Re: [R] an apply question
On Jan 18, 2013, at 9:17 PM, m p wrote:
Hello,
It should be easu but I cannot figure out how to use apply function.
Unless this is a homework question then using `apply` seems inefficient.
I am
trying to replace negative values in an array with these values + 24.
Would appreciate help. Thanks,
Mark
shours - apply(fhours, function(x){if (x 0) x - x+24})
Error in match.fun(FUN) : argument FUN is missing, with no default
You should not use the assignment operator in the expression that
forms the consequent for `ifelse`. (Furthermore apply takes three
arguments and you only have two.)
Vectorize:
mat1-matrix(sample(-10:10,40,replace=TRUE),ncol=5)
mat1[mat1 0] - mat1[mat1 0]+24
mat1
[,1] [,2] [,3] [,4] [,5]
[1,]24 2310
[2,] 187 103 16
[3,] 10 16 16 160
[4,]336 173
[5,] 21069 16
[6,] 104600
[7,]78 210 20
[8,] 197 15 195
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Re: [R] How to re-project ease( Equal Area Scalable Earth) grid with a ~25 km cylindrical projection to WGS84 0.25 degree?
On Fri, Jan 18, 2013 at 5:11 PM, Jonsson amen.alya...@bordeaux.inra.fr wrote: -raster(C:\\Users\\aalyaari\\Desktop\\SM_RE01_MIR_CLF31D_20100812T00_20100812T235959_246_001_7.nc, varname = Soil_Moisture) d: class : RasterLayer dimensions : 586, 1383, 810438 (nrow, ncol, ncell) resolution : 0.2603037, 0.2916659 (x, y) extent : -180, 180, -85.4581, 85.4581 (xmin, xmax, ymin, ymax) coord. ref. : +proj=longlat +datum=WGS84 names : Retrieved.soil.moisture.value zvar: Soil_Moisture a - spTransform(d, CRS (+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs)) but I got this error: Error in function (classes, fdef, mtable) : unable to find an inherited method for function ‘spTransform’ for signature ‘RasterLayer, CRS’ And what is the error telling you? That there's no method for spTransform that applies to RasterLayers. To transform a raster from one projection to another you need to use projectRaster from the raster package. Note that generally this can involve warping a raster and interpolating the new values to get a grid of cells in the new coordinate system. But... you were trying to do this: a - spTransform(d, CRS (+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs)) where d was: coord. ref. : +proj=longlat +datum=WGS84 - which is a no-op. The source and destination have the same coordinate reference system. You need to tell raster what the coordinate system of the source is. See ?projection - note this doesn't change the raster or do any projection, its just to tell the system what the coordinates in the data represent - lat,long or metres or whatever.. I looked in the HDR file and saw nothing about the projection, so I don't know how to specify what you've got. Also, you didn't point us to the .nc file you used in your example. Also also, you should probably be posting to R-sig-geo. Barry __ 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] import data (txt) separated by many blank spaces and lines with variable names that correspond to multiple observations.
Hello, I have read other posts and in part I tried to solve my problem. I have a txt file but the values as well as being separated by many blank spaces and lines eg.var_a var_b var_c 1 2 4 5 2 62 have an encoding problem in the header, let me explain: some of the variables grouping multiple observations throughout the text egvar_a = 1var_b = 2,4,5 var_c=2 etc. now I have tried to achieve by removing the header and doubling the name of the variable where needed but the problem still remains to convert the data that come out like this: istr-scan(file.choose(), what = numeric, sep=\n,quote=\', n = -1, dec = .,flush = FALSE, fill = FALSE, strip.white = TRUE, quiet = FALSE, blank.lines.skip = TRUE, multi.line = TRUE) [25877] 1\t\t \t \t \t1\t \t1\t1\t1\t \t2\t4\t [25878] t5\t\t\t\t2\t6\t\t\t\t2 write.table(istr, qmethod = double) 25877 1 2 4 25878 5 2 6 2 but remains the problem: - all numbers are in a unique quote (i would like a separeted cells) - in txt format variables are not exhausted all in the first line, but for example from the first to the fifth however, when R imports, each line seems to be an observation in my case an individual (n) how to solve it? -- View this message in context: http://r.789695.n4.nabble.com/import-data-txt-separated-by-many-blank-spaces-and-lines-with-variable-names-that-correspond-to-mult-tp4656041.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] importing large datasets in R
take a look at ff package On Jan 19, 2013 7:04 AM, gaurav singh gauravonlin...@gmail.com wrote: Hi Everyone, I am a little new to R and the first problem I am facing is the dilemma whether R is suitable for files of size 2 GB's and slightly more then 2 Million rows. When I try importing the data using read.table, it seems to take forever and I have to cancel the command. Are there any special techniques or methods which i can use or some tricks of the game that I should keep in mind in order to be able to do data analysis on such large files using R? -- Regards Gaurav Singh [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] importing large datasets in R
On 13-01-19 3:28 AM, gaurav singh wrote: Hi Everyone, I am a little new to R and the first problem I am facing is the dilemma whether R is suitable for files of size 2 GB's and slightly more then 2 Million rows. When I try importing the data using read.table, it seems to take forever and I have to cancel the command. Are there any special techniques or methods which i can use or some tricks of the game that I should keep in mind in order to be able to do data analysis on such large files using R? Specifying the type of each column with colClasses will speed up read.table a lot in a big file. You have a lot of data, so having a lot of memory will help. You may want to work in 64 bit R, which has access to a lot more than 32 bit R sees. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] calculating mean matrix
Hi list, Thank you vey much for reading this post. I have a data frame, I am trying to split it into a couple of data frame using one of the columns, say, x. After I get the data frames, I am planning to treat them as matrices and trying to calculate an element by element mean matrix. Could anyone give me some advice how to do it? So far, I know that if I have a couple of matrices, say data1,data2,data3,data4...dataN, I can do it like this: data=array(cbind(data1,data2,data3,data4,dataN), c(2, 3, N)) #2 refers to row number of matrix, 3 refers to column number of matrix, N refers to number of matrices to be averaged. meanmtrx=apply(data,1:2,mean) but I do not know how to use the resulting data frames with cbind(). Maybe there are other better ways. Any advice is appreciated. Thank you very much. Have a nice day. ya [[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] calculating mean matrix
I'm not sure I understand your question. It is always better to use an example: set.seed(42) dataN - array(sapply(1:5, function(i) assign(paste0(data,i), + matrix(rnorm(6), 2, 3))), c(2, 3, 5)) meanmtrx - apply(dataN,1:2,mean) meanmtrx [,1] [,2] [,3] [1,] 0.189669255 0.3368646 0.34261301 [2,] -0.009700353 -0.4676745 0.01974906 The result is a matrix, not a data frame, and certainly not resulting data frames. What are you trying to cbind? -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of ya Sent: Saturday, January 19, 2013 8:50 AM To: r-help Subject: [R] calculating mean matrix Hi list, Thank you vey much for reading this post. I have a data frame, I am trying to split it into a couple of data frame using one of the columns, say, x. After I get the data frames, I am planning to treat them as matrices and trying to calculate an element by element mean matrix. Could anyone give me some advice how to do it? So far, I know that if I have a couple of matrices, say data1,data2,data3,data4...dataN, I can do it like this: data=array(cbind(data1,data2,data3,data4,dataN), c(2, 3, N)) #2 refers to row number of matrix, 3 refers to column number of matrix, N refers to number of matrices to be averaged. meanmtrx=apply(data,1:2,mean) but I do not know how to use the resulting data frames with cbind(). Maybe there are other better ways. Any advice is appreciated. Thank you very much. Have a nice day. ya [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to re-project ease( Equal Area Scalable Earth) grid with a ~25 km cylindrical projection to WGS84 0.25 degree?
In fact,it is netcdf file(even if the extension is DBL). I am new to prjections and i just tried that spTransform,I did not know projectraster. Could you please tell me what is the command using project raster.I wonder if you have tried to re-project the file? -- View this message in context: http://r.789695.n4.nabble.com/How-to-re-project-ease-Equal-Area-Scalable-Earth-grid-with-a-25-km-cylindrical-projection-to-WGS84-0-tp4655977p4656055.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] Need help with Wavelet transformation
Dear R users, I am trying to perform a Wavelet transformation for time series data. I found R package called: wavelets. But as far as I have tried - no luck. I need to get something like that: http://www.jssm.org/combat/2/5/fig1.gif Maybe some of you are familiar with this problem? Thanks for your help. p.s. I do also need FFT something like that: http://www.aanda.org/index.php?option=com_imageformat=rawurl=/articles/aa/full_html/2009/06/aa09551-08/img36.gif -- Simonas Kecorius ** [[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] Hclust tree to Figtree w/ branch lengths
Hi, This worked: fit - hclust(d, method=ward) library(ape) p - (as.phylo(fit)) write.tree(p, file=MyNewick.tre) Cheers, J -- View this message in context: http://r.789695.n4.nabble.com/Hclust-tree-to-Figtree-w-branch-lengths-tp4655990p4656057.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] Tinn-R and R problem
Hello,
This seems to be a Tinn-R question, to be addressed to its team, not to
R-Help. Anyway, since you're using R 2.12.1, maybe the error goes away
if you update your version of R.
Hope this helps,
Rui Barradas
Em 19-01-2013 04:30, Roslina Zakaria escreveu:
Dear r-users,
Actually, this is not a big problem, however it is a bit annoying. Everytime I
want to use Tinn-R and R. I have to do this step first before I can excute a
set of R codes:
R-- configure -- temporarily (current session)
if not it will give this message:
.trPaths - paste(paste(Sys.getenv('APPDATA'), '\\Tinn-R\\tmp\\', sep=''),
c('', 'search.txt', 'objects.txt', 'file.r', 'selection.r', 'block.r', 'lines.r'),
sep=''
source('C:/Users/Owner/AppData/Roaming/Tinn-R/custom/Rconfigure_default.r')
Hope somebody can explain to me and help me to solve this problem?
R version 2.12.1 (2010-12-16)
Thank you so much for your help.
[[alternative HTML version deleted]]
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Re: [R] Tinn-R and R problem
Yes, Rui.
And, even more, the Tinn-R docs explain what to do and there's even a
Tinn-R menu item (R --Configure -- Permanent) that should fix the
matter.
For manual configuration of such things in R, see (in R) ?Startup
-- Bert
On Sat, Jan 19, 2013 at 8:28 AM, Rui Barradas ruipbarra...@sapo.pt wrote:
Hello,
This seems to be a Tinn-R question, to be addressed to its team, not to
R-Help. Anyway, since you're using R 2.12.1, maybe the error goes away if
you update your version of R.
Hope this helps,
Rui Barradas
Em 19-01-2013 04:30, Roslina Zakaria escreveu:
Dear r-users,
Actually, this is not a big problem, however it is a bit annoying.
Everytime I want to use Tinn-R and R. I have to do this step first before I
can excute a set of R codes:
R-- configure -- temporarily (current session)
if not it will give this message:
.trPaths - paste(paste(Sys.getenv('APPDATA'), '\\Tinn-R\\tmp\\',
sep=''), c('', 'search.txt', 'objects.txt', 'file.r', 'selection.r',
'block.r', 'lines.r'), sep=''
source('C:/Users/Owner/AppData/Roaming/Tinn-R/custom/Rconfigure_default.r')
Hope somebody can explain to me and help me to solve this problem?
R version 2.12.1 (2010-12-16)
Thank you so much for your help.
[[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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--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
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[R] Deformulation and R
Dear All, I hope this is not too off-topic. Essentially, I need to know if there is any R package which can help me with a deformulation project. Suppose e.g. that you know from a chemical analysis the fat, mineral, vitamin, energy [and so on] content of a certain food product. You also know the ingredients of this product (e.g. milk, lactose, vegetable oil) and you know the chemical composition of each ingredient in terms of fat, minerals, vitamins etc... At this point the question, assuming that the procedure to create the product from the ingredients does not alter the chemical composition of any ingredient, is to determine the amount of each ingredient (milk, lactose, vegetable oil) in the final product. Can anyone point me in the right direction? Many thanks Lorenzo __ 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] Deformulation and R
Algebra 1? --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Lorenzo Isella lorenzo.ise...@gmail.com wrote: Dear All, I hope this is not too off-topic. Essentially, I need to know if there is any R package which can help me with a deformulation project. Suppose e.g. that you know from a chemical analysis the fat, mineral, vitamin, energy [and so on] content of a certain food product. You also know the ingredients of this product (e.g. milk, lactose, vegetable oil) and you know the chemical composition of each ingredient in terms of fat, minerals, vitamins etc... At this point the question, assuming that the procedure to create the product from the ingredients does not alter the chemical composition of any ingredient, is to determine the amount of each ingredient (milk, lactose, vegetable oil) in the final product. Can anyone point me in the right direction? Many thanks Lorenzo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in mer_finalize(ans) : Downdated X'X is not positive definite, 8.
Yoav Avneon Avneony at bgu.ac.il writes: I have conducted an experiment in order to examine predation pressure in the surroundings of potential wildlife road-crossing structures. I have documented predation occurrence (binary…) in these structures and calculated several possible explanatory variables describing the spatial heterogeneity in several scales. At the landscape scale I have calculated the percentage of different land-uses (7) in buffers around the structures with changing radii (100m, 250m, 500m, 1000m and 2000m). For each radii I have generated a set of all possible models from the given 7 variables related to this radii. I have tried to account for random effects. A spatial random effect – the structure itself as a repeated measurement, by adding the term (1|Road_Structure). A temporal random effect – the observation session (is it correct to say that this examines possible learning in time ?), by adding the term (1|Session.ord). I have generated 4 sets for each radii: 1) with both random effects, 2+3) only one (each) random effect, and 4) none. I have tried to model the relationships using glm, glmer and lmer. The problem is that in the full model (all 7 variables) of some sets with random effects I get the following error: *Error in mer_finalize(ans) : Downdated X'X is not positive definite, 8.* The only record of this error I have found in the internet is for data with missing observation. This doesn't comply with my data set. I think it might be a singularity problem but I don't know how to check it, and as a result, I obviously don't know how to fix it. I have attached example R scripts (for the radius 2000) and the data table. Any help is highly appreciated ! Thanks and all the best, Questions like this (and follow-ups) should probably go to r-sig-mixed-mod...@r-project.org. I don't have time to dig into this in detail, but I would start by (1) centering and scaling all of your variables (see ?scale, and Schielzeth 2010 _Methods in Ecology and Evolution_ and (2) checking the correlations among your variables; if they are strongly correlated you have lots of options (none of them perfect), much discussed on the internet, including discarding some variables or using PCA. __ 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] calculating mean matrix
One way using `Reduce`:
set.seed(45)
grp - factor(rep(letters[1:10], each=10)) # equivalent of your column x
# dummy data
df - as.data.frame(matrix(sample(1:1000, replace=T),
ncol=length(levels(grp
# solution
Reduce('+', split(df, grp))/length(levels(grp))
Arun
On Saturday, January 19, 2013 at 3:49 PM, ya wrote:
Hi list,
Thank you vey much for reading this post.
I have a data frame, I am trying to split it into a couple of data frame
using one of the columns, say, x. After I get the data frames, I am planning
to treat them as matrices and trying to calculate an element by element mean
matrix. Could anyone give me some advice how to do it?
So far, I know that if I have a couple of matrices, say
data1,data2,data3,data4...dataN, I can do it like this:
data=array(cbind(data1,data2,data3,data4,dataN), c(2, 3, N))
#2 refers to row number of matrix, 3 refers to column number of matrix, N
refers to number of matrices to be averaged.
meanmtrx=apply(data,1:2,mean)
but I do not know how to use the resulting data frames with cbind(). Maybe
there are other better ways. Any advice is appreciated.
Thank you very much.
Have a nice day.
ya
[[alternative HTML version deleted]]
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[R] Merge 2 columns into 1 column
Hey everyone, I just canât wrap my head around this problem: I got 2 Columns with 4 columns. They basically look like this: 1 2 3 4 ⦠⦠⦠⦠I want to merge the two CSVs into a two-column list, which should look like this: 1 3 2 4 ⦠⦠⦠⦠This is what I came up with so far: files - paste(list.files(files.dir, pattern = *.csv), sep = )# Scan mergedfiles - do.call(rbind, lapply(files, read.csv)) # Merge Obviously this will only merge the two CSVs into a four column list. Is there any way to merge columns 1 3 and columns 2 4 of both files into a single list? Thanks and all the best Kenji [[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] Is it possible to create color ramp legend in spplot for discontinuous data ?
Hello All, I have a discontinuous dataset and I used spplot to plot the points. I was wondering whether it is possible to show the legend of the plot as color ramp. I saw that on continuous data. If anyone could tell me that would be great. Another thing I would like to know is how can we create the horizontal legend. By default, the legend is vertical. I was able to shift the legend inside the plot but not horizontal. Some of the code I used is as follows: ##Polygon as major plot and contour as layout ## Put north icon on the map l2 = list(SpatialPolygonsRescale, layout.north.arrow(), offset = c(439000,3368000), scale = 4000) l3 = list(SpatialPolygonsRescale, layout.scale.bar(), offset = c(46,3352000), scale = 5000, fill=c(transparent,black)) l4 = list(sp.text,c(46,3351500),0) l5 = list(sp.text,c(465000,3351500),100 m) cuts=c(0,5,10,15,20,25,30,35,37,39,40) p1 - spplot(data1,sp.layout=list(list(sp.polygons,hello),l2,l3,l4,l5),axes=T,xlab=Eastings,cuts=cuts, ylab=Northings,lwd=2,cex=1.2,col.regions = rainbow(100, start = 3/15, end = 1)) # Legend in Spplot names(p1$legend) - inside p1$legend$inside$x - 0.15 p1$legend$inside$y - 0.9 plot(p1) Thank you so much. Janesh [[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] calculating mean matrix
Dear Arun and David, Thank you very much for the response. Arun's code works. Thank you very much. David, I am sorry that I did not quite get the mean of your code, but still, thank you very much for helping. Best regards, ya -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of ya Sent: Saturday, January 19, 2013 8:50 AM To: r-help Subject: [R] calculating mean matrix Hi list, Thank you vey much for reading this post. I have a data frame, I am trying to split it into a couple of data frame using one of the columns, say, x. After I get the data frames, I am planning to treat them as matrices and trying to calculate an element by element mean matrix. Could anyone give me some advice how to do it? So far, I know that if I have a couple of matrices, say data1,data2,data3,data4...dataN, I can do it like this: data=array(cbind(data1,data2,data3,data4,dataN), c(2, 3, N)) #2 refers to row number of matrix, 3 refers to column number of matrix, N refers to number of matrices to be averaged. meanmtrx=apply(data,1:2,mean) but I do not know how to use the resulting data frames with cbind(). Maybe there are other better ways. Any advice is appreciated. Thank you very much. Have a nice day. ya [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Doing mixed stock analysis with predict function using DFA
Dear R Help Mailing List Members, I have some baseline data (attached) on which I plan to run a DFA in R to find out the best predictor variables that best allow discrimination between the different stocks. I then need to apply this DFA function to the mixed data set (attached), which contains all the predictor variables of the baseline data set, but does not contain a stock variable, as their origin is unknown and I am trying to classify the mixed stock fish back to their origin stock using the DFA function generated from the baseline data. My question is whether it is possible to use the predict function with the generated DFA function and provide the mixed data set as the newdata argument within this to generate the classification, even though the mixed data set does not contain the stock variable? Unfortunately, the mixstock package that has recently become available is not capable of dealing with continuous variables at this time, so I am unable to use it. I would be grateful for any guidance you may be able to provide. Thank you, Melanie Melanie Zölck (Zoelck) PhD Candidate Galway-Mayo Institute of Technology Marine and Freshwater Research Centre Commercial Fisheries Research Group Department of Life Science Dublin Road Galway Republic of Ireland E-mail: mzoe...@hotmaill.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] dummy encoding in metafor
Hi, I am quite new to R and in need of some advice. I am trying to conduct a meta regression over a some studies with about 7 mod variables which I have to dummy encode. I have found the following piece of code in the manual for the metafor library: ### manual dummy coding of the allocation factor alloc.random - ifelse(dat$alloc == random, 1, 0) alloc.alternate - ifelse(dat$alloc == alternate, 1, 0) alloc.systematic - ifelse(dat$alloc == systematic, 1, 0) ### test the allocation factor (in the presence of the other moderators) ### note: alternate is the reference level of the allocation factor ### note: the intercept is the first coefficient, so btt=c(2,3) rma(yi, vi, mods=cbind(alloc.random, alloc.systematic, year, ablat), data=dat, method=REML, btt=c(2,3)) What I do not understand is the following: How does R know which columns in my data.frame are related to the dummy encoded variables? It is clear that in the call of cbind I just do not use the reference variable as a parameter but I do not get it how R knows that alloc.random and alloc.systematic refer to the column alloc in the data frame. Thank you very much in advance for your help, kind regards, Alma [[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] Cluster Analysis and PCoA (mixt variables)
Hello everyone,
I mail you because of my lake of knowlegde regarding statistics.
I'm using the CA and PCoA (but maybe should I use some other techniques) to
determine the differences and similarities between a large sample of plants
using different kind of traits through matrix of mixte variables.
I understood that the daisy() function using the gower metric and defining
the different type of variable is a good way to deal with such mixt
variable. And in fact, my plots (cluster{agnes})(more that my PCoA) are
quite reflecting what I was expecting from the aspect of those different
plants.
My problem :
The problem now is that I need to understand wich variables are considered
to produce the dissimilarity matrix that is used for the cluster analysis
or the PCoA. In other word, how are construct the branch of my Cluster
Analysis tree?
It has been one month since I tried to figured most of the things out of
what I know today in data analysis and R software world. So, I'm really
sorry for asking so simple things that do not exactly focus on the R issues
but I tried in many ways but I just can't figure it out.
Thank you
Julien Mehl Vettori
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Re: [R] Merge 2 columns into 1 column
On Jan 19, 2013, at 8:08 AM, qt2ho...@gmail.com wrote: Hey everyone, I just can’t wrap my head around this problem: I got 2 Columns with 4 columns. OK, this is simply incoherent. They basically look like this: 1 2 3 4 … … … … I want to merge the two CSVs into a two-column list, which should look like this: 1 3 2 4 … … … … This is what I came up with so far: files - paste(list.files(files.dir, pattern = *.csv), sep = )# Scan mergedfiles - do.call(rbind, lapply(files, read.csv)) # Merge Obviously this will only merge the two CSVs into a four column list. I doubt that claim. Can you provide a reproducible example to prove me wrong? Is there any way to merge columns 1 3 and columns 2 4 of both files into a single list? Thanks and all the best Kenji [[alternative HTML version deleted]] -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] a confidence interval from an ANOVA model
Dear R People: I have a data set with trt and resp: trt resp A 23 A 28 A 37 A 30 B 37 B 44 B 31 B 35 C 42 C 47 C 52 C 38 And I did read.table, constructed an aov object and ran the summary on the aov object. I also ran the TukeyHSD function. All is well so far. My question is: is there a way to put together a confidence interval from the aov object on a particular mean, please? It seems like there should be. Thanks, Have a great night/day, Sincerely, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: a confidence interval from an ANOVA model solved
Just use confint -- Forwarded message -- From: Erin Hodgess erinm.hodg...@gmail.com Date: Sat, Jan 19, 2013 at 8:11 PM Subject: [R] a confidence interval from an ANOVA model To: R help r-h...@stat.math.ethz.ch Dear R People: I have a data set with trt and resp: trt resp A 23 A 28 A 37 A 30 B 37 B 44 B 31 B 35 C 42 C 47 C 52 C 38 And I did read.table, constructed an aov object and ran the summary on the aov object. I also ran the TukeyHSD function. All is well so far. My question is: is there a way to put together a confidence interval from the aov object on a particular mean, please? It seems like there should be. Thanks, Have a great night/day, Sincerely, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@gmail.com -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@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] calculating mean matrix
Hi,
This could be also done by:
#Using Arun's example:
res- Reduce('+', split(df, grp))/length(levels(grp))
res
# V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
#1 417.3 792.2 504.2 506.1 513.9 480.7 545.4 564.4 473.7 486.2
#2 585.8 416.6 409.5 417.8 480.1 586.4 436.1 615.1 449.8 501.2
#3 459.3 449.1 542.0 411.6 404.6 507.6 472.0 344.0 363.2 485.1
#4 591.1 448.4 482.6 464.0 554.0 374.1 567.9 450.0 477.9 488.0
#5 433.1 438.2 441.4 596.4 356.9 461.6 356.7 457.4 434.9 510.4
6 # 425.7 498.3 452.0 489.4 302.8 538.1 270.6 418.6 564.1 545.8
#7 755.1 526.4 615.2 559.9 483.3 379.7 439.3 458.8 528.5 564.0
#8 599.7 579.4 473.2 585.1 508.3 643.7 432.1 587.2 547.6 506.2
#9 471.8 321.0 375.8 394.4 355.5 434.4 532.1 640.5 490.1 619.1
#10 356.6 434.3 403.9 445.0 416.2 532.8 570.9 548.9 697.9 488.8
library(plyr)
res1-aaply(laply(split(df,((1:nrow(df)-1)%/% 10)+1),as.matrix),c(2,3),mean)
res1
# X2
#X1 V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
# 1 417.3 792.2 504.2 506.1 513.9 480.7 545.4 564.4 473.7 486.2
# 2 585.8 416.6 409.5 417.8 480.1 586.4 436.1 615.1 449.8 501.2
# 3 459.3 449.1 542.0 411.6 404.6 507.6 472.0 344.0 363.2 485.1
# 4 591.1 448.4 482.6 464.0 554.0 374.1 567.9 450.0 477.9 488.0
# 5 433.1 438.2 441.4 596.4 356.9 461.6 356.7 457.4 434.9 510.4
# 6 425.7 498.3 452.0 489.4 302.8 538.1 270.6 418.6 564.1 545.8
# 7 755.1 526.4 615.2 559.9 483.3 379.7 439.3 458.8 528.5 564.0
#8 599.7 579.4 473.2 585.1 508.3 643.7 432.1 587.2 547.6 506.2
#9 471.8 321.0 375.8 394.4 355.5 434.4 532.1 640.5 490.1 619.1
#10 356.6 434.3 403.9 445.0 416.2 532.8 570.9 548.9 697.9 488.8
A.K.
- Original Message -
From: ya xinxi...@126.com
To: r-help r-help@r-project.org
Cc:
Sent: Saturday, January 19, 2013 9:49 AM
Subject: [R] calculating mean matrix
Hi list,
Thank you vey much for reading this post.
I have a data frame, I am trying to split it into a couple of data frame using
one of the columns, say, x. After I get the data frames, I am planning to treat
them as matrices and trying to calculate an element by element mean matrix.
Could anyone give me some advice how to do it?
So far, I know that if I have a couple of matrices, say
data1,data2,data3,data4...dataN, I can do it like this:
data=array(cbind(data1,data2,data3,data4,dataN), c(2, 3, N))
#2 refers to row number of matrix, 3 refers to column number of matrix, N
refers to number of matrices to be averaged.
meanmtrx=apply(data,1:2,mean)
but I do not know how to use the resulting data frames with cbind(). Maybe
there are other better ways. Any advice is appreciated.
Thank you very much.
Have a nice day.
ya
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and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is it possible to create color ramp legend in spplot for discontinuous data ?
Hi Janesh, I'm going to ask you the same thing you were asked when you posted this question on the r-sig-Geo list: What is data1? Please give us the output of dput(data1), or make another example that we can reproduce. Best, Ista On Sat, Jan 19, 2013 at 7:16 AM, Jd Devkota janesh.devk...@gmail.com wrote: Hello All, I have a discontinuous dataset and I used spplot to plot the points. I was wondering whether it is possible to show the legend of the plot as color ramp. I saw that on continuous data. If anyone could tell me that would be great. Another thing I would like to know is how can we create the horizontal legend. By default, the legend is vertical. I was able to shift the legend inside the plot but not horizontal. Some of the code I used is as follows: ##Polygon as major plot and contour as layout ## Put north icon on the map l2 = list(SpatialPolygonsRescale, layout.north.arrow(), offset = c(439000,3368000), scale = 4000) l3 = list(SpatialPolygonsRescale, layout.scale.bar(), offset = c(46,3352000), scale = 5000, fill=c(transparent,black)) l4 = list(sp.text,c(46,3351500),0) l5 = list(sp.text,c(465000,3351500),100 m) cuts=c(0,5,10,15,20,25,30,35,37,39,40) p1 - spplot(data1,sp.layout=list(list(sp.polygons,hello),l2,l3,l4,l5),axes=T,xlab=Eastings,cuts=cuts, ylab=Northings,lwd=2,cex=1.2,col.regions = rainbow(100, start = 3/15, end = 1)) # Legend in Spplot names(p1$legend) - inside p1$legend$inside$x - 0.15 p1$legend$inside$y - 0.9 plot(p1) Thank you so much. Janesh [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Merge 2 columns into 1 column
HI, Not clear what you are trying to do: set.seed(25) df1-as.data.frame(matrix(sample(1:40,20,replace=TRUE),ncol=4)) set.seed(15) df2-as.data.frame(matrix(sample(1:40,20,replace=TRUE),ncol=4)) do.call(rbind,lapply(list(df1,df2),`[`,c(2,4))) # V2 V4 #1 40 6 #2 26 22 #3 14 30 #4 3 20 #5 12 30 #6 40 34 #7 33 18 #8 11 39 #9 28 6 #10 34 32 do.call(rbind,lapply(list(df1,df2),`[`,c(1,3))) #in reading from read.csv() do.call(rbind,lapply(lapply(files,read.csv),`[`,c(1,3))) A.K. - Original Message - From: qt2ho...@gmail.com qt2ho...@gmail.com To: r-help@r-project.org Cc: Sent: Saturday, January 19, 2013 11:08 AM Subject: [R] Merge 2 columns into 1 column Hey everyone, I just can’t wrap my head around this problem: I got 2 Columns with 4 columns. They basically look like this: 1 2 3 4 … … … … I want to merge the two CSVs into a two-column list, which should look like this: 1 3 2 4 … … … … This is what I came up with so far: files - paste(list.files(files.dir, pattern = *.csv), sep = )# Scan mergedfiles - do.call(rbind, lapply(files, read.csv)) # Merge Obviously this will only merge the two CSVs into a four column list. Is there any way to merge columns 1 3 and columns 2 4 of both files into a single list? Thanks and all the best Kenji [[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] Data interpolation using R from the user given data
I have a time series of more than 2500 points. I also have observed data set but it is not continuous. I want to use the observed data set and find out the modeled data from the time series data. After the modeled data has been found out for the same time I want to plot the correlation plot and display the equation and coefficient of correlation on the plot. The sample time series can be found on the following link https://www.dropbox.com/s/uxg0g1h7vbhxp3z/33010G10.csv The observed data is as follows: 260.323 25.170 267.316 25.520 274.313 24.950 281.333 25.140 288.326 24.130 295.319 19.540 302.330 10.280 309.323 17.340 317.326 18.300 323.323 11.280 329.355 12.450 337.333 9.050 351.323 14.620 364.389 16.350 372.368 19.400 379.382 10.980 393.382 14.260 414.377 11.640 421.382 10.660 428.378 3.950 435.382 18.950 442.378 18.180 449.378 20.570 456.368 18.400 463.375 11.770 470.382 18.130 477.372 18.370 484.368 21.310 491.375 24.200 498.378 24.070 505.382 18.600 512.389 24.670 526.392 28.310 533.406 28.310 540.399 28.700 547.375 28.400 554.389 27.050 Please let me know how can I efficiently arrange the dataset so that I could repeat this for several other locations. Thank you so much. Best Regards, J Dev [[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] select rows with identical columns from a data frame
* Rui Barradas ehvconeen...@fncb.cg [2013-01-18 21:02:20 +]: Try the following. complete.cases(f) apply(f, 1, function(x) all(x == x[1])) thanks, this works, but is horribly slow (dim(f) is 766,950x2) -- Sam Steingold (http://sds.podval.org/) on Ubuntu 12.04 (precise) X 11.0.11103000 http://www.childpsy.net/ http://truepeace.org http://palestinefacts.org http://thereligionofpeace.com http://honestreporting.com http://ffii.org usually: can't pay == don't buy. software: can't buy == don't pay __ 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] select rows with identical columns from a data frame
But David W. and Bill Dunlap gave you solutions that also work and are much faster, no?! -- Bert On Sat, Jan 19, 2013 at 9:41 PM, Sam Steingold s...@gnu.org wrote: * Rui Barradas ehvconeen...@fncb.cg [2013-01-18 21:02:20 +]: Try the following. complete.cases(f) apply(f, 1, function(x) all(x == x[1])) thanks, this works, but is horribly slow (dim(f) is 766,950x2) -- Sam Steingold (http://sds.podval.org/) on Ubuntu 12.04 (precise) X 11.0.11103000 http://www.childpsy.net/ http://truepeace.org http://palestinefacts.org http://thereligionofpeace.com http://honestreporting.com http://ffii.org usually: can't pay == don't buy. software: can't buy == don't pay __ 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ 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.
