "group2"))
Usually there is output in the console where the Flash animation has been
produced such as:
Flash has been created at:
C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ\file2.swf
When I run my code, there is the output below. Yet, the Flash file is not
produced, and there is no error message. I am still able to enter commands.
Thanks in advance for your help.
Executing: "C:\Program Files (x86)\SWFTools\png2swf.exe"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file1.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file2.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file3.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file4.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file5.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file6.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file7.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file8.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file9.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00010.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00011.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00012.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00013.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00014.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00015.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00016.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00017.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00018.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00019.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00020.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00021.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00022.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00023.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00024.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00025.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00026.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00027.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00028.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00029.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00030.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00031.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00032.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00033.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00034.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00035.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00036.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00037.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00038.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00039.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00040.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00041.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00042.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00043.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00044.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00045.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00046.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00047.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00048.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00049.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00050.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00051.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00052.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00053.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00054.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00055.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00056.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00057.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00058.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00059.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00060.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00061.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00062.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00063.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00064.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00065.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00066.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00067.png"
"C:\Users\CHERYL\AppData\Local\Temp\RtmpqayKkJ/file00
[R] Must array methods be defined for user defined classes?
Here's a simple example:
setClass("foo", contains="numeric")
x <- new("foo", 4)
# Division by scalar works
> x / 2
An object of class "foo"
[1] 2
# Division by array blows up
y <- array(2, c(2, 2))
> x / y
Error in getDataPart(c(2, 2, 2, 2)) : node stack overflow
# Not sure I understand the error message, but in any case, based on
the success of ...
> x / as.numeric(y)
[1] 2 2 2 2
# ... wrote a division method for arrays, which worked.
> setMethod("/", signature = c("foo", "array"), function(e1, e2) e1 /
> as.numeric(e2))
[1] "/"
> x / y
[1] 2 2 2 2
Is it always necessary to define "array" methods for arithmetic on
user defined classes? Maybe the answer has to do with the error
message I did not understand.
Thanks,
Dan Murphy
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252LC_MONETARY=English_United States.1252 LC_NUMERIC=C
LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.1.0
>
__
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] From long to wide format
Hi Arun,
Thank you very much for your suggestion.
While running some tests, I came across the following:
# sample data
n <- 2000
p <- 1000
x2 <- data.frame(variable = rep(paste0('x', 1:p), each = n), id =
rep(paste0('p', 1:p), n), outcome = sample(0:2, n*p, TRUE), rate =
runif(n*p, 0.5, 1))
str(x2)
library(dplyr)
library(tidyr)
# Arun's suggestion
system.time({wide1 <- x2%>%
select(-rate) %>%
mutate(variable=factor(variable,
levels=unique(variable)),id=factor(id, levels=unique(id))) %>%
spread(variable,outcome)
colnames(wide1)[-1] <- paste("outcome",colnames(wide1)[-1],sep=".")
})
# Error: C stack usage 18920219 is too close to the limit
# Timing stopped at: 13.833 0.251 14.085
Do you happen to know what can be done to avoid this?
Thank you.
Best,
Jorge.-
On Mon, Jun 30, 2014 at 6:51 PM, arun wrote:
>
>
> Hi Jorge,
>
> You may try:
> library(dplyr)
> library(tidyr)
>
> #Looks like this is faster than the other methods.
> system.time({wide1 <- x2%>%
> select(-rate) %>%
> mutate(variable=factor(variable,
> levels=unique(variable)),id=factor(id, levels=unique(id)))
> %>%
> spread(variable,outcome)
> colnames(wide1)[-1] <- paste("outcome",colnames(wide1)[-1],sep=".")
> })
>
> #user system elapsed
> # 0.0060.000.006
>
>
>
> system.time(wide <- reshape(x2[, -4], v.names = "outcome", idvar = "id",
>timevar = "variable", direction = "wide"))
> #user system elapsed
> # 0.169 0.000 0.169
>
>
>
> system.time({
> sel <- unique(x2$variable)
> id <- unique(x2$id)
> X <- matrix(NA, ncol = length(sel) + 1, nrow = length(id))
> X[, 1] <- id
> colnames(X) <- c('id', sel)
> r <- mclapply(seq_along(sel), function(i){
> out <- x2[x2$variable == sel[i], ][, 3]
> }, mc.cores = 4)
> X[, -1] <- do.call(rbind, r)
> X
> })
>
> # user system elapsed
> # 0.125 0.011 0.074
>
>
> wide2 <- wide1
> wide2$id <- as.character(wide2$id)
> wide$id <- as.character(wide$id)
> all.equal(wide, wide2, check.attributes=F)
> #[1] TRUE
>
> A.K.
>
>
>
> On Sunday, June 29, 2014 11:48 PM, Jorge I Velez
> wrote:
> Dear R-help,
>
> I am working with some data stored as "filename.txt.gz" in my working
> directory.
> After reading the data in using read.table(), I can see that each of them
> has four columns (variable, id, outcome, and rate) and the following
> structure:
>
> # sample data
> x2 <- data.frame(variable = rep(paste0('x', 1:100), each = 100), id =
> rep(paste0('p', 1:100), 100), outcome = sample(0:2, 1, TRUE), rate =
> runif(1, 0.5, 1))
> str(x2)
>
> Each variable, i.e., x1, x2,..., x100 is repeated as many times as the
> number of unique IDs (100 in this example). What I would like to do is to
> transform the data above
> in a long format. I can do this by using
>
> # reshape
> wide <- reshape(x2[, -4], v.names = "outcome", idvar = "id",
> timevar = "variable", direction = "wide")
> str(wide)
>
> # or a "hack" with mclapply:
>
> require(parallel)
> sel <- as.character(unique(x2$variable))
> id <- as.character(unique(x2$id))
> X <- matrix(NA, ncol = length(sel) + 1, nrow = length(id))
> X[, 1] <- id
> colnames(X) <- c('id', sel)
> r <- mclapply(seq_along(sel), function(i){
> out <- x2[x2$variable == sel[i], ][, 3]
> }, mc.cores = 4)
> X[, -1] <- do.call(rbind, r)
> X
>
> However, I was wondering if it is possible to come up with another solution
> , hopefully faster than these
> . Unfortunately, either one of these takes a very long time to process,
> specially when the number of variables is very large
> (> 250,000) and the number of ids is ~2000.
>
> I would very much appreciate your suggestions. At the end of this message
> is my sessionInfo().
>
> Thank you very much in advance.
>
> Best regards,
> Jorge Velez.-
>
>
> R> sessionInfo()
>
> R version 3.0.2 Patched (2013-12-11 r64449)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
> attached base packages:
> [1] graphics grDevices utils datasets parallel compiler stats
> [8] methods base
>
> other attached packages:
> [1] knitr_1.6.3ggplot2_1.0.0 slidifyLibraries_0.3.1
> [4] slidify_0.3.52
>
> loaded via a namespace (and not attached):
> [1] colorspace_1.2-4 digest_0.6.4 evaluate_0.5.5 formatR_0.10
> [5] grid_3.0.2 gtable_0.1.2 markdown_0.7.1 MASS_7.3-33
> [9] munsell_0.4.2plyr_1.8.1 proto_0.3-10 Rcpp_0.11.2
> [13] reshape2_1.4 scales_0.2.4 stringr_0.6.2tools_3.0.2
> [17] whisker_0.4 yaml_2.1.13
>
> [[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-containe
Re: [R] Getting data from Table in RStudio
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Shanae Clarke > Sent: Monday, June 30, 2014 1:58 PM > To: r-help@r-project.org > Subject: [R] Getting data from Table in RStudio > > Hello, > > I am new to R progaming and have just started using this program since > last week. What i want to achieve is to use R to determine patterns in > sales/ customer complaint etc. information located in a mysql database. > I am not sure how to approach this or which technique i should use to > do so. However, i had proceeded to add a dataset to RStudio using the > following code: > library(RODBC) > dsn.name <- "MySQLlocal" > user.name <- "orange" > pwd <- "" > ch <- odbcConnect(dsn=dsn.name,uid=user.name,pwd = pwd) > res <- sqlFetch(ch, "") > odbcQuery(ch, "Select * from ") > odbcClose(ch) > > When the code is run all that is returned is > > library (RODBC) > > dsn.name <- "MySQLlocal" > > user.name <- "orange" > > pwd <- "" > > ch <- odbcConnect(dsn=dsn.name,uid=user.name,pwd = pwd) > > res <- sqlFetch(ch, "") > > odbcQuery(ch, "Select * from ") > [1] 1 > > odbcClose(ch) > > No other results. > I was expecting to see the table values or some other data. Not that. > Maybe I am misunderstanding the whole concept of how R works. > If so could someone please help me to clarify what the problem is and > perhaps point me to a tutorial or somewhere i can get a information and > get a better understanding. > > Thank you. Your Help will be greatly appreciated. > > Gayon Clarke > [[alternative HTML version deleted]] 1. For future reference, you should read the posting guide linked at the bottom of each email, and post only in plain text (no HTML). 2. You should read the help files for each of the functions you are trying use. 3. Did you try to look at the object, res, that you created? That should have contained the table that you fetched from the MySQL database. You could have typed res and the table would have printed out. You also could have used head(res) to look at the first few records, or used str(res) to examine the structure of res. There is also an R-sig-DB list where you can get more specific help with database connectivity questions. https://stat.ethz.ch/mailman/listinfo/r-sig-db Hope this is helpful, Dan Daniel J. Nordlund Research and Data Analysis Division Services & Enterprise Support Administration Washington State Department of Social and Health Services __ 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] yet another regular expression
On Mon, 30 Jun 2014 11:13:18 PM Jim Lemon wrote:
> Hi all,
> I have managed, with the help of glob2rx() to get two parts of a text
> manipulation working. I have successfully gotten rid of the first and
> second bits, but I have hit the wall trying to get rid of the last bit.
> Here's an example:
>
> initString<-
> "\"Delete this\":value1,\"Delete this too\":value2},Delete last bit"
> sub("\"Delete this too\":","",
> sub(glob2rx("*this\":*"),"",initString),fixed=TRUE)
>
> This gives me:
>
> [1] "value1,value2},Delete last bit"
>
> and glob2rx("},*") just won't get rid of the last bit. I throw myself upon
> the mercy of the regular expression gurus.
>
Hi again,
Sorry, but my "minimal reproducible example" was apparently
misleading. "value1" and "value2" are not fixed strings, but varying
numbers. After a night's sleep I solved the problem using strsplit(), which
gave me a big list of strings that I could process without wearing out the
"\" key. Thanks for the suggestions.
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.
[R] Getting data from Table in RStudio
Hello, I am new to R progaming and have just started using this program since last week. What i want to achieve is to use R to determine patterns in sales/ customer complaint etc. information located in a mysql database. I am not sure how to approach this or which technique i should use to do so. However, i had proceeded to add a dataset to RStudio using the following code: library(RODBC) dsn.name <- "MySQLlocal" user.name <- "orange" pwd <- "" ch <- odbcConnect(dsn=dsn.name,uid=user.name,pwd = pwd) res <- sqlFetch(ch, "") odbcQuery(ch, "Select * from ") odbcClose(ch) When the code is run all that is returned is > library (RODBC) > dsn.name <- "MySQLlocal" > user.name <- "orange" > pwd <- "" > ch <- odbcConnect(dsn=dsn.name,uid=user.name,pwd = pwd) > res <- sqlFetch(ch, "") > odbcQuery(ch, "Select * from ") [1] 1 > odbcClose(ch) No other results. I was expecting to see the table values or some other data. Not that. Maybe I am misunderstanding the whole concept of how R works. If so could someone please help me to clarify what the problem is and perhaps point me to a tutorial or somewhere i can get a information and get a better understanding. Thank you. Your Help will be greatly appreciated. Gayon Clarke [[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] Delaunay triangles with LONG/LAT + biomass
On 01/07/14 04:31, Trevor Davies wrote:
Hello,
I was hoping someone could point me in the direction towards a package
where I can use delaunay triangulation to create a polygon set where the
inside of the triangles are tagged with an estimate of a mean value of the
points making up the points of the triangle. This is fisheries trawl data
if that helps add context.
For those familiar with the system, it's to make plots similar to those
made by the Dept of Fisheries and Oceans Canada in ACON (which has now
stopped being maintained). Although freely available, I'm on a mac and it
would be nice to just get it sorted out in R going forward.
Ref here:
http://www2.mar.dfo-mpo.gc.ca/science/acon/Examples/ShadedContours.html
The deldir package has the capacity to tag points with values, and the
triang.list() function creates a list of data frames corresponding to
each triangle, the last column of these data frames (named "z") being
the "values" associated with the corners of the triangles.
The means of these values can be calculated using sapply().
E.g.:
set.seed(42)
x <- runif(20)
y <- runif(20)
z <- sample(1:5,20,TRUE)
dxy <- deldir(x,y,z=z)
txy <- triang.list(dxy)
mxy <- sapply(txy,function(u){mean(u[["z"]])})
You could "tag" the triangles with these mean values by assigning the
values as attributes of the components of txy, using lapply(), possibly.
Note that deldir() treats coordinates as ***Euclidean*** coordinates.
This is only an approximation to a triangulation on a sphere. Whether
the approximation is good enough is up to you, I guess.
cheers,
Rolf Turner
__
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] How to combine/join/merge etc PCA and Cluster?
Insert
data(dune)
data(dune.env)
after library(vegan)
David C.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of David L Carlson
Sent: Monday, June 30, 2014 4:47 PM
To: Jackson Rodrigues; r-help@r-project.org
Subject: Re: [R] How to combine/join/merge etc PCA and Cluster?
This is a long way from being a reproducible example with no data. You also
don't mention that you are using package vegan. I'll use the dune, dune.env
data included in that package:
library(vegan)
mydata.pca <- rda(dune)
mydata.w <- hclust(dist(dune), "ward")
plot(mydata.w, hang=-1)
rect.hclust(mydata.w, 5)
gr <- cutree(mydata.w, k=5)
# Don't need grl <- levels(factor(gr))
sit.sc1 <- scores(mydata.pca, display="w", scaling=3)
p <- plot(mydata.pca, display="wa", scaling=3, type="n",
main="Mydata PCA and clusters")
# Don't need either abline() functions since plot() adds these.
# symbol = cluster (5 groups), color = Moisture (4 groups)
# Note, pch=16 and pch=19 are the same symbol so you don't want pch=15:19
points(sit.sc1, pch=as.numeric(gr), col=as.numeric(dune.env$Moisture))
# or
points(sit.sc1, pch=as.numeric(gr)+20, bg=as.numeric(dune.env$Moisture))
# I'll skip the text labels
The legend will be complicated since there are groups*ecosytems combinations.
-
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Jackson Rodrigues
Sent: Monday, June 30, 2014 9:03 AM
To: r-help@r-project.org
Subject: [R] How to combine/join/merge etc PCA and Cluster?
Hello everybody,
I Would like to get some help to plot together, Principal Components
Analysis (PCA) and clusters.
I am handling environmental data from 25 locations spread across 5
different ecosystems.When grouped into 5 clusters, locations from different
ecosystems are arranged in the same group.
So, I want to plot together PCA and Clusters, in a such way that locations
belonging to the same ecosystem are displayed with the same COLORS, and
locations grouped in the same cluster, have the same SHAPE. For example:
I have 1 site from Savanna and 1 site from Serengeti that are in the same
cluster, Thus I would like to plot both with different colors blue and
green, respectively due different ecosystem classification and with the
same shape (triangle) because they are in the same group. So, I would have
a cluster with 2 triangles one green and another blue.
How to make this combination?
There is command lines below that I'm using to make my combination, as
presented by Bocard in Numerical Ecology Analysis with R chapter 4 or 5.
with this code, it is possible to join PCA and Cluster however, without
differentiating the colors of each ecosystem.
#PCA
mydata.pca<-rda(mydata)
#Cluster
mydata.w <- hclust(dist(Sqchord.mydata), "ward")
plot(mydata.w, hang=-1)
rect.hclust(mydata.w, 5)
# Cut the dendrogram to yield 5 groups
gr <- cutree(mydata.w, k=5)
grl <- levels(factor(gr))
# Get the site scores, scaling 1
sit.sc1 <- scores(mydata.pca, display="w", scaling=3)
# Plot the sites with cluster symbols and colours (scaling 3)
p <- plot(mydata.pca, display="wa", scaling=3, type="n",
main="Mydata PCA and clusters")
abline(v=0, lty="dotted")
abline(h=0, lty="dotted")
for (i in 1:length(grl))
{ points(sit.sc1[gr==i,], pch=(14+i), cex=2.5, col=i+1)}
text(sit.sc1, row.names(Pre_euro_veg.1.all), cex=0.7, pos=3)
# Add legend interactively
legend(locator(1), paste("Cluster", c(1:length(grl))),
pch=14+c(1:length(grl)),
col=1+c(1:length(grl)), pt.cex=2)
Thank you for any help.
Jackson Rodrigues
[[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.
__
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] How to combine/join/merge etc PCA and Cluster?
This is a long way from being a reproducible example with no data. You also
don't mention that you are using package vegan. I'll use the dune, dune.env
data included in that package:
library(vegan)
mydata.pca <- rda(dune)
mydata.w <- hclust(dist(dune), "ward")
plot(mydata.w, hang=-1)
rect.hclust(mydata.w, 5)
gr <- cutree(mydata.w, k=5)
# Don't need grl <- levels(factor(gr))
sit.sc1 <- scores(mydata.pca, display="w", scaling=3)
p <- plot(mydata.pca, display="wa", scaling=3, type="n",
main="Mydata PCA and clusters")
# Don't need either abline() functions since plot() adds these.
# symbol = cluster (5 groups), color = Moisture (4 groups)
# Note, pch=16 and pch=19 are the same symbol so you don't want pch=15:19
points(sit.sc1, pch=as.numeric(gr), col=as.numeric(dune.env$Moisture))
# or
points(sit.sc1, pch=as.numeric(gr)+20, bg=as.numeric(dune.env$Moisture))
# I'll skip the text labels
The legend will be complicated since there are groups*ecosytems combinations.
-
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Jackson Rodrigues
Sent: Monday, June 30, 2014 9:03 AM
To: r-help@r-project.org
Subject: [R] How to combine/join/merge etc PCA and Cluster?
Hello everybody,
I Would like to get some help to plot together, Principal Components
Analysis (PCA) and clusters.
I am handling environmental data from 25 locations spread across 5
different ecosystems.When grouped into 5 clusters, locations from different
ecosystems are arranged in the same group.
So, I want to plot together PCA and Clusters, in a such way that locations
belonging to the same ecosystem are displayed with the same COLORS, and
locations grouped in the same cluster, have the same SHAPE. For example:
I have 1 site from Savanna and 1 site from Serengeti that are in the same
cluster, Thus I would like to plot both with different colors blue and
green, respectively due different ecosystem classification and with the
same shape (triangle) because they are in the same group. So, I would have
a cluster with 2 triangles one green and another blue.
How to make this combination?
There is command lines below that I'm using to make my combination, as
presented by Bocard in Numerical Ecology Analysis with R chapter 4 or 5.
with this code, it is possible to join PCA and Cluster however, without
differentiating the colors of each ecosystem.
#PCA
mydata.pca<-rda(mydata)
#Cluster
mydata.w <- hclust(dist(Sqchord.mydata), "ward")
plot(mydata.w, hang=-1)
rect.hclust(mydata.w, 5)
# Cut the dendrogram to yield 5 groups
gr <- cutree(mydata.w, k=5)
grl <- levels(factor(gr))
# Get the site scores, scaling 1
sit.sc1 <- scores(mydata.pca, display="w", scaling=3)
# Plot the sites with cluster symbols and colours (scaling 3)
p <- plot(mydata.pca, display="wa", scaling=3, type="n",
main="Mydata PCA and clusters")
abline(v=0, lty="dotted")
abline(h=0, lty="dotted")
for (i in 1:length(grl))
{ points(sit.sc1[gr==i,], pch=(14+i), cex=2.5, col=i+1)}
text(sit.sc1, row.names(Pre_euro_veg.1.all), cex=0.7, pos=3)
# Add legend interactively
legend(locator(1), paste("Cluster", c(1:length(grl))),
pch=14+c(1:length(grl)),
col=1+c(1:length(grl)), pt.cex=2)
Thank you for any help.
Jackson Rodrigues
[[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] R Console Output
What do you mean by "stops"? Can you at least show what was on the console. Can you continue to enter commands? It is not clear what you are talking about. 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 Mon, Jun 30, 2014 at 10:56 AM, Cheryl Johnson < johnson.cheryl...@gmail.com> wrote: > When I run code in R, my R console output stops before all the code has > complied. There are no error messages, but there must be an error > somewhere. Thanks in advance for any guidance. > > [[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. > [[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] matrix
t[1, 1] <- 50 t[3, 2] <- 90 t[5, 3] <- 100 Jean On Mon, Jun 30, 2014 at 10:27 AM, IZHAK shabsogh wrote: > > > kindly guide me on how i can delete and replace an element from a matrix t > below > > for example delete first element in column one and replace it with 50, > third element in column 2 by 90 and fifth element in column 3 by 100 > > > t1<-c(1,2,3,4,5) > t2<-c(6,7,8,9,10) > t3<-c(11,12,13,14,15) > t<-cbind(t1,t2,t3) > > > thanks > [[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. > [[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 Console Output
When I run code in R, my R console output stops before all the code has complied. There are no error messages, but there must be an error somewhere. Thanks in advance for any guidance. [[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] How to combine/join/merge etc PCA and Cluster?
Hello everybody,
I Would like to get some help to plot together, Principal Components
Analysis (PCA) and clusters.
I am handling environmental data from 25 locations spread across 5
different ecosystems.When grouped into 5 clusters, locations from different
ecosystems are arranged in the same group.
So, I want to plot together PCA and Clusters, in a such way that locations
belonging to the same ecosystem are displayed with the same COLORS, and
locations grouped in the same cluster, have the same SHAPE. For example:
I have 1 site from Savanna and 1 site from Serengeti that are in the same
cluster, Thus I would like to plot both with different colors blue and
green, respectively due different ecosystem classification and with the
same shape (triangle) because they are in the same group. So, I would have
a cluster with 2 triangles one green and another blue.
How to make this combination?
There is command lines below that I'm using to make my combination, as
presented by Bocard in Numerical Ecology Analysis with R chapter 4 or 5.
with this code, it is possible to join PCA and Cluster however, without
differentiating the colors of each ecosystem.
#PCA
mydata.pca<-rda(mydata)
#Cluster
mydata.w <- hclust(dist(Sqchord.mydata), "ward")
plot(mydata.w, hang=-1)
rect.hclust(mydata.w, 5)
# Cut the dendrogram to yield 5 groups
gr <- cutree(mydata.w, k=5)
grl <- levels(factor(gr))
# Get the site scores, scaling 1
sit.sc1 <- scores(mydata.pca, display="w", scaling=3)
# Plot the sites with cluster symbols and colours (scaling 3)
p <- plot(mydata.pca, display="wa", scaling=3, type="n",
main="Mydata PCA and clusters")
abline(v=0, lty="dotted")
abline(h=0, lty="dotted")
for (i in 1:length(grl))
{ points(sit.sc1[gr==i,], pch=(14+i), cex=2.5, col=i+1)}
text(sit.sc1, row.names(Pre_euro_veg.1.all), cex=0.7, pos=3)
# Add legend interactively
legend(locator(1), paste("Cluster", c(1:length(grl))),
pch=14+c(1:length(grl)),
col=1+c(1:length(grl)), pt.cex=2)
Thank you for any help.
Jackson Rodrigues
[[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] matrix
kindly guide me on how i can delete and replace an element from a matrix t below for example delete first element in column one and replace it with 50, third element in column 2 by 90 and fifth element in column 3 by 100 t1<-c(1,2,3,4,5) t2<-c(6,7,8,9,10) t3<-c(11,12,13,14,15) t<-cbind(t1,t2,t3) thanks [[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] yet another regular expression
Hi Jim,
May be this helps:
library(stringr)
paste(str_extract_all(initString,
perl('(?<=\\:)[[:alnum:]]+,?'))[[1]],collapse="")
#[1] "value1,value2"
A.K.
On Monday, June 30, 2014 9:58 AM, Jim Lemon wrote:
Hi all,
I have managed, with the help of glob2rx() to get two parts of a text
manipulation working. I have successfully gotten rid of the first and
second bits, but I have hit the wall trying to get rid of the last bit. Here's
an example:
initString<-
"\"Delete this\":value1,\"Delete this too\":value2},Delete last bit"
sub("\"Delete this too\":","",
sub(glob2rx("*this\":*"),"",initString),fixed=TRUE)
This gives me:
[1] "value1,value2},Delete last bit"
and glob2rx("},*") just won't get rid of the last bit. I throw myself upon
the mercy of the regular expression gurus.
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.
__
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] Delaunay triangles with LONG/LAT + biomass
One place to start would be the "Spatial" task view on CRAN. The other would be to ask on R-sig-geo, where people who specialize in spatial data "hang out". Delaunay triangulation is available in several packages. A simple search for "delaunay" on the CRAN packages page will easily find at least one. You will also need the sp package for sure. Assigning a value to each triangle may or may not be easy, it will depend, probably among other things, on the data structure returned by whatever function you end up using to create the triangles. Based on a quick look at your acon web page, you might be happy with akima::interp Gridded Bivariate Interpolation for Irregular Data -Don -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 6/30/14 9:31 AM, "Trevor Davies" wrote: >Hello, > >I was hoping someone could point me in the direction towards a package >where I can use delaunay triangulation to create a polygon set where the >inside of the triangles are tagged with an estimate of a mean value of the >points making up the points of the triangle. This is fisheries trawl data >if that helps add context. > >For those familiar with the system, it's to make plots similar to those >made by the Dept of Fisheries and Oceans Canada in ACON (which has now >stopped being maintained). Although freely available, I'm on a mac and it >would be nice to just get it sorted out in R going forward. > >Ref here: >http://www2.mar.dfo-mpo.gc.ca/science/acon/Examples/ShadedContours.html > >Thanks for the help. >Cheers, >Trevor > > [[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] mixing grid and traditional graphics
Hi, Greg: Thanks. Just what I asked. Spencer
On 6/30/2014 10:24 AM, Greg Snow wrote:
If you really want to mix base and grid graphics (they don't play
nicely together as you have noticed) then you should really use the
gridBase package. There is at least one package for doing maps using
grid (ggmap or ggMaps or something similar) and there is the regular
text function for adding text to a base graph, either of those may be
easier than mixing.
Since you are plotting the map after the text, whether the text is
visible or not depends on the background drawn for the map, I expect
that this differs for the different devices. Would you be surprised
if you wrote some text on a piece of paper, then layed a paper map
over the top and could not read the paper? If you want the text
visible on top of the map, do the text after the map.
On Sun, Jun 29, 2014 at 5:56 PM, Spencer Graves
wrote:
I'm confused with the results I'm getting from mixing grid and
traditional graphics. A toy example appears below: The png file created by
gridFn() shows "a label" over Africa, as expected. However, when run
interactively, "a label" appears for roughly half a second, then disappears.
Can someone explain these results?
Thanks,
Spencer
gridFn <- function(){
pushViewport(plotViewport())
grid.text(label='a label')
popViewport()
map()
}
library(grid)
library(maps)
gridFn()
png('gridTst.png')
gridFn()
dev.off()
sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] maps_2.3-7
loaded via a namespace (and not attached):
[1] tools_3.1.0
__
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] standard error of survfit.coxph()
Thank you Terry for the explanation!
John
From: "Therneau, Terry M., Ph.D."
Sent: Monday, June 30, 2014 6:04 AM
Subject: Re: standard error of survfit.coxph()
1. The computations "behind the scenes" produce the variance of the cumulative
hazard.
This is true for both an ordinary Kaplan-Meier and a Cox model.
Transformations to other
scales are done using simple Taylor series.
H = cumulative hazard = log(S); S=survival
var(H) = var(log(S)) = the starting point
S = exp(log(S)), so var(S) is approx [deriv of exp(x)]^2 * var(log(S)) =
S^2 var(H)
var(log(log(S)) is approx (1/S^2) var(H)
2. At the time it was written, summary.survfit was used only for printing out
the survival
curve at selected times, and the audience for the printout wanted std(S).
True, that was
20 years ago, but I don't recall anyone ever asking for summary to do anything
else. Your
request is not a bad idea.
Note however that the primary impact of using log(S) or S or log(log(S))
scale is is on
the confidence intervals, and they do appear per request in the summary output.
Terry T.
On 06/28/2014 05:00 AM, r-help-requ...@r-project.org wrote:
> Message: 9
> Date: Fri, 27 Jun 2014 12:39:29 -0700
> To:"r-help@r-project.org"
> Subject: [R] standard error of survfit.coxph()
> Message-ID:
> <1403897969.91269.yahoomail...@web122906.mail.ne1.yahoo.com>
> Content-Type: text/plain
>
> Hi, can anyone help me to understand the standard errors printed in the
> output of survfit.coxph()?
>
> time<-sample(1:15,100,replace=T)
>
> status<-as.numeric(runif(100,0,1)<0.2)
> x<-rnorm(100,10,2)
>
> fit<-coxph(Surv(time,status)~x)
> ??? ### method 1
>
> survfit(fit, newdata=data.frame(time=time,status=status,x=x)[1:5,],
> conf.type='log')$std.err
>
> [,1]??? [,2]??? [,3]??? [,4]?? [,5]
> ?[1,] 0.0 0.0 0.0 0.0 0.
> ?[2,] 0.008627644 0.008567253 0.008773699 0.009354788 0.01481819
> ?[3,] 0.008627644 0.008567253 0.008773699 0.009354788 0.01481819
> ?[4,] 0.013800603 0.013767977 0.013889971 0.014379928 0.02353371
> ?[5,] 0.013800603 0.013767977 0.013889971 0.014379928 0.02353371
> ?[6,] 0.013800603 0.013767977 0.013889971 0.014379928 0.02353371
> ?[7,] 0.030226811 0.030423883 0.029806263 0.028918817 0.05191161
> ?[8,] 0.030226811 0.030423883 0.029806263 0.028918817 0.05191161
> ?[9,] 0.036852571 0.037159980 0.036186931 0.034645002 0.06485394
> [10,] 0.044181716 0.044621159 0.043221145 0.040872939 0.07931028
> [11,] 0.044181716 0.044621159 0.043221145 0.040872939 0.07931028
> [12,] 0.055452631 0.056018832 0.054236881 0.051586391 0.10800413
> [13,] 0.070665160 0.071363749 0.069208056 0.066655730 0.14976433
> [14,] 0.124140400 0.125564637 0.121281571 0.118002021 0.30971860
> [15,] 0.173132357 0.175309455 0.168821266 0.164860523 0.46393111
>
> survfit(fit, newdata=data.frame(time=time,status=status,x=x)[1:5,],
> conf.type='log')$time
> ?[1]? 1? 2? 3? 4? 5? 6? 7? 8? 9 10 11 12 13 14 15
>
> ??? ### method 2
>
> summary(survfit(fit, newdata=data.frame(time=time,status=status,x=x)[1:5,],
> conf.type='log'),time=10)$std.err
>
> ? 1? 2? 3? 4? 5
> [1,] 0.04061384 0.04106186 0.03963184 0.03715246 0.06867532
>
> By reading the help of ?survfit.object and ?summary.survfit, the standard
> error provided in the output of method 1 (survfit()) was for cumulative
> hazard-log(survival), while the standard error provided in the output of
> method 2 (summary.survfit()) was for survival itself, regardless of how you
> choose the value for "conf.type" ('log', 'log-log' or 'plain'). This explains
> why the standard error output is different between method 1 (10th row) and
> method 2.
>
> My question is how do I get standard error estimates for log(-log(survival))?
>
> Thanks!
>
> John
[[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] How to plot individual pdf files for each wrapped plot with ggplot2?
I think the easiest most straight forward way would be to just throw it
into a loop and subset the data on each loop around (untested code below
but I'm sure you get the gist). ~Trevor
sex1<-unique(tips$sex)
day1<-unique(tips$day)
for (i in 1:length(sex1)){
for (j in 1:length(day1)){
pdf(paste('example_',sex1[i],day1[j],'.pdf',sep=''))
data1<-subset(tips, sex==sex1[i] & day==day1[j])
sp <- ggplot(data1,aes(x=total_bill, y = tip/total_bill)) +
geom_point(shape=1)
plot(sp)
dev.off()
}
}
On Mon, Jun 30, 2014 at 10:23 AM, Bea GD wrote:
> Hi,
>
> I'm working with tips data from reshape package.
>
> library(reshape2)
>
> I'm saving my plots as pdf and I was wondering whether it was possible
> to print a different pdf for each 'wrapped' plot. Using the code below
> as an example, I'd like to get 8 independent pdf files for each sex ~
> day combination.
>
> sp <- ggplot(tips,aes(x=total_bill, y = tip/total_bill)) +
> geom_point(shape=1) +
> facet_grid(sex ~ day)
> plot(sp)
>
> Thanks a lot for your help!
>
> [[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.
>
[[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] mixing grid and traditional graphics
If you really want to mix base and grid graphics (they don't play
nicely together as you have noticed) then you should really use the
gridBase package. There is at least one package for doing maps using
grid (ggmap or ggMaps or something similar) and there is the regular
text function for adding text to a base graph, either of those may be
easier than mixing.
Since you are plotting the map after the text, whether the text is
visible or not depends on the background drawn for the map, I expect
that this differs for the different devices. Would you be surprised
if you wrote some text on a piece of paper, then layed a paper map
over the top and could not read the paper? If you want the text
visible on top of the map, do the text after the map.
On Sun, Jun 29, 2014 at 5:56 PM, Spencer Graves
wrote:
> I'm confused with the results I'm getting from mixing grid and
> traditional graphics. A toy example appears below: The png file created by
> gridFn() shows "a label" over Africa, as expected. However, when run
> interactively, "a label" appears for roughly half a second, then disappears.
>
>
> Can someone explain these results?
>
>
> Thanks,
> Spencer
>
>
> gridFn <- function(){
> pushViewport(plotViewport())
> grid.text(label='a label')
> popViewport()
> map()
> }
>
> library(grid)
> library(maps)
> gridFn()
>
> png('gridTst.png')
> gridFn()
> dev.off()
>
>
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] maps_2.3-7
>
> loaded via a namespace (and not attached):
> [1] tools_3.1.0
>>
>
> __
> 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.
--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.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.
[R] How to plot individual pdf files for each wrapped plot with ggplot2?
Hi, I'm working with tips data from reshape package. library(reshape2) I'm saving my plots as pdf and I was wondering whether it was possible to print a different pdf for each 'wrapped' plot. Using the code below as an example, I'd like to get 8 independent pdf files for each sex ~ day combination. sp <- ggplot(tips,aes(x=total_bill, y = tip/total_bill)) + geom_point(shape=1) + facet_grid(sex ~ day) plot(sp) Thanks a lot for your help! [[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] Delaunay triangles with LONG/LAT + biomass
Hello, I was hoping someone could point me in the direction towards a package where I can use delaunay triangulation to create a polygon set where the inside of the triangles are tagged with an estimate of a mean value of the points making up the points of the triangle. This is fisheries trawl data if that helps add context. For those familiar with the system, it's to make plots similar to those made by the Dept of Fisheries and Oceans Canada in ACON (which has now stopped being maintained). Although freely available, I'm on a mac and it would be nice to just get it sorted out in R going forward. Ref here: http://www2.mar.dfo-mpo.gc.ca/science/acon/Examples/ShadedContours.html Thanks for the help. Cheers, Trevor [[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] A Question about read.table and Data Frames in R
You are also missing the fact that loops are often not required in R. In this
case print() has a method for printing data frames and that method is
automatically used when you simply type the data.frame name or if you
explicitly call it with print(stockList):
> stockList <- read.table(text="symbol,shares
+ XOM,1000
+ APA,400
+ CVX,200", header = T, sep=",")
>
> stockList
symbol shares
1XOM 1000
2APA400
3CVX200
You will save yourself hours of frustration by reading some of the official and
unofficial documentation for R:
http://cran.r-project.org/manuals.html
http://www.r-project.org/other-docs.html
http://cran.r-project.org/other-docs.html
David Carlson
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of David Winsemius
Sent: Sunday, June 29, 2014 5:58 PM
To: Robert Sherry
Cc: r-help@r-project.org
Subject: Re: [R] A Question about read.table and Data Frames in R
On Jun 29, 2014, at 3:22 PM, Robert Sherry wrote:
> I created the following file:
>
> symbol,shares
> XOM,1000
> APA,400
> CVX,200
>
> I then read the file in R using the command:
> stockList=read.table("/NotesOnR/stockList", header = T, sep=",")
>
> I would then expect the following expression to evaluate to the simple
> string APA:
> stockList$symbol[2]
> However when I type that in on the command line, I get:
> [1] APA
> Levels: APA CVX XOM
>
> I would also expect to be able to print out the table by using the
> command:
> for( i in 1:3 ) {
> print( stockList$symbol[i] )
> print ( stockList$shares[i] )
> }
>
> However, as part of the output I get:
> Levels: APA CVX XOM
> I do not understand what is going on. Also, when I try passing the
> expression stockList$symbol to a standard function in R, it does not
> work.
>
> I think that I am missing something here but I am not sure what I am
> missing.
You are missing the fact that a factor variable was created. If you
had added stringsAsFactors=FALSE to your read.table code, you would
ahve gotten what you expected.
> Should I be writing code like:
> for ( i in stockList$smybol )
> However, given the symbol, I am not sure how to get the share count
> that is
> in the same row.
>
> I thank the group in advance for their responses.
>
> Bob
>
> __
> 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.
David Winsemius, MD
Alameda, CA, USA
__
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] Change database in SQL Server using RODBC
Hi
I can see that you do have troubles understanding how all this works using the
RODBC package. Peter wasn't really being helpful to you.
This is something that is quite difficult to help with not sitting beside you.
Do you not having some local help from e.g. the IT department?
However for a start please let me know how you managed to get
con = odbcConnect("SQLServer2012")
to work.
It seems like that some DSN was set up.
From there we can probably find a solution.
Br. Frede
Sendt fra Samsung mobil
Oprindelig meddelelse
Fra: Ira Sharenow
Dato:30/06/2014 16.42 (GMT+01:00)
Til: Peter Crowther ,R list
Emne: Re: [R] Change database in SQL Server using RODBC
Thanks for everyoneâs feedback.
library(RODBC)
con = odbcConnect("SQLServer2012")
orders1 = sqlFetch(con,"dbo.orders")
odbcClose(con)
Allowed me to close the connection properly. Thanks.
However, I still cannot figure out how to connect to the second database
and table.
library(RODBC)
>con2 = odbcConnect("[sportsDB].dbo.sports")
Warning messages:
1: In odbcDriverConnect("DSN=[sportsDB].dbo.sports") :
[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager]
Data source name not found and no default driver specified
2: In odbcDriverConnect("DSN=[sportsDB].dbo.sports") :
ODBC connection failed
>con2 = odbcConnect("[sportsDB].[dbo].sports")
Warning messages:
1: In odbcDriverConnect("DSN=[sportsDB].[dbo].sports") :
[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager]
Data source name not found and no default driver specified
2: In odbcDriverConnect("DSN=[sportsDB].[dbo].sports") :
ODBC connection failed
>con2 = odbcConnect("[sportsDB].[dbo].[sports]")
Warning messages:
1: In odbcDriverConnect("DSN=[sportsDB].[dbo].[sports]") :
[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager]
Data source name not found and no default driver specified
2: In odbcDriverConnect("DSN=[sportsDB].[dbo].[sports]") :
ODBC connection failed
>con3 = odbcConnect("SQLServer2012")
>orders3 = sqlFetch(con3, "sportsDB.dbo.sports")
Error in odbcTableExists(channel, sqtable) :
âsportsDB.dbo.sportsâ: table not found on channel
On 6/30/2014 1:34 AM, Peter Crowther wrote:
> On 30 June 2014 02:44, Ira Sharenow wrote:
>> I wish to query tables that are NOT in the default SQL Server 2012 database.
>> Now for the problem. I also want to read in the table dbo.sports. That
>> table is in the database sportsDB. I did not see any way to do so from
>> within R.
> Can you not use sportsDB.dbo.sports to reference the table?
>
> In general, table reference syntax is [ [ [ serverName '.' ]
> databaseName '.' ] [schema ] '.' ] tableName, where the names need
> only be surrounded by [...] if they are not valid SQL Server
> identifiers. Many people may suggest you reference
> [sportsDB].[dbo].[sports]; this is unnecessary verbiage.
>
> Cheers,
>
> - Peter
>
[[alternative HTML version deleted]]
[[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] Change database in SQL Server using RODBC
Please post here using the plain text option in your email software because the
HTML is not coming through undamaged.
The first argument to the odbcConnect function is never SQL syntax... for SQL
Server it is always a "Data Source Name" (DSN) that has been predefined in the
ODBC administration tool (control panel on Windows).
If the databases you are trying to access are managed by the same server and
your authentication gives you access to all the databases and tables that you
need access to, then you can construct SQL queries that refer to other tables
in other databases on that server using the "dot" notation mentioned by Peter,
and pass all those queries through the same DSN.
Something like
library(RODBC)
con <- odbcConnect("SQLServer2012")
orders1 <- sqlFetch(con,"sportsDB.dbo.sports")
odbcClose(con)
---
Jeff NewmillerThe . . Go Live...
DCN:Basics: ##.#. ##.#. 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 June 30, 2014 7:39:25 AM PDT, Ira Sharenow wrote:
>Thanks for everyone���s feedback.
>
>library(RODBC)
>
>con = odbcConnect("SQLServer2012")
>
>orders1 = sqlFetch(con,"dbo.orders")
>
>odbcClose(con)
>
>Allowed me to close the connection properly. Thanks.
>
>However, I still cannot figure out how to connect to the second
>database
>and table.
>
>library(RODBC)
>
>>con2 = odbcConnect("[sportsDB].dbo.sports")
>
>Warning messages:
>
>1: In odbcDriverConnect("DSN=[sportsDB].dbo.sports") :
>
>[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver
>Manager] Data source name not found and no default driver specified
>
>2: In odbcDriverConnect("DSN=[sportsDB].dbo.sports") :
>
> ODBC connection failed
>
>>con2 = odbcConnect("[sportsDB].[dbo].sports")
>
>Warning messages:
>
>1: In odbcDriverConnect("DSN=[sportsDB].[dbo].sports") :
>
>[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver
>Manager] Data source name not found and no default driver specified
>
>2: In odbcDriverConnect("DSN=[sportsDB].[dbo].sports") :
>
> ODBC connection failed
>
>>con2 = odbcConnect("[sportsDB].[dbo].[sports]")
>
>Warning messages:
>
>1: In odbcDriverConnect("DSN=[sportsDB].[dbo].[sports]") :
>
>[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver
>Manager] Data source name not found and no default driver specified
>
>2: In odbcDriverConnect("DSN=[sportsDB].[dbo].[sports]") :
>
> ODBC connection failed
>
>>con3 = odbcConnect("SQLServer2012")
>
>>orders3 = sqlFetch(con3, "sportsDB.dbo.sports")
>
>Error in odbcTableExists(channel, sqtable) :
>
> ���sportsDB.dbo.sports���: table not found on channel
>
>On 6/30/2014 1:34 AM, Peter Crowther wrote:
>> On 30 June 2014 02:44, Ira Sharenow wrote:
>>> I wish to query tables that are NOT in the default SQL Server 2012
>database.
>>> Now for the problem. I also want to read in the table dbo.sports.
>That
>>> table is in the database sportsDB. I did not see any way to do so
>from
>>> within R.
>> Can you not use sportsDB.dbo.sports to reference the table?
>>
>> In general, table reference syntax is [ [ [ serverName '.' ]
>> databaseName '.' ] [schema ] '.' ] tableName, where the names need
>> only be surrounded by [...] if they are not valid SQL Server
>> identifiers. Many people may suggest you reference
>> [sportsDB].[dbo].[sports]; this is unnecessary verbiage.
>>
>> Cheers,
>>
>> - Peter
>>
>
>
> [[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] Change database in SQL Server using RODBC
Thanks for everyoneâs feedback.
library(RODBC)
con = odbcConnect("SQLServer2012")
orders1 = sqlFetch(con,"dbo.orders")
odbcClose(con)
Allowed me to close the connection properly. Thanks.
However, I still cannot figure out how to connect to the second database
and table.
library(RODBC)
>con2 = odbcConnect("[sportsDB].dbo.sports")
Warning messages:
1: In odbcDriverConnect("DSN=[sportsDB].dbo.sports") :
[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager]
Data source name not found and no default driver specified
2: In odbcDriverConnect("DSN=[sportsDB].dbo.sports") :
ODBC connection failed
>con2 = odbcConnect("[sportsDB].[dbo].sports")
Warning messages:
1: In odbcDriverConnect("DSN=[sportsDB].[dbo].sports") :
[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager]
Data source name not found and no default driver specified
2: In odbcDriverConnect("DSN=[sportsDB].[dbo].sports") :
ODBC connection failed
>con2 = odbcConnect("[sportsDB].[dbo].[sports]")
Warning messages:
1: In odbcDriverConnect("DSN=[sportsDB].[dbo].[sports]") :
[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager]
Data source name not found and no default driver specified
2: In odbcDriverConnect("DSN=[sportsDB].[dbo].[sports]") :
ODBC connection failed
>con3 = odbcConnect("SQLServer2012")
>orders3 = sqlFetch(con3, "sportsDB.dbo.sports")
Error in odbcTableExists(channel, sqtable) :
âsportsDB.dbo.sportsâ: table not found on channel
On 6/30/2014 1:34 AM, Peter Crowther wrote:
> On 30 June 2014 02:44, Ira Sharenow wrote:
>> I wish to query tables that are NOT in the default SQL Server 2012 database.
>> Now for the problem. I also want to read in the table dbo.sports. That
>> table is in the database sportsDB. I did not see any way to do so from
>> within R.
> Can you not use sportsDB.dbo.sports to reference the table?
>
> In general, table reference syntax is [ [ [ serverName '.' ]
> databaseName '.' ] [schema ] '.' ] tableName, where the names need
> only be surrounded by [...] if they are not valid SQL Server
> identifiers. Many people may suggest you reference
> [sportsDB].[dbo].[sports]; this is unnecessary verbiage.
>
> Cheers,
>
> - Peter
>
[[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] yet another regular expression
If everything Regular Expressions could do could be done with globbing then RE
would likely not exist.
I have interpreted your problem as:
Start at the beginning of the string ("^")
match stuff that is not a colon ("[^:]")
match a colon (":')
keep stuff that is not a comma ("([^,]*)")
match a comma (",")
keep stuff that is not a right brace ("([^}]*)")
match a right brace and comma ("},")
match any characters (".*")
up to the end of the string ("$")
and then substitute that whole matched string with
the first kept match ("\\1")
a comma (",")
the second kept match ("\\2")
which gives
sub("^[^:]*:([^,]*),[^:]*:([^}]*)},.*$","\\1,\\2",initString)
The separator comma could be wrapped with the first and second kept matches in
this case to make a single kept match.. I was just methodically working my way
through your pattern finding pieces of interest.
---
Jeff NewmillerThe . . Go Live...
DCN:Basics: ##.#. ##.#. 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 June 30, 2014 6:13:18 AM PDT, Jim Lemon wrote:
>Hi all,
>I have managed, with the help of glob2rx() to get two parts of a text
>manipulation working. I have successfully gotten rid of the first and
>second bits, but I have hit the wall trying to get rid of the last bit.
>Here's
>an example:
>
>initString<-
> "\"Delete this\":value1,\"Delete this too\":value2},Delete last bit"
>sub("\"Delete this too\":","",
> sub(glob2rx("*this\":*"),"",initString),fixed=TRUE)
>
>This gives me:
>
>[1] "value1,value2},Delete last bit"
>
>and glob2rx("},*") just won't get rid of the last bit. I throw myself
>upon
>the mercy of the regular expression gurus.
>
>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.
__
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] yet another regular expression
Hi Jim
What about trying to use what you want to keep
m=gregexpr('\\":value[12]+[}]?,', initString)
regmatches(initString, m)
[[1]]
[1] "\":value1," "\":value2},"
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mac...@northnet.com.au
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Jim Lemon
Sent: Monday, 30 June 2014 23:13
To: r-help@r-project.org
Subject: [R] yet another regular expression
Hi all,
I have managed, with the help of glob2rx() to get two parts of a text
manipulation working. I have successfully gotten rid of the first and
second bits, but I have hit the wall trying to get rid of the last bit.
Here's
an example:
initString<-
"\"Delete this\":value1,\"Delete this too\":value2},Delete last bit"
sub("\"Delete this too\":","",
sub(glob2rx("*this\":*"),"",initString),fixed=TRUE)
This gives me:
[1] "value1,value2},Delete last bit"
and glob2rx("},*") just won't get rid of the last bit. I throw myself upon
the mercy of the regular expression gurus.
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.
__
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] regular expression help
Hi, Bill
Thank you so much for your kind explanation. It's very clear too for someone
like me.
I should've remember this but somehow forgot that [] have a special meaning in
regular expression.
Lin
> From: wdun...@tibco.com
> Date: Sun, 29 Jun 2014 13:16:26 -0700
> Subject: Re: [R] regular expression help
> To: bac...@hotmail.com
> CC: dwinsem...@comcast.net; r-help@r-project.org
>
>> what's the difference between [:space:]+ and[[:space:]]+ ?
>
> The pattern '[:space:]' matches any of ':', 's', 'p', 'a', 'c', and
> 'e' (the second colon is superfluous). I.e., it has no magic meaning.
> Inside of [] it does have a special meaning.
>
> The pattern '[[:space:]]' matches a space, a newline, and other
> whitespace characters. The pattern '[a-c[:space:]z[:digit:]]' matches
> 'a', 'b', 'c', any decimal digit, and any whitespace character.
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Fri, Jun 27, 2014 at 6:27 AM, C Lin wrote:
>> Thank you all for your help.
>>
>> Bill, thanks for making it compact and I did mean any amount of whitespace.
>>
>> To break it down, so I know why this pattern work:
>> The first parenthesis means that before AARSD1 it can be
>> ^: begins with nothing
>> |: or
>> //: double slash or
>> [[:space:]]+: one or more whitespace character
>>
>> For the second parenthesis:
>> $: ending with nothing
>>
>> Do this sound correct?
>>
>> I missed the fact that I need the ^ and $ and I always do [:space:]+ instead
>> of [[:space:]]+
>> what's the difference between [:space:]+ and[[:space:]]+ ?
>>
>> Thanks so much!
>> Lin
>>
>>
>>> From: wdun...@tibco.com
>>> Date: Fri, 27 Jun 2014 02:35:54 -0700
>>> Subject: Re: [R] regular expression help
>>> To: dwinsem...@comcast.net
>>> CC: bac...@hotmail.com; r-help@r-project.org
>>>
>>> You can use parentheses to factor out the common string in David's
>>> pattern, as in
>>> grep(value=TRUE, "(^|//|[[:space:]]+)AARSD1($|//|[[:space:]]+)", test)
>>>
>>> (By 'whitespace' I could not tell if you meant any amount of
>>> whitespace or a single
>>> whitespace character. I use '+' to match one or more whitespace characters.)
>>>
>>> Bill Dunlap
>>> TIBCO Software
>>> wdunlap tibco.com
>>>
>>>
>>> On Thu, Jun 26, 2014 at 10:12 PM, David Winsemius
>>> wrote:
On Jun 26, 2014, at 6:11 PM, C Lin wrote:
> Hi Duncan,
>
> Thanks for trying to help. Sorry for not being clear.
> The string I'd like to get is 'AARSD1'
> It can be followed or preceded by white space or // or nothing
>
> so, from test <- c('AARSD11','AARSD1-','AARSD1//','AARSD1
> //','//AARSD1','AARSD1');
>
> I want to match only 'AARSD1//','AARSD1 //','//AARSD1','AARSD1'
Perhaps you want jsut
grepl('^AARSD1//$|^AARSD1 //$|^//AARSD1$|^AARSD1', test)
> grepl('^AARSD1//$|^AARSD1 //$|^//AARSD1$|^AARSD1$', test)
[1] FALSE FALSE TRUE TRUE TRUE TRUE
--
David.
>
> Thanks,
> Lin
>
>
>> From: dulca...@bigpond.com
>> To: bac...@hotmail.com; r-help@r-project.org
>> Subject: RE: [R] regular expression help
>> Date: Fri, 27 Jun 2014 10:59:29 +1000
>>
>> Hi
>>
>> You only have a vector of length 5 and I am not quite sure of the string
>> you
>> are testing
>> so try this
>>
>> grep('[/]*\\[/]*',test)
>>
>> Duncan
>>
>> Duncan Mackay
>> Department of Agronomy and Soil Science
>> University of New England
>> Armidale NSW 2351
>> Email: home: mac...@northnet.com.au
>>
>> -Original Message-
>> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
>> On
>> Behalf Of C Lin
>> Sent: Friday, 27 June 2014 10:05
>> To: r-help@r-project.org
>> Subject: [R] regular expression help
>>
>> Dear R users,
>>
>> I need to match a string. It can be followed or preceded by whitespace
>> or //
>> or nothing.
>> How do I code it in R?
>>
>> For example:
>> test <- c('AARSD11','AARSD1-','AARSD1//','AARSD1 //','//AARSD1');
>> grep('AARSD1(\\s*//*)',test);
>>
>> should return 3,4,5 and 6.
>>
>
David Winsemius
Alameda, CA, USA
__
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] Population growthrate with Euler-Lotka
Thank you Simon and David for your suggestions. They were most helpful. The
Skript is now working as it was originally planed.
Greetings
Mark
Gesendet: Montag, 30. Juni 2014 um 13:06 Uhr
Von: "Simon Blomberg"
An: "Mark Christjani"
Cc: "r-help@r-project.org"
Betreff: Re: Aw: Re: [R] Population growthrate with Euler-Lotka
Hmm. Try setting extendInt="yes" in the call to uniroot. You should also
look at the help page for uniroot. help(uniroot) May give you a clue. It's
difficult for me to debug code on my iphone. Well, more difficult than
usual.
Best,
Simon.
Sent from my iPhone
On 30 Jun 2014, at 8:53 pm, "Mark Christjani" <[1]m_christj...@gmx.de>
wrote:
Thank you, Simon, for your input.
Data import works fine now, but the final equation still won`t work.
Console reads now:
> setwd("c:/Mark")
>
> table <- read.table("r-TCO-Scene-Kontrolle.csv", header=TRUE, sep=";")
>
> table
x lx mx
1 1 1.0 0.0
2 2 1.0 0.0
3 3 1.0 0.0
4 4 1.0 0.0
5 5 1.0 0.0
6 6 1.0 0.0
7 7 1.0 0.0
8 8 1.0 0.0
9 9 1.0 0.0
10 10 1.0 0.0
11 11 0.2 3.5
>
> x <- c(table$x)
> L <- c(table$lx)
> m <- c(table$mx)
> r.range<- c(0, 5)
>
> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
f() values at end points not of opposite sign
>
> res$root
Error: object 'res' not found
Any idea on this "Error in uniroot(f = eulerlotka, interval = r.range, tol =
1e-08) :
f() values at end points not of opposite sign"-matter?
Kind regards,
Mark
Gesendet: Montag, 30. Juni 2014 um 12:41 Uhr
Von: "Simon Blomberg" <[2]s.blombe...@uq.edu.au>
An: "Mark Christjani" <[3]m_christj...@gmx.de>
Cc: "[4]r-help@r-project.org" <[5]r-help@r-project.org>
Betreff: Re: [R] Population growthrate with Euler-Lotka
Your script is failing at the first hurdle because you data are not being
imported properly. You should include
header=TRUE. sep=";"
In the call to read.table.
Cheers.
Simon.
Sent from my iPhone
Sent from my iPhone
> On 30 Jun 2014, at 7:10 pm, "Mark Christjani" <[6]m_christj...@gmx.de>
wrote:
>
>
> Hi everybody,
>
> I`m Mark and I do my PhD in biology. I try using R to calculate a
population
> growth rate of animals grown on different types of food. Our workgroup has
a
> R-skript to do so, but sadly nobody, who knows how this works. I`ve never
> used R before, but got some stuff figured out myself. The skript goes:
>
> setwd("c:/Mark")
> table <- read.table("r-TCO-Scene-Kontrolle.csv")
> table
> x <- c(table$x)
> L <- c(table$lx)
> m <- c(table$mx)
> r.range<- c(0, 5)
> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> res$root
>
> I understood that the first 3 lines are simply to load my data and show it
> in the workspace console. The next 4 lines define variables of my .csv
table
> for R. Thus far, everything works fine. Now comes the Euler-Lotka
equation,
> but somehow, this does not seem to work out as supposed. I tried to find a
> solution on the internet, but I think this formula is somewhat special so
I
> could not find a suitible solution for my special problem. The console
says:
>
>
>> setwd("c:/Mark")
>>
>> table <- read.table("r-TCO-Scene-Kontrolle.csv")
>>
>> table
> V1
> 1 x;lx;mx
> 2 1;1;0
> 3 2;1;0
> 4 3;1;0
> 5 4;1;0
> 6 5;1;0
> 7 6;1;0
> 8 7;1;0
> 9 8;1;0
> 10 9;1;0
> 11 10;1;0
> 12 11;0.2;3.5
>>
>> x <- c(table$x)
>> L <- c(table$lx)
>> m <- c(table$mx)
>> r.range<- c(0, 5)
>>
>> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
>> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
> f() values at end points not of opposite sign
>>
>> res$root
>
> Does anybody have an idea how to get this running?
>
> Thanks in advance
>
> Kind regards
> Mark
> __
> [7]R-help@r-project.org mailing list
> [8]https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
[9]http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
References
1. file://localhost/tmp/m_christj...@gmx.de
2. file://localhost/tmp/s.blombe...@uq.edu.au
3. file://localhost/tmp/m_christj...@gmx.de
4. file://localhost/tmp/r-help@r-project.org
5. file://localhost/tmp/r-help@r-project.org
6. file://localhost/tmp/m_christj...@gmx.de
7. file://localhost/tmp/R-help@r-project.org
8. https:/
[R] yet another regular expression
Hi all,
I have managed, with the help of glob2rx() to get two parts of a text
manipulation working. I have successfully gotten rid of the first and
second bits, but I have hit the wall trying to get rid of the last bit. Here's
an example:
initString<-
"\"Delete this\":value1,\"Delete this too\":value2},Delete last bit"
sub("\"Delete this too\":","",
sub(glob2rx("*this\":*"),"",initString),fixed=TRUE)
This gives me:
[1] "value1,value2},Delete last bit"
and glob2rx("},*") just won't get rid of the last bit. I throw myself upon
the mercy of the regular expression gurus.
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] standard error of survfit.coxph()
1. The computations "behind the scenes" produce the variance of the cumulative hazard.
This is true for both an ordinary Kaplan-Meier and a Cox model. Transformations to other
scales are done using simple Taylor series.
H = cumulative hazard = log(S); S=survival
var(H) = var(log(S)) = the starting point
S = exp(log(S)), so var(S) is approx [deriv of exp(x)]^2 * var(log(S)) = S^2
var(H)
var(log(log(S)) is approx (1/S^2) var(H)
2. At the time it was written, summary.survfit was used only for printing out the survival
curve at selected times, and the audience for the printout wanted std(S). True, that was
20 years ago, but I don't recall anyone ever asking for summary to do anything else. Your
request is not a bad idea.
Note however that the primary impact of using log(S) or S or log(log(S)) scale is is on
the confidence intervals, and they do appear per request in the summary output.
Terry T.
On 06/28/2014 05:00 AM, r-help-requ...@r-project.org wrote:
Message: 9
Date: Fri, 27 Jun 2014 12:39:29 -0700
From: array chip
To:"r-help@r-project.org"
Subject: [R] standard error of survfit.coxph()
Message-ID:
<1403897969.91269.yahoomail...@web122906.mail.ne1.yahoo.com>
Content-Type: text/plain
Hi, can anyone help me to understand the standard errors printed in the output
of survfit.coxph()?
time<-sample(1:15,100,replace=T)
status<-as.numeric(runif(100,0,1)<0.2)
x<-rnorm(100,10,2)
fit<-coxph(Surv(time,status)~x)
??? ### method 1
survfit(fit, newdata=data.frame(time=time,status=status,x=x)[1:5,],
conf.type='log')$std.err
[,1]??? [,2]??? [,3]??? [,4]?? [,5]
?[1,] 0.0 0.0 0.0 0.0 0.
?[2,] 0.008627644 0.008567253 0.008773699 0.009354788 0.01481819
?[3,] 0.008627644 0.008567253 0.008773699 0.009354788 0.01481819
?[4,] 0.013800603 0.013767977 0.013889971 0.014379928 0.02353371
?[5,] 0.013800603 0.013767977 0.013889971 0.014379928 0.02353371
?[6,] 0.013800603 0.013767977 0.013889971 0.014379928 0.02353371
?[7,] 0.030226811 0.030423883 0.029806263 0.028918817 0.05191161
?[8,] 0.030226811 0.030423883 0.029806263 0.028918817 0.05191161
?[9,] 0.036852571 0.037159980 0.036186931 0.034645002 0.06485394
[10,] 0.044181716 0.044621159 0.043221145 0.040872939 0.07931028
[11,] 0.044181716 0.044621159 0.043221145 0.040872939 0.07931028
[12,] 0.055452631 0.056018832 0.054236881 0.051586391 0.10800413
[13,] 0.070665160 0.071363749 0.069208056 0.066655730 0.14976433
[14,] 0.124140400 0.125564637 0.121281571 0.118002021 0.30971860
[15,] 0.173132357 0.175309455 0.168821266 0.164860523 0.46393111
survfit(fit, newdata=data.frame(time=time,status=status,x=x)[1:5,],
conf.type='log')$time
?[1]? 1? 2? 3? 4? 5? 6? 7? 8? 9 10 11 12 13 14 15
??? ### method 2
summary(survfit(fit, newdata=data.frame(time=time,status=status,x=x)[1:5,],
conf.type='log'),time=10)$std.err
? 1? 2? 3? 4? 5
[1,] 0.04061384 0.04106186 0.03963184 0.03715246 0.06867532
By reading the help of ?survfit.object and ?summary.survfit, the standard error provided
in the output of method 1 (survfit()) was for cumulative hazard-log(survival), while the
standard error provided in the output of method 2 (summary.survfit()) was for survival
itself, regardless of how you choose the value for "conf.type" ('log',
'log-log' or 'plain'). This explains why the standard error output is different between
method 1 (10th row) and method 2.
My question is how do I get standard error estimates for log(-log(survival))?
Thanks!
John
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Population growthrate with Euler-Lotka
Thank you, Simon, for your input.
Data import works fine now, but the final equation still won`t work.
Console reads now:
> setwd("c:/Mark")
>
> table <- read.table("r-TCO-Scene-Kontrolle.csv", header=TRUE, sep=";")
>
> table
x lx mx
1 1 1.0 0.0
2 2 1.0 0.0
3 3 1.0 0.0
4 4 1.0 0.0
5 5 1.0 0.0
6 6 1.0 0.0
7 7 1.0 0.0
8 8 1.0 0.0
9 9 1.0 0.0
10 10 1.0 0.0
11 11 0.2 3.5
>
> x <- c(table$x)
> L <- c(table$lx)
> m <- c(table$mx)
> r.range<- c(0, 5)
>
> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
f() values at end points not of opposite sign
>
> res$root
Error: object 'res' not found
Any idea on this "Error in uniroot(f = eulerlotka, interval = r.range, tol =
1e-08) :
f() values at end points not of opposite sign"-matter?
Kind regards,
Mark
Gesendet: Montag, 30. Juni 2014 um 12:41 Uhr
Von: "Simon Blomberg"
An: "Mark Christjani"
Cc: "r-help@r-project.org"
Betreff: Re: [R] Population growthrate with Euler-Lotka
Your script is failing at the first hurdle because you data are not being
imported properly. You should include
header=TRUE. sep=";"
In the call to read.table.
Cheers.
Simon.
Sent from my iPhone
Sent from my iPhone
> On 30 Jun 2014, at 7:10 pm, "Mark Christjani" wrote:
>
>
> Hi everybody,
>
> I`m Mark and I do my PhD in biology. I try using R to calculate a
population
> growth rate of animals grown on different types of food. Our workgroup has
a
> R-skript to do so, but sadly nobody, who knows how this works. I`ve never
> used R before, but got some stuff figured out myself. The skript goes:
>
> setwd("c:/Mark")
> table <- read.table("r-TCO-Scene-Kontrolle.csv")
> table
> x <- c(table$x)
> L <- c(table$lx)
> m <- c(table$mx)
> r.range<- c(0, 5)
> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> res$root
>
> I understood that the first 3 lines are simply to load my data and show it
> in the workspace console. The next 4 lines define variables of my .csv
table
> for R. Thus far, everything works fine. Now comes the Euler-Lotka
equation,
> but somehow, this does not seem to work out as supposed. I tried to find a
> solution on the internet, but I think this formula is somewhat special so
I
> could not find a suitible solution for my special problem. The console
says:
>
>
>> setwd("c:/Mark")
>>
>> table <- read.table("r-TCO-Scene-Kontrolle.csv")
>>
>> table
> V1
> 1 x;lx;mx
> 2 1;1;0
> 3 2;1;0
> 4 3;1;0
> 5 4;1;0
> 6 5;1;0
> 7 6;1;0
> 8 7;1;0
> 9 8;1;0
> 10 9;1;0
> 11 10;1;0
> 12 11;0.2;3.5
>>
>> x <- c(table$x)
>> L <- c(table$lx)
>> m <- c(table$mx)
>> r.range<- c(0, 5)
>>
>> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
>> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
> f() values at end points not of opposite sign
>>
>> res$root
>
> Does anybody have an idea how to get this running?
>
> Thanks in advance
>
> Kind regards
> Mark
> __
> R-help@r-project.org mailing list
> [1]https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
[2]http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
References
1. https://stat.ethz.ch/mailman/listinfo/r-help
2. http://www.R-project.org/posting-guide.html
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Population growthrate with Euler-Lotka
There may be something wrong with your data: in all but one case you have lx=1
and mx=0. Uniroot may be having difficulty because of this.
Simon.
Sent from my iPhone
> On 30 Jun 2014, at 9:09 pm, "Simon Blomberg" wrote:
>
> Hmm. Try setting extendInt="yes" in the call to uniroot. You should also look
> at the help page for uniroot. help(uniroot) May give you a clue. It's
> difficult for me to debug code on my iphone. Well, more difficult than usual.
>
> Best,
>
> Simon.
>
> Sent from my iPhone
>
> On 30 Jun 2014, at 8:53 pm, "Mark Christjani"
> mailto:m_christj...@gmx.de>> wrote:
>
> Thank you, Simon, for your input.
>
> Data import works fine now, but the final equation still won`t work.
>
> Console reads now:
>
>> setwd("c:/Mark")
>>
>> table <- read.table("r-TCO-Scene-Kontrolle.csv", header=TRUE, sep=";")
>>
>> table
>x lx mx
> 1 1 1.0 0.0
> 2 2 1.0 0.0
> 3 3 1.0 0.0
> 4 4 1.0 0.0
> 5 5 1.0 0.0
> 6 6 1.0 0.0
> 7 7 1.0 0.0
> 8 8 1.0 0.0
> 9 9 1.0 0.0
> 10 10 1.0 0.0
> 11 11 0.2 3.5
>>
>> x <- c(table$x)
>> L <- c(table$lx)
>> m <- c(table$mx)
>> r.range<- c(0, 5)
>>
>> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
>> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
> f() values at end points not of opposite sign
>>
>> res$root
> Error: object 'res' not found
>
> Any idea on this "Error in uniroot(f = eulerlotka, interval = r.range, tol =
> 1e-08) :
> f() values at end points not of opposite sign"-matter?
>
> Kind regards,
> Mark
>
>
>
> Gesendet: Montag, 30. Juni 2014 um 12:41 Uhr
> Von: "Simon Blomberg" mailto:s.blombe...@uq.edu.au>>
> An: "Mark Christjani" mailto:m_christj...@gmx.de>>
> Cc: "r-help@r-project.org"
> mailto:r-help@r-project.org>>
> Betreff: Re: [R] Population growthrate with Euler-Lotka
> Your script is failing at the first hurdle because you data are not being
> imported properly. You should include
>
> header=TRUE. sep=";"
>
> In the call to read.table.
>
> Cheers.
>
> Simon.
>
> Sent from my iPhone
>
> Sent from my iPhone
>> On 30 Jun 2014, at 7:10 pm, "Mark Christjani"
>> mailto:m_christj...@gmx.de>> wrote:
>>
>>
>> Hi everybody,
>>
>> I`m Mark and I do my PhD in biology. I try using R to calculate a population
>> growth rate of animals grown on different types of food. Our workgroup has a
>> R-skript to do so, but sadly nobody, who knows how this works. I`ve never
>> used R before, but got some stuff figured out myself. The skript goes:
>>
>> setwd("c:/Mark")
>> table <- read.table("r-TCO-Scene-Kontrolle.csv")
>> table
>> x <- c(table$x)
>> L <- c(table$lx)
>> m <- c(table$mx)
>> r.range<- c(0, 5)
>> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
>> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
>> res$root
>>
>> I understood that the first 3 lines are simply to load my data and show it
>> in the workspace console. The next 4 lines define variables of my .csv table
>> for R. Thus far, everything works fine. Now comes the Euler-Lotka equation,
>> but somehow, this does not seem to work out as supposed. I tried to find a
>> solution on the internet, but I think this formula is somewhat special so I
>> could not find a suitible solution for my special problem. The console says:
>>
>>
>>> setwd("c:/Mark")
>>>
>>> table <- read.table("r-TCO-Scene-Kontrolle.csv")
>>>
>>> table
>> V1
>> 1 x;lx;mx
>> 2 1;1;0
>> 3 2;1;0
>> 4 3;1;0
>> 5 4;1;0
>> 6 5;1;0
>> 7 6;1;0
>> 8 7;1;0
>> 9 8;1;0
>> 10 9;1;0
>> 11 10;1;0
>> 12 11;0.2;3.5
>>>
>>> x <- c(table$x)
>>> L <- c(table$lx)
>>> m <- c(table$mx)
>>> r.range<- c(0, 5)
>>>
>>> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
>>> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
>> Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
>> f() values at end points not of opposite sign
>>>
>>> res$root
>>
>> Does anybody have an idea how to get this running?
>>
>> Thanks in advance
>>
>> Kind regards
>> Mark
>> __
>> 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.
>
>[[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 co
Re: [R] Population growthrate with Euler-Lotka
Mark - good on you for jumping into R with both feet.
In addition to Simon's advice, the error message you are getting means
that the two endpoints (r.range in your case) do not give function
values that are of the opposite sign and so either the function has no
roots on the interval or has and even number of roots on the interval
(2,4,6,...). Neither situation is good for your case because uniroot
finds the single root (where the y-value = 0) on the interval. Once the
reading issues are settled, try narrowing or expanding the r.range. A
good way to find a proper r.range is to plot the function vs. r and
locate the range of r where the function crosses zero. Then use the
region of r around that point as your r.range. You also learn a lot
about that function by studying that plot.
Regards
David
On 6/30/2014 1:39 AM, Mark Christjani wrote:
Hi everybody,
I`m Mark and I do my PhD in biology. I try using R to calculate a population
growth rate of animals grown on different types of food. Our workgroup has a
R-skript to do so, but sadly nobody, who knows how this works. I`ve never
used R before, but got some stuff figured out myself. The skript goes:
setwd("c:/Mark")
table <- read.table("r-TCO-Scene-Kontrolle.csv")
table
x <- c(table$x)
L <- c(table$lx)
m <- c(table$mx)
r.range<- c(0, 5)
eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
res$root
I understood that the first 3 lines are simply to load my data and show it
in the workspace console. The next 4 lines define variables of my .csv table
for R. Thus far, everything works fine. Now comes the Euler-Lotka equation,
but somehow, this does not seem to work out as supposed. I tried to find a
solution on the internet, but I think this formula is somewhat special so I
could not find a suitible solution for my special problem. The console says:
> setwd("c:/Mark")
>
> table <- read.table("r-TCO-Scene-Kontrolle.csv")
>
> table
V1
1 x;lx;mx
2 1;1;0
3 2;1;0
4 3;1;0
5 4;1;0
6 5;1;0
7 6;1;0
8 7;1;0
9 8;1;0
10 9;1;0
11 10;1;0
12 11;0.2;3.5
>
> x <- c(table$x)
> L <- c(table$lx)
> m <- c(table$mx)
> r.range<- c(0, 5)
>
> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
f() values at end points not of opposite sign
>
> res$root
Does anybody have an idea how to get this running?
Thanks in advance
Kind regards
Mark
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
David K Stevens, P.E., Ph.D.
Professor and Head, Environmental Engineering
Civil and Environmental Engineering
Utah Water Research Laboratory
8200 Old Main Hill
Logan, UT 84322-8200
435 797 3229 - voice
435 797 1363 - fax
david.stev...@usu.edu
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Population growthrate with Euler-Lotka
Hmm. Try setting extendInt="yes" in the call to uniroot. You should also look
at the help page for uniroot. help(uniroot) May give you a clue. It's difficult
for me to debug code on my iphone. Well, more difficult than usual.
Best,
Simon.
Sent from my iPhone
On 30 Jun 2014, at 8:53 pm, "Mark Christjani"
mailto:m_christj...@gmx.de>> wrote:
Thank you, Simon, for your input.
Data import works fine now, but the final equation still won`t work.
Console reads now:
> setwd("c:/Mark")
>
> table <- read.table("r-TCO-Scene-Kontrolle.csv", header=TRUE, sep=";")
>
> table
x lx mx
1 1 1.0 0.0
2 2 1.0 0.0
3 3 1.0 0.0
4 4 1.0 0.0
5 5 1.0 0.0
6 6 1.0 0.0
7 7 1.0 0.0
8 8 1.0 0.0
9 9 1.0 0.0
10 10 1.0 0.0
11 11 0.2 3.5
>
> x <- c(table$x)
> L <- c(table$lx)
> m <- c(table$mx)
> r.range<- c(0, 5)
>
> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
f() values at end points not of opposite sign
>
> res$root
Error: object 'res' not found
Any idea on this "Error in uniroot(f = eulerlotka, interval = r.range, tol =
1e-08) :
f() values at end points not of opposite sign"-matter?
Kind regards,
Mark
Gesendet: Montag, 30. Juni 2014 um 12:41 Uhr
Von: "Simon Blomberg" mailto:s.blombe...@uq.edu.au>>
An: "Mark Christjani" mailto:m_christj...@gmx.de>>
Cc: "r-help@r-project.org"
mailto:r-help@r-project.org>>
Betreff: Re: [R] Population growthrate with Euler-Lotka
Your script is failing at the first hurdle because you data are not being
imported properly. You should include
header=TRUE. sep=";"
In the call to read.table.
Cheers.
Simon.
Sent from my iPhone
Sent from my iPhone
> On 30 Jun 2014, at 7:10 pm, "Mark Christjani"
> mailto:m_christj...@gmx.de>> wrote:
>
>
> Hi everybody,
>
> I`m Mark and I do my PhD in biology. I try using R to calculate a population
> growth rate of animals grown on different types of food. Our workgroup has a
> R-skript to do so, but sadly nobody, who knows how this works. I`ve never
> used R before, but got some stuff figured out myself. The skript goes:
>
> setwd("c:/Mark")
> table <- read.table("r-TCO-Scene-Kontrolle.csv")
> table
> x <- c(table$x)
> L <- c(table$lx)
> m <- c(table$mx)
> r.range<- c(0, 5)
> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> res$root
>
> I understood that the first 3 lines are simply to load my data and show it
> in the workspace console. The next 4 lines define variables of my .csv table
> for R. Thus far, everything works fine. Now comes the Euler-Lotka equation,
> but somehow, this does not seem to work out as supposed. I tried to find a
> solution on the internet, but I think this formula is somewhat special so I
> could not find a suitible solution for my special problem. The console says:
>
>
>> setwd("c:/Mark")
>>
>> table <- read.table("r-TCO-Scene-Kontrolle.csv")
>>
>> table
> V1
> 1 x;lx;mx
> 2 1;1;0
> 3 2;1;0
> 4 3;1;0
> 5 4;1;0
> 6 5;1;0
> 7 6;1;0
> 8 7;1;0
> 9 8;1;0
> 10 9;1;0
> 11 10;1;0
> 12 11;0.2;3.5
>>
>> x <- c(table$x)
>> L <- c(table$lx)
>> m <- c(table$mx)
>> r.range<- c(0, 5)
>>
>> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
>> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
> f() values at end points not of opposite sign
>>
>> res$root
>
> Does anybody have an idea how to get this running?
>
> Thanks in advance
>
> Kind regards
> Mark
> __
> 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.
[[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] x,y scatterplots, with averaging by a column
On Mon, 30 Jun 2014 10:42:28 AM Tim Richter-Heitmann wrote:
> Hallo!
>
> I have this matrix:
>
> SampleID, Day, Species1, Species2,Species3,...,Speciesn
> 1,Monday,abundance values
> 2,Monday,abundance values
> 11,Tuesday,abundance values
> 12,Tuesday,abundance values
> 21,Wednesday,abundance values
> 22,Wednesday,abundance values
>
> I would like to plot the Days on the x-axis, and the species
abundance
> data on the y-axis. Each pair of values (i just have two
measurements
> for each day) should be represented by their mean with absolute
error
> bars (so we have basically a vertical min,max-range) and whiskers.
The
> means for each Species observation should be connected with lines.
> Also of interest would be annotating the whispers with their sample
ID
> (because the whiskers basically represent the values for y1,2
(11,12;
> 21,22)).
Hi Tim,
I think this might get you started:
trhdf<-data.frame(SampleID=seq(0,50,by=10)+(1:2),
Day=factor(rep( c("Monday","Tuesday","Wednesday",
"Thursday","Friday","Saturday"),
each=2),levels=c("Monday","Tuesday","Wednesday",
"Thursday","Friday","Saturday")),
Species1=sample(0:20,12),Species2=sample(0:20,12),
Species3=sample(0:20,12),Species4=sample(0:20,12),
Species5=sample(0:20,12))
rollfunc<-function(x,FUN="mean",roll=2) {
lenx<-length(x)
xmeans<-rep(NA,lenx/2)
start<-1
for(xm in 1:(lenx/2)) {
xmeans[xm]<-do.call(FUN,list(x[start:(start+roll-1)]))
start<-start+roll
}
return(xmeans)
}
xpos<-rep(1:6,5)+seq(-0.4,0.4,by=0.2)
ypos<-as.vector(sapply(trhdf[,3:7],rollfunc))
ymin<-as.vector(sapply(trhdf[,3:7],rollfunc,"min"))
ymax<-as.vector(sapply(trhdf[,3:7],rollfunc,"max"))
library(plotrix)
plot(xpos,ypos,pch=c("1","2","3","4","5"),ylim=c(0,20),
xaxt="n",xlab="Day",ylab="Abundance")
dispersion(xpos,ypos,ymax,ymin,interval=FALSE)
staxlab(1,at=1:6,
labels=c("Monday","Tuesday","Wednesday",
"Thursday","Friday","Saturday"))
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.
[R] solving pde with given boundary condition (heat equation)
Dear R-helpers, I have 3 thermometers measuring soil temperature at 3 levels every 10 minutes. I want to determine the soil diffusivity, by solving the heat equation. The heat equation is a partial differential equation. In my case, the initial values are know and the boundary conditions are given by 2 time series: Tz1 and Tz3. These are measured temperatures at 2 levels. I tried deSolve and bvpSolve, but apparently they do not provide a numerical solution for this kind of boundary conditions (dirichlet boundary condition?). Help would be appreciated, since my calculus was selectively forgotten some 10 years ago All the best, J -- José Miguel Delgado Lisboa Portugal [[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] Population growthrate with Euler-Lotka
Your script is failing at the first hurdle because you data are not being
imported properly. You should include
header=TRUE. sep=";"
In the call to read.table.
Cheers.
Simon.
Sent from my iPhone
Sent from my iPhone
> On 30 Jun 2014, at 7:10 pm, "Mark Christjani" wrote:
>
>
> Hi everybody,
>
> I`m Mark and I do my PhD in biology. I try using R to calculate a population
> growth rate of animals grown on different types of food. Our workgroup has a
> R-skript to do so, but sadly nobody, who knows how this works. I`ve never
> used R before, but got some stuff figured out myself. The skript goes:
>
> setwd("c:/Mark")
> table <- read.table("r-TCO-Scene-Kontrolle.csv")
> table
> x <- c(table$x)
> L <- c(table$lx)
> m <- c(table$mx)
> r.range<- c(0, 5)
> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> res$root
>
> I understood that the first 3 lines are simply to load my data and show it
> in the workspace console. The next 4 lines define variables of my .csv table
> for R. Thus far, everything works fine. Now comes the Euler-Lotka equation,
> but somehow, this does not seem to work out as supposed. I tried to find a
> solution on the internet, but I think this formula is somewhat special so I
> could not find a suitible solution for my special problem. The console says:
>
>
>> setwd("c:/Mark")
>>
>> table <- read.table("r-TCO-Scene-Kontrolle.csv")
>>
>> table
> V1
> 1 x;lx;mx
> 2 1;1;0
> 3 2;1;0
> 4 3;1;0
> 5 4;1;0
> 6 5;1;0
> 7 6;1;0
> 8 7;1;0
> 9 8;1;0
> 10 9;1;0
> 11 10;1;0
> 12 11;0.2;3.5
>>
>> x <- c(table$x)
>> L <- c(table$lx)
>> m <- c(table$mx)
>> r.range<- c(0, 5)
>>
>> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
>> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
> f() values at end points not of opposite sign
>>
>> res$root
>
> Does anybody have an idea how to get this running?
>
> Thanks in advance
>
> Kind regards
> Mark
> __
> 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] merge question
Rolf, I hear you. But, after reflection, ie I looked at my situation again, it is great :-)-O el Sent from Dr Lisse's iPad mini > On Jun 30, 2014, at 0:48, Rolf Turner wrote: > > >> On 30/06/14 10:32, Dr Eberhard W Lisse wrote: >> >> Thanks, >> >> I then set NA to 0, and can do the sutraction, >> >> great. > > Not so great. I haven't gone through the issues underlying this post, but > replacing NA by 0 will almost surely yield nonsense. "Missing" is ***not*** > the same thing as "zero". Pretending that it is will have disastrous > consequences. Think through what you are trying to do more clearly. > > cheers, > > Rolf Turner __ 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] convergence warning in betamix()
Hi, I am running some rather complex mixtures of beta regressions using the betamix() command from the betareg package (V. 3.0-4). If I am doing exploratory regressions with only one random starting value (nstart=1) I obtain results which converge after about 100 iterations. However, if I run regressions with nstart=100 random starting values I obtain solutions amended with a warning that no convergence resulted after 200 iterations. I conclude that 1) the initial regression converges to a local optimum, 2) the likelihood function is flat. However, at least in theory the EM algorithm should converge to an optimum. Thus, I am wondering about the meaning of the warning: does it mean "no convergence at all, i.e. after 5000 iterations of the BFGS algorithm" or convergence but after more than 200 iterations? Moreover, is there a way out the flat trap? I have started to experiment with the SANN algorithm within the betamix() function but it is slow (as expected)... Thanks for any hints Chris -- View this message in context: http://r.789695.n4.nabble.com/convergence-warning-in-betamix-tp4693249.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] From long to wide format
Hi Jorge,
You may try:
library(dplyr)
library(tidyr)
#Looks like this is faster than the other methods.
system.time({wide1 <- x2%>%
select(-rate) %>%
mutate(variable=factor(variable, levels=unique(variable)),id=factor(id,
levels=unique(id))) %>%
spread(variable,outcome)
colnames(wide1)[-1] <- paste("outcome",colnames(wide1)[-1],sep=".")
})
#user system elapsed
# 0.006 0.00 0.006
system.time(wide <- reshape(x2[, -4], v.names = "outcome", idvar = "id",
timevar = "variable", direction = "wide"))
#user system elapsed
# 0.169 0.000 0.169
system.time({
sel <- unique(x2$variable)
id <- unique(x2$id)
X <- matrix(NA, ncol = length(sel) + 1, nrow = length(id))
X[, 1] <- id
colnames(X) <- c('id', sel)
r <- mclapply(seq_along(sel), function(i){
out <- x2[x2$variable == sel[i], ][, 3]
}, mc.cores = 4)
X[, -1] <- do.call(rbind, r)
X
})
# user system elapsed
# 0.125 0.011 0.074
wide2 <- wide1
wide2$id <- as.character(wide2$id)
wide$id <- as.character(wide$id)
all.equal(wide, wide2, check.attributes=F)
#[1] TRUE
A.K.
On Sunday, June 29, 2014 11:48 PM, Jorge I Velez
wrote:
Dear R-help,
I am working with some data stored as "filename.txt.gz" in my working
directory.
After reading the data in using read.table(), I can see that each of them
has four columns (variable, id, outcome, and rate) and the following
structure:
# sample data
x2 <- data.frame(variable = rep(paste0('x', 1:100), each = 100), id =
rep(paste0('p', 1:100), 100), outcome = sample(0:2, 1, TRUE), rate =
runif(1, 0.5, 1))
str(x2)
Each variable, i.e., x1, x2,..., x100 is repeated as many times as the
number of unique IDs (100 in this example). What I would like to do is to
transform the data above
in a long format. I can do this by using
# reshape
wide <- reshape(x2[, -4], v.names = "outcome", idvar = "id",
timevar = "variable", direction = "wide")
str(wide)
# or a "hack" with mclapply:
require(parallel)
sel <- as.character(unique(x2$variable))
id <- as.character(unique(x2$id))
X <- matrix(NA, ncol = length(sel) + 1, nrow = length(id))
X[, 1] <- id
colnames(X) <- c('id', sel)
r <- mclapply(seq_along(sel), function(i){
out <- x2[x2$variable == sel[i], ][, 3]
}, mc.cores = 4)
X[, -1] <- do.call(rbind, r)
X
However, I was wondering if it is possible to come up with another solution
, hopefully faster than these
. Unfortunately, either one of these takes a very long time to process,
specially when the number of variables is very large
(> 250,000) and the number of ids is ~2000.
I would very much appreciate your suggestions. At the end of this message
is my sessionInfo().
Thank you very much in advance.
Best regards,
Jorge Velez.-
R> sessionInfo()
R version 3.0.2 Patched (2013-12-11 r64449)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] graphics grDevices utils datasets parallel compiler stats
[8] methods base
other attached packages:
[1] knitr_1.6.3 ggplot2_1.0.0 slidifyLibraries_0.3.1
[4] slidify_0.3.52
loaded via a namespace (and not attached):
[1] colorspace_1.2-4 digest_0.6.4 evaluate_0.5.5 formatR_0.10
[5] grid_3.0.2 gtable_0.1.2 markdown_0.7.1 MASS_7.3-33
[9] munsell_0.4.2 plyr_1.8.1 proto_0.3-10 Rcpp_0.11.2
[13] reshape2_1.4 scales_0.2.4 stringr_0.6.2 tools_3.0.2
[17] whisker_0.4 yaml_2.1.13
[[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.
[R] x,y scatterplots, with averaging by a column
Hallo! I have this matrix: SampleID, Day, Species1, Species2,Species3,...,Speciesn 1,Monday,abundance values 2,Monday,abundance values 11,Tuesday,abundance values 12,Tuesday,abundance values 21,Wednesday,abundance values 22,Wednesday,abundance values I would like to plot the Days on the x-axis, and the species abundance data on the y-axis. Each pair of values (i just have two measurements for each day) should be represented by their mean with absolute error bars (so we have basically a vertical min,max-range) and whiskers. The means for each Species observation should be connected with lines. Also of interest would be annotating the whispers with their sample ID (because the whiskers basically represent the values for y1,2 (11,12; 21,22)). Any help is welcome! I am new to R, so please bear with me. Thank you! -- Tim Richter-Heitmann (M.Sc.) PhD Candidate International Max-Planck Research School for Marine Microbiology University of Bremen Microbial Ecophysiology Group (AG Friedrich) FB02 - Biologie/Chemie Leobener Straße (NW2 A2130) D-28359 Bremen Tel.: 0049(0)421 218-63062 Fax: 0049(0)421 218-63069 __ 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] getPairListElement()
hi. "Writing R Extensions" provides a simple routine getListElement(),
said to be based on a similar routine in the package stats, for C code
to call to find a named element of a list . however, it doesn't work
for the argument list passed to a .External(), as that is a PairList
rather than a List.
below is a simple reworking (with slightly different semantics) that
appears to work with PairLists. the argument "cmd" is used in producing
an error() in the case where this the requested element is not found.
(the original getListElement() would return R_NilValue, but for *my* use
i found throwing the error easier at this lower level; possibly i should
have parameterized that behavior.)
here is an example of use:
static SEXP
rimageread(SEXP args) {
...
file = CHAR(STRING_ELT(getPairListElement(args, "file", "rimageread"), 0));
usemagick = LOGICAL(getPairListElement(args, "usemagickwand",
"rimageread"))[0];
...
}
anyway, in the hope this may be of some use to someone.
cheers, Greg Minshall
/* get the list element named str, or report an error() */
static SEXP
getPairListElement(SEXP pairs, const char *str, const char *cmd) {
for (pairs = CDR(pairs); pairs != R_NilValue; pairs = CDR(pairs)) {
if (!isNull(TAG(pairs))) {
if (strcmp(CHAR(PRINTNAME(TAG(pairs))), str) == 0) {
return CAR(pairs);
}
}
}
error("%s: required parameter '%s' not specified", cmd, str);
/*NOTREACHED*/
}
__
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] Population growthrate with Euler-Lotka
Hi everybody,
I`m Mark and I do my PhD in biology. I try using R to calculate a population
growth rate of animals grown on different types of food. Our workgroup has a
R-skript to do so, but sadly nobody, who knows how this works. I`ve never
used R before, but got some stuff figured out myself. The skript goes:
setwd("c:/Mark")
table <- read.table("r-TCO-Scene-Kontrolle.csv")
table
x <- c(table$x)
L <- c(table$lx)
m <- c(table$mx)
r.range<- c(0, 5)
eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
res$root
I understood that the first 3 lines are simply to load my data and show it
in the workspace console. The next 4 lines define variables of my .csv table
for R. Thus far, everything works fine. Now comes the Euler-Lotka equation,
but somehow, this does not seem to work out as supposed. I tried to find a
solution on the internet, but I think this formula is somewhat special so I
could not find a suitible solution for my special problem. The console says:
> setwd("c:/Mark")
>
> table <- read.table("r-TCO-Scene-Kontrolle.csv")
>
> table
V1
1 x;lx;mx
2 1;1;0
3 2;1;0
4 3;1;0
5 4;1;0
6 5;1;0
7 6;1;0
8 7;1;0
9 8;1;0
10 9;1;0
11 10;1;0
12 11;0.2;3.5
>
> x <- c(table$x)
> L <- c(table$lx)
> m <- c(table$mx)
> r.range<- c(0, 5)
>
> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
f() values at end points not of opposite sign
>
> res$root
Does anybody have an idea how to get this running?
Thanks in advance
Kind regards
Mark
__
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] perform a double poisson in R
Good morning,
for my data I've perform a Quasi-Poisson distribution and now I want to
perform a Double Poisson distribution
Could someone tell me if it is possible and how do it in R
I attach below my data
Tanks for help, best regards
Roberta Marino
> intdata<- read.table("dati-traffico-guide.dat")
> intdata
V1 V2 V3 V4 V5
1 1 4 4 21.193913 3.053714
2 2 4 2 8.400438 2.128284
3 3 4 0 20.443000 3.017641
4 4 3 3 14.434567 2.669626
5 5 3 5 28.549402 3.351636
6 6 5 2 8.400438 2.128284
7 7 4 1 3.329605 1.202854
8 8 3 4 21.193913 3.053714
9 9 4 3 14.434567 2.669626
10 10 5 1 3.329605 1.202854
11 11 4 3 14.434567 2.669626
12 12 5 1 3.329605 1.202854
13 13 4 1 3.329605 1.202854
14 14 3 3 14.434567 2.669626
15 15 3 2 8.400438 2.128284
16 16 4 4 21.193913 3.053714
17 17 5 5 28.549402 3.351636
18 18 5 1 3.329605 1.202854
19 19 4 2 8.400438 2.128284
20 20 3 6 36.417738 3.595056
21 21 5 3 14.434567 2.669626
22 22 4 4 21.193913 3.053714
23 23 4 3 14.434567 2.669626
24 24 4 6 36.417738 3.595056
25 25 4 5 28.549402 3.351636
26 26 5 1 3.329605 1.202854
27 27 4 0 15.678000 2.752258
28 28 4 3 14.434567 2.669626
29 29 4 2 8.400438 2.128284
30 30 4 1 3.329605 1.202854
31 31 4 7 44.739851 3.800865
32 32 4 6 36.417738 3.595056
33 33 5 5 28.549402 3.351636
34 34 5 3 14.434567 2.669626
35 35 4 3 14.434567 2.669626
36 36 4 2 8.400438 2.128284
37 37 5 4 21.193913 3.053714
38 38 5 4 21.193913 3.053714
39 39 4 5 28.549402 3.351636
40 40 4 3 14.434567 2.669626
41 41 4 2 8.400438 2.128284
42 42 4 6 36.417738 3.595056
43 43 5 2 8.400438 2.128284
44 44 3 2 8.400438 2.128284
45 45 3 2 8.400438 2.128284
46 46 4 1 3.329605 1.202854
47 47 3 3 14.434567 2.669626
48 48 6 0 40.723000 3.706793
49 49 5 7 44.739851 3.800865
50 50 5 3 14.434567 2.669626
51 51 4 3 14.434567 2.669626
52 52 5 5 28.549402 3.351636
53 53 4 1 3.329605 1.202854
54 54 3 3 14.434567 2.669626
55 55 4 4 21.193913 3.053714
56 56 3 6 36.417738 3.595056
57 57 4 3 14.434567 2.669626
58 58 4 7 44.739851 3.800865
59 59 4 0 46.851000 3.846972
60 60 3 1 3.329605 1.202854
61 61 4 7 44.739851 3.800865
62 62 3 9 62.577007 4.136398
63 63 4 3 14.434567 2.669626
64 64 4 0 13.21 2.580974
65 65 3 1 3.329605 1.202854
66 66 4 1 3.329605 1.202854
67 67 4 3 14.434567 2.669626
68 68 4 4 21.193913 3.053714
69 69 4 3 14.434567 2.669626
70 70 3 3 14.434567 2.669626
71 71 4 3 14.434567 2.669626
72 72 3 4 21.193913 3.053714
73 73 4 3 14.434567 2.669626
74 74 5 4 21.193913 3.053714
75 75 3 5 28.549402 3.351636
76 76 4 5 28.549402 3.351636
77 77 3 5 28.549402 3.351636
78 78 3 6 36.417738 3.595056
79 79 3 3 14.434567 2.669626
80 80 5 7 44.739851 3.800865
81 81 3 1 3.329605 1.202854
82 82 3 0 5.184000 1.645577
83 83 3 0 7.742000 2.046660
84 84 6 2 8.400438 2.128284
85 85 5 0 80.941000 4.393720
86 86 3 14 112.876553 4.726295
87 87 4 17 146.278901 4.985515
88 88 4 7 44.739851 3.800865
89 89 5 3 14.434567 2.669626
90 90 5 3 14.434567 2.669626
91 91 4 4 21.193913 3.053714
92 92 3 5 28.549402 3.351636
93 93 4 2 8.400438 2.128284
94 94 3 7 44.739851 3.800865
95 95 4 8 53.471253 3.979144
96 96 4 2 8.400438 2.128284
97 97 3 5 28.549402 3.351636
98 98 6 1 3.329605 1.202854
99 99 5 3 14.434567 2.669626
100 100 4 7 44.739851 3.800865
101 101 4 8 53.471253 3.979144
102 102 3 5 28.549402 3.351636
103 103 4 3 14.434567 2.669626
104 104 5 3 14.434567 2.669626
105 105 3 5 28.549402 3.351636
106 106 4 9 62.577007 4.136398
107 107 4 5 28.549402 3.351636
108 108 4 4 21.193913 3.053714
109 109 4 7 44.739851 3.800865
110 110 4 9 62.577007 4.136398
111 111 3 1 3.329605 1.202854
112 112 3 1 3.329605 1.202854
113 113 4 2 8.400438 2.128284
114 114 4 2 8.400438 2.128284
115 115 4 4 21.193913 3.053714
116 116 3 4 21.193913 3.053714
117 117 3 3 14.434567 2.669626
118 118 5 2 8.400438 2.128284
119 119 4 4 21.193913 3.053714
120 120 3 1 3.329605 1.202854
121 121 4 3 14.434567 2.669626
122 122 4 5 28.549402 3.351636
123 123 4 5 28.549402 3.351636
124 124 4 4 21.193913 3.053714
125 125 3 4 21.193913 3.053714
126 126 3 3 14.434567 2.669626
127 127 4 2 8.400438 2.128284
128 128 5 0 6.436000 1.861907
129 129 5 1 3.329605 1.202854
130 130 5 1 3.329605 1.202854
131 131 5 1 3.329605 1.202854
132 132 4 3 14.434567 2.669626
133 133 3 1
[R] How to document an S3 class?
Hi, How do I document an S3 class with roxygen2? I create the class at the end of the method with: class(res) <- "myclass" but how do I create an documentation entry for this class, where I can describe the fields of the class (in case of myclass these are just list entries)? regards -- Witold Eryk Wolski __ 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] Change database in SQL Server using RODBC
On 30 June 2014 02:44, Ira Sharenow wrote: > I wish to query tables that are NOT in the default SQL Server 2012 database. > Now for the problem. I also want to read in the table dbo.sports. That > table is in the database sportsDB. I did not see any way to do so from > within R. Can you not use sportsDB.dbo.sports to reference the table? In general, table reference syntax is [ [ [ serverName '.' ] databaseName '.' ] [schema ] '.' ] tableName, where the names need only be surrounded by [...] if they are not valid SQL Server identifiers. Many people may suggest you reference [sportsDB].[dbo].[sports]; this is unnecessary verbiage. Cheers, - Peter __ 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] Time series
Hi Not much to cook from. Maybe ?approx Regards Petr > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of So > Sent: Monday, June 30, 2014 7:05 AM > To: r-help@r-project.org > Subject: [R] Time series > > Hi There! > I have a time series data for 13 years with freqency of 23 per year. I > have plot the curve on R. > Is it possible to refer to the point inbetween the nodes... > eg. say the time series ts1 has ts1[1] 0.25 and ts1[2]=0.4. is it > possible to get the time when ts1 reach to 0.3?? > > > > -- > View this message in context: http://r.789695.n4.nabble.com/Time- > series-tp4693234.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. Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. V případě, že je tento e-mail součástí obchodního jednání: - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou. - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech. - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient. __ 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] Time series
Hi There! I have a time series data for 13 years with freqency of 23 per year. I have plot the curve on R. Is it possible to refer to the point inbetween the nodes... eg. say the time series ts1 has ts1[1] 0.25 and ts1[2]=0.4. is it possible to get the time when ts1 reach to 0.3?? -- View this message in context: http://r.789695.n4.nabble.com/Time-series-tp4693234.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.
