[R] how to sort data frame order by column?
I have a data frame, for exampe dat - data.frame(a=rnorm(5),b=rnorm(5),c=rnorm(5)) ab c 1 -0.1731141 0.002453991 0.1180976 2 1.2142024 -0.413897606 0.7617472 3 -0.9428484 -0.609312786 0.5132441 4 0.1343336 0.178208961 0.7509650 5 -0.1402286 -0.333476839 -0.4959459 How to make dat2 from dat, where source data frame be ordered by any column? [[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] OT ; Interview with David Smith, REvolution Computing
Dear R community, Here is an interview with David Smith, Director of Community at REvolution Computing. David talks of the exciting work being done at REvolution to help make R reach out to even more users. http://www.decisionstats.com/2009/05/29/interview-david-smith-revolution-computing/ Best, Ajay Ohri [[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 sort data frame order by column?
e.g. dat[ order(dat$a), ] On Sun, May 31, 2009 at 2:34 PM, Угодай n/a ugo...@gmail.com wrote: I have a data frame, for exampe dat - data.frame(a=rnorm(5),b=rnorm(5),c=rnorm(5)) a b c 1 -0.1731141 0.002453991 0.1180976 2 1.2142024 -0.413897606 0.7617472 3 -0.9428484 -0.609312786 0.5132441 4 0.1343336 0.178208961 0.7509650 5 -0.1402286 -0.333476839 -0.4959459 How to make dat2 from dat, where source data frame be ordered by any column? [[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] logical vector as a matrix
Thanks a lot! :) Grześ wrote: I have a vector like this: h - c(4, 6, NA, 12) and I create the secound logical vector like this: g - c(TRUE, TRUE, FALSE, TRUE) And my problem is that I would like to get a new m vector as a rasult h and g( as dot-matrix printer) but with missed NA value, for example: m = (4,6,12) Do you have any idea? -- View this message in context: http://www.nabble.com/logical-vector-as-a--matrix-tp23785253p23796738.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] logical vector as a matrix
Thanks a lot! :) Linlin Yan wrote: On Sat, May 30, 2009 at 2:48 AM, Grześ gregori...@gmail.com wrote: I have a vector like this: h - c(4, 6, NA, 12) and I create the secound logical vector like this: g - c(TRUE, TRUE, FALSE, TRUE) Why don't you create vector g like this: g - ! is.na(h) And my problem is that I would like to get a new m vector as a rasult h and m but with missed NA value, for example: m = (4,6,12) Do you have any idea? As what you tried to do: m - h[g] # which got (4,6,12) you can directly use: m - h[ ! is.na(h) ] __ 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. -- View this message in context: http://www.nabble.com/logical-vector-as-a--matrix-tp23785253p23796761.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] logical vector as a matrix
Thanks Jorge Ivan Velez! -- View this message in context: http://www.nabble.com/logical-vector-as-a--matrix-tp23785253p23796796.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] IP-Address
edwin Sendjaja wrote:
Hi VQ,
Thank you. It works like charm. But I think Peter's code is faster. What is
the difference?
i think peter's code is more r-elegant, though less generic. here's a
quick test, with not so surprising results. gsubfn is implemented in r,
not c, and it is painfully slow in this test. i also added gabor's
suggestion.
library(gsubfn)
library(gtools)
library(rbenchmark)
n = 1000
df = data.frame(
a=rnorm(n),
b = rnorm(n),
c = rnorm(n),
ip = replicate(n, paste(sample(255, 4), collapse='.'),
simplify=TRUE))
benchmark(columns=c('test', 'elapsed'), replications=10, order=NULL,
peda={
connection = textConnection(as.character(df$ip))
o = do.call(order, read.table(connection, sep='.'))
close(connection)
df[o, ] },
waku=df[order(gsubfn(perl=TRUE,
'[0-9]+',
~ sprintf('%03d', as.integer(x)),
as.character(df$ip))), ],
gagr=df[mixedorder(df$ip), ] )
# peda 0.070
# waku 7.070
# gagr 4.710
vQ
__
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] mapply
well, you do not have to compute the pairwise difference each time; for
instance, you could use something like this (untested):
out1 - outer(a, c, -)
out2 - outer(b, c, -)
u - v - 1:5
mat - matrix(0, length(u), length(u))
for (i in seq_len(u)) {
for (j in seq_len(v)) {
res1 - colSums(abs(out1 - i) == 0) 0
res2 - colSums(abs(out2 - j) == 0) 0
mat[i, j] - sum(res1 res2)
}
}
mat
I hope it helps.
Best,
Dimitris
KARAVASILIS GEORGE wrote:
Hello, R users.
I would like to count the number of triples (r_i, s_j, t_k) with r_i,
s_j, t_k distinct and abs((r_i-t_k)-u)=0 and abs((s_j-t_k)-v)=0, where
r_i, s_j, t_k are the elements of three vectors a,b,c with different
lengths and u,v=1:n. I have solved this problem writing a subroutine in
Fortran an calling .Fortran(). I would like to find another way to use
functions like mapply. I tried this one:
xx - mapply( function(u,v) {
kk - outer(a, c, function(s,t) abs((s-t)-u)==0)
ll - outer(b, c, function(s,t) abs((s-t)-v)==0)
sum( outer( which(kk==TRUE, TRUE)[,2], which(ll==TRUE, TRUE)[,2],
function(s,t) s==t) ) },
rep(1:n, each=n), rep(1:n, times=n))
xx - matrix(xx, nrow=n, ncol=n, byrow=TRUE)
It works but it is rather slow. Taking into account that my vectors have
lengths 3000, and n is from 50 to 200, can I do something to improve the
running time of the above 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.
--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
__
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] Spatiotemporal correlation function
This is a new one on me. Do you mean the Kronecker delta, or the Kronecker product? The Kronecker product is more likely. In which case try ?kronecker. It is available as an operator, %x%, as well. Bill Venables. From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of FMH [kagba2...@yahoo.com] Sent: 30 May 2009 18:24 To: r-help@r-project.org Subject: [R] Spatiotemporal correlation function Hi, I'm trying to compute the spatiotemporal correlation matrix by using Delta Kronecker products of spatial and temporal correlation matrix in R, but didn't find any delta Kronecker's operator in R. The operators in matrix such as multiplication, addition, eigen values/vector and etc is easily to find and used. Could someone help me, please? Cheers. Firdaus [[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] strange behavior when reading csv - line wraps
Dear Jim, with the help of Ted, we diagnosed that the cause is in the extreme variability in line length during reading in. As the table column number is apparently determined fro mthe first five lines, what exceeds this length gets automatically on the next line. I am now trying to find a way to read in the data despite this. I have no control over the table extent, the only thing that would make sense according to my data would be to read in a fixed number of columns and merge all remaining columns as a long string in the last one. No idea how to do this, though. Thanks Martin jim holtman wrote: It is still not clear to me exactly how you want to read the lines in. If the lines have a variable number of fields, and some of the lines might be wrapped, is there some way to determine where the start of each line is. If you are reading them in with read.csv, then the system is assuming that each line starts a new row. If this is not the case, then you will have to state the rules that determine where the lines start. You can always read the data in with 'scan' to separate each line and then do whatever processing is required to put together the rows in a data frame that you want. In one of your examples, you indicated that the line was split starting at the word kempten; if this is in the middle of the line, then you would have to create the break after reading the line in with 'scan' and then creating the rows in the dataframe. All of this can be done in R if you can state what the criteria is. On Sat, May 30, 2009 at 4:32 AM, Martin Tomko martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch wrote: Jim, the two lines I put in are the actual problematic input lines. In these examples, there are no quotes nor # signs, although I have no means to make sure they do not occur in the inputs (any hints how I could deal with that?). I am trying to avoid as much pre-processing outside R as possible, and I have to process about 500 files with up to 3000 records each, so I need a more or less automated/batch solution. - so any string substitution will have to occur in R. But for the moment, I do not see a reaason for substitution, and the wrapping still occurs. Cheers Martin jim holtman wrote: You need to supply the actual input line so we can see what is happening. Are you sure you do not have unbalanced quotes in your input (try quote='') or do you have comment characters (#) in your input? On Fri, May 29, 2009 at 3:15 PM, Martin Tomko martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch wrote: Dear All, I am observing a strange behavior and searching the archives and help pages didn't help much. I have a csv with a variable number of fields in each line. I use dataPoints - read.csv(inputFile, head=FALSE, sep=;,fill =TRUE); to read it in, and it works. But - some lines are long and 'wrap', or split and continue on the next line. So when I check the dim of the frame, they are not correct and I can see when I do a printout that the lines is split into two in the frame. I checked the input file and all is good. an example of the input is: 37;2175168475;13;8.522729;47.19537;16366...@n00;30;sculpture;bird;tourism;animal;statue;canon;eos;rebel;schweiz;switzerland;eagle;swiss;adler;skulptur;zug;1750;28;tamron;f28;canton;tourismus;vogel;baar;kanton;xti;tamron1750;1750mm;tamron1750mm;400d;rabbitriotnet; where the last values occurs on the next line in the data frame. It does not have to be the last value, as in the follwong example, the word kempten starts the next line: 39;167757703;12;10.309295;47.724545;21903...@n00;36;white;building;tower;clock;clouds;germany;bayern;deutschland;bavaria;europa;europe;eagle;adler;eu;wolke;dome;townhall;rathaus;turm;weiss;allemagne;europeanunion;bundesrepublik;gebaeude;glocke;brd;allgau;kuppel;europ;kempten;niemcy;europo;federalrepublic;europaischeunion;europaeischeunion;germanio; What could be the reason? I ws thinking about solving the issue by using a different separator, that I would use for the first 7 fields and concatenating all of the remaining values into a single stirng value, but could not figure out how to do such a substitution in R. Unfortunately, on my system I cannot specify a range for sed... Thanks for any help/pointers Martin __ R-help@r-project.org mailto:R-help@r-project.org
[R] Bug in truncgof package?
Dear R-helpers,
I was testing the truncgof CRAN package, found something that looked
like a bug, and did my job: contacted the maintainer. But he did not
reply, so I am resending my query here.
I installed package truncgof and run the example for function ad.test. I
got the following output:
set.seed(123)
treshold - 10
xc - rlnorm(100, 2, 2)# complete sample
xt - xc[xc = treshold]# left truncated sample
ad.test(xt, plnorm, list(meanlog = 2, sdlog = 2), H = 10)
Supremum Class Anderson-Darling Test
data: xt
AD = 3.124, p-value = 0.12
alternative hypothesis: two.sided
treshold = 10, simulations: 100
So I cannot reject the hipothesis (at a standard confidence level) that
the original sample comes from a lognormal distribution (as it is the
case).
But let us try to iterate on this example:
set.seed( 123 )
treshold - 10
foo - function(){
xc - rlnorm(100, 2, 2) # complete sample
xt - xc[xc = treshold] # left truncated sample
ks.test(xt, plnorm, list(meanlog = 2, sdlog = 2), H =
10)$p.value
}
results - replicate( 100, foo() )
Then:
table( results )
results
0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.1 0.11 0.16 0.18
0.19 0.2
257931234112211
32
0.21 0.22 0.26 0.27 0.28 0.3 0.31 0.32 0.33 0.36 0.38 0.4 0.44 0.49
0.54 0.55
22131211121211
21
0.56 0.57 0.62 0.7 0.76 0.78 0.96 0.98
12111111
This is, in a 45% of the cases, you would reject the H_0 hypothesis,
which happens to be true, at the 5% standard confidence level.
Do you think this behaviour is buggy? If so, given that the maintainer
does not seem to be contactable, what would be the next step to take?
Best regards,
Carlos J. Gil Bellosta
http://www.datanalytics.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] Bug in gmodels CrossTable()?
Is the code below showing a bug in Crosstable()? My expectation was that the values produced by xtabs were rounded instead of truncated: library(gmodels) abc - c(a, a, b, b, c, c) def - c(d, e, f, f, d, e) wgt - c(0.8, 0.6, 0.4, 0.5, 1.4, 1.3) xtabs(wgt ~ abc + def) CrossTable(xtabs(wgt ~ abc + def), prop.r = F, prop.c = F, prop.t = F, prop.chisq = F) -- Jakson Aquino Professor of Political Science Federal University of Ceara, Brazil __ 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] grid.edit() for ggplot2
Dear all, I'm trying to access and modify grobs in a ggplot2 plot. The basic idea for raw Grid objects I understand from Paul Murrell's R graphics book, or this page of examples, http://www.stat.auckland.ac.nz/~paul/grid/copygrob/copygrobs.R However I can't figure out how to apply this to a ggplot (basically I don't know how to write a syntactically correct gPath), p - # minimal example qplot(0,0)+ annotate(text,0,0,label=test) g - # store the plot as a grob ggplotGrob(p) # structure of the grob grid.ls(g) # rather large! # find a particular grob in the gTree getGrob(g,texts, grep = T) # next step, modify, say, the colour of these grobs grid.edit() # what do I put in here? Thanks for any piece of advice, baptiste __ 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] convert the contents of a date.frame to a matrix
Dear R user, I am trying to convert the contents of a date.frame to a matrix. Since there are negative values in the date.frame, when I use data.matrix(x, rownames.force = NA), the resulting matrix is not the same as the original one. Basically I think R treats the numbers in the date.frame as character and converts it to corresponding numerics. Any idea on this issue? Many Thanks, Hongyuan x[1:3,] ALL ALL.1 ALL.2 ALL.3 ALL.4 ALL.5 ALL.6 ALL.7 ALL.8 ALL.9 ALL.10 ALL.11 2 -214 -139 -76 -135 -106 -138 -72 -413 5 -88 -165-67 3 -153 -73 -49 -114 -125 -85 -144 -260 -127 -105 -155-93 4 -58-1 -307 265 -76 215 238 7 10642-71 84 ALL.12 ALL.13 ALL.14 ALL.15 ALL.16 ALL.17 ALL.18 ALL.19 ALL.20 ALL.21 ALL.22 2-92 -113 -107 -117 -476-81-44 17 -144 -247 -74 3 -119 -147-72 -219 -213 -150-51 -229 -199-90 -321 4-31 -118 -126-50-18 -119100 79 -157 -168 -11 ALL.23 ALL.24 ALL.25 ALL.26 AML AML.1 AML.2 AML.3 AML.4 AML.5 AML.6 AML.7 2 -120-81 -112 -273 -20 7 -213 -25 -72-415 -318 3 -263 -150 -233 -327 -207 -100 -252 -20 -139 -116 -114 -192 4 -114-85-78-76 -50 -57 136 124-1 -125 2 -95 AML.8 AML.9 AML.10 ALL.27 ALL.28 ALL.29 ALL.30 ALL.31 ALL.32 ALL.33 ALL.34 2 -32 -124 -135 -342-87 22 -243 -130 -256-62 86 3 -49 -79 -186 -200 -248 -153 -218 -177 -249-23-36 449 -37-70 41262 17 -163-28 -410 -7 -141 ALL.35 ALL.36 ALL.37 ALL.38 ALL.39 ALL.40 ALL.41 ALL.42 ALL.43 ALL.44 ALL.45 2 -146 -187-56-55-59 -131 -154-79-76-34 -95 3-74 -187-43-44 -114 -126 -136 -118-98 -144 -118 4170312 43 12 23-50 49-30 -153-17 59 ALL.46 AML.11 AML.12 AML.13 AML.14 AML.15 AML.16 AML.17 AML.18 AML.19 AML.20 2-12-21 -202 -112 -118-90 -137 -157 -172-47 -62 3 -172-13 -274 -185 -142-87-51 -370 -122 -442 -198 4 12 8 59 24212102-82-77 38-21 -5 AML.21 AML.22 AML.23 AML.24 2-58 -161-48 -176 3 -217 -215 -531 -284 4 63-46 -124-81 help(as.matrix) y = data.matrix(x, rownames.force = NA) y[1:3,] ALL ALL.1 ALL.2 ALL.3 ALL.4 ALL.5 ALL.6 ALL.7 ALL.8 ALL.9 ALL.10 ALL.11 2 19575 620761358 466 399 1967 472 97377 3 106 533 4673739 43389 2786812 83432 4 499 1 315 1458 407 891 1096 1819 718 1320476 1436 ALL.12 ALL.13 ALL.14 ALL.15 ALL.16 ALL.17 ALL.18 ALL.19 ALL.20 ALL.21 ALL.22 2446 25 11 30489428308 1156 52178 381 3 30 87438159244 61346188103482 196 4219 33 37383186 28474 2449 64101 23 ALL.23 ALL.24 ALL.25 ALL.26 AML AML.1 AML.2 AML.3 AML.4 AML.5 AML.6 AML.7 2 35485 23278 173 1178 186 254 545 362 602 318 3203 81167330 181 1 228 190753920 181 4 26496467596 443 276 869 867 155 775 676 AML.8 AML.9 AML.10 ALL.27 ALL.28 ALL.29 ALL.30 ALL.31 ALL.32 ALL.33 ALL.34 2 27367102169544 1043 87 63272294 1226 3 386 615190 94196 86 74130267109170 4 1569 360611 1004 1162897 43241404308 48 ALL.35 ALL.36 ALL.37 ALL.38 ALL.39 ALL.40 ALL.41 ALL.42 ALL.43 ALL.44 ALL.45 2 55130253281376 38 89466361133 329 3372130213238 24 33 66 32397 36 25 4725 1231 1041488 1028316 1748222 60 50 1020 ALL.46 AML.11 AML.12 AML.13 AML.14 AML.15 AML.16 AML.17 AML.18 AML.19 AML.20 2 22131170 21 47381 36 67 77279 403 3 52 42245100 97374236166 28265 130 4397 1714 1932915 1289409316293 1054136 351 AML.21 AML.22 AML.23 AML.24 2218132324 76 3 74209344140 4 1015420 65342 [[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] Bug in gmodels CrossTable()?
On May 31, 2009, at 7:51 AM, Jakson Alves de Aquino wrote: Is the code below showing a bug in Crosstable()? My expectation was that the values produced by xtabs were rounded instead of truncated: library(gmodels) abc - c(a, a, b, b, c, c) def - c(d, e, f, f, d, e) wgt - c(0.8, 0.6, 0.4, 0.5, 1.4, 1.3) xtabs(wgt ~ abc + def) CrossTable(xtabs(wgt ~ abc + def), prop.r = F, prop.c = F, prop.t = F, prop.chisq = F) CrossTable() is designed to take one or two vectors, which are then [cross-]tabulated to yield integer counts, OR a matrix of integer counts, not fractional values. In the latter case, it is presumed that the matrix is the result of an 'a priori' cross-tabulation operation such as the use of table(). The output of xtabs() above is: xtabs(wgt ~ abc + def) def abc d e f a 0.8 0.6 0.0 b 0.0 0.0 0.9 c 1.4 1.3 0.0 The relevant output of CrossTable() in your example above shows: | def abc | d | e | f | Row Total | -|---|---|---|---| a | 0 | 0 | 0 | 1 | -|---|---|---|---| b | 0 | 0 | 0 | 0 | -|---|---|---|---| c | 1 | 1 | 0 | 2 | -|---|---|---|---| Column Total | 2 | 1 | 0 | 5 | -|---|---|---|---| The internal table object that would be generated here is effectively: addmargins(xtabs(wgt ~ abc + def)) def abc d e f Sum a 0.8 0.6 0.0 1.4 b 0.0 0.0 0.9 0.9 c 1.4 1.3 0.0 2.7 Sum 2.2 1.9 0.9 5.0 The textual output of CrossTable() is internally formatted using formatC(..., format = d), which is an integer based format: formatC(addmargins(xtabs(wgt ~ abc + def)), format = d) def abc d e f Sum a 0 0 0 1 b 0 0 0 0 c 1 1 0 2 Sum 2 1 0 5 In other words, you are getting the integer coerced values of the individual cells and then the same for the column, row and table totals: matrix(as.integer(addmargins(xtabs(wgt ~ abc + def))), 4, 4) [,1] [,2] [,3] [,4] [1,]0001 [2,]0000 [3,]1102 [4,]2105 If you review ?as.integer, you will note the following in the 'Value' section: Non-integral numeric values are truncated towards zero (i.e., as.integer(x) equals trunc(x) there) The output is correct, if confusing, but you are really using the function in a fashion that is not intended. HTH, Marc Schwartz __ 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] Bug in gmodels CrossTable()?
Dear Marc Schwartz, You are correct: there is no bug in CrossTable(). To get what I want I should have done: CrossTable(round(xtabs(wgt ~ abc + def)), prop.r = F, prop.c = F, prop.t = F, prop.chisq = F) Thank you for the explanation! Jakson Marc Schwartz wrote: On May 31, 2009, at 7:51 AM, Jakson Alves de Aquino wrote: Is the code below showing a bug in Crosstable()? My expectation was that the values produced by xtabs were rounded instead of truncated: library(gmodels) abc - c(a, a, b, b, c, c) def - c(d, e, f, f, d, e) wgt - c(0.8, 0.6, 0.4, 0.5, 1.4, 1.3) xtabs(wgt ~ abc + def) CrossTable(xtabs(wgt ~ abc + def), prop.r = F, prop.c = F, prop.t = F, prop.chisq = F) CrossTable() is designed to take one or two vectors, which are then [cross-]tabulated to yield integer counts, OR a matrix of integer counts, not fractional values. In the latter case, it is presumed that the matrix is the result of an 'a priori' cross-tabulation operation such as the use of table(). The output of xtabs() above is: xtabs(wgt ~ abc + def) def abc d e f a 0.8 0.6 0.0 b 0.0 0.0 0.9 c 1.4 1.3 0.0 The relevant output of CrossTable() in your example above shows: | def abc | d | e | f | Row Total | -|---|---|---|---| a | 0 | 0 | 0 | 1 | -|---|---|---|---| b | 0 | 0 | 0 | 0 | -|---|---|---|---| c | 1 | 1 | 0 | 2 | -|---|---|---|---| Column Total | 2 | 1 | 0 | 5 | -|---|---|---|---| The internal table object that would be generated here is effectively: addmargins(xtabs(wgt ~ abc + def)) def abc d e f Sum a 0.8 0.6 0.0 1.4 b 0.0 0.0 0.9 0.9 c 1.4 1.3 0.0 2.7 Sum 2.2 1.9 0.9 5.0 The textual output of CrossTable() is internally formatted using formatC(..., format = d), which is an integer based format: formatC(addmargins(xtabs(wgt ~ abc + def)), format = d) def abc d e f Sum a 0 0 0 1 b 0 0 0 0 c 1 1 0 2 Sum 2 1 0 5 In other words, you are getting the integer coerced values of the individual cells and then the same for the column, row and table totals: matrix(as.integer(addmargins(xtabs(wgt ~ abc + def))), 4, 4) [,1] [,2] [,3] [,4] [1,]0001 [2,]0000 [3,]1102 [4,]2105 If you review ?as.integer, you will note the following in the 'Value' section: Non-integral numeric values are truncated towards zero (i.e., as.integer(x) equals trunc(x) there) The output is correct, if confusing, but you are really using the function in a fashion that is not intended. HTH, Marc Schwartz __ 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] convert the contents of a date.frame to a matrix
Unable to reproduce: ?data.matrix x - read.table(textConnection( ALL ALL.1 ALL.2 ALL.3 ALL.4 ALL.5 ALL.6 ALL.7 ALL.8 ALL.9 ALL.10 ALL.11 + 2 -214 -139 -76 -135 -106 -138 -72 -413 5 -88 -165-67 + 3 -153 -73 -49 -114 -125 -85 -144 -260 -127 -105 -155-93 + 4 -58-1 -307 265 -76 215 238 7 10642 -71 84), header=TRUE) x ALL ALL.1 ALL.2 ALL.3 ALL.4 ALL.5 ALL.6 ALL.7 ALL.8 ALL.9 ALL.10 ALL.11 2 -214 -139 -76 -135 -106 -138 -72 -413 5 -88 -165 -67 3 -153 -73 -49 -114 -125 -85 -144 -260 -127 -105 -155 -93 4 -58-1 -307 265 -76 215 238 7 10642 -71 84 data.matrix(x) ALL ALL.1 ALL.2 ALL.3 ALL.4 ALL.5 ALL.6 ALL.7 ALL.8 ALL.9 ALL.10 ALL.11 2 -214 -139 -76 -135 -106 -138 -72 -413 5 -88 -165 -67 3 -153 -73 -49 -114 -125 -85 -144 -260 -127 -105 -155 -93 4 -58-1 -307 265 -76 215 238 7 10642 -71 84 You may have something else in that dataframe that is not apparent on a simple print display. Can you instead provide the results of dput(x)? -- David Winsemius On May 31, 2009, at 9:29 AM, Hongyuan Cao wrote: Dear R user, I am trying to convert the contents of a date.frame to a matrix. Since there are negative values in the date.frame, when I use data.matrix(x, rownames.force = NA), the resulting matrix is not the same as the original one. Basically I think R treats the numbers in the date.frame as character and converts it to corresponding numerics. Any idea on this issue? Many Thanks, Hongyuan x[1:3,] ALL ALL.1 ALL.2 ALL.3 ALL.4 ALL.5 ALL.6 ALL.7 ALL.8 ALL.9 ALL.10 ALL.11 2 -214 -139 -76 -135 -106 -138 -72 -413 5 -88 -165-67 3 -153 -73 -49 -114 -125 -85 -144 -260 -127 -105 -155-93 4 -58-1 -307 265 -76 215 238 7 10642 -71 84 ALL.12 ALL.13 ALL.14 ALL.15 ALL.16 ALL.17 ALL.18 ALL.19 ALL.20 ALL.21 ALL.22 2-92 -113 -107 -117 -476-81-44 17 -144 -247 -74 3 -119 -147-72 -219 -213 -150-51 -229 -199 -90 -321 4-31 -118 -126-50-18 -119100 79 -157 -168 -11 ALL.23 ALL.24 ALL.25 ALL.26 AML AML.1 AML.2 AML.3 AML.4 AML.5 AML. 6 AML.7 2 -120-81 -112 -273 -20 7 -213 -25 -72-4 15 -318 3 -263 -150 -233 -327 -207 -100 -252 -20 -139 -116 -114 -192 4 -114-85-78-76 -50 -57 136 124-1 -125 2 -95 AML.8 AML.9 AML.10 ALL.27 ALL.28 ALL.29 ALL.30 ALL.31 ALL.32 ALL.33 ALL.34 2 -32 -124 -135 -342-87 22 -243 -130 -256 -62 86 3 -49 -79 -186 -200 -248 -153 -218 -177 -249 -23-36 449 -37-70 41262 17 -163-28 -410 -7 -141 ALL.35 ALL.36 ALL.37 ALL.38 ALL.39 ALL.40 ALL.41 ALL.42 ALL.43 ALL.44 ALL.45 2 -146 -187-56-55-59 -131 -154-79-76 -34 -95 3-74 -187-43-44 -114 -126 -136 -118-98 -144 -118 4170312 43 12 23-50 49-30 -153 -17 59 ALL.46 AML.11 AML.12 AML.13 AML.14 AML.15 AML.16 AML.17 AML.18 AML.19 AML.20 2-12-21 -202 -112 -118-90 -137 -157 -172 -47 -62 3 -172-13 -274 -185 -142-87-51 -370 -122 -442 -198 4 12 8 59 24212102-82-77 38 -21 -5 AML.21 AML.22 AML.23 AML.24 2-58 -161-48 -176 3 -217 -215 -531 -284 4 63-46 -124-81 help(as.matrix) y = data.matrix(x, rownames.force = NA) y[1:3,] ALL ALL.1 ALL.2 ALL.3 ALL.4 ALL.5 ALL.6 ALL.7 ALL.8 ALL.9 ALL.10 ALL.11 2 19575 620761358 466 399 1967 472 97377 3 106 533 4673739 43389 2786812 83432 4 499 1 315 1458 407 891 1096 1819 718 1320476 1436 ALL.12 ALL.13 ALL.14 ALL.15 ALL.16 ALL.17 ALL.18 ALL.19 ALL.20 ALL.21 ALL.22 2446 25 11 30489428308 1156 52 178 381 3 30 87438159244 61346188103 482 196 4219 33 37383186 28474 2449 64 101 23 ALL.23 ALL.24 ALL.25 ALL.26 AML AML.1 AML.2 AML.3 AML.4 AML.5 AML.6 AML.7 2 35485 23278 173 1178 186 254 545 362 602 318 3203 81167330 181 1 228 1907539 20 181 4 26496467596 443 276 869 867 155 775 676 AML.8 AML.9 AML.10 ALL.27 ALL.28 ALL.29 ALL.30 ALL.31 ALL.32 ALL.33 ALL.34 2 27367102169544 1043 87 63272 294 1226 3 386 615190 94196 86 74130267 109170 4 1569 360611 1004 1162897 43241404 308 48 ALL.35 ALL.36
Re: [R] strange behavior when reading csv - line wraps
You can do something like this: count the number of fields in each line of the file and use the max to determine the number of columns for read.table: file - '/tempxx.txt' maxFields - max(count.fields(file)) # max # now setup read.table for max number input - read.table(file, colClasses=rep(NA, maxFields), fill=TRUE, col.names=paste(V, seq(maxFields), sep='')) On Sun, May 31, 2009 at 6:06 AM, Martin Tomko martin.to...@geo.uzh.chwrote: Dear Jim, with the help of Ted, we diagnosed that the cause is in the extreme variability in line length during reading in. As the table column number is apparently determined fro mthe first five lines, what exceeds this length gets automatically on the next line. I am now trying to find a way to read in the data despite this. I have no control over the table extent, the only thing that would make sense according to my data would be to read in a fixed number of columns and merge all remaining columns as a long string in the last one. No idea how to do this, though. Thanks Martin jim holtman wrote: It is still not clear to me exactly how you want to read the lines in. If the lines have a variable number of fields, and some of the lines might be wrapped, is there some way to determine where the start of each line is. If you are reading them in with read.csv, then the system is assuming that each line starts a new row. If this is not the case, then you will have to state the rules that determine where the lines start. You can always read the data in with 'scan' to separate each line and then do whatever processing is required to put together the rows in a data frame that you want. In one of your examples, you indicated that the line was split starting at the word kempten; if this is in the middle of the line, then you would have to create the break after reading the line in with 'scan' and then creating the rows in the dataframe. All of this can be done in R if you can state what the criteria is. On Sat, May 30, 2009 at 4:32 AM, Martin Tomko martin.to...@geo.uzh.chmailto: martin.to...@geo.uzh.ch wrote: Jim, the two lines I put in are the actual problematic input lines. In these examples, there are no quotes nor # signs, although I have no means to make sure they do not occur in the inputs (any hints how I could deal with that?). I am trying to avoid as much pre-processing outside R as possible, and I have to process about 500 files with up to 3000 records each, so I need a more or less automated/batch solution. - so any string substitution will have to occur in R. But for the moment, I do not see a reaason for substitution, and the wrapping still occurs. Cheers Martin jim holtman wrote: You need to supply the actual input line so we can see what is happening. Are you sure you do not have unbalanced quotes in your input (try quote='') or do you have comment characters (#) in your input? On Fri, May 29, 2009 at 3:15 PM, Martin Tomko martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch wrote: Dear All, I am observing a strange behavior and searching the archives and help pages didn't help much. I have a csv with a variable number of fields in each line. I use dataPoints - read.csv(inputFile, head=FALSE, sep=;,fill =TRUE); to read it in, and it works. But - some lines are long and 'wrap', or split and continue on the next line. So when I check the dim of the frame, they are not correct and I can see when I do a printout that the lines is split into two in the frame. I checked the input file and all is good. an example of the input is: 37;2175168475;13;8.522729;47.19537;16366...@n00 ;30;sculpture;bird;tourism;animal;statue;canon;eos;rebel;schweiz;switzerland;eagle;swiss;adler;skulptur;zug;1750;28;tamron;f28;canton;tourismus;vogel;baar;kanton;xti;tamron1750;1750mm;tamron1750mm;400d;rabbitriotnet; where the last values occurs on the next line in the data frame. It does not have to be the last value, as in the follwong example, the word kempten starts the next line: 39;167757703;12;10.309295;47.724545;21903...@n00 ;36;white;building;tower;clock;clouds;germany;bayern;deutschland;bavaria;europa;europe;eagle;adler;eu;wolke;dome;townhall;rathaus;turm;weiss;allemagne;europeanunion;bundesrepublik;gebaeude;glocke;brd;allgau;kuppel;europ;kempten;niemcy;europo;federalrepublic;europaischeunion;europaeischeunion;germanio; What could be the reason? I ws thinking about solving the issue by using a different separator, that I would use for the first 7 fields and
Re: [R] strange behavior when reading csv - line wraps
Ah!!! It was count.fields() which we had overlooked! We discoveered a work-round which involved using Data0 - readLines(file) to create a vector of strings, one for each line of the input file, and then using NF - unlist(lapply(R0,function(x) length(unlist(gregexpr(;,x,fixed=TRUE,useBytes=TRUE)) to count the number of occurrences of ; (the separator) in each line. (NF+1) produces the same result as count.fields(file,sep=;). Thanks for pointing out the existence of count.fields()! Ted. On 31-May-09 15:04:23, jim holtman wrote: You can do something like this: count the number of fields in each line of the file and use the max to determine the number of columns for read.table: file - '/tempxx.txt' maxFields - max(count.fields(file)) # max # now setup read.table for max number input - read.table(file, colClasses=rep(NA, maxFields), fill=TRUE, col.names=paste(V, seq(maxFields), sep='')) On Sun, May 31, 2009 at 6:06 AM, Martin Tomko martin.to...@geo.uzh.chwrote: Dear Jim, with the help of Ted, we diagnosed that the cause is in the extreme variability in line length during reading in. As the table column number is apparently determined fro mthe first five lines, what exceeds this length gets automatically on the next line. I am now trying to find a way to read in the data despite this. I have no control over the table extent, the only thing that would make sense according to my data would be to read in a fixed number of columns and merge all remaining columns as a long string in the last one. No idea how to do this, though. Thanks Martin jim holtman wrote: It is still not clear to me exactly how you want to read the lines in. If the lines have a variable number of fields, and some of the lines might be wrapped, is there some way to determine where the start of each line is. If you are reading them in with read.csv, then the system is assuming that each line starts a new row. If this is not the case, then you will have to state the rules that determine where the lines start. You can always read the data in with 'scan' to separate each line and then do whatever processing is required to put together the rows in a data frame that you want. In one of your examples, you indicated that the line was split starting at the word kempten; if this is in the middle of the line, then you would have to create the break after reading the line in with 'scan' and then creating the rows in the dataframe. All of this can be done in R if you can state what the criteria is. On Sat, May 30, 2009 at 4:32 AM, Martin Tomko martin.to...@geo.uzh.chmailto: martin.to...@geo.uzh.ch wrote: Jim, the two lines I put in are the actual problematic input lines. In these examples, there are no quotes nor # signs, although I have no means to make sure they do not occur in the inputs (any hints how I could deal with that?). I am trying to avoid as much pre-processing outside R as possible, and I have to process about 500 files with up to 3000 records each, so I need a more or less automated/batch solution. - so any string substitution will have to occur in R. But for the moment, I do not see a reaason for substitution, and the wrapping still occurs. Cheers Martin jim holtman wrote: You need to supply the actual input line so we can see what is happening. Are you sure you do not have unbalanced quotes in your input (try quote='') or do you have comment characters (#) in your input? On Fri, May 29, 2009 at 3:15 PM, Martin Tomko martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch wrote: Dear All, I am observing a strange behavior and searching the archives and help pages didn't help much. I have a csv with a variable number of fields in each line. I use dataPoints - read.csv(inputFile, head=FALSE, sep=;,fill =TRUE); to read it in, and it works. But - some lines are long and 'wrap', or split and continue on the next line. So when I check the dim of the frame, they are not correct and I can see when I do a printout that the lines is split into two in the frame. I checked the input file and all is good. an example of the input is: 37;2175168475;13;8.522729;47.19537;16366...@n00 ;30;sculpture;bird;tourism;animal;statue;canon;eos;rebel;schweiz;switz erland;eagle;swiss;adler;skulptur;zug;1750;28;tamron;f28;canton;touris mus;vogel;baar;kanton;xti;tamron1750;1750mm;tamron1750mm;400d;rabbitri otnet; where the last values occurs on the next line in the data frame. It does not have to be the last value, as in the follwong example,
[R] renaming column names
I am trying to rename the column names of a data frame called data. It has 177 columns. I have used : colnames(data) - a where a is a vector with 177 character names. I don't get any error message, but the column names don't change because when I then type : colnames(data) I get the same set of names as before, so the assignment doesnt seem to have worked. Any ideas or suggestions gratefully received. Benny Chain Benjamin Chain Division of Infection and Immunity Windeyer Building UCL, 46 Cleveland St. London W1T 4JF Fax 00 44 20 7679 9301 [[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] convert the contents of a date.frame to a matrix
On May 31, 2009, at 10:49 AM, Hongyuan Cao wrote: x = read.table(hongyuan_5_30_forsafe.txt, sep = \t) x = read.table(/Users/davidwinsemius/Downloads/ hongyuan_5_30_forsafe.txt, sep = \t) str(x) 'data.frame': 7131 obs. of 74 variables: $ V1 : Factor w/ 7131 levels ,A28102_at,..: 1 934 120 122 118 126 124 130 128 134 ... $ V2 : Factor w/ 5528 levels ,2-Sep,6-Mar,..: 1 5528 NA NA NA NA NA NA NA NA ... $ V3 : Factor w/ 2375 levels -1,-10,-100,..: 2374 2375 195 106 499 2262 287 483 1254 143 ... $ V4 : Factor w/ 2326 levels -1,-10,-100,..: 2325 2326 75 533 1 1442 231 357 299 117 ... My guess (which became a conclusion after testing) was that you have encountered the stringsAsFactors pitfall. (It's probably in the R Inferno someplace bu my favorite quote is from Terry Terneau: .) Try reading the table in with stringsAsFactors=FALSE or as.is=TRUE. After doing that and applying the rest of your code, I get: head(y) X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 X14 X15 X16 X17 AFFX-BioB-5_at -214 -139 -76 -135 -106 -138 -72 -4135 -88 -165 -67 -92 -113 -107 -117 -476 AFFX-BioB-M_at -153 -73 -49 -114 -125 -85 -144 -260 -127 -105 -155 -93 -119 -147 -72 -219 -213 AFFX-BioB-3_at -58 -1 -307 265 -76 215 2387 106 42 -71 84 -31 -118 -126 -50 -18 AFFX-BioC-5_at88 283 309 12 168 71 55 -2 268 219 82 25 173 243 149 257 301 AFFX-BioC-3_at -295 -264 -376 -419 -230 -272 -399 -541 -210 -178 -163 -179 -233 -127 -205 -218 -403 AFFX-BioDn-5_at -558 -400 -650 -585 -284 -558 -551 -790 -535 -246 -430 -323 -227 -398 -284 -402 -394 . ...snipped the rest of the output. You replied to me only personally which is against R-help practice, so I am adding back the list to the address list. (You should also configure your maile-client so that it sends plain text to the r-help list.) -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] renaming column names
Cannot reproduce with a toy example: data - data.frame(a=1:3, b=4:6, c=6:8) colnames(data) - c(d,e,f) colnames(data) [1] d e f Perhaps you need to produce more detail. Surely offering the results of dput(a) would not tax the limits of the R-mail server. -- David On May 31, 2009, at 11:58 AM, Benny Chain wrote: I am trying to rename the column names of a data frame called data. It has 177 columns. I have used : colnames(data) - a where a is a vector with 177 character names. I don't get any error message, but the column names don't change because when I then type : colnames(data) I get the same set of names as before, so the assignment doesnt seem to have worked. Any ideas or suggestions gratefully received. Benny Chain Benjamin Chain Division of Infection and Immunity Windeyer Building UCL, 46 Cleveland St. London W1T 4JF Fax 00 44 20 7679 9301 [[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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] convert the contents of a date.frame to a matrix
On May 31, 2009, at 12:03 PM, David Winsemius wrote: On May 31, 2009, at 10:49 AM, Hongyuan Cao wrote: x = read.table(hongyuan_5_30_forsafe.txt, sep = \t) x = read.table(/Users/davidwinsemius/Downloads/ hongyuan_5_30_forsafe.txt, sep = \t) str(x) 'data.frame': 7131 obs. of 74 variables: $ V1 : Factor w/ 7131 levels ,A28102_at,..: 1 934 120 122 118 126 124 130 128 134 ... $ V2 : Factor w/ 5528 levels ,2-Sep,6-Mar,..: 1 5528 NA NA NA NA NA NA NA NA ... $ V3 : Factor w/ 2375 levels -1,-10,-100,..: 2374 2375 195 106 499 2262 287 483 1254 143 ... $ V4 : Factor w/ 2326 levels -1,-10,-100,..: 2325 2326 75 533 1 1442 231 357 299 117 ... My guess (which became a conclusion after testing) was that you have encountered the stringsAsFactors pitfall. (It's probably in the R Inferno someplace but my favorite quote is from Terry Terneau(sic): The default action of turning every character string into a factor is a plague on the S language. ---Terry Therneau, from s-news, 2004 -- David Winsemius Heritage Laboratories West Hartford, CT __ 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 set a filter during reading tables
Thanks, Juliet.
It works for filtering columns.
I am also wondering if there is a way to filter rows.
Thanks again.
-james
One can use colClasses to set which columns get read in. For the
columns you don't
want you can set those to NULL. For example,
cc - c(NULL,rep(numeric,9))
myData -
read.table(myFile.txt,header=TRUE,colClasses=cc,nrow=numRows).
On Wed, May 27, 2009 at 12:27 PM, g...@ucalgary.ca wrote:
We are reading big tables, such as,
Chemicals -
read.table('ftp://ftp.bls.gov/pub/time.series/wp/wp.data.7.Chemicals',header
= TRUE, sep = '\t', as.is =T)
I was wondering if it is possible to set a filter during loading so
that
we just load what we want not the whole table each time. Thanks,
-james
__
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 set a filter during reading tables
I think you can use readLines(n=1) in loop to skip unwanted rows.
On Mon, Jun 1, 2009 at 12:56 AM, g...@ucalgary.ca wrote:
Thanks, Juliet.
It works for filtering columns.
I am also wondering if there is a way to filter rows.
Thanks again.
-james
One can use colClasses to set which columns get read in. For the
columns you don't
want you can set those to NULL. For example,
cc - c(NULL,rep(numeric,9))
myData -
read.table(myFile.txt,header=TRUE,colClasses=cc,nrow=numRows).
On Wed, May 27, 2009 at 12:27 PM, g...@ucalgary.ca wrote:
We are reading big tables, such as,
Chemicals -
read.table('ftp://ftp.bls.gov/pub/time.series/wp/wp.data.7.Chemicals',header
= TRUE, sep = '\t', as.is =T)
I was wondering if it is possible to set a filter during loading so
that
we just load what we want not the whole table each time. Thanks,
-james
__
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.
[R] using chron vector with boxplot
Hi,
I'm having trouble using dates (created using library(chron)) as
groupings for a boxplot. I have 10 repeat measurements of a variable
within an individual day. The measurements were done over 10 days. I
would like to plot the measurements as a box and wisker plot (using
boxplot or something similar) where the days (as chron object) would be
the grouping and the repeated measurements of the variable make up the
box and wisker plot. I would like the spacing of the individual
boxplots to reflect the time between measurements:
Example using random numbers:
### Create date vector of measurement dates
library(chron)
time=c(39083, 39085, 39095, 39096, 39103, 39104, 39105, 39110, 39113,
39120);
orig =chron(01/01/1900)
date = orig + time-2;
### Data for B and W plot
data = data.frame();
mean=rnorm(10, mean=0, sd=1);
for(i in 1:10){data[1:10,i] =rnorm(10, mean=mean[i], sd=1)};
### Plot
boxplot(data, range=0); # works, but doesn't reflect the different time
intervals between measurements dates!
boxplot(data~date, range=0) # tried using formula, gives error:
Error in model.frame.default(formula = data ~ date) :
invalid type (list) for variable 'data'
Not sure what to try next. Any suggestions?
Thanks,
ken
kat...@psu.edu
[[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] IP-Address
library(gsubfn)
library(gtools)
library(rbenchmark)
n - 1
df - data.frame(
a = rnorm(n),
b = rnorm(n),
c = rnorm(n),
ip = replicate(n, paste(sample(255, 4), collapse='.'), simplify=TRUE)
)
res - benchmark(columns=c('test', 'elapsed'), replications=10, order=NULL,
peda = {
connection - textConnection(as.character(df$ip))
o - do.call(order, read.table(connection, sep='.'))
close(connection)
df[o, ]
},
peda2 = {
connection - textConnection(as.character(df$ip))
dfT - read.table(connection, sep='.', colClasses=rep(integer,
4), quote=, na.strings=NULL, blank.lines.skip=FALSE)
close(connection)
o - do.call(order, dfT)
df[o, ]
},
hb = {
ip - strsplit(as.character(df$ip), split=., fixed=TRUE)
ip - unlist(ip, use.names=FALSE)
ip - as.integer(ip)
dim(ip) - c(4, nrow(df))
ip - 256^3*ip[1,] + 256^2*ip[2,] + 256*ip[3,] + ip[4,]
o - order(ip)
df[o, ]
},
hb2 = {
ip - strsplit(as.character(df$ip), split=., fixed=TRUE)
ip - unlist(ip, use.names=FALSE)
ip - as.integer(ip);
dim(ip) - c(4, nrow(df))
o - sort.list(ip[4,], method=radix, na.last=TRUE)
for (kk in 3:1) {
o - o[sort.list(ip[kk,o], method=radix, na.last=TRUE)]
}
df[o, ]
}
)
print(res)
test elapsed
1 peda4.12
2 peda24.08
3hb0.28
4 hb20.25
On Sun, May 31, 2009 at 12:42 AM, Wacek Kusnierczyk
waclaw.marcin.kusnierc...@idi.ntnu.no wrote:
edwin Sendjaja wrote:
Hi VQ,
Thank you. It works like charm. But I think Peter's code is faster. What is
the difference?
i think peter's code is more r-elegant, though less generic. here's a
quick test, with not so surprising results. gsubfn is implemented in r,
not c, and it is painfully slow in this test. i also added gabor's
suggestion.
library(gsubfn)
library(gtools)
library(rbenchmark)
n = 1000
df = data.frame(
a=rnorm(n),
b = rnorm(n),
c = rnorm(n),
ip = replicate(n, paste(sample(255, 4), collapse='.'),
simplify=TRUE))
benchmark(columns=c('test', 'elapsed'), replications=10, order=NULL,
peda={
connection = textConnection(as.character(df$ip))
o = do.call(order, read.table(connection, sep='.'))
close(connection)
df[o, ] },
waku=df[order(gsubfn(perl=TRUE,
'[0-9]+',
~ sprintf('%03d', as.integer(x)),
as.character(df$ip))), ],
gagr=df[mixedorder(df$ip), ] )
# peda 0.070
# waku 7.070
# gagr 4.710
vQ
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to set a filter during reading tables
The sqldf package can read a subset of rows and columns into R without
reading the entire file into R. There are a few caveats:
- It does not support ftp so you will need to download the file to your
computer first as shown in the example below
- since value is an SQL keyword it turns value into value__1 to avoid
a collision.
- you will have to convert the value column to numeric yourself as shown:
library(sqldf)
download.file(ftp://ftp.bls.gov/pub/time.series/wp/wp.data.7.Chemicals;,
Chemicals.txt, method = wget)
# define wp as a file with indicated format
wp - file(Chemicals.txt)
attr(wp, file.format) - list(sep = \t, header = TRUE)
# use sqldf to read it in keeping only indicated rows
wp.df - sqldf(select * from wp where footnote_codes = 'p' and period = 'M01')
# fix up type of value__1
wp.df$value__1 - as.numeric(as.character(wp.df$value__1))
head(wp.df)
See http://sqldf.googlecode.com
On Wed, May 27, 2009 at 12:27 PM, g...@ucalgary.ca wrote:
We are reading big tables, such as,
Chemicals -
read.table('ftp://ftp.bls.gov/pub/time.series/wp/wp.data.7.Chemicals',header
= TRUE, sep = '\t', as.is =T)
I was wondering if it is possible to set a filter during loading so that
we just load what we want not the whole table each time. Thanks,
-james
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] using chron vector with boxplot
Try this:
boxplot(as.matrix(data) ~ as.Date(date), cex.axis = 0.5, las = 2)
or if all the dates are in the same year and month as they are here
then you might want to just display the day of the month:
boxplot(as.matrix(data) ~ month.day.year(date)$day)
On Sun, May 31, 2009 at 1:45 PM, Kenneth Takagi kat...@psu.edu wrote:
Hi,
I'm having trouble using dates (created using library(chron)) as
groupings for a boxplot. I have 10 repeat measurements of a variable
within an individual day. The measurements were done over 10 days. I
would like to plot the measurements as a box and wisker plot (using
boxplot or something similar) where the days (as chron object) would be
the grouping and the repeated measurements of the variable make up the
box and wisker plot. I would like the spacing of the individual
boxplots to reflect the time between measurements:
Example using random numbers:
### Create date vector of measurement dates
library(chron)
time=c(39083, 39085, 39095, 39096, 39103, 39104, 39105, 39110, 39113,
39120);
orig =chron(01/01/1900)
date = orig + time-2;
### Data for B and W plot
data = data.frame();
mean=rnorm(10, mean=0, sd=1);
for(i in 1:10){data[1:10,i] =rnorm(10, mean=mean[i], sd=1)};
### Plot
boxplot(data, range=0); # works, but doesn't reflect the different time
intervals between measurements dates!
boxplot(data~date, range=0) # tried using formula, gives error:
Error in model.frame.default(formula = data ~ date) :
invalid type (list) for variable 'data'
Not sure what to try next. Any suggestions?
Thanks,
ken
kat...@psu.edu
[[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] How to set a filter during reading tables
Since there are many rows, using read.table we spent too much on reading
in rows that we do not want. We are wondering if there is a way to read
only rows that we are interested in. Thanks,
-james
I think you can use readLines(n=1) in loop to skip unwanted rows.
On Mon, Jun 1, 2009 at 12:56 AM, g...@ucalgary.ca wrote:
Thanks, Juliet.
It works for filtering columns.
I am also wondering if there is a way to filter rows.
Thanks again.
-james
One can use colClasses to set which columns get read in. For the
columns you don't
want you can set those to NULL. For example,
cc - c(NULL,rep(numeric,9))
myData -
read.table(myFile.txt,header=TRUE,colClasses=cc,nrow=numRows).
On Wed, May 27, 2009 at 12:27 PM, Â g...@ucalgary.ca wrote:
We are reading big tables, such as,
Chemicals -
read.table('ftp://ftp.bls.gov/pub/time.series/wp/wp.data.7.Chemicals',header
= TRUE, sep = '\t', as.is =T)
I was wondering if it is possible to set a filter during loading so
that
we just load what we want not the whole table each time. Thanks,
-james
__
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] a simple trick to get autoclose parenthesis on windows
Gabor Grothendieck wrote:
Hi, I was looking for your sendcodetoR.ahk autohotkey script
but couldn't find it. Would you be able to point me to it.
Thanks.
Here's what I have right now, it also maps right alt to send code to R.
You should change the ahk_class to your editor of choice (here it's
vim). To get the ahk_class, you need to run the atoit_spy (comes with
every autohotkey install).
HTH,
-Jose
; F3 and right alt will send selection to open Rgui
#WinActivateForce
F3::
IfWinExist, ahk_class Rgui
{
Send ^c; copy selection to clipboard
WinActivate ; R Console
save = %clipboard%
sendinput, {Raw}%save%
sendinput,{enter}
Sleep 1000
WinActivate, ahk_class Vim
}
Ralt::
IfWinExist, ahk_class Rgui
{
Send ^c; copy selection to clipboard
WinActivate ; R Console
save = %clipboard%
sendinput, {Raw}%save%
sendinput,{enter}
Sleep 1000
WinActivate, ahk_class Vim
}
return
--
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-,
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/
__
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] renaming column names
Dear David Problem solved ! Remarkably, I saw your previous post about stringsasFactors - false and that was the root of the problem. I was trying to rename the columns according to contents of one of the rows of the data frame, which were being interpreted as factors (which I hadn't realised) and that's why the assignment as new column names didn't work ! Thanks for your help, albeit inadvertent ! Benny Benjamin Chain Division of Infection and Immunity Windeyer Building UCL, 46 Cleveland St. London W1T 4JF Fax 00 44 20 7679 9301 -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: 31 May 2009 17:11 To: Benny Chain Cc: r-help@r-project.org Subject: Re: [R] renaming column names Cannot reproduce with a toy example: data - data.frame(a=1:3, b=4:6, c=6:8) colnames(data) - c(d,e,f) colnames(data) [1] d e f Perhaps you need to produce more detail. Surely offering the results of dput(a) would not tax the limits of the R-mail server. -- David On May 31, 2009, at 11:58 AM, Benny Chain wrote: I am trying to rename the column names of a data frame called data. It has 177 columns. I have used : colnames(data) - a where a is a vector with 177 character names. I don't get any error message, but the column names don't change because when I then type : colnames(data) I get the same set of names as before, so the assignment doesnt seem to have worked. Any ideas or suggestions gratefully received. Benny Chain Benjamin Chain Division of Infection and Immunity Windeyer Building UCL, 46 Cleveland St. London W1T 4JF Fax 00 44 20 7679 9301 [[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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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 simple trick to get autoclose parenthesis on windows
Thanks very much. Regards.
On Sun, May 31, 2009 at 2:20 PM, Jose Quesada ques...@gmail.com wrote:
Gabor Grothendieck wrote:
Hi, I was looking for your sendcodetoR.ahk autohotkey script
but couldn't find it. Would you be able to point me to it.
Thanks.
Here's what I have right now, it also maps right alt to send code to R.
You should change the ahk_class to your editor of choice (here it's
vim). To get the ahk_class, you need to run the atoit_spy (comes with
every autohotkey install).
HTH,
-Jose
; F3 and right alt will send selection to open Rgui
#WinActivateForce
F3::
IfWinExist, ahk_class Rgui
{
Send ^c ; copy selection to clipboard
WinActivate ; R Console
save = %clipboard%
sendinput, {Raw}%save%
sendinput,{enter}
Sleep 1000
WinActivate, ahk_class Vim
}
Ralt::
IfWinExist, ahk_class Rgui
{
Send ^c ; copy selection to clipboard
WinActivate ; R Console
save = %clipboard%
sendinput, {Raw}%save%
sendinput,{enter}
Sleep 1000
WinActivate, ahk_class Vim
}
return
--
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-,
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/
__
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] Can I Compile R with MS Access 2003 Developer Extensions?
Hi: I have an application that uses MS Access as front end interacting with Excel,Word,Sigmaplot and R in the background. I use the programs to do different tasks but I mainly use R to create graphics on my Access forms without having to manually open R. To make this short, I was wondering if R can be compiled from Access using the Developer Extensions. I know that the MS office programs can be compiled with it but don't know if it can be done including R. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, 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] Can I Compile R with MS Access 2003 Developer Extensions?
Hi: I have an application that uses MS Access as front end interacting with Excel,Word,Sigmaplot and R in the background. I use the programs to do different tasks but I mainly use R to create graphics on my Access forms without having to manually open R. To make this short, I was wondering if R can be compiled from Access using the Developer Extensions. I know that the MS office programs can be compiled with it but don't know if it can be done including R. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, 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.
Re: [R] Can I Compile R with MS Access 2003 Developer Extensions?
Le dimanche 31 mai 2009 à 12:08 -0700, Felipe Carrillo a écrit : Hi: I have an application that uses MS Access as front end interacting with Excel,Word,Sigmaplot and R in the background. I use the programs to do different tasks but I mainly use R to create graphics on my Access forms without having to manually open R. To make this short, I was wondering if R can be compiled from Access using the Developer Extensions. I know that the MS office programs can be compiled with it but don't know if it can be done including R. Somehow, I strongly doubt it : R compilation needs tools totally alien to Microsoft's world vision. However, ISTR that there exists some sort of R-WinWorld bridge. Have a look here : http://cran.miroir-francais.fr/contrib/extra/dcom/ Note that I can't vouch for it myself : I didn't touch a Windows computer for years... HTH, Emmanuel Charpentier __ 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] strange behavior when reading csv - line wraps
Big thanks to Ted and Jim for all the help. Martin (Ted Harding) wrote: Ah!!! It was count.fields() which we had overlooked! We discoveered a work-round which involved using Data0 - readLines(file) to create a vector of strings, one for each line of the input file, and then using NF - unlist(lapply(R0,function(x) length(unlist(gregexpr(;,x,fixed=TRUE,useBytes=TRUE)) to count the number of occurrences of ; (the separator) in each line. (NF+1) produces the same result as count.fields(file,sep=;). Thanks for pointing out the existence of count.fields()! Ted. On 31-May-09 15:04:23, jim holtman wrote: You can do something like this: count the number of fields in each line of the file and use the max to determine the number of columns for read.table: file - '/tempxx.txt' maxFields - max(count.fields(file)) # max # now setup read.table for max number input - read.table(file, colClasses=rep(NA, maxFields), fill=TRUE, col.names=paste(V, seq(maxFields), sep='')) On Sun, May 31, 2009 at 6:06 AM, Martin Tomko martin.to...@geo.uzh.chwrote: Dear Jim, with the help of Ted, we diagnosed that the cause is in the extreme variability in line length during reading in. As the table column number is apparently determined fro mthe first five lines, what exceeds this length gets automatically on the next line. I am now trying to find a way to read in the data despite this. I have no control over the table extent, the only thing that would make sense according to my data would be to read in a fixed number of columns and merge all remaining columns as a long string in the last one. No idea how to do this, though. Thanks Martin jim holtman wrote: It is still not clear to me exactly how you want to read the lines in. If the lines have a variable number of fields, and some of the lines might be wrapped, is there some way to determine where the start of each line is. If you are reading them in with read.csv, then the system is assuming that each line starts a new row. If this is not the case, then you will have to state the rules that determine where the lines start. You can always read the data in with 'scan' to separate each line and then do whatever processing is required to put together the rows in a data frame that you want. In one of your examples, you indicated that the line was split starting at the word kempten; if this is in the middle of the line, then you would have to create the break after reading the line in with 'scan' and then creating the rows in the dataframe. All of this can be done in R if you can state what the criteria is. On Sat, May 30, 2009 at 4:32 AM, Martin Tomko martin.to...@geo.uzh.chmailto: martin.to...@geo.uzh.ch wrote: Jim, the two lines I put in are the actual problematic input lines. In these examples, there are no quotes nor # signs, although I have no means to make sure they do not occur in the inputs (any hints how I could deal with that?). I am trying to avoid as much pre-processing outside R as possible, and I have to process about 500 files with up to 3000 records each, so I need a more or less automated/batch solution. - so any string substitution will have to occur in R. But for the moment, I do not see a reaason for substitution, and the wrapping still occurs. Cheers Martin jim holtman wrote: You need to supply the actual input line so we can see what is happening. Are you sure you do not have unbalanced quotes in your input (try quote='') or do you have comment characters (#) in your input? On Fri, May 29, 2009 at 3:15 PM, Martin Tomko martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch mailto:martin.to...@geo.uzh.ch wrote: Dear All, I am observing a strange behavior and searching the archives and help pages didn't help much. I have a csv with a variable number of fields in each line. I use dataPoints - read.csv(inputFile, head=FALSE, sep=;,fill =TRUE); to read it in, and it works. But - some lines are long and 'wrap', or split and continue on the next line. So when I check the dim of the frame, they are not correct and I can see when I do a printout that the lines is split into two in the frame. I checked the input file and all is good. an example of the input is: 37;2175168475;13;8.522729;47.19537;16366...@n00 ;30;sculpture;bird;tourism;animal;statue;canon;eos;rebel;schweiz;switz erland;eagle;swiss;adler;skulptur;zug;1750;28;tamron;f28;canton;touris mus;vogel;baar;kanton;xti;tamron1750;1750mm;tamron1750mm;400d;rabbitri otnet; where the last values occurs on the next line in the data frame. It does not have to be the last value, as in the follwong example, the
Re: [R] IP-Address
wow! :)
vQ
Henrik Bengtsson wrote:
library(gsubfn)
library(gtools)
library(rbenchmark)
n - 1
df - data.frame(
a = rnorm(n),
b = rnorm(n),
c = rnorm(n),
ip = replicate(n, paste(sample(255, 4), collapse='.'), simplify=TRUE)
)
res - benchmark(columns=c('test', 'elapsed'), replications=10, order=NULL,
peda = {
connection - textConnection(as.character(df$ip))
o - do.call(order, read.table(connection, sep='.'))
close(connection)
df[o, ]
},
peda2 = {
connection - textConnection(as.character(df$ip))
dfT - read.table(connection, sep='.', colClasses=rep(integer,
4), quote=, na.strings=NULL, blank.lines.skip=FALSE)
close(connection)
o - do.call(order, dfT)
df[o, ]
},
hb = {
ip - strsplit(as.character(df$ip), split=., fixed=TRUE)
ip - unlist(ip, use.names=FALSE)
ip - as.integer(ip)
dim(ip) - c(4, nrow(df))
ip - 256^3*ip[1,] + 256^2*ip[2,] + 256*ip[3,] + ip[4,]
o - order(ip)
df[o, ]
},
hb2 = {
ip - strsplit(as.character(df$ip), split=., fixed=TRUE)
ip - unlist(ip, use.names=FALSE)
ip - as.integer(ip);
dim(ip) - c(4, nrow(df))
o - sort.list(ip[4,], method=radix, na.last=TRUE)
for (kk in 3:1) {
o - o[sort.list(ip[kk,o], method=radix, na.last=TRUE)]
}
df[o, ]
}
)
print(res)
test elapsed
1 peda4.12
2 peda24.08
3hb0.28
4 hb20.25
__
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] warning message when running quantile regression
Hi All, I am running quantile regression in a for loop starting with 1 variable and adding a variable at a time reaching a maximum of 20 variables. I get the following warning messages after my for loop runs. Should I be concerned about these messages? I am building predictive models and am not interested in inference. Warning messages: 1: In summary.rq(quantreg.emaff) : 3 non-positive fis - I don't understand this message - is this a cause for concern? 2: In summary.rq(quantreg.emaff) : 3 non-positive fis 3: In summary.rq(quantreg.emaff) : 5 non-positive fis 4: In rq.fit.br(x, y, tau = tau, ...) : Solution may be nonunique 5: In summary.rq(quantreg.emaff) : 6 non-positive fis 6: In summary.rq(quantreg.emaff) : 5 non-positive fis 7: In summary.rq(quantreg.emaff) : 5 non-positive fis 8: In summary.rq(quantreg.emaff) : 7 non-positive fis 9: In summary.rq(quantreg.emaff) : 10 non-positive fis 10: In summary.rq(quantreg.emaff) : 9 non-positive fis 11: In summary.rq(quantreg.emaff) : 8 non-positive fis 12: In summary.rq(quantreg.emaff) : 9 non-positive fis 13: In summary.rq(quantreg.emaff) : 8 non-positive fis 14: In summary.rq(quantreg.emaff) : 11 non-positive fis I understand the non-unique solution message. Thanks in advance, Jude Ryan ___ Jude Ryan Director, Client Analytical Services Strategy Business Development UBS Financial Services Inc. 1200 Harbor Boulevard, 4th Floor Weehawken, NJ 07086-6791 Tel. 201-352-1935 Fax 201-272-2914 Email: jude.r...@ubs.com Please do not transmit orders or instructions regarding a UBS account electronically, including but not limited to e-mail, fax, text or instant messaging. The information provided in this e-mail or any attachments is not an official transaction confirmation or account statement. For your protection, do not include account numbers, Social Security numbers, credit card numbers, passwords or other non-public information in your e-mail. Because the information contained in this message may be privileged, confidential, proprietary or otherwise protected from disclosure, please notify us immediately by replying to this message and deleting it from your computer if you have received this communication in error. Thank you. UBS Financial Services Inc. UBS International Inc. UBS Financial Services Incorporated of Puerto Rico UBS AG UBS reserves the right to retain all messages. Messages are protected and accessed only in legally justified cases.__ 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] Problem with reshaping of data
Hi, i have to reshape a dataset. my data have the following format: ID; x1; x2; x3; x4; v1; ... v20 1; 0.1; 0.3; 0.4; 0.2; 2; ... 3 2; 0.3; 0.7; 0.1; 0.2; 1; ... 4 ... 999; 0.9; 0.6; 0.3; 0.1; 4; ... 2 1000; 0.2; 0.6; 0.7; 0.8; 1; ... 5 ID is the number of persons (here 1000 persons) x are descriptive variables and v1-v20 are values of satisfaction on holidays for 20 days and now i should reshape the data such that each record contains only one participiant on one day could somebody help me? i don't know how to do this?! thank you _ [[elided Hotmail spam]] [[elided Hotmail spam]] [[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] Error:non-numeric argument in my function
Hello!
I have a function:
zywnoscCalosc- function( jedzenie, n1, n2, n3, n4, d1, d2, d3, d4 ) {
ndf - data.frame(nn1=n1,nn2=n2,nn3=n3,nn4=n4)
ddf - data.frame(dd1=d1,dd2=d2,dd3=d3,dd4=d4)
for (i in 1:length(n1)){
wekt_n = ndf[i,]
wekt_n_ok = wekt_n[!is.na(wekt_n)]
dl_n = length(wekt_n_ok)
wynik = (1*wekt_n_ok)/(1*dl_n)
}
}
and I get an error like this:
Error in 1 * wekt_n_ok : non-numeric argument to binary operator
Anybody can help me?
--
View this message in context:
http://www.nabble.com/Error%3Anon-numeric-argument-in-my-function-tp23807218p23807218.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] Error:non-numeric argument in my function
Message is very clear:
1 * 'a'
Error in 1 * a : non-numeric argument to binary operator
wekt_n_ok must be non-numeric. You need to provide a reproducible
script. You also need to learn about debugging. 'str(wekt_n_ok )' when the
error occurred may have helped to pinpoint the problem.
On Sun, May 31, 2009 at 5:43 PM, Grze¶ gregori...@gmail.com wrote:
Hello!
I have a function:
zywnoscCalosc- function( jedzenie, n1, n2, n3, n4, d1, d2, d3, d4 ) {
ndf - data.frame(nn1=n1,nn2=n2,nn3=n3,nn4=n4)
ddf - data.frame(dd1=d1,dd2=d2,dd3=d3,dd4=d4)
for (i in 1:length(n1)){
wekt_n = ndf[i,]
wekt_n_ok = wekt_n[!is.na(wekt_n)]
dl_n = length(wekt_n_ok)
wynik = (1*wekt_n_ok)/(1*dl_n)
}
}
and I get an error like this:
Error in 1 * wekt_n_ok : non-numeric argument to binary operator
Anybody can help me?
--
View this message in context:
http://www.nabble.com/Error%3Anon-numeric-argument-in-my-function-tp23807218p23807218.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.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[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] Problem with reshaping of data
x - data.frame(id=1:100, x1=sample(100), x2=sample(100), s1=1, s2=2, s3=3, s4=4) require(reshape) z - melt(x, id=1:3) # first three columns are ids head(z,10) # should be what you want id x1 x2 variable value 1 1 97 43 s1 1 2 2 89 5 s1 1 3 3 59 97 s1 1 4 4 91 86 s1 1 5 5 11 73 s1 1 6 6 27 79 s1 1 7 7 19 85 s1 1 8 8 24 26 s1 1 9 9 10 30 s1 1 10 10 38 67 s1 1 On Sun, May 31, 2009 at 2:06 PM, Christian Schmitt christian_...@hotmail.com wrote: Hi, i have to reshape a dataset. my data have the following format: ID; x1; x2; x3; x4; v1; ... v20 1; 0.1; 0.3; 0.4; 0.2; 2; ... 3 2; 0.3; 0.7; 0.1; 0.2; 1; ... 4 ... 999; 0.9; 0.6; 0.3; 0.1; 4; ... 2 1000; 0.2; 0.6; 0.7; 0.8; 1; ... 5 ID is the number of persons (here 1000 persons) x are descriptive variables and v1-v20 are values of satisfaction on holidays for 20 days and now i should reshape the data such that each record contains only one participiant on one day could somebody help me? i don't know how to do this?! thank you _ [[elided Hotmail spam]] [[elided Hotmail spam]] [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] Problem with reshaping of data
a shorter example: n - 4 x - data.frame(id=1:n, x1=sample(n), x2=sample(n), s1=1, s2=2, s3=3, s4=4) require(reshape) z - melt(x, id=1:3) # first three columns are ids x id x1 x2 s1 s2 s3 s4 1 1 3 1 1 2 3 4 2 2 4 2 1 2 3 4 3 3 1 4 1 2 3 4 4 4 2 3 1 2 3 4 z # should be what you want id x1 x2 variable value 1 1 3 1 s1 1 2 2 4 2 s1 1 3 3 1 4 s1 1 4 4 2 3 s1 1 5 1 3 1 s2 2 6 2 4 2 s2 2 7 3 1 4 s2 2 8 4 2 3 s2 2 9 1 3 1 s3 3 10 2 4 2 s3 3 11 3 1 4 s3 3 12 4 2 3 s3 3 13 1 3 1 s4 4 14 2 4 2 s4 4 15 3 1 4 s4 4 16 4 2 3 s4 4 On Sun, May 31, 2009 at 2:06 PM, Christian Schmitt christian_...@hotmail.com wrote: Hi, i have to reshape a dataset. my data have the following format: ID; x1; x2; x3; x4; v1; ... v20 1; 0.1; 0.3; 0.4; 0.2; 2; ... 3 2; 0.3; 0.7; 0.1; 0.2; 1; ... 4 ... 999; 0.9; 0.6; 0.3; 0.1; 4; ... 2 1000; 0.2; 0.6; 0.7; 0.8; 1; ... 5 ID is the number of persons (here 1000 persons) x are descriptive variables and v1-v20 are values of satisfaction on holidays for 20 days and now i should reshape the data such that each record contains only one participiant on one day could somebody help me? i don't know how to do this?! thank you _ [[elided Hotmail spam]] [[elided Hotmail spam]] [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] IP-Address
Not really, just the old saying that any piece of code can be made
twice as fast (which often holds true recursively). /Henrik
On Sun, May 31, 2009 at 1:58 PM, Wacek Kusnierczyk
waclaw.marcin.kusnierc...@idi.ntnu.no wrote:
wow! :)
vQ
Henrik Bengtsson wrote:
library(gsubfn)
library(gtools)
library(rbenchmark)
n - 1
df - data.frame(
a = rnorm(n),
b = rnorm(n),
c = rnorm(n),
ip = replicate(n, paste(sample(255, 4), collapse='.'), simplify=TRUE)
)
res - benchmark(columns=c('test', 'elapsed'), replications=10, order=NULL,
peda = {
connection - textConnection(as.character(df$ip))
o - do.call(order, read.table(connection, sep='.'))
close(connection)
df[o, ]
},
peda2 = {
connection - textConnection(as.character(df$ip))
dfT - read.table(connection, sep='.', colClasses=rep(integer,
4), quote=, na.strings=NULL, blank.lines.skip=FALSE)
close(connection)
o - do.call(order, dfT)
df[o, ]
},
hb = {
ip - strsplit(as.character(df$ip), split=., fixed=TRUE)
ip - unlist(ip, use.names=FALSE)
ip - as.integer(ip)
dim(ip) - c(4, nrow(df))
ip - 256^3*ip[1,] + 256^2*ip[2,] + 256*ip[3,] + ip[4,]
o - order(ip)
df[o, ]
},
hb2 = {
ip - strsplit(as.character(df$ip), split=., fixed=TRUE)
ip - unlist(ip, use.names=FALSE)
ip - as.integer(ip);
dim(ip) - c(4, nrow(df))
o - sort.list(ip[4,], method=radix, na.last=TRUE)
for (kk in 3:1) {
o - o[sort.list(ip[kk,o], method=radix, na.last=TRUE)]
}
df[o, ]
}
)
print(res)
test elapsed
1 peda 4.12
2 peda2 4.08
3 hb 0.28
4 hb2 0.25
__
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 set a filter during reading tables
There are several things you can tell read.table to make it faster.
First, as mentioned, setting colClasses helps. I think telling read.table how
many rows and columns there are also helps.
When this was not sufficient, I've had to do the data processing
using Python, Perl, or awk.
If that had not been convenient I would have tried the sqldf solution that was
mentioned.
That covers all the options I'm familiar with. I'm also curious about other ways
to selectively read in rows in R. Let me know what ends up working.
On Sun, May 31, 2009 at 2:17 PM, g...@ucalgary.ca wrote:
Since there are many rows, using read.table we spent too much on reading
in rows that we do not want. We are wondering if there is a way to read
only rows that we are interested in. Thanks,
-james
I think you can use readLines(n=1) in loop to skip unwanted rows.
On Mon, Jun 1, 2009 at 12:56 AM, g...@ucalgary.ca wrote:
Thanks, Juliet.
It works for filtering columns.
I am also wondering if there is a way to filter rows.
Thanks again.
-james
One can use colClasses to set which columns get read in. For the
columns you don't
want you can set those to NULL. For example,
cc - c(NULL,rep(numeric,9))
myData -
read.table(myFile.txt,header=TRUE,colClasses=cc,nrow=numRows).
On Wed, May 27, 2009 at 12:27 PM, g...@ucalgary.ca wrote:
We are reading big tables, such as,
Chemicals -
read.table('ftp://ftp.bls.gov/pub/time.series/wp/wp.data.7.Chemicals',header
= TRUE, sep = '\t', as.is =T)
I was wondering if it is possible to set a filter during loading so
that
we just load what we want not the whole table each time. Thanks,
-james
__
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] 'options=utils::recover' not working in .Rprofile or within R
On May 31, 2009, at 12:22 AM, Duncan Murdoch wrote:
David Winsemius wrote:
You are wiping out all of the default options with that approach.
Actually, I think it hid the options() function.
Since I was doing this at the RGui and became concerned that it
appeared I no longer had any options, I restarted. Could I have saved
time by just executing rm(options)?
Try (after restarting R to get the other options back to what they
should be):
op=options() # so you can reset back to baseline
options(error=utils::recover) # do not think the utils:: is needed
Not if you run it in the console, but it is needed in .Rprofile.
Because it might be executed before the loading of the default packages?
--
David
Saving the old option could be done as
olderror - options(error=utils::recover)
Duncan Murdoch
my.func - function(x){
y - x + 12
nonsense
y
}
my.func(14)
Error in my.func(14) : object nonsense not found
Enter a frame number, or 0 to exit
1: my.func(14)
Selection:
On May 30, 2009, at 10:24 PM, Mark Kimpel wrote:
Duncan,
I've pared down my .Rprofile so that it has just the options
line, started R
from terminal (instead of using ESS-emacs) and I still have the
problem. Am
I specifying the options incorrectly? I believe I took this
directly from
the help page.
Not what the examples look like on my machine.
See my output of .Rprofile, the code example that doesn't
work as we think it ought, and my sessionInfo(). Thanks, Mark
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
read.table(~/.Rprofile)
V1
1 options=utils::recover
my.func - function(x){
+ y - x + 12
+ nonsense
+ y
+ }
my.func(14)
Error in my.func(14) : object 'nonsense' not found
sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE = en_US .UTF -8 ;LC_NUMERIC = C ;LC_TIME = en_US .UTF
-8 ;LC_COLLATE = en_US .UTF -8 ;LC_MONETARY = C ;LC_MESSAGES =
en_US .UTF -8 ;LC_PAPER = en_US .UTF -8 ;LC_NAME = C ;LC_ADDRESS
=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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] Error:non-numeric argument in my function
On Sun, May 31, 2009 at 6:10 PM, jim holtman jholt...@gmail.com wrote: Message is very clear: 1 * 'a' Error in 1 * a : non-numeric argument to binary operator Though the user should have been able to figure this out, perhaps the error message could be improved? After all, it is not the fact that the operator is *binary* that implies that its argument must be numeric, but that it is *arithmetic*. The binary operator %in%, for example, takes non-numeric arguments. Suggested replacement error message: non-numeric argument to arithmetic operator -s [[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] Error:non-numeric argument in my function
Thanks jholtman! But I'm not sure what and where I should change my code... :( wekt_n = ndf[i,] wekt_n_ok = wekt_n[!is.na(wekt_n)] If before this line I should change wekt_n_ok as numeric? but if I wrote as.numeric(wekt_n_ok) it's also not correct and I also don't understand why wekt_n_ok is not numeric? -- View this message in context: http://www.nabble.com/Error%3Anon-numeric-argument-in-my-function-tp23807218p23807873.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] grid.edit() for ggplot2
If you enter the code in this post first: https://stat.ethz.ch/pipermail/r-help/2009-May/198791.html then this post shows an example of how to do it with lattice: https://stat.ethz.ch/pipermail/r-help/2009-May/199146.html but I think there is a bug in grid since similar code does not seem to work with your example of grid graphics generated by ggplot2. On Sun, May 31, 2009 at 9:01 AM, baptiste auguie ba...@exeter.ac.uk wrote: Dear all, I'm trying to access and modify grobs in a ggplot2 plot. The basic idea for raw Grid objects I understand from Paul Murrell's R graphics book, or this page of examples, http://www.stat.auckland.ac.nz/~paul/grid/copygrob/copygrobs.R However I can't figure out how to apply this to a ggplot (basically I don't know how to write a syntactically correct gPath), p - # minimal example qplot(0,0)+ annotate(text,0,0,label=test) g - # store the plot as a grob ggplotGrob(p) # structure of the grob grid.ls(g) # rather large! # find a particular grob in the gTree getGrob(g,texts, grep = T) # next step, modify, say, the colour of these grobs grid.edit() # what do I put in here? Thanks for any piece of advice, baptiste __ 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] Error:non-numeric argument in my function
What you need to do is to see that is in 'wekt_n_ok' at that point in your program. You should be able to see it with str(wekt_n_ok) when the error occurs. You can also add a print statement in the loop to print out the value before it is used with the binary operator. It would help if you provided 'str' of the various objects you are using, or maybe some reproducible code. Somehow you are creating a non-numeric value in your code; you need to debug it and check all the values before you use them. On Sun, May 31, 2009 at 7:05 PM, Grze¶ gregori...@gmail.com wrote: Thanks jholtman! But I'm not sure what and where I should change my code... :( wekt_n = ndf[i,] wekt_n_ok = wekt_n[!is.na(wekt_n)] If before this line I should change wekt_n_ok as numeric? but if I wrote as.numeric(wekt_n_ok) it's also not correct and I also don't understand why wekt_n_ok is not numeric? -- View this message in context: http://www.nabble.com/Error%3Anon-numeric-argument-in-my-function-tp23807218p23807873.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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] (no subject)
Hi R-users, I try to use sn package but it give me the following message: install.packages(repos=NULL,pkgs=c:\\Tinn-R\\sn_0.4-12.zip) Warning: package 'sn' is in use and will not be installed updating HTML package descriptions I did tried a few time to save the .zip file but it give me the same error message. Thank you so much for any help given. [[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] (no subject)
use _search()_ to see if the package is on the search path. If yes, use _detach(package:sn,unload=TRUE)_ to detach it and then try to install it again. Ronggui 2009/6/1 Roslina Zakaria zrosl...@yahoo.com: Hi R-users, I try to use sn package but it give me the following message: install.packages(repos=NULL,pkgs=c:\\Tinn-R\\sn_0.4-12.zip) Warning: package 'sn' is in use and will not be installed updating HTML package descriptions I did tried a few time to save the .zip file but it give me the same error message. Thank you so much for any help given. [[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. -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.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] 'options=utils::recover' not working in .Rprofile or within R
options(error=utils::recover)
Does indeed work, at least with the new install of R-devel (to be 2.10.0)
that I am running right now. I was sure I checked this with 2.9.0 last
night, but I am probably mistaken.
One point, the ?options help page is misleading in that the example is
Note that these need to
specified as e.g. 'options=utils::recover' in startup files
such as '.Rprofile'.
Since the use of utils:: is a new requirement, I think stemming from when
utils is loaded, this help page should be corrected as the example is
confusing/incorrect.
So, stick with what is in the first line above and, for now, ignore the help
page.
Mark
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, Mobile VoiceMail
(317) 399-1219 Home
Skype: mkimpel
The real problem is not whether machines think but whether men do. -- B.
F. Skinner
**
On Sat, May 30, 2009 at 10:49 PM, David Winsemius dwinsem...@comcast.netwrote:
You are wiping out all of the default options with that approach.
Try (after restarting R to get the other options back to what they should
be):
op=options() # so you can reset back to baseline
options(error=utils::recover) # do not think the utils:: is needed
my.func - function(x){
y - x + 12
nonsense
y
}
my.func(14)
Error in my.func(14) : object nonsense not found
Enter a frame number, or 0 to exit
1: my.func(14)
Selection:
On May 30, 2009, at 10:24 PM, Mark Kimpel wrote:
Duncan,
I've pared down my .Rprofile so that it has just the options line, started
R
from terminal (instead of using ESS-emacs) and I still have the problem.
Am
I specifying the options incorrectly? I believe I took this directly from
the help page.
Not what the examples look like on my machine.
See my output of .Rprofile, the code example that doesn't
work as we think it ought, and my sessionInfo(). Thanks, Mark
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
read.table(~/.Rprofile)
V1
1 options=utils::recover
my.func - function(x){
+ y - x + 12
+ nonsense
+ y
+ }
my.func(14)
Error in my.func(14) : object 'nonsense' not found
sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
[[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] 'options=utils::recover' not working in .Rprofile or within R
David Winsemius wrote: On May 31, 2009, at 12:22 AM, Duncan Murdoch wrote: David Winsemius wrote: You are wiping out all of the default options with that approach. Actually, I think it hid the options() function. Since I was doing this at the RGui and became concerned that it appeared I no longer had any options, I restarted. Could I have saved time by just executing rm(options)? Yes. Try (after restarting R to get the other options back to what they should be): op=options() # so you can reset back to baseline options(error=utils::recover) # do not think the utils:: is needed Not if you run it in the console, but it is needed in .Rprofile. Because it might be executed before the loading of the default packages? I think ?Startup documents it to do just that. I didn't check the actual source or test it, but usually the docs are right, even if sometimes they aren't. Duncan Murdoch __ 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] 'options=utils::recover' not working in .Rprofile or within R
Mark Kimpel wrote:
options(error=utils::recover)
Does indeed work, at least with the new install of R-devel (to be 2.10.0)
that I am running right now. I was sure I checked this with 2.9.0 last
night, but I am probably mistaken.
One point, the ?options help page is misleading in that the example is
Note that these need to
specified as e.g. 'options=utils::recover' in startup files
such as '.Rprofile'.
Yes, thanks, I'll fix that.
Duncan Murdoch
Since the use of utils:: is a new requirement, I think stemming from when
utils is loaded, this help page should be corrected as the example is
confusing/incorrect.
So, stick with what is in the first line above and, for now, ignore the help
page.
Mark
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, Mobile VoiceMail
(317) 399-1219 Home
Skype: mkimpel
The real problem is not whether machines think but whether men do. -- B.
F. Skinner
**
On Sat, May 30, 2009 at 10:49 PM, David Winsemius dwinsem...@comcast.netwrote:
You are wiping out all of the default options with that approach.
Try (after restarting R to get the other options back to what they should
be):
op=options() # so you can reset back to baseline
options(error=utils::recover) # do not think the utils:: is needed
my.func - function(x){
y - x + 12
nonsense
y
}
my.func(14)
Error in my.func(14) : object nonsense not found
Enter a frame number, or 0 to exit
1: my.func(14)
Selection:
On May 30, 2009, at 10:24 PM, Mark Kimpel wrote:
Duncan,
I've pared down my .Rprofile so that it has just the options line, started
R
from terminal (instead of using ESS-emacs) and I still have the problem.
Am
I specifying the options incorrectly? I believe I took this directly from
the help page.
Not what the examples look like on my machine.
See my output of .Rprofile, the code example that doesn't
work as we think it ought, and my sessionInfo(). Thanks, Mark
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
read.table(~/.Rprofile)
V1
1 options=utils::recover
my.func - function(x){
+ y - x + 12
+ nonsense
+ y
+ }
my.func(14)
Error in my.func(14) : object 'nonsense' not found
sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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] Sweave:Figures from plot (LME output) not getting generated (pdf or eps)
Hi,
I seem to be facing a strange problem when I use Sweave for creating a
LaTeX document of the R lme() output --- The EPS and PDF figure files
get created, but are empty. I have attached a reproducible example
below (taken from the R lme() help example).
\documentclass[a4paper,10pt]{article}
\usepackage{Sweave}
\SweaveOpts{keep.source=TRUE}
\begin{document}
=
fm1 - lme(distance ~ age, Orthodont, random = ~ age | Subject)
@
fig=TRUE=
plot(fm1, distance ~ fitted(.) | Subject, abline = c(0,1))
@
\end{document}
I don't seem to face this problem while plotting other objects. Any
help is appreciated.
Thanks,
-Girish
===
sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.
1252;LC_MONETARY=English_United States.
1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] grid splines stats graphics grDevices utils
datasets methods
[9] base
other attached packages:
[1] RWinEdt_1.8-1 coda_0.13-4verification_1.29
CircStats_0.2-3
[5] boot_1.2-36fields_5.02spam_0.15-4
waveslim_1.6.1
[9] lmtest_0.9-23 zoo_1.5-5 psychometric_2.1
multilevel_2.3
[13] MASS_7.2-46nlme_3.1-92languageR_0.953
lme4_0.999375-31
[17] Matrix_0.999375-26 zipfR_0.6-5lattice_0.17-22
gplots_2.7.0
[21] caTools_1.9bitops_1.0-4.1 gdata_2.4.2
gtools_2.5.0-1
[25] gmodels_2.14.1 ggplot2_0.8.3 reshape_0.8.3
plyr_0.1.8
[29] proto_0.3-8doBy_3.9 foreign_0.8-34
car_1.2-14
[33] Design_2.1-2 survival_2.35-4Hmisc_3.6-0
loaded via a namespace (and not attached):
[1] cluster_1.12.0 Formula_0.1-3kinship_1.1.0-22
plm_1.1-2sandwich_2.2-1
[6] tools_2.9.0
__
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] Bug in truncgof package?
Carlos J. Gil Bellosta wrote:
Dear R-helpers,
I was testing the truncgof CRAN package, found something that looked
like a bug, and did my job: contacted the maintainer. But he did not
reply, so I am resending my query here.
I installed package truncgof and run the example for function ad.test. I
got the following output:
set.seed(123)
treshold - 10
xc - rlnorm(100, 2, 2)# complete sample
xt - xc[xc = treshold]# left truncated sample
ad.test(xt, plnorm, list(meanlog = 2, sdlog = 2), H = 10)
Supremum Class Anderson-Darling Test
data: xt
AD = 3.124, p-value = 0.12
alternative hypothesis: two.sided
treshold = 10, simulations: 100
So I cannot reject the hipothesis (at a standard confidence level) that
the original sample comes from a lognormal distribution (as it is the
case).
But let us try to iterate on this example:
set.seed( 123 )
treshold - 10
foo - function(){
xc - rlnorm(100, 2, 2) # complete sample
xt - xc[xc = treshold] # left truncated sample
ks.test(xt, plnorm, list(meanlog = 2, sdlog = 2), H =
10)$p.value
}
results - replicate( 100, foo() )
Then:
table( results )
results
0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.1 0.11 0.16 0.18
0.19 0.2
257931234112211
32
0.21 0.22 0.26 0.27 0.28 0.3 0.31 0.32 0.33 0.36 0.38 0.4 0.44 0.49
0.54 0.55
22131211121211
21
0.56 0.57 0.62 0.7 0.76 0.78 0.96 0.98
12111111
This is, in a 45% of the cases, you would reject the H_0 hypothesis,
which happens to be true, at the 5% standard confidence level.
That looks to me that the test as implemented is not very good. This
could be an implementation bug, but it could also be a limitation of the
test itself. I don't know the theory underlying this particular test,
but a way to determine it is in implementation bug is to carefully
implement the test and see if you got the same answer.
Duncan Murdoch
Do you think this behaviour is buggy? If so, given that the maintainer
does not seem to be contactable, what would be the next step to take?
Best regards,
Carlos J. Gil Bellosta
http://www.datanalytics.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-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.
