[R] Sweave absolute path versus relative path
Sorry, I should have really started a new thread with this because really it
is a new question only loosely related to the first Q.
Thanks for the assist.
As suggested I switched over to sweave. I have a lot of .tex tables that I
have already created that I was previously inserting into my tex document
(using \input). The journal I plan on submitting to eventually wants the
final .tex file so I thought it would be a good idea to use Sweave, it makes
a tex doc with my tables generated and it should be all good.
I just spend a few hours trying to get the \SweaveInput commant to work
properly. I finally determined that I couldn't put the file in as an
absolute path but it had to be a relative path. I.e
\SweaveInput{/home/tdavies/Dropbox/CollapseRecovery_Shared/trevor/afterAFS/writing/sweave/blah.tex}
gave the error:
R CMD Sweave hitmiss.Rnw
Error in SweaveReadFile(c(ifile, file), syntax, encoding = encoding) :
no Sweave file with name
'.//home/tdavies/Dropbox/CollapseRecovery_Shared/trevor/afterAFS/writing/sweave/blah.tex'
found
Calls: Anonymous - Sweave - SweaveReadFile - SweaveReadFile
Execution halted
make: *** [hitmiss.tex] Error 1
However, when i use:
\SweaveInput{../../../../../../../../home/tdavies/Dropbox/CollapseRecovery_Shared/trevor/afterAFS/writing/sweave/blah.tex}
It works fine.
What am I missing here?
Thanks.
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Re: [R] Split an array into arbirtary sizes
sorry! vols=read.csv(file=C:/Documents and Settings/Hugh/My Documents/PhD/QuickDirtyVols.csv + , header=TRUE, sep=,) x-ts(vols[,2]) x so I have an ts object of 500 elements. I want to be able to split the array into say two parts of 250? How can I do it? I want to keep the elements in the same order -- View this message in context: http://r.789695.n4.nabble.com/Split-an-array-into-arbirtary-sizes-tp3948938p3949426.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help with ggplot backgrounds
Hi, I have two questions regarding plotting of this dataset: Product ColorStoreA StoreB StoreC Price A Red 4 2378 Blue 5 22 78 Greem4 3 2 80 B Red 3 And so on (Not all products have same colors). I made 2 plots: one is a scatter where x=Price and y=Values (of different stores). The different stores are facet_wrapped, and Color is indicated by point color while Product by point_shape. Second plot is a polar plot of geom_bars with position=dodge for all Products to differentiate the colors. The y value is the value for each store (Price is not represented). My questions: 1. for the first plot, I want to make a background area split into 3, top right is red (indicating high-price/high-values), middle is yellow, the rest is green (these are kind of reverse-log areas, like in heat maps). 2. for the second plot, the red-yellow green are just background geom_rects filled in, but I cant figure out how to specify the xmin and xmax for this (since they are discrete variables). Any help will be appreciated, thanks. -- View this message in context: http://r.789695.n4.nabble.com/help-with-ggplot-backgrounds-tp3949320p3949320.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problem with glsm.krige: trendd and trend l must have similar specifications error
Hello, I used glsm.mcmc and likfit.glsm to create model. Now I want to predict at different locations, but I can't get glsm.krige to work. I keep getting the error that trend.d and trend.l must have similar specifications. I have tried numerous ways to include the covariates in the glsm.krige model, and I keep getting the same error message. The bolded part is the part that doesn't work. Any help would be appreciated! reddmcmc=glsm.mcmc(geodata, coords=geodata$coords, data=geodata$data,model=list(family=poisson, cov.pars=c(50,8000),beta=c(-26,-.04,6.94),cov.model=spherical,nugget=5,trend=~powerb1+temp1),mcmc.input = mcmc.control(S.scale =.01 ,thin=10)) prepareredd1=prepare.likfit.glsm(reddmcmc) lik.redd1.1 - likfit.glsm(prepareredd1, ini.phi = 10,cov.model = spherical,trend=~powerb1 + temp1) # predict at new locations trendpred=trend.spatial(~habitat2$powerb + habitat2$avgtemp) test2 - glsm.krige(reddmcmc,coords,trend.l=trendpred) # trend.d and trend.l must have similar specifications ? test2 - glsm.krige(reddmcmc,coords,trend.l=habitat2$powerb + habitat2$avgtemp) # same error message... [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to plot survival data from multiple trials (simulations)?
Dear all: Could anyone please provide some R codes to plot the below survival data to compare two groups (0 vs 1) after 2 simulations (TRL)? need 95% prediction interval on the plot from these 2 trials. I would like to simulate 1000 trials later. Thanks a lot for your great help and consideration! yan TRL ID ECOG BASE PTR8 GROUP POP ST ind 1 1 1 1 2.2636717 0.255634126 1 1 99.4 F 3 1 2 1 24.7719223 0.756458142 0 1 8.1 T 5 1 3 0 4.7685832 0.908777937 1 0 2.6 T 7 1 4 0 2.5934492 -0.231564522 1 1 7.4 T 9 1 5 0 4.7309141 -2.455991696 0 1 0.4 T 11 1 6 1 3.5904766 -0.459694803 1 1 13.1 T 13 1 7 1 4.8592495 0.983131140 1 1 17.8 T 15 1 8 1 3.1308760 -1.136462783 0 0 10.6 T 17 1 9 1 5.8127637 -0.131647588 0 1 1.2 T 19 1 10 0 4.0875668 -3.567509428 0 1 0.4 T 21 1 11 1 14.7112528 0.900416367 1 1 15.2 T 23 1 12 0 6.7290298 -0.140283251 0 0 8.5 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 25 1 13 0 6.6118789 -0.095603854 0 1 13.8 T 27 1 14 1 1.1191479 0.735691765 1 1 60.5 F 29 1 15 0 11.9169275 0.796172293 0 0 40.1 F 31 1 16 1 6.7940011 0.845746271 1 1 68.1 F 33 1 17 0 4.7380330 0.582527179 1 1 11.7 T 35 1 18 0 12.0571049 0.165637187 0 0 25.0 T 37 1 19 1 3.1922217 0.891862148 1 1 34.0 T 39 1 20 0 10.6253830 -0.747701704 0 1 7.8 T 41 1 21 0 2.0178336 -2.732716143 0 1 0.8 T 43 1 22 1 13.8066137 0.706372607 0 1 58.2 F 45 1 23 1 11.8844261 0.842735359 1 1 13.9 T 47 1 24 1 3.9546421 0.193353044 0 1 2.7 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 49 1 25 0 27.0913396 0.970400135 1 1 19.1 T 51 1 26 1 12.0249672 0.886403017 1 1 27.1 T 53 1 27 1 5.9453281 0.964694968 1 1 21.2 T 55 1 28 0 6.8084911 -1.333850454 1 0 4.1 T 57 1 29 1 8.3642227 -0.024960757 0 1 4.4 T 59 1 30 0 26.6382483 0.714020234 0 0 3.9 T 61 1 31 1 13.1107410 0.372041597 0 1 26.2 T 63 1 32 0 4.2271255 0.056569282 1 1 14.3 T 65 1 33 0 17.7269456 0.252550311 0 0 11.2 T 67 1 34 1 3.6215522 -0.282323084 0 0 0.3 T 69 1 35 1 19.3787770 0.349288143 0 1 5.2 T 71 1 36 0 8.9546567 0.945492048 1 1 15.2 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 73 1 37 0 2.7796959 -3.119155682 0 0 12.3 T 75 1 38 0 9.4029912 -0.793046460 0 1 1.2 T 77 1 39 1 7.8146429 0.888593758 1 1 8.0 T 79 1 40 0 9.6419102 0.525301532 1 1 22.4 T 81 1 41 1 3.3174969 0.915870306 1 1 24.7 T 83 1 42 1 12.4030358 0.661856980 1 1 16.4 T 85 1 43 1 24.2982862 0.710967270 0 1 5.5 T 87 1 44 0 10.4332028 0.940833126 1 0 2.9 T 89 1 45 0 4.7520799 0.897518558 1 1 32.6 T 91 1 46 0 2.7028663 -3.484128492 0 1 0.2 T 93 1 47 1 2.7572158 0.890976979 1 0 30.9 T 95 1 48 0 7.2240161 -0.377073350 0 0 3.7 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 97 1 49 0 20.6156368 0.500864314 0 1 12.2 T 99 1 50 1 12.8547093 0.982784519 1 1 54.4 F 2 2 1 1 3.0862631 0.931988949 1 1 199.2 F 4 2 2 1 18.6633707 0.540651036 0 1 8.1 T 6 2 3 0 5.5728260 -1.851336117 1 0 3.0 T 8 2 4 0 4.0740408 0.021119280 1 1 10.1 T 10 2 5 0 14.2396242 0.465013972 0 1 6.6 T 12 2 6 1 37.5234448 0.986992132 1 1 30.5 T 14 2 7 1 11.2925748 0.922905093 1 1 14.0 T 16 2 8 1 15.2298842 0.459418082 0 0 12.6 T 18 2 9 1 5.3266590 -1.487487920 0 1 0.3 T 20 2 10 0 11.7956270 0.606294774 0 1 26.9 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 22 2 11 1 26.0051377 0.823996317 1 1 8.6 T 24 2 12 0 4.7851855 -1.635216564 0 0 10.7 T 26 2 13 0 5.4896572 -1.085740446 0 1 3.8 T 28 2 14 1 15.0284557 0.981428564 1 1 56.1 F 30 2 15 0 15.3001584 -0.101949376 0 0 36.7 T 32 2 16 1 4.1838899 -0.002416447 1 1 26.0 T 34 2 17 0 1.9213881 0.678721863 1 1 15.5 T 36 2 18 0 22.0870166 0.682030393 0 0 18.8 T 38 2 19 1 7.8815644 0.938210236 1 1 25.9 T 40 2 20 0 6.8308086 -0.774314088 0 1 8.5 T 42 2 21 0 6.0056206 -0.656448295 0 1 5.4 T 44 2 22 1 11.9301049 0.137476151 0 1 32.2 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 46 2 23 1 4.4453597 0.932378925 1 1 18.3 T 48 2 24 1 7.0352655 0.142463064 0 1 2.4 T 50 2 25 0 22.1603315 0.990013687 1 1 23.5 T 52 2 26 1 1.7582992 0.041687569 1 1 13.6 T 54 2 27 1 4.0864310 0.893550143 1 1 18.7 T 56 2 28 0 3.7564158 0.149721394 1 0 3.1 T 58 2 29 1 23.7880592 0.312680371 0 1 4.0 T 60 2 30 0 7.3082204 0.084729300 0 0 3.4 T 62 2 31 1 29.8669157 0.779756301 0 1 24.3 T 64 2 32 0 6.7967624 0.228897567 1 1 15.8 T 66 2 33 0 9.0048160 -1.073334969 0 0 9.5 T 68 2 34 1 9.3920052 0.183028557 0 0 0.3 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 70 2 35 1 17.0794700 0.575865059 0 1 6.7 T 72 2 36 0 5.8638675 0.986021171 1 1 18.2 T 74 2 37 0 12.7073727 0.808851125 0 0 11.6 T 76 2 38 0 6.6391834 -0.515246589 0 1 1.5 T 78 2 39 1 4.0731162 0.640324530 1 1 6.9 T 80 2 40 0 8.1501724 0.963706289 1 1 37.9 T 82 2 41 1 7.1095450 0.852592536 1 1 19.9 T 84 2 42 1 6.3169479 0.686874101 1 1 23.2 T 86 2 43 1 12.8719503 -0.442671821 0 1 2.5 T 88 2 44 0 19.2469239 0.982064666 1 0 3.3 T 90 2 45 0 6.7743672 0.724107074 1 1 24.1 T 92 2 46 0 7.9332652 0.050580084 0 1 5.9 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 94 2 47 1 0.6997334 -0.146007844 1 0 23.7 T 96 2 48 0 14.6486847 0.723251604 0 0 4.5 T 98 2 49 0 4.1576131 0.232732832 0 1 15.6 T 100 2 50 1 7.2583626 0.811803286 1 1 49.0 F
[R] Matching
I have a spatial weight file in csv that I want as listw object in R. The file has the following 3 variables (left to right in the file) -- OID_, NID and WEIGHTS. NID stands for the neighbors and OID_ as the origins. There are 217 origins with 4 neighbors each. I have been able to read the csv file as a data frame (test.csv). Then I tried to check whether the OID_ variable is in the right place in the dataframe. I used match for that using: o - match(OID_, OID_) I am not sure whether this is the right way to match. Please advice. Anyway, next I created a matrix object (m) using: m - as.matrix(test.csv[, -1]) Then I created object m1, using: m1 - m[o, o] Finally, I tried creating listw object using: mat2listw(m1) Here I get an error that x is not a square matrix. Not sure what to do now. Any helo appreciated! Thanks, Shishm __ 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] Extracting data by row
Thanks everyone for you help with my last question, and now I have one last one... Here is a sample of my data in .csv format site,time_local,time_utc,reef_type_code,sensor_type,sensor_depth_m,temperature_c 06,2006-04-09 10:20:00,2006-04-09 20:20:00,BAK,sb39, 2, 29.63 06,2006-04-09 10:40:00,2006-04-09 20:40:00,BAK,sb39, 2, 29.56 06,2006-04-09 11:00:00,2006-04-09 21:00:00,BAK,sb39, 2, 29.51 06,2006-04-09 11:20:00,2006-04-09 21:20:00,BAK,sb39, 2, 29.53 06,2006-04-09 11:40:00,2006-04-09 21:40:00,BAK,sb39, 10, 29.57 06,2006-04-09 12:00:00,2006-04-09 22:00:00,BAK,sb39, 2, 29.60 06,2006-04-09 12:20:00,2006-04-09 22:20:00,BAK,sb39, 2, 29.66 06,2006-04-09 12:40:00,2006-04-09 22:40:00,BAK,sb39, 10, 29.68 06,2006-04-09 13:00:00,2006-04-09 23:00:00,BAK,sb39, 2, 29.68 My goal was to extract all of the rows from a certain depth. Using the column sensor_depth_m to order my data by, I wanted all of the data from 10m. So this is what I wanted when I finished site,time_local,time_utc,reef_type_code,sensor_type,sensor_depth_m,temperature_c 06,2006-04-09 11:40:00,2006-04-09 21:40:00,BAK,sb39, 10, 29.57 06,2006-04-09 12:40:00,2006-04-09 22:40:00,BAK,sb39, 10, 29.68 06,2006-04-09 13:00:00,2006-04-09 23:00:00,BAK,sb39, 10, 29.68 To pull out all of the data from a 10m sensor depth I came up with the code: Ten-dataTable1[(dataTable1$sensor_depth_m==10),] But when I run it I just get an extra column tacked onto the end like this site,time_local,time_utc,reef_type_code,sensor_type,sensor_depth_m,temperature_c, sensor_depth_m 06,2006-04-09 10:20:00,2006-04-09 20:20:00,BAK,sb39, 2, 29.63,10 06,2006-04-09 10:40:00,2006-04-09 20:40:00,BAK,sb39, 2, 29.56,10 06,2006-04-09 11:00:00,2006-04-09 21:00:00,BAK,sb39, 2, 29.51,10 06,2006-04-09 11:20:00,2006-04-09 21:20:00,BAK,sb39, 2, 29.53,10 06,2006-04-09 11:40:00,2006-04-09 21:40:00,BAK,sb39, 10, 29.57,10 06,2006-04-09 12:00:00,2006-04-09 22:00:00,BAK,sb39, 2, 29.60,10 06,2006-04-09 12:20:00,2006-04-09 22:20:00,BAK,sb39, 2, 29.66,10 06,2006-04-09 12:40:00,2006-04-09 22:40:00,BAK,sb39, 10, 29.68,10 06,2006-04-09 13:00:00,2006-04-09 23:00:00,BAK,sb39, 10, 29.68,10 It seems pretty straight forward, I'm not sure what I am missing. Thanks V [[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] fPortfolio constraints
I have a list of 5 stocks consisting of IBM, AXP, XOM, BA, GE. I am able to solve the optimal portfolio without long only constraints along with group weight constraints. However, I am not able to add one more constraint regarding Beta of the portfolio with upper bound of 1.1 and lower bound of .9. The Beta of each individual stock is in a set of defined data. May anyone be able to help? Appreciated much. -- View this message in context: http://r.789695.n4.nabble.com/fPortfolio-constraints-tp3950116p3950116.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] alternative option in skewness and kurtosis tests?
On Oct 25, 2011, at 18:23 , Xiang Gao wrote: I have a question about the D'Agostino skewness test and the Anscombe-Glynn kurtosis test. agostino.test(x, alternative = c(two.sided, less, greater)) anscombe.test(x, alternative = c(two.sided, less, greater)) The option alternative in those two functions seems to be the null hypothesis. In the output, the statement about the alternative hypothesis is correct, which is opposite to what you specify in command. An example below: Certainly looks like a bug. You should contact the maintainers of the contributed package containing these tests. -pd skewdata = c(rep(44,5),rep(43,15),rep(42,10),rep(41,4),rep(40,3),rep(39,2),rep(38,1)) agostino.test(skewdata, alternative = greater) D'Agostino skewness test data: skewdata skew = -1.0014, z = -1.7209, p-value = 0.04264 alternative hypothesis: data have negative skewness anscombe.test(skewdata, alternative=„less) Anscombe-Glynn kurtosis test data: skewdata kurt = 3.4748, z = 1.0716, p-value = 0.1419 alternative hypothesis: kurtosis is greater than 3 -- [[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. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extracting data by row
On Friday 28 October 2011 18:04:59 Vinny Moriarty wrote: Thanks everyone for you help with my last question, and now I have one last one... Here is what I would do, based on my understanding of your question: # your data snippet as data frame x site time_localtime_utc reef_type_code sensor_type 16 2006-04-09 10:20:00 2006-04-09 20:20:00BAKsb39 26 2006-04-09 10:40:00 2006-04-09 20:40:00BAKsb39 36 2006-04-09 11:00:00 2006-04-09 21:00:00BAKsb39 46 2006-04-09 11:20:00 2006-04-09 21:20:00BAKsb39 56 2006-04-09 11:40:00 2006-04-09 21:40:00BAKsb39 66 2006-04-09 12:00:00 2006-04-09 22:00:00BAKsb39 76 2006-04-09 12:20:00 2006-04-09 22:20:00BAKsb39 86 2006-04-09 12:40:00 2006-04-09 22:40:00BAKsb39 96 2006-04-09 13:00:00 2006-04-09 23:00:00BAKsb39 sensor_depth_m temperature_c 1 2 29.63 2 2 29.56 3 2 29.51 4 2 29.53 5 10 29.57 6 2 29.60 7 2 29.66 8 10 29.68 9 2 29.68 # extracting all 10m depth sensors using subscripting Ten - x[x[sensor_depth_m]==10,] Ten site time_localtime_utc reef_type_code sensor_type 56 2006-04-09 11:40:00 2006-04-09 21:40:00BAKsb39 86 2006-04-09 12:40:00 2006-04-09 22:40:00BAKsb39 sensor_depth_m temperature_c 5 10 29.57 8 10 29.68 Does that help? Rgds, Rainer On Friday 28 October 2011 18:04:59 Vinny Moriarty wrote: Thanks everyone for you help with my last question, and now I have one last one... Here is a sample of my data in .csv format site,time_local,time_utc,reef_type_code,sensor_type,sensor_depth_m,temper ature_c 06,2006-04-09 10:20:00,2006-04-09 20:20:00,BAK,sb39, 2, 29.63 06,2006-04-09 10:40:00,2006-04-09 20:40:00,BAK,sb39, 2, 29.56 06,2006-04-09 11:00:00,2006-04-09 21:00:00,BAK,sb39, 2, 29.51 06,2006-04-09 11:20:00,2006-04-09 21:20:00,BAK,sb39, 2, 29.53 06,2006-04-09 11:40:00,2006-04-09 21:40:00,BAK,sb39, 10, 29.57 06,2006-04-09 12:00:00,2006-04-09 22:00:00,BAK,sb39, 2, 29.60 06,2006-04-09 12:20:00,2006-04-09 22:20:00,BAK,sb39, 2, 29.66 06,2006-04-09 12:40:00,2006-04-09 22:40:00,BAK,sb39, 10, 29.68 06,2006-04-09 13:00:00,2006-04-09 23:00:00,BAK,sb39, 2, 29.68 My goal was to extract all of the rows from a certain depth. Using the column sensor_depth_m to order my data by, I wanted all of the data from 10m. So this is what I wanted when I finished site,time_local,time_utc,reef_type_code,sensor_type,sensor_depth_m,temper ature_c 06,2006-04-09 11:40:00,2006-04-09 21:40:00,BAK,sb39, 10, 29.57 06,2006-04-09 12:40:00,2006-04-09 22:40:00,BAK,sb39, 10, 29.68 06,2006-04-09 13:00:00,2006-04-09 23:00:00,BAK,sb39, 10, 29.68 To pull out all of the data from a 10m sensor depth I came up with the code: Ten-dataTable1[(dataTable1$sensor_depth_m==10),] But when I run it I just get an extra column tacked onto the end like this site,time_local,time_utc,reef_type_code,sensor_type,sensor_depth_m,temper ature_c, sensor_depth_m 06,2006-04-09 10:20:00,2006-04-09 20:20:00,BAK,sb39, 2, 29.63,10 06,2006-04-09 10:40:00,2006-04-09 20:40:00,BAK,sb39, 2, 29.56,10 06,2006-04-09 11:00:00,2006-04-09 21:00:00,BAK,sb39, 2, 29.51,10 06,2006-04-09 11:20:00,2006-04-09 21:20:00,BAK,sb39, 2, 29.53,10 06,2006-04-09 11:40:00,2006-04-09 21:40:00,BAK,sb39, 10, 29.57,10 06,2006-04-09 12:00:00,2006-04-09 22:00:00,BAK,sb39, 2, 29.60,10 06,2006-04-09 12:20:00,2006-04-09 22:20:00,BAK,sb39, 2, 29.66,10 06,2006-04-09 12:40:00,2006-04-09 22:40:00,BAK,sb39, 10, 29.68,10 06,2006-04-09 13:00:00,2006-04-09 23:00:00,BAK,sb39, 10, 29.68,10 It seems pretty straight forward, I'm not sure what I am missing. Thanks V [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Add col in data.frame
Hello Gurus, I am still new to R. Here is my issue. I was trying to add column to data frame that was populated by read.spss(). When I used cbind to add a new variable(column). library(foreign) mydf-read.spss(file=C:/myspss.sav,use.value.labels=FALSE, to.data.frame=TRUE,use.missings=FALSE) attr(mydf,variable.labels) ## it gives you all the labels ##Adding a new variable(col) to mydf newcolm - list(frt=grapes) mydf - cbind(mydf, newrow) ##Now checking to see labels again attr(mydf,variable.labels) ## And you get NULL Can anyone please help me to achieve this without loosing any default attribute that was there? Thanks and Regards -- SmartG [[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] Add col in data.frame
On 10/29/2011 06:54 PM, Smart Guy wrote: Hello Gurus, I am still new to R. Here is my issue. I was trying to add column to data frame that was populated by read.spss(). When I used cbind to add a new variable(column). library(foreign) mydf-read.spss(file=C:/myspss.sav,use.value.labels=FALSE, to.data.frame=TRUE,use.missings=FALSE) attr(mydf,variable.labels) ## it gives you all the labels ##Adding a new variable(col) to mydf newcolm- list(frt=grapes) mydf- cbind(mydf, newrow) ##Now checking to see labels again attr(mydf,variable.labels) ## And you get NULL Can anyone please help me to achieve this without loosing any default attribute that was there? Hi SmartG, I assume that the newcolm-newrow is just a typo in the example above. Assuming that you are managing to get your new column in mydf, you can add the new variable name like this: oldvl-attr(mydf,variable.labels) mydf-cbind(mydf,newrow) attr(mydf,variable.labels)-c(oldvl,newvar) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Add col in data.frame
Hi Jim, I am sorry for the typo. Thats 'newcolm' everywhere. Thanks for the help. I think this should work now. :) Thanks and Regards SmartG On 29 October 2011 13:34, Jim Lemon j...@bitwrit.com.au wrote: On 10/29/2011 06:54 PM, Smart Guy wrote: Hello Gurus, I am still new to R. Here is my issue. I was trying to add column to data frame that was populated by read.spss(). When I used cbind to add a new variable(column). library(foreign) mydf-read.spss(file=C:/**myspss.sav,use.value.labels=**FALSE, to.data.frame=TRUE,use.**missings=FALSE) attr(mydf,variable.labels) ## it gives you all the labels ##Adding a new variable(col) to mydf newcolm- list(frt=grapes) mydf- cbind(mydf, newrow) ##Now checking to see labels again attr(mydf,variable.labels) ## And you get NULL Can anyone please help me to achieve this without loosing any default attribute that was there? Hi SmartG, I assume that the newcolm-newrow is just a typo in the example above. Assuming that you are managing to get your new column in mydf, you can add the new variable name like this: oldvl-attr(mydf,variable.**labels) mydf-cbind(mydf,newrow) attr(mydf,variable.labels)-**c(oldvl,newvar) Jim -- SmartG [[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] Sweave absolute path versus relative path
On 11-10-29 1:58 AM, Trevor Davies wrote:
Sorry, I should have really started a new thread with this because really it
is a new question only loosely related to the first Q.
Thanks for the assist.
I haven't looked at the Sweave sources, so I don't know why a relative
path is needed, but I think you can probably use the LaTeX \input
command (or possibly \include, but it sounds as though \input is better)
rather than SweaveInput. You would use SweaveInput if the file includes
markup that needs to be processed by Sweave. If it's just some .tex to
include, let LaTeX do it.
Duncan Murdoch
As suggested I switched over to sweave. I have a lot of .tex tables that I
have already created that I was previously inserting into my tex document
(using \input). The journal I plan on submitting to eventually wants the
final .tex file so I thought it would be a good idea to use Sweave, it makes
a tex doc with my tables generated and it should be all good.
I just spend a few hours trying to get the \SweaveInput commant to work
properly. I finally determined that I couldn't put the file in as an
absolute path but it had to be a relative path. I.e
\SweaveInput{/home/tdavies/Dropbox/CollapseRecovery_Shared/trevor/afterAFS/writing/sweave/blah.tex}
gave the error:
R CMD Sweave hitmiss.Rnw
Error in SweaveReadFile(c(ifile, file), syntax, encoding = encoding) :
no Sweave file with name
'.//home/tdavies/Dropbox/CollapseRecovery_Shared/trevor/afterAFS/writing/sweave/blah.tex'
found
Calls:Anonymous - Sweave - SweaveReadFile - SweaveReadFile
Execution halted
make: *** [hitmiss.tex] Error 1
However, when i use:
\SweaveInput{../../../../../../../../home/tdavies/Dropbox/CollapseRecovery_Shared/trevor/afterAFS/writing/sweave/blah.tex}
It works fine.
What am I missing here?
Thanks.
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Re: [R] program never enters browser mode when I add browser()
I see two possibilities:
1) the call to 'browser' is inside an 'if'
clause that doesn't exectute.
2) the call forgets the parentheses, so it is:
browser
rather than
browser()
On 28/10/2011 20:04, M. Tran wrote:
Dear All
I have a program that breaks at the following lines of code:
bigfunction =
{
...
object1 = myfunction(x)
object2 = strsplit(object1, ,)[[1]]
...
}
where myfunction is defined elsewhere outside of bigfunction.
The error I get is error in strsplit() -- object1 not found.
However, when I insert browser() into my code so that the above reads,
bigfunction =
{
...
browser()
object1 = myfunction(x)
object2 = strsplit(object1, ,)[[1]]
...
}
my entire program runs successfully, and oddly *never enters browser mode*.
Has anyone encountered a similar problem? Any advice would be greatly
appreciated.
Thank you,
Michelle
--
View this message in context:
http://r.789695.n4.nabble.com/program-never-enters-browser-mode-when-I-add-browser-tp3948920p3948920.html
Sent from the R help mailing list archive at Nabble.com.
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--
Patrick Burns
pbu...@pburns.seanet.com
twitter: @portfolioprobe
http://www.portfolioprobe.com/blog
http://www.burns-stat.com
(home of 'Some hints for the R beginner'
and 'The R Inferno')
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Re: [R] Graphics Reciprocal labeling
Thank you both so very much. -- View this message in context: http://r.789695.n4.nabble.com/Graphics-Reciprocal-labeling-tp3949054p3950480.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] Contrasts with an interaction. How does one specify the dummy variables for the interaction
John, There is a good example of one way of doing this in multcomp-examples.pdf of package multcomp. See pages 8 to 10. Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com/Contrasts-with-an-interaction-How-does-one-specify-the-dummy-variables-for-the-interaction-tp3948792p3950225.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] Split an array into arbirtary sizes
The short answer is that you need to use the window() command with ts objects. The (ever so slightly) longer answer is that no one really likes ts objects and that's why a proliferation of contributed packages exist to deal with their idiosyncracies. The most popular for finance are zoo and xts and I heartily recommend you start using those for your analysis if at all possible. If you use those, you can use simple commands like x[1:250] to get the first 250 elements or you can subset by time for xts which is very nice. Michael On Fri, Oct 28, 2011 at 6:59 PM, Bazman76 h_a_patie...@hotmail.com wrote: sorry! vols=read.csv(file=C:/Documents and Settings/Hugh/My Documents/PhD/QuickDirtyVols.csv + , header=TRUE, sep=,) x-ts(vols[,2]) x so I have an ts object of 500 elements. I want to be able to split the array into say two parts of 250? How can I do it? I want to keep the elements in the same order -- View this message in context: http://r.789695.n4.nabble.com/Split-an-array-into-arbirtary-sizes-tp3948938p3949426.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-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] Correllogram of Daily Time Series
I'm not an expert on these things, but I don't believe so. acf/pacf doesn't require a ts object so it doesn't really need things to fit the exact nuances of the ts class. You may have to be a little careful in interpretation however depending on the nature of the irregular spacing, but that's going to be problem dependent. Eitherway, take a look at the packages I endorsed in your other thread so you don't have deal with issues like lying to ts about your data. Michael On Thu, Oct 27, 2011 at 4:23 PM, Bazman76 h_a_patie...@hotmail.com wrote: I did it using the code below thank you. Will the fact I have used a ts object but the observations are not really equally spaced invalidate the results? vols=read.csv(file=C:/Documents and Settings/Hugh/My Documents/PhD/Swaption vols.csv + , header=TRUE, sep=,) x-ts(vols[,2]) x acf(x) -- View this message in context: http://r.789695.n4.nabble.com/Correllogram-of-Daily-Time-Series-tp3944094p3945927.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R help with different combinations of vectors of different sizes
Hi, I am trying to get different combinations of a vector of different size and find their sum. For example, if I have a vector (i,j) where i and j can be anything from 0 to 5, i get these combinations (0,0), (0,1), (1,0), (1,1), (2,0), .. (5,5) and find sum of these as 0, 1, 1, 2, . , 10. I used outer functions to get this and it worked. What if I have a vector (i,j,k) where all i, j , and k can be anything from 0 to 5. I want to do the same thing here. Get all the combinations and sum them up. (0,0,0) (0,0,1), (0,1,0), (1,0,0), (5,5,5) How can I get these combinations and find their sums? Thank you very much in advance. Uka [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R help with different combinations of vectors of different sizes
Just add another outer wrapper:
outer(1:5, outer(1:5, 1:5, +), +)
If you are going to arbitrarily long tuples, it may be worthwhile to
put this in a wrapper like so:
tupleSums - function(vec, n){
stopifnot(all.equal(n, as.integer(n)))
n - as.integer(n)
if (n == 1L) return(vec)
ans - outer(vec, vec, +)
if (n == 2L) return(ans)
else{
for (i in 3:n) ans - outer(vec, ans, +)
}
return(ans)
}
Though this really could be made much more efficient if you want:
e.g., for the n = 4 case, it would be better to take outer( outer(vec,
vec, +), outer(vec, vec, +), +).
Michael
On Sat, Oct 29, 2011 at 9:08 AM, Suleyman K s.ka...@gmail.com wrote:
Hi,
I am trying to get different combinations of a vector of different size and
find their sum. For example, if I have a vector (i,j) where i and j can be
anything from 0 to 5, i get these combinations (0,0), (0,1), (1,0), (1,1),
(2,0), .. (5,5) and find sum of these as 0, 1, 1, 2, . , 10. I used
outer functions to get this and it worked. What if I have a vector (i,j,k)
where all i, j , and k can be anything from 0 to 5. I want to do the same
thing here. Get all the combinations and sum them up. (0,0,0) (0,0,1),
(0,1,0), (1,0,0), (5,5,5) How can I get these combinations and find
their sums? Thank you very much in advance.
Uka
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [R] R help with different combinations of vectors of different sizes
Another approach is to use expand.grid to create a
data.frame of all possible combinations of elements
of its input vectors:
rowSums(expand.grid(0:5, 0:5, 0:5))
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of R. Michael
Weylandt
Sent: Saturday, October 29, 2011 7:46 AM
To: Suleyman K
Cc: r-help@r-project.org
Subject: Re: [R] R help with different combinations of vectors of different
sizes
Just add another outer wrapper:
outer(1:5, outer(1:5, 1:5, +), +)
If you are going to arbitrarily long tuples, it may be worthwhile to
put this in a wrapper like so:
tupleSums - function(vec, n){
stopifnot(all.equal(n, as.integer(n)))
n - as.integer(n)
if (n == 1L) return(vec)
ans - outer(vec, vec, +)
if (n == 2L) return(ans)
else{
for (i in 3:n) ans - outer(vec, ans, +)
}
return(ans)
}
Though this really could be made much more efficient if you want:
e.g., for the n = 4 case, it would be better to take outer( outer(vec,
vec, +), outer(vec, vec, +), +).
Michael
On Sat, Oct 29, 2011 at 9:08 AM, Suleyman K s.ka...@gmail.com wrote:
Hi,
I am trying to get different combinations of a vector of different size and
find their sum. For example, if I have a vector (i,j) where i and j can be
anything from 0 to 5, i get these combinations (0,0), (0,1), (1,0), (1,1),
(2,0), .. (5,5) and find sum of these as 0, 1, 1, 2, . , 10. I used
outer functions to get this and it worked. What if I have a vector (i,j,k)
where all i, j , and k can be anything from 0 to 5. I want to do the same
thing here. Get all the combinations and sum them up. (0,0,0) (0,0,1),
(0,1,0), (1,0,0), (5,5,5) How can I get these combinations and find
their sums? Thank you very much in advance.
Uka
[[alternative HTML version deleted]]
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Re: [R] R help with different combinations of vectors of different sizes
On Oct 29, 2011, at 9:08 AM, Suleyman K wrote: Hi, I am trying to get different combinations of a vector of different size and find their sum. For example, if I have a vector (i,j) where i and j can be anything from 0 to 5, i get these combinations (0,0), (0,1), (1,0), (1,1), (2,0), .. (5,5) and find sum of these as 0, 1, 1, 2, . , 10. I used outer functions to get this and it worked. What if I have a vector (i,j,k) where all i, j , and k can be anything from 0 to 5. I want to do the same thing here. Get all the combinations and sum them up. (0,0,0) (0,0,1), (0,1,0), (1,0,0), (5,5,5) How can I get these combinations and find their sums? Thank you very much in advance. You did say combinations rather than permutations, so: colSums(combn(0:5, 3)) [1] 3 4 5 6 5 6 7 7 8 9 6 7 8 8 9 10 9 10 11 12 If you instead meant permutations, then consider this: rowSums(expand.grid(0:5,0:5, 0:5)) [1] 0 1 2 3 4 5 1 2 3 4 5 6 2 3 4 5 6 7 3 4 5 6 7 8 4 5 6 7 8 9 5 6 7 [34] 8 9 10 1 2 3 4 5 6 2 3 4 5 6 7 3 4 5 6 7 8 4 5 6 7 8 9 5 6 7 8 9 10 [67] 6 7 8 9 10 11 2 3 4 5 6 7 3 4 5 6 7 8 4 5 6 7 8 9 5 6 7 8 9 10 6 7 8 [100] 9 10 11 7 8 9 10 11 12 3 4 5 6 7 8 4 5 6 7 8 9 5 6 7 8 9 10 6 7 8 9 10 11 [133] 7 8 9 10 11 12 8 9 10 11 12 13 4 5 6 7 8 9 5 6 7 8 9 10 6 7 8 9 10 11 7 8 9 [166] 10 11 12 8 9 10 11 12 13 9 10 11 12 13 14 5 6 7 8 9 10 6 7 8 9 10 11 7 8 9 10 11 12 [199] 8 9 10 11 12 13 9 10 11 12 13 14 10 11 12 13 14 15 table(rowSums(expand.grid(0:5,0:5, 0:5))) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 1 3 6 10 15 21 25 27 27 25 21 15 10 6 3 1 A056150 Number of combinations for each possible sum when throwing 3 (normal) dice. http://oeis.org/A056150 Uka [[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 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] Email out of R (code)
R has packages for almost everything, so there is sendmailR
Uwe Ligges
On 28.10.2011 20:04, MacQueen, Don wrote:
The various suggestions seem kind of complex to me, at least on a
unix-like system (including Mac OS X).
This is what I do:
sink('tmp.txt')
cat('This is the body of the message\n')
sink()
system('cat tmp.txt | mail -s A test email macque...@llnl.gov')
One could probably avoid the temporary external text file using
connections, but I haven't had that need.
For attachments, the following approach works on at least some systems
(RHEL for one):
pdf('temp.pdf')
## create a plot
dev.off()
sink('tmp.txt')
## print() and cat() commands
sink()
cmd- '/bin/mailx -s Subject line text
-a temp.pdf -S replyto=macque...@llnl.gov
recipi...@some.host tmp.txt'
system(cmd)
It's not hard, of course, to wrap such a thing up in a function with
arguments for various elements such as the subject, the file names, the
email address(es), and then construct the cmd using paste().
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Re: [R] R help with different combinations of vectors of different sizes
Thank you very much both! That's exactly what I was trying to get. -- View this message in context: http://r.789695.n4.nabble.com/R-help-with-different-combinations-of-vectors-of-different-sizes-tp3950940p3950997.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Luis Miguel Delgado Gomez/BBK está ausente de la oficina.
__ 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] lme4 + R 2.11.0 + mac unavailable
I had a similar problem installing lme4 on my mac in R 2.12.1. The information on this thread helped me troubleshoot the problem, but I arrived at a different solution. When I tried to load lme4 from the source as advised by one author, it failed and I got an error message regarding the package 'Matrix' (see below if you're interested). Before diving in on some of the other suggestions to deal with the Matrix issue, I simply got the 'Matrix' package I already had installed going, and then installed lme4 successfully. library(Matrix) install.packages(lme4) That did the trick. Andy * installing *source* package ‘Matrix’ ... ** libs *** arch - i386 sh: make: command not found ERROR: compilation failed for package ‘Matrix’ * removing ‘/Users/darwin/Library/R/2.12/library/Matrix’ * installing *source* package ‘lme4’ ... ** libs *** arch - i386 sh: make: command not found ERROR: compilation failed for package ‘lme4’ * removing ‘/Users/darwin/Library/R/2.12/library/lme4’ The downloaded packages are in ‘/private/var/folders/Ts/TsMLZGaEF3W3JOTfdmIGDTU/-Tmp-/RtmpAXhRpJ/downloaded_packages’ Warning messages: 1: In install.packages(lme4, type = source) : installation of package 'Matrix' had non-zero exit status 2: In install.packages(lme4, type = source) : installation of package 'lme4' had non-zero exit status -- View this message in context: http://r.789695.n4.nabble.com/lme4-R-2-11-0-mac-unavailable-tp2220331p3951179.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] installing FastRWeb
hi, I am working on Ubuntu and tried to install FastRWeb, but am getting the following error for installation of cairo.h. install.packages(FastRWeb,dep=TRUE) Installing package(s) into /home/ba/R/i686-pc-linux-gnu-library/2.12 (as lib is unspecified) also installing the dependency Cairo trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Cairo_1.5-0.tar.gz' Content type 'application/x-gzip' length 81214 bytes (79 Kb) opened URL == downloaded 79 Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/FastRWeb_1.0-0.tar.gz' Content type 'application/x-gzip' length 71072 bytes (69 Kb) opened URL == downloaded 69 Kb * installing *source* package Cairo ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... no configure: CAIRO_LIBS is unset, attempting to guess it. configure: CAIRO_CFLAGS= checking if R was compiled with the RConn patch... no checking cairo.h usability... no checking cairo.h presence... no checking for cairo.h... no configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly. ERROR: configuration failed for package Cairo * removing /home/ba/R/i686-pc-linux-gnu-library/2.12/Cairo ERROR: dependency Cairo is not available for package FastRWeb * removing /home/ba/R/i686-pc-linux-gnu-library/2.12/FastRWeb The downloaded packages are in /tmp/Rtmpla4fs8/downloaded_packages Warning messages: 1: In install.packages(FastRWeb, dep = TRUE) : installation of package 'Cairo' had non-zero exit status 2: In install.packages(FastRWeb, dep = TRUE) : installation of package 'FastRWeb' had non-zero exit status so, I tried to install Cairo, but I get the following error: install.packages(Cairo) Installing package(s) into /home/ba/R/i686-pc-linux-gnu-library/2.12 (as lib is unspecified) trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Cairo_1.5-0.tar.gz' Content type 'application/x-gzip' length 81214 bytes (79 Kb) opened URL == downloaded 79 Kb * installing *source* package Cairo ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... no configure: CAIRO_LIBS is unset, attempting to guess it. configure: CAIRO_CFLAGS= checking if R was compiled with the RConn patch... no checking cairo.h usability... no checking cairo.h presence... no checking for cairo.h... no configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly. ERROR:
Re: [R] How to plot survival data from multiple trials (simulations)?
I'm assuming you want to plot the Kaplan-Meier curves. First, load your data into a data.frame, e.g. surv_data It looks like ST is your survival time and ind is your event indicator. The following code should get you started: # create your survival object: mySurv = Surv(surv_data$ST,surv_data$ind) # use survfit, which will generate KM curves: survFit = survfit(mySurv~surv_data$GROUP) # plot your curves. plot(survFit,conf.int=TRUE,xlab=time,ylab=survival pct) -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Zheng Lu Sent: Friday, October 28, 2011 10:30 PM To: r-help@r-project.org Subject: [R] How to plot survival data from multiple trials (simulations)? Dear all: Could anyone please provide some R codes to plot the below survival data to compare two groups (0 vs 1) after 2 simulations (TRL)? need 95% prediction interval on the plot from these 2 trials. I would like to simulate 1000 trials later. Thanks a lot for your great help and consideration! yan TRL ID ECOG BASE PTR8 GROUP POP ST ind 1 1 1 1 2.2636717 0.255634126 1 1 99.4 F 3 1 2 1 24.7719223 0.756458142 0 1 8.1 T 5 1 3 0 4.7685832 0.908777937 1 0 2.6 T 7 1 4 0 2.5934492 -0.231564522 1 1 7.4 T 9 1 5 0 4.7309141 -2.455991696 0 1 0.4 T 11 1 6 1 3.5904766 -0.459694803 1 1 13.1 T 13 1 7 1 4.8592495 0.983131140 1 1 17.8 T 15 1 8 1 3.1308760 -1.136462783 0 0 10.6 T 17 1 9 1 5.8127637 -0.131647588 0 1 1.2 T 19 1 10 0 4.0875668 -3.567509428 0 1 0.4 T 21 1 11 1 14.7112528 0.900416367 1 1 15.2 T 23 1 12 0 6.7290298 -0.140283251 0 0 8.5 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 25 1 13 0 6.6118789 -0.095603854 0 1 13.8 T 27 1 14 1 1.1191479 0.735691765 1 1 60.5 F 29 1 15 0 11.9169275 0.796172293 0 0 40.1 F 31 1 16 1 6.7940011 0.845746271 1 1 68.1 F 33 1 17 0 4.7380330 0.582527179 1 1 11.7 T 35 1 18 0 12.0571049 0.165637187 0 0 25.0 T 37 1 19 1 3.1922217 0.891862148 1 1 34.0 T 39 1 20 0 10.6253830 -0.747701704 0 1 7.8 T 41 1 21 0 2.0178336 -2.732716143 0 1 0.8 T 43 1 22 1 13.8066137 0.706372607 0 1 58.2 F 45 1 23 1 11.8844261 0.842735359 1 1 13.9 T 47 1 24 1 3.9546421 0.193353044 0 1 2.7 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 49 1 25 0 27.0913396 0.970400135 1 1 19.1 T 51 1 26 1 12.0249672 0.886403017 1 1 27.1 T 53 1 27 1 5.9453281 0.964694968 1 1 21.2 T 55 1 28 0 6.8084911 -1.333850454 1 0 4.1 T 57 1 29 1 8.3642227 -0.024960757 0 1 4.4 T 59 1 30 0 26.6382483 0.714020234 0 0 3.9 T 61 1 31 1 13.1107410 0.372041597 0 1 26.2 T 63 1 32 0 4.2271255 0.056569282 1 1 14.3 T 65 1 33 0 17.7269456 0.252550311 0 0 11.2 T 67 1 34 1 3.6215522 -0.282323084 0 0 0.3 T 69 1 35 1 19.3787770 0.349288143 0 1 5.2 T 71 1 36 0 8.9546567 0.945492048 1 1 15.2 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 73 1 37 0 2.7796959 -3.119155682 0 0 12.3 T 75 1 38 0 9.4029912 -0.793046460 0 1 1.2 T 77 1 39 1 7.8146429 0.888593758 1 1 8.0 T 79 1 40 0 9.6419102 0.525301532 1 1 22.4 T 81 1 41 1 3.3174969 0.915870306 1 1 24.7 T 83 1 42 1 12.4030358 0.661856980 1 1 16.4 T 85 1 43 1 24.2982862 0.710967270 0 1 5.5 T 87 1 44 0 10.4332028 0.940833126 1 0 2.9 T 89 1 45 0 4.7520799 0.897518558 1 1 32.6 T 91 1 46 0 2.7028663 -3.484128492 0 1 0.2 T 93 1 47 1 2.7572158 0.890976979 1 0 30.9 T 95 1 48 0 7.2240161 -0.377073350 0 0 3.7 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 97 1 49 0 20.6156368 0.500864314 0 1 12.2 T 99 1 50 1 12.8547093 0.982784519 1 1 54.4 F 2 2 1 1 3.0862631 0.931988949 1 1 199.2 F 4 2 2 1 18.6633707 0.540651036 0 1 8.1 T 6 2 3 0 5.5728260 -1.851336117 1 0 3.0 T 8 2 4 0 4.0740408 0.021119280 1 1 10.1 T 10 2 5 0 14.2396242 0.465013972 0 1 6.6 T 12 2 6 1 37.5234448 0.986992132 1 1 30.5 T 14 2 7 1 11.2925748 0.922905093 1 1 14.0 T 16 2 8 1 15.2298842 0.459418082 0 0 12.6 T 18 2 9 1 5.3266590 -1.487487920 0 1 0.3 T 20 2 10 0 11.7956270 0.606294774 0 1 26.9 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 22 2 11 1 26.0051377 0.823996317 1 1 8.6 T 24 2 12 0 4.7851855 -1.635216564 0 0 10.7 T 26 2 13 0 5.4896572 -1.085740446 0 1 3.8 T 28 2 14 1 15.0284557 0.981428564 1 1 56.1 F 30 2 15 0 15.3001584 -0.101949376 0 0 36.7 T 32 2 16 1 4.1838899 -0.002416447 1 1 26.0 T 34 2 17 0 1.9213881 0.678721863 1 1 15.5 T 36 2 18 0 22.0870166 0.682030393 0 0 18.8 T 38 2 19 1 7.8815644 0.938210236 1 1 25.9 T 40 2 20 0 6.8308086 -0.774314088 0 1 8.5 T 42 2 21 0 6.0056206 -0.656448295 0 1 5.4 T 44 2 22 1 11.9301049 0.137476151 0 1 32.2 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 46 2 23 1 4.4453597 0.932378925 1 1 18.3 T 48 2 24 1 7.0352655 0.142463064 0 1 2.4 T 50 2 25 0 22.1603315 0.990013687 1 1 23.5 T 52 2 26 1 1.7582992 0.041687569 1 1 13.6 T 54 2 27 1 4.0864310 0.893550143 1 1 18.7 T 56 2 28 0 3.7564158 0.149721394 1 0 3.1 T 58 2 29 1 23.7880592 0.312680371 0 1 4.0 T 60 2 30 0 7.3082204 0.084729300 0 0 3.4 T 62 2 31 1 29.8669157 0.779756301 0 1 24.3 T 64 2 32 0 6.7967624 0.228897567 1 1 15.8 T 66 2 33 0 9.0048160 -1.073334969 0 0 9.5 T 68 2 34 1 9.3920052 0.183028557 0 0 0.3 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 70 2 35 1
Re: [R] lme4 + R 2.11.0 + mac unavailable
On 29.10.2011 18:33, ADosmann wrote: I had a similar problem installing lme4 on my mac in R 2.12.1. The information on this thread helped me troubleshoot the problem, but I arrived at a different solution. When I tried to load lme4 from the source as advised by one author, it failed and I got an error message regarding the package 'Matrix' (see below if you're interested). Before diving in on some of the other suggestions to deal with the Matrix issue, I simply got the 'Matrix' package I already had installed going, and then installed lme4 successfully. library(Matrix) install.packages(lme4) That did the trick. Yes, but given the output below, it looks like make is not available. Uwe Ligges Andy * installing *source* package ‘Matrix’ ... ** libs *** arch - i386 sh: make: command not found ERROR: compilation failed for package ‘Matrix’ * removing ‘/Users/darwin/Library/R/2.12/library/Matrix’ * installing *source* package ‘lme4’ ... ** libs *** arch - i386 sh: make: command not found ERROR: compilation failed for package ‘lme4’ * removing ‘/Users/darwin/Library/R/2.12/library/lme4’ The downloaded packages are in ‘/private/var/folders/Ts/TsMLZGaEF3W3JOTfdmIGDTU/-Tmp-/RtmpAXhRpJ/downloaded_packages’ Warning messages: 1: In install.packages(lme4, type = source) : installation of package 'Matrix' had non-zero exit status 2: In install.packages(lme4, type = source) : installation of package 'lme4' had non-zero exit status -- View this message in context: http://r.789695.n4.nabble.com/lme4-R-2-11-0-mac-unavailable-tp2220331p3951179.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-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] installing FastRWeb
Please do read the output, it tells you: Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly. And that is exactly what you need to do, it cannot be solved by installing R packages Best, Uwe Ligges On 29.10.2011 18:24, financial engineer wrote: hi, I am working on Ubuntu and tried to install FastRWeb, but am getting the following error for installation of cairo.h. install.packages(FastRWeb,dep=TRUE) Installing package(s) into ‘/home/ba/R/i686-pc-linux-gnu-library/2.12’ (as ‘lib’ is unspecified) also installing the dependency ‘Cairo’ trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Cairo_1.5-0.tar.gz' Content type 'application/x-gzip' length 81214 bytes (79 Kb) opened URL == downloaded 79 Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/FastRWeb_1.0-0.tar.gz' Content type 'application/x-gzip' length 71072 bytes (69 Kb) opened URL == downloaded 69 Kb * installing *source* package ‘Cairo’ ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... no configure: CAIRO_LIBS is unset, attempting to guess it. configure: CAIRO_CFLAGS= checking if R was compiled with the RConn patch... no checking cairo.h usability... no checking cairo.h presence... no checking for cairo.h... no configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly. ERROR: configuration failed for package ‘Cairo’ * removing ‘/home/ba/R/i686-pc-linux-gnu-library/2.12/Cairo’ ERROR: dependency ‘Cairo’ is not available for package ‘FastRWeb’ * removing ‘/home/ba/R/i686-pc-linux-gnu-library/2.12/FastRWeb’ The downloaded packages are in ‘/tmp/Rtmpla4fs8/downloaded_packages’ Warning messages: 1: In install.packages(FastRWeb, dep = TRUE) : installation of package 'Cairo' had non-zero exit status 2: In install.packages(FastRWeb, dep = TRUE) : installation of package 'FastRWeb' had non-zero exit status so, I tried to install Cairo, but I get the following error: install.packages(Cairo) Installing package(s) into ‘/home/ba/R/i686-pc-linux-gnu-library/2.12’ (as ‘lib’ is unspecified) trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Cairo_1.5-0.tar.gz' Content type 'application/x-gzip' length 81214 bytes (79 Kb) opened URL == downloaded 79 Kb * installing *source* package ‘Cairo’ ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... no configure: CAIRO_LIBS is unset, attempting to guess it. configure:
Re: [R] Graphics Reciprocal labeling
I need just a little more education. I still haven't got back into attempting R programs, but I have appreciated your information. The linear-in-frequency horizontal-axis scale is natural for frequency analysis, and so labeling in period is applicable. Also applicable for better view is an exponential scale like factA*pow(2,-freq*factB) or related negative exponential properly scaled. Can I do similar period labeling for this situation also? Can I even get the exponential scale? I thought of this scale when I thought of the 5,2,1 US money system. -- View this message in context: http://r.789695.n4.nabble.com/Graphics-Reciprocal-labeling-tp3949054p3951313.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] installing FastRWeb
A missing X11/Intrinsic.h: suggests you also have to install some X11 header files that are still missing ... Uwe Ligges On 29.10.2011 19:44, financial engineer wrote: hi Uwe, thanks for your response. I ran the following as per the instructions on the Cairo website: sudo apt-get install libcairo2-dev following which I tried to install FastRWeb again (hopefully I have not missed any steps in between)can you pls. tell me how I can fix this error.. install.packages(FastRWeb,dep=TRUE) Installing package(s) into ‘/home/ba/R/i686-pc-linux-gnu-library/2.12’ (as ‘lib’ is unspecified) also installing the dependency ‘Cairo’ trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Cairo_1.5-0.tar.gz' Content type 'application/x-gzip' length 81214 bytes (79 Kb) opened URL == downloaded 79 Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/FastRWeb_1.0-0.tar.gz' Content type 'application/x-gzip' length 71072 bytes (69 Kb) opened URL == downloaded 69 Kb * installing *source* package ‘Cairo’ ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... yes checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender configure: CAIRO_CFLAGS=-pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1 checking if R was compiled with the RConn patch... no checking cairo.h usability... yes checking cairo.h presence... yes checking for cairo.h... yes checking for PNG support in Cairo... yes checking for ATS font support in Cairo... no configure: CAIRO_LIBS=-L/usr/lib/i386-linux-gnu -lfreetype -lpng12 -lz -lXrender -lcairo -lX11 checking for library containing deflate... none required checking whether Cairo programs can be compiled... yes checking whether cairo_image_surface_get_format is declared... no checking for FreeType support in cairo... yes checking whether FreeType needs additional flags... no checking wheter libjpeg works... yes checking wheter libtiff works... no configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/cconfig.h ** libs gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairobem.c -o cairobem.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairogd.c -o cairogd.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairotalk.c -o cairotalk.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c img-backend.c -o img-backend.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c
Re: [R] installing FastRWeb
On 29.10.2011 19:48, financial engineer wrote: I understand... can you please tell me where I can locate those to be able to install them. I am not familiar with X11. Depends on the OS, if this is Ubuntu, probably in libxt-dev So go ahead with apt-get install libxt-dev and please do not bother the list with basic sysadmin questions anymore, but ask for local advice on how to set up your system. Best, Uwe Ligges Date: Sat, 29 Oct 2011 19:46:16 +0200 From: lig...@statistik.tu-dortmund.de To: fin_e...@hotmail.com CC: r-help@r-project.org Subject: Re: [R] installing FastRWeb A missing X11/Intrinsic.h: suggests you also have to install some X11 header files that are still missing ... Uwe Ligges On 29.10.2011 19:44, financial engineer wrote: hi Uwe, thanks for your response. I ran the following as per the instructions on the Cairo website: sudo apt-get install libcairo2-dev following which I tried to install FastRWeb again (hopefully I have not missed any steps in between)can you pls. tell me how I can fix this error.. install.packages(FastRWeb,dep=TRUE) Installing package(s) into ‘/home/ba/R/i686-pc-linux-gnu-library/2.12’ (as ‘lib’ is unspecified) also installing the dependency ‘Cairo’ trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Cairo_1.5-0.tar.gz' Content type 'application/x-gzip' length 81214 bytes (79 Kb) opened URL == downloaded 79 Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/FastRWeb_1.0-0.tar.gz' Content type 'application/x-gzip' length 71072 bytes (69 Kb) opened URL == downloaded 69 Kb * installing *source* package ‘Cairo’ ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... yes checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender configure: CAIRO_CFLAGS=-pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1 checking if R was compiled with the RConn patch... no checking cairo.h usability... yes checking cairo.h presence... yes checking for cairo.h... yes checking for PNG support in Cairo... yes checking for ATS font support in Cairo... no configure: CAIRO_LIBS=-L/usr/lib/i386-linux-gnu -lfreetype -lpng12 -lz -lXrender -lcairo -lX11 checking for library containing deflate... none required checking whether Cairo programs can be compiled... yes checking whether cairo_image_surface_get_format is declared... no checking for FreeType support in cairo... yes checking whether FreeType needs additional flags... no checking wheter libjpeg works... yes checking wheter libtiff works... no configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/cconfig.h ** libs gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairobem.c -o cairobem.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairogd.c -o cairogd.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairotalk.c -o cairotalk.o gcc
Re: [R] installing FastRWeb
hi Uwe, thanks for your response. I ran the following as per the instructions on the Cairo website: sudo apt-get install libcairo2-dev following which I tried to install FastRWeb again (hopefully I have not missed any steps in between)can you pls. tell me how I can fix this error.. install.packages(FastRWeb,dep=TRUE) Installing package(s) into /home/ba/R/i686-pc-linux-gnu-library/2.12 (as lib is unspecified) also installing the dependency Cairo trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Cairo_1.5-0.tar.gz' Content type 'application/x-gzip' length 81214 bytes (79 Kb) opened URL == downloaded 79 Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/FastRWeb_1.0-0.tar.gz' Content type 'application/x-gzip' length 71072 bytes (69 Kb) opened URL == downloaded 69 Kb * installing *source* package Cairo ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... yes checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender configure: CAIRO_CFLAGS=-pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1 checking if R was compiled with the RConn patch... no checking cairo.h usability... yes checking cairo.h presence... yes checking for cairo.h... yes checking for PNG support in Cairo... yes checking for ATS font support in Cairo... no configure: CAIRO_LIBS=-L/usr/lib/i386-linux-gnu -lfreetype -lpng12 -lz -lXrender -lcairo -lX11 checking for library containing deflate... none required checking whether Cairo programs can be compiled... yes checking whether cairo_image_surface_get_format is declared... no checking for FreeType support in cairo... yes checking whether FreeType needs additional flags... no checking wheter libjpeg works... yes checking wheter libtiff works... no configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/cconfig.h ** libs gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairobem.c -o cairobem.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairogd.c -o cairogd.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairotalk.c -o cairotalk.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c img-backend.c -o img-backend.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c img-jpeg.c -o img-jpeg.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12
Re: [R] installing FastRWeb
I understand... can you please tell me where I can locate those to be able to install them. I am not familiar with X11. Date: Sat, 29 Oct 2011 19:46:16 +0200 From: lig...@statistik.tu-dortmund.de To: fin_e...@hotmail.com CC: r-help@r-project.org Subject: Re: [R] installing FastRWeb A missing X11/Intrinsic.h: suggests you also have to install some X11 header files that are still missing ... Uwe Ligges On 29.10.2011 19:44, financial engineer wrote: hi Uwe, thanks for your response. I ran the following as per the instructions on the Cairo website: sudo apt-get install libcairo2-dev following which I tried to install FastRWeb again (hopefully I have not missed any steps in between)can you pls. tell me how I can fix this error.. install.packages(FastRWeb,dep=TRUE) Installing package(s) into /home/ba/R/i686-pc-linux-gnu-library/2.12 (as lib is unspecified) also installing the dependency Cairo trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Cairo_1.5-0.tar.gz' Content type 'application/x-gzip' length 81214 bytes (79 Kb) opened URL == downloaded 79 Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/FastRWeb_1.0-0.tar.gz' Content type 'application/x-gzip' length 71072 bytes (69 Kb) opened URL == downloaded 69 Kb * installing *source* package Cairo ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... yes checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender configure: CAIRO_CFLAGS=-pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1 checking if R was compiled with the RConn patch... no checking cairo.h usability... yes checking cairo.h presence... yes checking for cairo.h... yes checking for PNG support in Cairo... yes checking for ATS font support in Cairo... no configure: CAIRO_LIBS=-L/usr/lib/i386-linux-gnu -lfreetype -lpng12 -lz -lXrender -lcairo -lX11 checking for library containing deflate... none required checking whether Cairo programs can be compiled... yes checking whether cairo_image_surface_get_format is declared... no checking for FreeType support in cairo... yes checking whether FreeType needs additional flags... no checking wheter libjpeg works... yes checking wheter libtiff works... no configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/cconfig.h ** libs gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairobem.c -o cairobem.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairogd.c -o cairogd.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/cairo -I/usr/include/pixman-1-I. -Iinclude-std=gnu99 -O3 -pipe -g -fpic -std=gnu99 -O3 -pipe -g -c cairotalk.c -o cairotalk.o gcc -I/usr/share/R/include -pthread -I/usr/include/glib-2.0
Re: [R] installing FastRWeb
Hi, I don't know what FastRWeb does, but it appears to me that you need the developmental files for Cairo installed. I don't use ubuntu, but perhaps installing cairo-dev might help? HTH, Ranjan On Sat, 29 Oct 2011 11:24:04 -0500 financial engineer fin_e...@hotmail.com wrote: hi, I am working on Ubuntu and tried to install FastRWeb, but am getting the following error for installation of cairo.h. install.packages(FastRWeb,dep=TRUE) Installing package(s) into ‘/home/ba/R/i686-pc-linux-gnu-library/2.12’ (as ‘lib’ is unspecified) also installing the dependency ‘Cairo’ trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Cairo_1.5-0.tar.gz' Content type 'application/x-gzip' length 81214 bytes (79 Kb) opened URL == downloaded 79 Kb trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/FastRWeb_1.0-0.tar.gz' Content type 'application/x-gzip' length 71072 bytes (69 Kb) opened URL == downloaded 69 Kb * installing *source* package ‘Cairo’ ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... no configure: CAIRO_LIBS is unset, attempting to guess it. configure: CAIRO_CFLAGS= checking if R was compiled with the RConn patch... no checking cairo.h usability... no checking cairo.h presence... no checking for cairo.h... no configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly. ERROR: configuration failed for package ‘Cairo’ * removing ‘/home/ba/R/i686-pc-linux-gnu-library/2.12/Cairo’ ERROR: dependency ‘Cairo’ is not available for package ‘FastRWeb’ * removing ‘/home/ba/R/i686-pc-linux-gnu-library/2.12/FastRWeb’ The downloaded packages are in ‘/tmp/Rtmpla4fs8/downloaded_packages’ Warning messages: 1: In install.packages(FastRWeb, dep = TRUE) : installation of package 'Cairo' had non-zero exit status 2: In install.packages(FastRWeb, dep = TRUE) : installation of package 'FastRWeb' had non-zero exit status so, I tried to install Cairo, but I get the following error: install.packages(Cairo) Installing package(s) into ‘/home/ba/R/i686-pc-linux-gnu-library/2.12’ (as ‘lib’ is unspecified) trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Cairo_1.5-0.tar.gz' Content type 'application/x-gzip' length 81214 bytes (79 Kb) opened URL == downloaded 79 Kb * installing *source* package ‘Cairo’ ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config
Re: [R] How to plot survival data from multiple trials (simulations)?
Thank you very much for your consideration and response. you are right and the codes you provided was the one I am using now. But my question is if I simulate 1000 trials (due to limited space, I only provide the results here from 2 trials), TRL is from 1 to 1000 in the dataset, how can I creat KM curve with 95% prediction interval instead of confidence interval. Thanks again. From: robert.lancas...@orbitz.com To: luy...@hotmail.com; r-help@r-project.org Date: Sat, 29 Oct 2011 11:49:25 -0500 Subject: RE: [R] How to plot survival data from multiple trials (simulations)? I'm assuming you want to plot the Kaplan-Meier curves. First, load your data into a data.frame, e.g. surv_data It looks like ST is your survival time and ind is your event indicator. The following code should get you started: # create your survival object: mySurv = Surv(surv_data$ST,surv_data$ind) # use survfit, which will generate KM curves: survFit = survfit(mySurv~surv_data$GROUP) # plot your curves. plot(survFit,conf.int=TRUE,xlab=time,ylab=survival pct) -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Zheng Lu Sent: Friday, October 28, 2011 10:30 PM To: r-help@r-project.org Subject: [R] How to plot survival data from multiple trials (simulations)? Dear all: Could anyone please provide some R codes to plot the below survival data to compare two groups (0 vs 1) after 2 simulations (TRL)? need 95% prediction interval on the plot from these 2 trials. I would like to simulate 1000 trials later. Thanks a lot for your great help and consideration! yan TRL ID ECOG BASE PTR8 GROUP POP ST ind 1 1 1 1 2.2636717 0.255634126 1 1 99.4 F 3 1 2 1 24.7719223 0.756458142 0 1 8.1 T 5 1 3 0 4.7685832 0.908777937 1 0 2.6 T 7 1 4 0 2.5934492 -0.231564522 1 1 7.4 T 9 1 5 0 4.7309141 -2.455991696 0 1 0.4 T 11 1 6 1 3.5904766 -0.459694803 1 1 13.1 T 13 1 7 1 4.8592495 0.983131140 1 1 17.8 T 15 1 8 1 3.1308760 -1.136462783 0 0 10.6 T 17 1 9 1 5.8127637 -0.131647588 0 1 1.2 T 19 1 10 0 4.0875668 -3.567509428 0 1 0.4 T 21 1 11 1 14.7112528 0.900416367 1 1 15.2 T 23 1 12 0 6.7290298 -0.140283251 0 0 8.5 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 25 1 13 0 6.6118789 -0.095603854 0 1 13.8 T 27 1 14 1 1.1191479 0.735691765 1 1 60.5 F 29 1 15 0 11.9169275 0.796172293 0 0 40.1 F 31 1 16 1 6.7940011 0.845746271 1 1 68.1 F 33 1 17 0 4.7380330 0.582527179 1 1 11.7 T 35 1 18 0 12.0571049 0.165637187 0 0 25.0 T 37 1 19 1 3.1922217 0.891862148 1 1 34.0 T 39 1 20 0 10.6253830 -0.747701704 0 1 7.8 T 41 1 21 0 2.0178336 -2.732716143 0 1 0.8 T 43 1 22 1 13.8066137 0.706372607 0 1 58.2 F 45 1 23 1 11.8844261 0.842735359 1 1 13.9 T 47 1 24 1 3.9546421 0.193353044 0 1 2.7 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 49 1 25 0 27.0913396 0.970400135 1 1 19.1 T 51 1 26 1 12.0249672 0.886403017 1 1 27.1 T 53 1 27 1 5.9453281 0.964694968 1 1 21.2 T 55 1 28 0 6.8084911 -1.333850454 1 0 4.1 T 57 1 29 1 8.3642227 -0.024960757 0 1 4.4 T 59 1 30 0 26.6382483 0.714020234 0 0 3.9 T 61 1 31 1 13.1107410 0.372041597 0 1 26.2 T 63 1 32 0 4.2271255 0.056569282 1 1 14.3 T 65 1 33 0 17.7269456 0.252550311 0 0 11.2 T 67 1 34 1 3.6215522 -0.282323084 0 0 0.3 T 69 1 35 1 19.3787770 0.349288143 0 1 5.2 T 71 1 36 0 8.9546567 0.945492048 1 1 15.2 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 73 1 37 0 2.7796959 -3.119155682 0 0 12.3 T 75 1 38 0 9.4029912 -0.793046460 0 1 1.2 T 77 1 39 1 7.8146429 0.888593758 1 1 8.0 T 79 1 40 0 9.6419102 0.525301532 1 1 22.4 T 81 1 41 1 3.3174969 0.915870306 1 1 24.7 T 83 1 42 1 12.4030358 0.661856980 1 1 16.4 T 85 1 43 1 24.2982862 0.710967270 0 1 5.5 T 87 1 44 0 10.4332028 0.940833126 1 0 2.9 T 89 1 45 0 4.7520799 0.897518558 1 1 32.6 T 91 1 46 0 2.7028663 -3.484128492 0 1 0.2 T 93 1 47 1 2.7572158 0.890976979 1 0 30.9 T 95 1 48 0 7.2240161 -0.377073350 0 0 3.7 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 97 1 49 0 20.6156368 0.500864314 0 1 12.2 T 99 1 50 1 12.8547093 0.982784519 1 1 54.4 F 2 2 1 1 3.0862631 0.931988949 1 1 199.2 F 4 2 2 1 18.6633707 0.540651036 0 1 8.1 T 6 2 3 0 5.5728260 -1.851336117 1 0 3.0 T 8 2 4 0 4.0740408 0.021119280 1 1 10.1 T 10 2 5 0 14.2396242 0.465013972 0 1 6.6 T 12 2 6 1 37.5234448 0.986992132 1 1 30.5 T 14 2 7 1 11.2925748 0.922905093 1 1 14.0 T 16 2 8 1 15.2298842 0.459418082 0 0 12.6 T 18 2 9 1 5.3266590 -1.487487920 0 1 0.3 T 20 2 10 0 11.7956270 0.606294774 0 1 26.9 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 22 2 11 1 26.0051377 0.823996317 1 1 8.6 T 24 2 12 0 4.7851855 -1.635216564 0 0 10.7 T 26 2 13 0 5.4896572 -1.085740446 0 1 3.8 T 28 2 14 1 15.0284557 0.981428564 1 1 56.1 F 30 2 15 0 15.3001584 -0.101949376 0 0 36.7 T 32 2 16 1 4.1838899 -0.002416447 1 1 26.0 T 34 2 17 0 1.9213881 0.678721863 1 1 15.5 T 36 2 18 0 22.0870166 0.682030393 0 0 18.8 T 38 2 19 1 7.8815644 0.938210236 1 1 25.9 T 40 2 20 0 6.8308086 -0.774314088 0 1 8.5 T 42 2 21
Re: [R] Matching
Your post is unlikely to solicit a helpful response. As you do not adhere to the posting guide, it is quite impossible for us to figure out from your description what is going wrong. Please provide a self-contained example that reproduces the problem (i.e., code with simulated or actual data that we can copy paste to the R-prompt). Moreover, chances are that when you try to reproduce the error with simulated code, you will figure out what your mistake is. Best, Daniel shish matt wrote: I have a spatial weight file in csv that I want as listw object in R. The file has the following 3 variables (left to right in the file) -- OID_, NID and WEIGHTS. NID stands for the neighbors and OID_ as the origins. There are 217 origins with 4 neighbors each. I have been able to read the csv file as a data frame (test.csv). Then I tried to check whether the OID_ variable is in the right place in the dataframe. I used match for that using: o - match(OID_, OID_) I am not sure whether this is the right way to match. Please advice. Anyway, next I created a matrix object (m) using: m - as.matrix(test.csv[, -1]) Then I created object m1, using: m1 - m[o, o] Finally, I tried creating listw object using: mat2listw(m1) Here I get an error that x is not a square matrix. Not sure what to do now. Any helo appreciated! Thanks, Shishm __ R-help@ 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://r.789695.n4.nabble.com/Matching-tp3950158p3951527.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] Extracting data by row
You didn't show the details of what you did before Ten-dataTable1[(dataTable1$sensor_depth_m==10),] but that line makes me suspicious that you did some experimentation with syntax before coming up with that line. In particular, why did you use parentheses around (dataTable1$sensor_depth_m==10) and why did you use quotes around the 10? Here is an example of why you might have started using the unnecessary (and misleading) parentheses. I'll use a narrow dataset so its R printout does not get line-wrapped by a rogue mailer. d - data.frame(one=c(3,1,1,2), ten=c(3,1,1,2)*10) # first, use = instead of == for comparison d[ d$one = 1, ] Error: unexpected '=' in d[ d$one = # react to error message by adding parentheses d[ (d$one = 1), ] one ten 1 3 30 # That is definitely the wrong answer. # The parentheses hid that problem that you were using = # instead of == and did d$one-1, then d[1,] returned row 1. # Note that now d has been changed! d one ten 1 1 30 2 1 10 3 1 10 4 1 20 That may explain how you got a column of 10's (after a ...=10), but I don't know what you may have done to get a second column called sensor_depth_m. Nor do I have a guess as to why you put quotes around the number 10. This is why R-help asks to see exactly what you did in R, not just a synopsis. (When I copied what you showed into R, adding a read.csv(header=TRUE, textConnection(...data...)), I got the correct 2 lines of output, not the incorrect 3 lines you indicated that you wanted.) Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Vinny Moriarty Sent: Friday, October 28, 2011 6:05 PM To: r-help@r-project.org Subject: [R] Extracting data by row Thanks everyone for you help with my last question, and now I have one last one... Here is a sample of my data in .csv format site,time_local,time_utc,reef_type_code,sensor_type,sensor_depth_m,temperature_c 06,2006-04-09 10:20:00,2006-04-09 20:20:00,BAK,sb39, 2, 29.63 06,2006-04-09 10:40:00,2006-04-09 20:40:00,BAK,sb39, 2, 29.56 06,2006-04-09 11:00:00,2006-04-09 21:00:00,BAK,sb39, 2, 29.51 06,2006-04-09 11:20:00,2006-04-09 21:20:00,BAK,sb39, 2, 29.53 06,2006-04-09 11:40:00,2006-04-09 21:40:00,BAK,sb39, 10, 29.57 06,2006-04-09 12:00:00,2006-04-09 22:00:00,BAK,sb39, 2, 29.60 06,2006-04-09 12:20:00,2006-04-09 22:20:00,BAK,sb39, 2, 29.66 06,2006-04-09 12:40:00,2006-04-09 22:40:00,BAK,sb39, 10, 29.68 06,2006-04-09 13:00:00,2006-04-09 23:00:00,BAK,sb39, 2, 29.68 My goal was to extract all of the rows from a certain depth. Using the column sensor_depth_m to order my data by, I wanted all of the data from 10m. So this is what I wanted when I finished site,time_local,time_utc,reef_type_code,sensor_type,sensor_depth_m,temperature_c 06,2006-04-09 11:40:00,2006-04-09 21:40:00,BAK,sb39, 10, 29.57 06,2006-04-09 12:40:00,2006-04-09 22:40:00,BAK,sb39, 10, 29.68 06,2006-04-09 13:00:00,2006-04-09 23:00:00,BAK,sb39, 10, 29.68 To pull out all of the data from a 10m sensor depth I came up with the code: Ten-dataTable1[(dataTable1$sensor_depth_m==10),] But when I run it I just get an extra column tacked onto the end like this site,time_local,time_utc,reef_type_code,sensor_type,sensor_depth_m,temperature_c, sensor_depth_m 06,2006-04-09 10:20:00,2006-04-09 20:20:00,BAK,sb39, 2, 29.63,10 06,2006-04-09 10:40:00,2006-04-09 20:40:00,BAK,sb39, 2, 29.56,10 06,2006-04-09 11:00:00,2006-04-09 21:00:00,BAK,sb39, 2, 29.51,10 06,2006-04-09 11:20:00,2006-04-09 21:20:00,BAK,sb39, 2, 29.53,10 06,2006-04-09 11:40:00,2006-04-09 21:40:00,BAK,sb39, 10, 29.57,10 06,2006-04-09 12:00:00,2006-04-09 22:00:00,BAK,sb39, 2, 29.60,10 06,2006-04-09 12:20:00,2006-04-09 22:20:00,BAK,sb39, 2, 29.66,10 06,2006-04-09 12:40:00,2006-04-09 22:40:00,BAK,sb39, 10, 29.68,10 06,2006-04-09 13:00:00,2006-04-09 23:00:00,BAK,sb39, 10, 29.68,10 It seems pretty straight forward, I'm not sure what I am missing. Thanks V [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plot genes on chr locations
Hello, I have a list of genes in a txt file and the chromosome locations where they occur. I want to make a plot that will show all the chromosomes (1-22,X,Y) and the genes which occur in that chr position. Does anyone know if it can be done in R? -- View this message in context: http://r.789695.n4.nabble.com/Plot-genes-on-chr-locations-tp3951479p3951479.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] How to plot survival data from multiple trials (simulations)?
Oh sorry, I misread. You'll only be able to get the confidence interval out of the object returned by survfit. From: Zheng Lu [mailto:luy...@hotmail.com] Sent: Saturday, October 29, 2011 1:04 PM To: Lancaster, Robert (Orbitz); r-help@r-project.org Subject: RE: [R] How to plot survival data from multiple trials (simulations)? Thank you very much for your consideration and response. you are right and the codes you provided was the one I am using now. But my question is if I simulate 1000 trials (due to limited space, I only provide the results here from 2 trials), TRL is from 1 to 1000 in the dataset, how can I creat KM curve with 95% prediction interval instead of confidence interval. Thanks again. From: robert.lancas...@orbitz.com To: luy...@hotmail.com; r-help@r-project.org Date: Sat, 29 Oct 2011 11:49:25 -0500 Subject: RE: [R] How to plot survival data from multiple trials (simulations)? I'm assuming you want to plot the Kaplan-Meier curves. First, load your data into a data.frame, e.g. surv_data It looks like ST is your survival time and ind is your event indicator. The following code should get you started: # create your survival object: mySurv = Surv(surv_data$ST,surv_data$ind) # use survfit, which will generate KM curves: survFit = survfit(mySurv~surv_data$GROUP) # plot your curves. plot(survFit,conf.int=TRUE,xlab=time,ylab=survival pct) -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Zheng Lu Sent: Friday, October 28, 2011 10:30 PM To: r-help@r-project.org Subject: [R] How to plot survival data from multiple trials (simulations)? Dear all: Could anyone please provide some R codes to plot the below survival data to compare two groups (0 vs 1) after 2 simulations (TRL)? need 95% prediction interval on the plot from these 2 trials. I would like to simulate 1000 trials later. Thanks a lot for your great help and consideration! yan TRL ID ECOG BASE PTR8 GROUP POP ST ind 1 1 1 1 2.2636717 0.255634126 1 1 99.4 F 3 1 2 1 24.7719223 0.756458142 0 1 8.1 T 5 1 3 0 4.7685832 0.908777937 1 0 2.6 T 7 1 4 0 2.5934492 -0.231564522 1 1 7.4 T 9 1 5 0 4.7309141 -2.455991696 0 1 0.4 T 11 1 6 1 3.5904766 -0.459694803 1 1 13.1 T 13 1 7 1 4.8592495 0.983131140 1 1 17.8 T 15 1 8 1 3.1308760 -1.136462783 0 0 10.6 T 17 1 9 1 5.8127637 -0.131647588 0 1 1.2 T 19 1 10 0 4.0875668 -3.567509428 0 1 0.4 T 21 1 11 1 14.7112528 0.900416367 1 1 15.2 T 23 1 12 0 6.7290298 -0.140283251 0 0 8.5 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 25 1 13 0 6.6118789 -0.095603854 0 1 13.8 T 27 1 14 1 1.1191479 0.735691765 1 1 60.5 F 29 1 15 0 11.9169275 0.796172293 0 0 40.1 F 31 1 16 1 6.7940011 0.845746271 1 1 68.1 F 33 1 17 0 4.7380330 0.582527179 1 1 11.7 T 35 1 18 0 12.0571049 0.165637187 0 0 25.0 T 37 1 19 1 3.1922217 0.891862148 1 1 34.0 T 39 1 20 0 10.6253830 -0.747701704 0 1 7.8 T 41 1 21 0 2.0178336 -2.732716143 0 1 0.8 T 43 1 22 1 13.8066137 0.706372607 0 1 58.2 F 45 1 23 1 11.8844261 0.842735359 1 1 13.9 T 47 1 24 1 3.9546421 0.193353044 0 1 2.7 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 49 1 25 0 27.0913396 0.970400135 1 1 19.1 T 51 1 26 1 12.0249672 0.886403017 1 1 27.1 T 53 1 27 1 5.9453281 0.964694968 1 1 21.2 T 55 1 28 0 6.8084911 -1.333850454 1 0 4.1 T 57 1 29 1 8.3642227 -0.024960757 0 1 4.4 T 59 1 30 0 26.6382483 0.714020234 0 0 3.9 T 61 1 31 1 13.1107410 0.372041597 0 1 26.2 T 63 1 32 0 4.2271255 0.056569282 1 1 14.3 T 65 1 33 0 17.7269456 0.252550311 0 0 11.2 T 67 1 34 1 3.6215522 -0.282323084 0 0 0.3 T 69 1 35 1 19.3787770 0.349288143 0 1 5.2 T 71 1 36 0 8.9546567 0.945492048 1 1 15.2 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 73 1 37 0 2.7796959 -3.119155682 0 0 12.3 T 75 1 38 0 9.4029912 -0.793046460 0 1 1.2 T 77 1 39 1 7.8146429 0.888593758 1 1 8.0 T 79 1 40 0 9.6419102 0.525301532 1 1 22.4 T 81 1 41 1 3.3174969 0.915870306 1 1 24.7 T 83 1 42 1 12.4030358 0.661856980 1 1 16.4 T 85 1 43 1 24.2982862 0.710967270 0 1 5.5 T 87 1 44 0 10.4332028 0.940833126 1 0 2.9 T 89 1 45 0 4.7520799 0.897518558 1 1 32.6 T 91 1 46 0 2.7028663 -3.484128492 0 1 0.2 T 93 1 47 1 2.7572158 0.890976979 1 0 30.9 T 95 1 48 0 7.2240161 -0.377073350 0 0 3.7 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 97 1 49 0 20.6156368 0.500864314 0 1 12.2 T 99 1 50 1 12.8547093 0.982784519 1 1 54.4 F 2 2 1 1 3.0862631 0.931988949 1 1 199.2 F 4 2 2 1 18.6633707 0.540651036 0 1 8.1 T 6 2 3 0 5.5728260 -1.851336117 1 0 3.0 T 8 2 4 0 4.0740408 0.021119280 1 1 10.1 T 10 2 5 0 14.2396242 0.465013972 0 1 6.6 T 12 2 6 1 37.5234448 0.986992132 1 1 30.5 T 14 2 7 1 11.2925748 0.922905093 1 1 14.0 T 16 2 8 1 15.2298842 0.459418082 0 0 12.6 T 18 2 9 1 5.3266590 -1.487487920 0 1 0.3 T 20 2 10 0 11.7956270 0.606294774 0 1 26.9 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 22 2 11 1 26.0051377 0.823996317 1 1 8.6 T 24 2 12 0 4.7851855 -1.635216564 0 0 10.7 T 26 2 13 0 5.4896572 -1.085740446 0 1 3.8 T 28 2 14 1
[R] Redundancy canonical analysis plot problem in 3D using VEGAN
Hi Guys, First, English is not my native language so sorry if the question is too difficult to understand. I can rephrase it if necessary. I have 32-bit Windows Xp SP3, i use R version 2.12.0 (2010-10-15), and the question is about Redundancy canonical analysis plot problem in 3D using VEGAN, RGL, SCATTERPLOT3D and SFSMISC. I noticed the following code to explain as clearly as possible the problems encountered. I am not able to add species scores from RDA results in 3D plot like i can in 2D plot. With the code i used , i get errors like ; ERROR dans t$sites : $ operator is invalid for atomic vectors, Erreur dans match.arg (display, items) : 'arg' should be one of xyz.convert, points3d, plane3d, box3d, points, arrows I saw that I can use other functions, but it is impossible to extract the 3D scores ( and add species to 3d plot ), Other fonctions works but, add elements in a 2D space. How can I add the species scores (sites and arrows are added correctly) to the 3D plot as with the 2D plot. Thank you for your help, Sincerely, Thomas University of Quebec at Trois-Rivieres , Canada Environmental science MSC student. rouss...@uqtr.ca, thomasbeaum...@hotmail.com Here is the noticed code I used; - CODE # Load library library(vegan) library(rgl) library(scatterplot3d) library(sfsmisc) # Import data ALLMAS - read.table(C:/data.txt, header=TRUE, sep=, na.strings=NA, dec=., strip.white=TRUE # Define var. X -ALLMAS[,c(10,14,15,16,18,19,22)] # env. (7) var. Y -ALLMAS[,c(9,3:6)] # y. (4) var Z -ALLMAS[,c(25)] # Z. (1) var covariate ENVIESRDA -rda(Y,X,Z) # Redundancy canonical analysis pl - ordiplot3d(ENVIESRDA, angle=15, type=n) # Get $Points (1:2) , get $arrows (1:2) text(pl, arrows, col=blue, pos=3, cex = 1) # Text env. var in plot text(pl, points, col=red, pos=1, cex = 0.5) # Point sites (y.var) in plot text(pl, species, col=blue, cex=0.8) # Text species in plot , # I get the following error message: # Erreur dans match.arg(display, items) : # 'arg' should be one of xyz.convert, points3d, plane3d, box3d, points, arrows # I saw that I can use other functions, but it is impossible to extract the 3D scores. Other features add elements in a 2D space. # Then I try the following code, which works well in 2D when I extract the summary of the results of the RDA. t -summary(ENVIESRDA,scal=2) # t -summary(pl,scal=2) # I get ; # Length Class Mode # xyz.convert 1 -none- function # points3d 1 -none- function # plane3d 1 -none- function # box3d 1 -none- function # points 48 -none- numeric # arrows 14 -none- numeric # Points = sites but where is species scores ? X =t$sites[,1] # ERROR dans t$sites : $ operator is invalid for atomic vectors Y =t$sites[,2] t$sites summary(ENVIESRDA, step=1000, perm.max=1000) # Summary anova(ENVIESRDA, step=1000, perm.max=1000) # Anova # Draw arrows to connect the sites with each other before / after study. # But I can't get the new coordinates of 3D graphics using the function summary. stn2= p.arrows(X[1],Y[1], X[13],Y[13],fill=red,width=1) stn3= p.arrows(X[2],Y[2], X[14],Y[14],fill=yellow,width=1) stn4= p.arrows(X[3],Y[3], X[15],Y[15],fill=yellow,width=1) stn5= p.arrows(X[4],Y[4], X[16],Y[16],fill=red,width=1) stn6= p.arrows(X[5],Y[5], X[17],Y[17],fill=yellow,width=1) stn7= p.arrows(X[6],Y[6], X[18],Y[18],fill=red,width=1) stn9= p.arrows(X[7],Y[7], X[19],Y[19],fill=yellow,width=1) stn10= p.arrows(X[8],Y[8], X[20],Y[20],fill=yellow,width=1) stn11= p.arrows(X[9],Y[9], X[21],Y[21],fill=red,width=1) stn12= p.arrows(X[10],Y[10], X[22],Y[22],fill=yellow,width=1) stn13= p.arrows(X[11],Y[11], X[23],Y[23],fill=red,width=1) stn18= p.arrows(X[12],Y[12], X[24],Y[24],fill=red,width=1) stn19= p.arrows(X[13],Y[13], X[25],Y[25],fill=red,width=1) # END - Courriel expédié via https://courriel.uqtr.ca __ 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] Unscribe me please!
-- Hello, Kindly unsubscribe me from R emailing list And confirm me by email I do not want any further email Regards Mahesh Krishnan __ The information of this email is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should notify us immediately and destroy this email. [[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] Plot genes on chr locations
Perhaps this question is better suited for the bioconductor list: they can probably get you an answer quickly. Michael On Oct 29, 2011, at 3:10 PM, lumos lumos.lumos.lu...@gmail.com wrote: Hello, I have a list of genes in a txt file and the chromosome locations where they occur. I want to make a plot that will show all the chromosomes (1-22,X,Y) and the genes which occur in that chr position. Does anyone know if it can be done in R? -- View this message in context: http://r.789695.n4.nabble.com/Plot-genes-on-chr-locations-tp3951479p3951479.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-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] Unscribe me please!
Dear Mahesh, What you have done is the social equivalent of walking into a large retail store, getting on the store intercom, and saying, so that thousands of customers can hear you, Kindly get me out of this store. There are two problems with this: 1) It is inconsiderate to bother thousands of bystanders with your request which is really directed at management 2) It is actually a task you perform yourself---you presumably subscribed yourself in the first place and when you went through that process you would have learned how to unsubscribe. But supposing you forgot or lost that email, the truly trivial step of searching on google for: unsubscribe from R help list gives tons of pages, the very first one of which links you to a page with clear, simple, easy, instructions for how to unsubscribe. It is not asking for help that is a problem, it is the implicit, 3 minutes of my time to search and do it myself is too much to spend, I want someone else to do it for me. Indeed, since you use gmail, you would not even have to point your browser to www.google.com, you would just have to use the built in search and click the 'search the web' button, but evidently, you would rather have someone else do that for you and then send you an email stating as much. That's where I come in. I offer a specialized service, and for only 20 USD, I will gladly submit anyone's email to be unsubscribed from this list, and send you a follow up email to alert you of as much. If you are interested in this service, please email me off list and let me know when you have transferred the funds to my paypal account (same email address as I am using here). I look forward to doing business with you, Josh On Sat, Oct 29, 2011 at 3:14 PM, Mahesh Krishnan bhangisoluti...@gmail.com wrote: -- Hello, Kindly unsubscribe me from R emailing list And confirm me by email I do not want any further email Regards Mahesh Krishnan __ The information of this email is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should notify us immediately and destroy this email. [[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. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.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] Matching
Hi Shishm, Part of what you do seems reasonable. My guess is that: o - match(OID_, OID_) is not doing what you want/think. What happens when you look at the results? e.g.,: print(o) You use that later on as row and column indices to extract from m, to create m1. The fact taht mat2listw complains that m1 is not square, makes me guess the indices used to create m1 are not working correctly, which points back to o - match(). With a more detailed example we can give more detailed suggestions Hope this helps some, Josh On Fri, Oct 28, 2011 at 3:22 PM, shish matt shi...@yahoo.com wrote: I have a spatial weight file in csv that I want as listw object in R. The file has the following 3 variables (left to right in the file) -- OID_, NID and WEIGHTS. NID stands for the neighbors and OID_ as the origins. There are 217 origins with 4 neighbors each. I have been able to read the csv file as a data frame (test.csv). Then I tried to check whether the OID_ variable is in the right place in the dataframe. I used match for that using: o - match(OID_, OID_) I am not sure whether this is the right way to match. Please advice. Anyway, next I created a matrix object (m) using: m - as.matrix(test.csv[, -1]) Then I created object m1, using: m1 - m[o, o] Finally, I tried creating listw object using: mat2listw(m1) Here I get an error that x is not a square matrix. Not sure what to do now. Any helo appreciated! Thanks, Shishm __ 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. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.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] Parametric tests
Hello, I am interested in parametric multi comparison tests such as Dunnett, Duncan, Tukey, Newman-Keuls, Bonferonni, Scheffe, and non-parametric tests such as Kruskal-Wallis, and Mann-Whitney U. Are there packages that include most of these tests in each category? Many packages exist for an individual test but their outputs vary in great detail (test statistics, p-values, etc.) formats. It is desirable to have one that allows comparison of different test results such as Tukey versus Duncan. Cem Cem Girit [[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.
