date:20170502

Re: [R] nested for loop with data table

2017-05-02 Thread Jim Lemon

Hi Ek,
I think you want your example to look like this:

Sample<-read.table(text=
"Num Color Grade Value Month Day
1 yellow A 20 May 1
2 green B 25 June 2
3 green A 10 April 3
4 black A 17 August 3
5 red C 5 December 5
6 orange D 0 January 13
7 orange E 12 January 5
8 orange F 11 February 8
9 orange F 99 July 23
10 orange F 70 May 7
11 black A 77 June 11
12 green B 87 April 33
13 black A 79 August 9
14 green A 68 December 14
15 black C 90 January 31
16 green D 79 January 11
17 black E 101 February 17
18 red F 90 July 21
19 red F 112 February 13
20 red F 101 July 20",
header=TRUE)
AAA<-Sample[Sample$Num < 5 & Sample$Day < 3,]
BBB<-Sample[Sample$Num > 15 & Sample$Day > 13,]
for(i in 1:length(AAA)) {
 for(j in 1:length(BBB)) {
  ...
 }
}

except in data.table notation. However, I can't work out what you want
to do in the loop.

Jim


On Wed, May 3, 2017 at 2:35 AM, Ek Esawi  wrote:
> I have a huge data file; a sample is listed below. I am using the package
> data table to process the file and I am stuck on one issue and need some
> feedback. I used fread to create a data table. Then I divided the data
> table (named File1) into 10 general subsets using common table commands
> such as:
>
>
>
> AAA <- File1[Num<5>15]
>
> BBB <- File1[Num>15<10]
>
> …..
>
> …..
>
> …..
>
> …..
>
> …..
>
> …..
>
>
>
> I wanted to divide and count each of the above subsets based on a set of
> parameters common to all subsets. I did the following to go through each
> subset and it works:
>
> For (I in 1: length (AAA)) {
>
>   aa <- c(AAA[color==”green”==”a”,month==”Januray” .N],[
> AAA[color==”green”==”b”& month==”June”’ .N])
>
> }
>
>
>
> The question: I don’t want to have a separate loop for each subset (10
> loops). Instead, I was hoping to have 2 nested loops in the form below:
>
>
>
> For (I in 1:N)){
>
>   For (j in 1:M){
>
>
>
> }
>
> }
>
>
>
>  Sample
>
>
> Num
>
> Color
>
> Grade
>
> Value
>
> Month
>
> Day
>
> 1
>
> yellow
>
> A
>
> 20
>
> May
>
> 1
>
> 2
>
> green
>
> B
>
> 25
>
> June
>
> 2
>
> 3
>
> green
>
> A
>
> 10
>
> April
>
> 3
>
> 4
>
> black
>
> A
>
> 17
>
> August
>
> 3
>
> 5
>
> red
>
> C
>
> 5
>
> December
>
> 5
>
> 6
>
> orange
>
> D
>
> 0
>
> January
>
> 13
>
> 7
>
> orange
>
> E
>
> 12
>
> January
>
> 5
>
> 8
>
> orange
>
> F
>
> 11
>
> February
>
> 8
>
> 9
>
> orange
>
> F
>
> 99
>
> July
>
> 23
>
> 10
>
> orange
>
> F
>
> 70
>
> May
>
> 7
>
> 11
>
> black
>
> A
>
> 77
>
> June
>
> 11
>
> 12
>
> green
>
> B
>
> 87
>
> April
>
> 33
>
> 13
>
> black
>
> A
>
> 79
>
> August
>
> 9
>
> 14
>
> green
>
> A
>
> 68
>
> December
>
> 14
>
> 15
>
> black
>
> C
>
> 90
>
> January
>
> 31
>
> 16
>
> green
>
> D
>
> 79
>
> January
>
> 11
>
> 17
>
> black
>
> E
>
> 101
>
> February
>
> 17
>
> 18
>
> red
>
> F
>
> 90
>
> July
>
> 21
>
> 19
>
> red
>
> F
>
> 112
>
> February
>
> 13
>
> 20
>
> red
>
> F
>
> 101
>
> July
>
> 20
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
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] install lapack for mac

2017-05-02 Thread William Michels via R-help

Have you tried R-GUI, in the R-distribution available below?

https://cran.r-project.org/bin/macosx/

Here's a similar question on SO:

http://stackoverflow.com/questions/13476736/r-lapack-routines-cannot-be-loaded

HTH, Bill.

William Michels, Ph.D.


On Tue, May 2, 2017 at 11:51 AM, Assa Yeroslaviz  wrote:
> Hi,
>
> I am running R under Rstudio for the analysis of single-cell RNA-Seq data.
>
> When trying to analyse some data I keep getting the message
>
>> slicer_traj_lle <- lle(t(deng[slicer_genes,]), m = 2, k)$Y
> finding neighbours
> calculating weights
> Error in eigen(G, symmetric = TRUE, only.values = TRUE) :
>   LAPACK routines cannot be loaded
>
>
> After searching the net I couldn't find a way to install LAPACK on a mac.
> When trying to install it via homebrew I get this message (this is a
> shorted message. the complete message is below):
>
> brew install lapack
>
> ...
>
> macOS already provides this software and installing another version in
>
> parallel can cause all kinds of trouble.
>
> For compilers to find this software you may need to set:
>
> LDFLAGS:  -L/usr/local/opt/lapack/lib
>
> CPPFLAGS: -I/usr/local/opt/lapack/include
>
> For pkg-config to find this software you may need to set:
>
> PKG_CONFIG_PATH: /usr/local/opt/lapack/lib/pkgconfig
>
>
> I truely don't understand why my mac can't find the lapack, if it already
> there and i still can't figure out, how to tell my R tool / RStudio, where
> to find lapack.
>
> Does anyone has an idea how to do this?
>
> thanks
>
> Assa
>> R.version
>_
> platform   x86_64-apple-darwin13.4.0
> arch   x86_64
> os darwin13.4.0
> system x86_64, darwin13.4.0
> status
> major  3
> minor  3.1
> year   2016
> month  06
> day21
> svn rev70800
> language   R
> version.string R version 3.3.1 (2016-06-21)
> nickname   Bug in Your Hair
>
>
>> sessionInfo()
> R version 3.3.1 (2016-06-21)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.12.4 (Sierra)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
>  [1] splines   stats4parallel  stats graphics  grDevices utils
> datasets  methods
> [10] base
>
> other attached packages:
>  [1] R.utils_2.5.0R.oo_1.21.0  R.methodsS3_1.7.1
>  Seurat_1.4.0.14
>  [5] cowplot_0.7.0SLICER_0.2.0 alphahull_2.1lle_1.1
>
>  [9] snowfall_1.84-6.1snow_0.4-2   MASS_7.3-47
>  scatterplot3d_0.3-40
> [13] igraph_1.0.1 destiny_2.0.8monocle_2.2.0
>  DDRTree_0.1.4
> [17] irlba_2.1.2  VGAM_1.0-3   ggplot2_2.2.1
>  Biobase_2.34.0
> [21] BiocGenerics_0.20.0  Matrix_1.2-8 M3Drop_1.0.0
> numDeriv_2016.8-1
> [25] TSCAN_1.12.0
>
> loaded via a namespace (and not attached):
>   [1] shinydashboard_0.5.3   lme4_1.1-13RSQLite_1.1-2
>   [4] AnnotationDbi_1.36.2   htmlwidgets_0.8grid_3.3.1
>   [7] combinat_0.0-8 trimcluster_0.1-2  ranger_0.7.0
>  [10] Rtsne_0.13 munsell_0.4.3  codetools_0.2-15
>  [13] statmod_1.4.29 colorspace_1.3-2   fastICA_1.2-0
>  [16] knitr_1.15.1   ROCR_1.0-7 robustbase_0.92-7
>  [19] vcd_1.4-3  tensor_1.5 VIM_4.7.0
>  [22] TTR_0.23-1 lars_1.2   slam_0.1-40
>  [25] splancs_2.01-40bbmle_1.0.19   mnormt_1.5-5
>  [28] polyclip_1.6-1 pheatmap_1.0.8 rprojroot_1.2
>  [31] diptest_0.75-7 R6_2.2.0   RcppEigen_0.3.2.9.1
>  [34] flexmix_2.3-14 bitops_1.0-6   spatstat.utils_1.4-1
>  [37] assertthat_0.2.0   scales_0.4.1   nnet_7.3-12
>  [40] gtable_0.2.0   goftest_1.1-1  MatrixModels_0.4-1
>  [43] lazyeval_0.2.0 ModelMetrics_1.1.0 acepack_1.4.1
>  [46] checkmate_1.8.2reshape2_1.4.2 abind_1.4-5
>  [49] backports_1.0.5httpuv_1.3.3   rsconnect_0.7
>  [52] Hmisc_4.0-2caret_6.0-76   tools_3.3.1
>  [55] gplots_3.0.1   RColorBrewer_1.1-2 proxy_0.4-16
>  [58] Rcpp_0.12.10   plyr_1.8.4 base64enc_0.1-3
>  [61] RCurl_1.95-4.8 rpart_4.1-11   deldir_0.1-14
>  [64] pbapply_1.3-2  viridis_0.4.0  S4Vectors_0.12.2
>  [67] zoo_1.8-0  cluster_2.0.6  magrittr_1.5
>  [70] data.table_1.10.4  SparseM_1.77   lmtest_0.9-35
>  [73] mvtnorm_1.0-6  matrixStats_0.52.2 mime_0.5
>  [76] evaluate_0.10  xtable_1.8-2   smoother_1.1
>  [79] pbkrtest_0.4-7 XML_3.98-1.6   mclust_5.2.3
>  [82] IRanges_2.8.2  gridExtra_2.2.1HSMMSingleCell_0.108.0
>  [85] biomaRt_2.30.0 tibble_1.3.0   KernSmooth_2.23-15
>  [88] minqa_1.2.4htmltools_0.3.6segmented_0.5-1.4
>  [91] mgcv_1.8-17

Re: [R] memory issue

2017-05-02 Thread Jeff Newmiller

Suggestions...

Post plain text (you reduce your own chances of getting feedback by failing to 
do this in your email program)

Provide sample data and code

Buy more RAM

use data.table package and fread

load and analyze subsets of data

Put the data into a database (e.g. sqlite?)

If these suggestions seem brief, or even if they don't, please be more explicit 
in your question. Read [1] and [2].

[1] 
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

[2] http://adv-r.had.co.nz/Reproducibility.html
-- 
Sent from my phone. Please excuse my brevity.

On May 2, 2017 12:09:21 PM PDT, Amit Sengupta via R-help  
wrote:
>HI,I am unable to read a 2.4 gig file into a table (using read.table)
>in a 64 bit R environment. Do you have any suggestions?Amit 
>
>   [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>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 -- To UNSUBSCRIBE and more, see
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] nested for loop with data table

2017-05-02 Thread Boris Steipe

There's a lot that doesn't make sense here. I think what you need to do is 
produce a small, reproducible example, post that with dput() and state your 
question more clearly - including what you have tried and what didn't work. 
You'll probably be amazed how quickly you will get good advice if 
_you_only_follow_the_posting_guide_.

B.




> On May 2, 2017, at 12:35 PM, Ek Esawi  wrote:
> 
> I have a huge data file; a sample is listed below. I am using the package
> data table to process the file and I am stuck on one issue and need some
> feedback. I used fread to create a data table. Then I divided the data
> table (named File1) into 10 general subsets using common table commands
> such as:
> 
> 
> 
> AAA <- File1[Num<5>15]
> 
> BBB <- File1[Num>15<10]
> 
> …..
> 
> …..
> 
> …..
> 
> …..
> 
> …..
> 
> …..
> 
> 
> 
> I wanted to divide and count each of the above subsets based on a set of
> parameters common to all subsets. I did the following to go through each
> subset and it works:
> 
> For (I in 1: length (AAA)) {
> 
>  aa <- c(AAA[color==”green”==”a”,month==”Januray” .N],[
> AAA[color==”green”==”b”& month==”June”’ .N])
> 
> }
> 
> 
> 
> The question: I don’t want to have a separate loop for each subset (10
> loops). Instead, I was hoping to have 2 nested loops in the form below:
> 
> 
> 
> For (I in 1:N)){
> 
>  For (j in 1:M){
> 
> 
> 
> }
> 
> }
> 
> 
> 
> Sample
> 
> 
> Num
> 
> Color
> 
> Grade
> 
> Value
> 
> Month
> 
> Day
> 
> 1
> 
> yellow
> 
> A
> 
> 20
> 
> May
> 
> 1
> 
> 2
> 
> green
> 
> B
> 
> 25
> 
> June
> 
> 2
> 
> 3
> 
> green
> 
> A
> 
> 10
> 
> April
> 
> 3
> 
> 4
> 
> black
> 
> A
> 
> 17
> 
> August
> 
> 3
> 
> 5
> 
> red
> 
> C
> 
> 5
> 
> December
> 
> 5
> 
> 6
> 
> orange
> 
> D
> 
> 0
> 
> January
> 
> 13
> 
> 7
> 
> orange
> 
> E
> 
> 12
> 
> January
> 
> 5
> 
> 8
> 
> orange
> 
> F
> 
> 11
> 
> February
> 
> 8
> 
> 9
> 
> orange
> 
> F
> 
> 99
> 
> July
> 
> 23
> 
> 10
> 
> orange
> 
> F
> 
> 70
> 
> May
> 
> 7
> 
> 11
> 
> black
> 
> A
> 
> 77
> 
> June
> 
> 11
> 
> 12
> 
> green
> 
> B
> 
> 87
> 
> April
> 
> 33
> 
> 13
> 
> black
> 
> A
> 
> 79
> 
> August
> 
> 9
> 
> 14
> 
> green
> 
> A
> 
> 68
> 
> December
> 
> 14
> 
> 15
> 
> black
> 
> C
> 
> 90
> 
> January
> 
> 31
> 
> 16
> 
> green
> 
> D
> 
> 79
> 
> January
> 
> 11
> 
> 17
> 
> black
> 
> E
> 
> 101
> 
> February
> 
> 17
> 
> 18
> 
> red
> 
> F
> 
> 90
> 
> July
> 
> 21
> 
> 19
> 
> red
> 
> F
> 
> 112
> 
> February
> 
> 13
> 
> 20
> 
> red
> 
> F
> 
> 101
> 
> July
> 
> 20
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
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] memory issue

2017-05-02 Thread Amit Sengupta via R-help

HI,I am unable to read a 2.4 gig file into a table (using read.table) in a 64 
bit R environment. Do you have any suggestions?Amit 

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] install lapack for mac

2017-05-02 Thread Assa Yeroslaviz

Hi,

I am running R under Rstudio for the analysis of single-cell RNA-Seq data.

When trying to analyse some data I keep getting the message

> slicer_traj_lle <- lle(t(deng[slicer_genes,]), m = 2, k)$Y
finding neighbours
calculating weights
Error in eigen(G, symmetric = TRUE, only.values = TRUE) :
  LAPACK routines cannot be loaded


After searching the net I couldn't find a way to install LAPACK on a mac.
When trying to install it via homebrew I get this message (this is a
shorted message. the complete message is below):

brew install lapack

...

macOS already provides this software and installing another version in

parallel can cause all kinds of trouble.

For compilers to find this software you may need to set:

LDFLAGS:  -L/usr/local/opt/lapack/lib

CPPFLAGS: -I/usr/local/opt/lapack/include

For pkg-config to find this software you may need to set:

PKG_CONFIG_PATH: /usr/local/opt/lapack/lib/pkgconfig


I truely don't understand why my mac can't find the lapack, if it already
there and i still can't figure out, how to tell my R tool / RStudio, where
to find lapack.

Does anyone has an idea how to do this?

thanks

Assa
> R.version
   _
platform   x86_64-apple-darwin13.4.0
arch   x86_64
os darwin13.4.0
system x86_64, darwin13.4.0
status
major  3
minor  3.1
year   2016
month  06
day21
svn rev70800
language   R
version.string R version 3.3.1 (2016-06-21)
nickname   Bug in Your Hair


> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.4 (Sierra)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] splines   stats4parallel  stats graphics  grDevices utils
datasets  methods
[10] base

other attached packages:
 [1] R.utils_2.5.0R.oo_1.21.0  R.methodsS3_1.7.1
 Seurat_1.4.0.14
 [5] cowplot_0.7.0SLICER_0.2.0 alphahull_2.1lle_1.1

 [9] snowfall_1.84-6.1snow_0.4-2   MASS_7.3-47
 scatterplot3d_0.3-40
[13] igraph_1.0.1 destiny_2.0.8monocle_2.2.0
 DDRTree_0.1.4
[17] irlba_2.1.2  VGAM_1.0-3   ggplot2_2.2.1
 Biobase_2.34.0
[21] BiocGenerics_0.20.0  Matrix_1.2-8 M3Drop_1.0.0
numDeriv_2016.8-1
[25] TSCAN_1.12.0

loaded via a namespace (and not attached):
  [1] shinydashboard_0.5.3   lme4_1.1-13RSQLite_1.1-2
  [4] AnnotationDbi_1.36.2   htmlwidgets_0.8grid_3.3.1
  [7] combinat_0.0-8 trimcluster_0.1-2  ranger_0.7.0
 [10] Rtsne_0.13 munsell_0.4.3  codetools_0.2-15
 [13] statmod_1.4.29 colorspace_1.3-2   fastICA_1.2-0
 [16] knitr_1.15.1   ROCR_1.0-7 robustbase_0.92-7
 [19] vcd_1.4-3  tensor_1.5 VIM_4.7.0
 [22] TTR_0.23-1 lars_1.2   slam_0.1-40
 [25] splancs_2.01-40bbmle_1.0.19   mnormt_1.5-5
 [28] polyclip_1.6-1 pheatmap_1.0.8 rprojroot_1.2
 [31] diptest_0.75-7 R6_2.2.0   RcppEigen_0.3.2.9.1
 [34] flexmix_2.3-14 bitops_1.0-6   spatstat.utils_1.4-1
 [37] assertthat_0.2.0   scales_0.4.1   nnet_7.3-12
 [40] gtable_0.2.0   goftest_1.1-1  MatrixModels_0.4-1
 [43] lazyeval_0.2.0 ModelMetrics_1.1.0 acepack_1.4.1
 [46] checkmate_1.8.2reshape2_1.4.2 abind_1.4-5
 [49] backports_1.0.5httpuv_1.3.3   rsconnect_0.7
 [52] Hmisc_4.0-2caret_6.0-76   tools_3.3.1
 [55] gplots_3.0.1   RColorBrewer_1.1-2 proxy_0.4-16
 [58] Rcpp_0.12.10   plyr_1.8.4 base64enc_0.1-3
 [61] RCurl_1.95-4.8 rpart_4.1-11   deldir_0.1-14
 [64] pbapply_1.3-2  viridis_0.4.0  S4Vectors_0.12.2
 [67] zoo_1.8-0  cluster_2.0.6  magrittr_1.5
 [70] data.table_1.10.4  SparseM_1.77   lmtest_0.9-35
 [73] mvtnorm_1.0-6  matrixStats_0.52.2 mime_0.5
 [76] evaluate_0.10  xtable_1.8-2   smoother_1.1
 [79] pbkrtest_0.4-7 XML_3.98-1.6   mclust_5.2.3
 [82] IRanges_2.8.2  gridExtra_2.2.1HSMMSingleCell_0.108.0
 [85] biomaRt_2.30.0 tibble_1.3.0   KernSmooth_2.23-15
 [88] minqa_1.2.4htmltools_0.3.6segmented_0.5-1.4
 [91] mgcv_1.8-17Formula_1.2-1  tclust_1.2-3
 [94] DBI_0.6-1  fpc_2.1-10 boot_1.3-19
 [97] car_2.1-4  sgeostat_1.0-27gdata_2.17.0
[100] sn_1.5-0   foreign_0.8-68 laeken_0.4.6
[103] sp_1.2-4   foreach_1.4.3  stringr_1.2.0
[106] digest_0.6.12  tsne_0.1-3 rmarkdown_1.5
[109] htmlTable_1.9  kernlab_0.9-25 shiny_1.0.3
[112] gtools_3.5.0   quantreg_5.33  modeltools_0.2-21
[115] nloptr_1.0.4   nlme_3.1-131

[R] memory problem

2017-05-02 Thread Amit Sengupta via R-help

Hi,I was unable to read a 2.4 gig file into an R object using read.table in 64 
bit R environment. Please let me have your suggestions.Amit Sengupta

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and provide commented, minimal, self-contained, reproducible code.

[R] nested for loop with data table

2017-05-02 Thread Ek Esawi

I have a huge data file; a sample is listed below. I am using the package
data table to process the file and I am stuck on one issue and need some
feedback. I used fread to create a data table. Then I divided the data
table (named File1) into 10 general subsets using common table commands
such as:



AAA <- File1[Num<5>15]

BBB <- File1[Num>15<10]

…..

…..

…..

…..

…..

…..



I wanted to divide and count each of the above subsets based on a set of
parameters common to all subsets. I did the following to go through each
subset and it works:

For (I in 1: length (AAA)) {

  aa <- c(AAA[color==”green”==”a”,month==”Januray” .N],[
AAA[color==”green”==”b”& month==”June”’ .N])

}



The question: I don’t want to have a separate loop for each subset (10
loops). Instead, I was hoping to have 2 nested loops in the form below:



For (I in 1:N)){

  For (j in 1:M){



}

}



 Sample


Num

Color

Grade

Value

Month

Day

1

yellow

A

20

May

1

2

green

B

25

June

2

3

green

A

10

April

3

4

black

A

17

August

3

5

red

C

5

December

5

6

orange

D

0

January

13

7

orange

E

12

January

5

8

orange

F

11

February

8

9

orange

F

99

July

23

10

orange

F

70

May

7

11

black

A

77

June

11

12

green

B

87

April

33

13

black

A

79

August

9

14

green

A

68

December

14

15

black

C

90

January

31

16

green

D

79

January

11

17

black

E

101

February

17

18

red

F

90

July

21

19

red

F

112

February

13

20

red

F

101

July

20

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] clip a raster according to a shape file in R.

2017-05-02 Thread Jeff Newmiller

The answer is yes. However there are quite a few online resources (including 
blogs and the CRAN Spatial Task View and vignettes for packages mentioned 
there) that describe various tools and step you through how to do this, and you 
have not provided a reproducible example, and there is a whole mailing list 
dedicated to the topic (R-sig-geo), so I will just suggest that you read the 
Posting Guide mentioned below and (if needed) show the R-sig-geo mailing list 
your best attempt so they know how to help you. 
-- 
Sent from my phone. Please excuse my brevity.

On May 1, 2017 8:30:19 PM PDT, "M.M saifuddin"  wrote:
>I have a grid data which has values of a variable (e.g: Temperature).
>My
>data has 6069 data points where each data point refers to different
>latitude and longitude. I want to transform this data to a raster file
>so
>that I can clip it according to a shapefile that has much smaller
>boundaries than the raster ( actually the shapefile basins fall inside
>the
>much larger raster file which covers the whole USA).
>
>Can I do it by R? I know that this can be done by ArcGIS but I want to
>do
>it with R.
>
>Please help me.
>
>TIA
>
>   [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>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.

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Unusual behavior in e1071?

2017-05-02 Thread Uwe Ligges

Look more carefully at y. If this is a factor, please note what is the 
first (reference) level and what the second. This determines the rule, 
not the value of the first observation.


Best,
Uwe Ligges

On 02.05.2017 07:25, Daniel Jeske wrote:

Hello -

I have noticed that when I run svm() the order of my data matters.  If the
first case in the data frame has y=+1 I get the expected decision rule that
says to classify as +1 if f(x)>0.  However, if the first case in the data
frame has y=-1 then apparently the decision rule being used says to
classify as +1 if f(x)<0, and in this case all the coefficients are
negative of their values compared to the first case.  So the two
classification rules are equivalent, but is a user really supposed to know
the difference?  It is likely they would assume the decision rule is always
to classify as +1 if f(x)>0.  Does anyone think the behavior I have noticed
is as intended, or is otherwise benign?

Thank you,
Daniel Jeske
Professor
Department of Statistics
University of California - Riverside

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and provide commented, minimal, self-contained, reproducible code.



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Re: [R] cannot load .sav-files in R 3.4.0

2017-05-02 Thread Anthony Damico

are you able to install anything from github?  like

devtools::install_github( "hadley/dplyr" )



On Tue, May 2, 2017 at 9:36 AM,  wrote:

> unfortunately it failed with the installation of lodown:
>
>> devtools::install_github("ajdamico/lodown")
>>
> Downloading GitHub repo ajdamico/lodown@master
> from URL https://api.github.com/repos/ajdamico/lodown/zipball/master
> Installing lodown
> "C:/PROGRA~1/R/R-33~1.3/bin/x64/R" --no-site-file --no-environ --no-save
> \
>   --no-restore --quiet CMD INSTALL  \
>   "C:/Users/mandersk/AppData/Local/Temp/Rtmpch0aTn/devtools18f
> 4305b4ab5/ajdamico-lodown-d235a3e"  \
>   --library="\\unetna01/mandersk$/Daten/R/win-library/3.3" --install-tests
>
> * installing *source* package 'lodown' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> *** arch - i386
> Warnung in library(pkg_name, lib.loc = lib, character.only = TRUE,
> logical.return = TRUE)
>   there is no package called 'lodown'
> Fehler: Laden fehlgeschlagen
> Ausführung angehalten
> *** arch - x64
> Warnung in library(pkg_name, lib.loc = lib, character.only = TRUE,
> logical.return = TRUE)
>   there is no package called 'lodown'
> Fehler: Laden fehlgeschlagen
> Ausführung angehalten
> ERROR: loading failed for 'i386', 'x64'
> * removing '\\unetna01/mandersk$/Daten/R/win-library/3.3/lodown'
> Error: Command failed (1)
>
> Am 01.05.2017 18:15 schrieb Anthony Damico:
>
>> did my code work?  thanks
>>
>> On Mon, May 1, 2017 at 11:35 AM, 
>> wrote:
>>
>> hi, thanks for the reply!
>>> it always worked until 3.4.0. i got warning but they did not stop R
>>> loading the file ...
>>>
>>> Am 01.05.2017 16:10 schrieb Anthony Damico:
>>> hi, i don't think foreign::read.spss or haven::read_spss have ever
>>> worked with a handful of the ess files, but library(memisc) does.
>>> you
>>> are better off loading ess with library(lodown) because the drudge
>>> work has already been done--
>>>
>>> library(devtools)
>>> devtools::install_github("ajdamico/lodown")
>>> library(lodown)
>>> ess_cat <- get_catalog( "ess" , output_dir = "C:/My
>>> Directory/ESS"
>>> )
>>>
>>> # which entries do you want?
>>> head(ess_cat)
>>>
>>> # how about wave 7 only
>>> sub_ess_cat <- subset( ess_cat , wave == 7 )
>>>
>>> # replace the email address with whatever you registered with
>>> lodown( "ess" , sub_ess_cat , your_email = "em...@address.com"
>>> )
>>>
>>> x <- readRDS( "C:/My Directory/ESS/2014/ESS7csCH.rds" )
>>>
>>> # looks good
>>> head( x )
>>>
>>> On Mon, May 1, 2017 at 6:22 AM, 
>>> wrote:
>>>
>>> after updating R from 3.3.3. to 3.4.0 i cannot import spss-data
>>> files anymore. for the european social survey
>>> (europeansocialsurvey.org [1] [1]) i get this warning:
>>> re-encoding from CP1252
>>> Fehler in levels<-(*tmp*, value = if (nl == nL)
>>> as.character(labels) else paste0(labels, :
>>> factor level [3] is duplicated
>>> Zusätzlich: Warnmeldung:
>>> In read.spss(file, use.value.labels = use.value.labels,
>>> to.data.frame = to.data.frame, :
>>> //filepath/ESS7CH.sav: Unrecognized record type 7, subtype 18
>>> encountered in system file
>>>
>>> using the package foreign does the same.
>>>
>>> __
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help [2] [2]
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html [3] [3]
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>> Links:
>>> --
>>> [1] http://europeansocialsurvey.org [1]
>>> [2] https://stat.ethz.ch/mailman/listinfo/r-help [2]
>>> [3] http://www.R-project.org/posting-guide.html [3]
>>>
>>
>>
>>
>> Links:
>> --
>> [1] http://europeansocialsurvey.org
>> [2] https://stat.ethz.ch/mailman/listinfo/r-help
>> [3] http://www.R-project.org/posting-guide.html
>>
>

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] How create columns for squared values from previous columns?

2017-05-02 Thread Mike C

Ah, that works! Thank you!


From: PIKAL Petr 
Sent: Tuesday, May 2, 2017 7:56:33 AM
To: C W; r-help
Subject: RE: [R] How create columns for squared values from previous columns?

Hi

you can use data.frame
data.frame(dat, dat[,1:3]^2)

and you can set names afterwards by names function.

Cheers
Petr


> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of C W
> Sent: Saturday, April 29, 2017 3:22 AM
> To: r-help 
> Subject: Re: [R] How create columns for squared values from previous
> columns?
>
> I came up with this solution,
>
> > cbind(dat, dat[, 1:3]^2)
>X1 X2 X3 X4  X5  X1
> X2X3
> 1  0.72776481 -1.1332612 -1.9857503 0.46189400 -0.09016379 0.529641625
> 1.28428102 3.9432044
> 2  0.05126592  0.2858707  0.9075806 1.27582713 -0.49438507 0.002628194
> 0.08172203 0.8237026
> 3 -0.40430146  0.5457195 -1.1924042 0.15025594  1.99710475 0.163459669
> 0.29780978 1.4218277
> 4  1.40746971 -1.2279416  0.3296075 0.84411774 -0.52371619 1.980970990
> 1.50784058 0.1086411
> 5 -0.53841150  0.4750082 -0.4705148 0.05591914 -0.31503500 0.289886944
> 0.22563275 0.2213842
> 6  0.90691210  0.7247171  0.8244184 0.73328097 -1.05284737 0.822489552
> 0.52521494 0.6796657
>
> But, you would NOT ONLY get undesired variable names, BUT ALSO
> duplicated names. I suppose I can use paste() to solve that?
>
> Any better ideas?
>
>
> On Fri, Apr 28, 2017 at 8:57 PM, C W  wrote:
>
> > Dear R list,
> >
> > I am am a little unsure what is the best way to approach this. I
> > suppose I have
> >
> > > dat <- matrix(rnorm(30), ncol = 5)
> > > dat <- data.frame(dat)
> > > dat
> >X1  X2  X3 X4  X5
> > 1 -1.1317 -0.87868106 -0.33000492  1.5241765 -0.92483388
> > 2 -0.56168006 -0.08837883  1.96237792 -0.5335615  0.02880586
> > 3  0.82800071 -1.89965562 -0.05438815 -0.9162857 -0.57470053
> > 4 -0.03218412 -0.23119263 -1.10671765 -0.2885518 -0.30953951
> > 5  1.70525779 -0.93854817 -1.05932636 -0.2983139 -0.21980145
> > 6  1.19047531  0.38301678 -0.20830015 -0.6668266  0.82578534
> >
> > Suppose I want to add columns X6, X7, X8, where
> > X6 = X1^2
> > X7 = X2^2
> > X8 = X3^2
> >
> > I am thinking of using apply(), but df asks for column names, what's a
> > quick way to generate names on the fly?
> >
> > Thank you very much!
> >
> >
>
>   [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.


Tento e-mail a jak�koliv k n�mu p�ipojen� dokumenty jsou d�v�rn� a jsou ur�eny 
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jeho odes�latele. Obsah tohoto emailu i s p��lohami a jeho kopie vyma�te ze 
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Nejste-li zam��len�m adres�tem tohoto emailu, nejste opr�vn�ni tento email 
jakkoliv u��vat, roz�i�ovat, kop�rovat �i zve�ej�ovat.
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zpo�d�n�m p�enosu e-mailu.

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- vyhrazuje si odes�latel pr�vo ukon�it kdykoliv jedn�n� o uzav�en� smlouvy, a 
to z jak�hokoliv d�vodu i bez uveden� d�vodu.
- a obsahuje-li nab�dku, je adres�t opr�vn�n nab�dku bezodkladn� p�ijmout; 
Odes�latel tohoto e-mailu (nab�dky) vylu�uje p�ijet� nab�dky ze strany p��jemce 
s dodatkem �i odchylkou.
- trv� odes�latel na tom, �e p��slu�n� smlouva je uzav�ena teprve v�slovn�m 
dosa�en�m shody na v�ech jej�ch n�le�itostech.
- odes�latel tohoto emailu informuje, �e nen� opr�vn�n uzav�rat za spole�nost 
��dn� smlouvy s v�jimkou p��pad�, kdy k tomu byl p�semn� zmocn�n nebo p�semn� 
pov��en a takov� pov��en� nebo pln� moc byly adres�tovi tohoto emailu p��padn� 
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Re: [R] How create columns for squared values from previous columns?

2017-05-02 Thread PIKAL Petr

Hi

you can use data.frame
data.frame(dat, dat[,1:3]^2)

and you can set names afterwards by names function.

Cheers
Petr


> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of C W
> Sent: Saturday, April 29, 2017 3:22 AM
> To: r-help 
> Subject: Re: [R] How create columns for squared values from previous
> columns?
>
> I came up with this solution,
>
> > cbind(dat, dat[, 1:3]^2)
>X1 X2 X3 X4  X5  X1
> X2X3
> 1  0.72776481 -1.1332612 -1.9857503 0.46189400 -0.09016379 0.529641625
> 1.28428102 3.9432044
> 2  0.05126592  0.2858707  0.9075806 1.27582713 -0.49438507 0.002628194
> 0.08172203 0.8237026
> 3 -0.40430146  0.5457195 -1.1924042 0.15025594  1.99710475 0.163459669
> 0.29780978 1.4218277
> 4  1.40746971 -1.2279416  0.3296075 0.84411774 -0.52371619 1.980970990
> 1.50784058 0.1086411
> 5 -0.53841150  0.4750082 -0.4705148 0.05591914 -0.31503500 0.289886944
> 0.22563275 0.2213842
> 6  0.90691210  0.7247171  0.8244184 0.73328097 -1.05284737 0.822489552
> 0.52521494 0.6796657
>
> But, you would NOT ONLY get undesired variable names, BUT ALSO
> duplicated names. I suppose I can use paste() to solve that?
>
> Any better ideas?
>
>
> On Fri, Apr 28, 2017 at 8:57 PM, C W  wrote:
>
> > Dear R list,
> >
> > I am am a little unsure what is the best way to approach this. I
> > suppose I have
> >
> > > dat <- matrix(rnorm(30), ncol = 5)
> > > dat <- data.frame(dat)
> > > dat
> >X1  X2  X3 X4  X5
> > 1 -1.1317 -0.87868106 -0.33000492  1.5241765 -0.92483388
> > 2 -0.56168006 -0.08837883  1.96237792 -0.5335615  0.02880586
> > 3  0.82800071 -1.89965562 -0.05438815 -0.9162857 -0.57470053
> > 4 -0.03218412 -0.23119263 -1.10671765 -0.2885518 -0.30953951
> > 5  1.70525779 -0.93854817 -1.05932636 -0.2983139 -0.21980145
> > 6  1.19047531  0.38301678 -0.20830015 -0.6668266  0.82578534
> >
> > Suppose I want to add columns X6, X7, X8, where
> > X6 = X1^2
> > X7 = X2^2
> > X8 = X3^2
> >
> > I am thinking of using apply(), but df asks for column names, what's a
> > quick way to generate names on the fly?
> >
> > Thank you very much!
> >
> >
>
>   [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.


Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny 
pouze jeho adresátům.
Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně 
jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze 
svého systému.
Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email 
jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či 
zpožděním přenosu e-mailu.

V případě, že je tento e-mail součástí obchodního jednání:
- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a 
to z jakéhokoliv důvodu i bez uvedení důvodu.
- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; 
Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce 
s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným 
dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost 
žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně 
pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně 
osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi 
či osobě jím zastoupené známá.

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[R] Unusual behavior in e1071?

2017-05-02 Thread Daniel Jeske

Hello -

I have noticed that when I run svm() the order of my data matters.  If the
first case in the data frame has y=+1 I get the expected decision rule that
says to classify as +1 if f(x)>0.  However, if the first case in the data
frame has y=-1 then apparently the decision rule being used says to
classify as +1 if f(x)<0, and in this case all the coefficients are
negative of their values compared to the first case.  So the two
classification rules are equivalent, but is a user really supposed to know
the difference?  It is likely they would assume the decision rule is always
to classify as +1 if f(x)>0.  Does anyone think the behavior I have noticed
is as intended, or is otherwise benign?

Thank you,
Daniel Jeske
Professor
Department of Statistics
University of California - Riverside

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[R] clip a raster according to a shape file in R.

2017-05-02 Thread M.M saifuddin

I have a grid data which has values of a variable (e.g: Temperature). My
data has 6069 data points where each data point refers to different
latitude and longitude. I want to transform this data to a raster file so
that I can clip it according to a shapefile that has much smaller
boundaries than the raster ( actually the shapefile basins fall inside the
much larger raster file which covers the whole USA).

Can I do it by R? I know that this can be done by ArcGIS but I want to do
it with R.

Please help me.

TIA

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Re: [R] Lattice xyplot

2017-05-02 Thread array chip via R-help

Thanks all for the clarification!

  From: Jeff Newmiller 
 To: r-help@r-project.org; Bert Gunter ; array chip 
 
Cc: "r-help@r-project.org" 
 Sent: Monday, May 1, 2017 10:53 AM
 Subject: Re: [R] Lattice xyplot
   
It is not a question of whether lattice "understands" the unsorted data... 
imagine trying to plot 4 points to form a square instead of a trend line... you 
would NOT want lattice to sort those points for you. That lattice leaves your 
data alone gives you more flexibility, even while it adds work for certain 
applications. 

-- 
Sent from my phone. Please excuse my brevity.

On May 1, 2017 7:34:09 AM PDT, Bert Gunter  wrote:
>Yes. type = "l" connects the points in the order given in the data, so
>if the x's are not already ordered, the plots will be different after
>ordering the x's.
>
>e.g.
>
>> x <- c(3,1,2,4,6,5)
>> y <- 11:16
>> xyplot(y~x. type = "l")
>
>
>As for why ... that's just the way it was designed. You can always
>order the data first, if you don't want this default.
>
>Cheers,
>Bert
>
>Bert Gunter
>
>"The trouble with having an open mind is that people keep coming along
>and sticking things into it."
>-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
>On Sun, Apr 30, 2017 at 6:07 PM, array chip via R-help
> wrote:
>> Dear all, I am new to lattice, so would appreciate anyone's help on
>the questions below. I am using xyplot to plot some trend in my
>dataset. Using the example dataset attached, I am trying to plot
>variable "y" over variable "time" for each subject "id":
>> dat<-read.table("dat.txt",sep='\t',header=T,row.names=NULL)
>> xyplot(y ~ time, data=dat, groups=id, aspect = "fill", type = c("p",
>"l"),  xlab = "Time", ylab = "Y")
>>
>> It appears that it just worked fine. But if I sort the "dat" first,
>the plot will look somewhat different!
>> dat<-dat[order(dat$id, dat$time),]xyplot(y ~ time, data=dat,
>groups=id, aspect = "fill", type = c("p", "l"),  xlab = "Time", ylab =
>"Y")
>> Why is that? Do you need to sort the data first before using xyplot?
>Why xyplot can not understand the dataset unless it is sorted first?
>> Thanks,
>> John
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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 -- To UNSUBSCRIBE and more, see
>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.

   
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[R] Unusual behavior in e1071?

[R] clip a raster according to a shape file in R.

Re: [R] Lattice xyplot

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