R: Difference between revisions
| Line 9: | Line 9: | ||
== Embedding R == | == Embedding R == | ||
Reference http://bioconductor.org/help/course-materials/2012/Seattle-Oct-2012/AdvancedR.pdf | Reference http://bioconductor.org/help/course-materials/2012/Seattle-Oct-2012/AdvancedR.pdf | ||
<pre> | <pre> | ||
| Line 219: | Line 220: | ||
ns> | ns> | ||
ns> | ns> | ||
</pre> | |||
Note that if I follow the instruction to put embed.c at the end of g++ command, I will get an error. | |||
<pre> | |||
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ g++ -I/home/mli/Downloads/R-2.15.2/include -L/home/mli/Downloads/R-2.15.2/lib -lR embed.c | |||
/tmp/cc7Vum5j.o: In function `main': | |||
embed.c:(.text+0x1c): undefined reference to `Rf_initEmbeddedR' | |||
embed.c:(.text+0x2b): undefined reference to `Rf_endEmbeddedR' | |||
/tmp/cc7Vum5j.o: In function `doSplinesExample()': | |||
embed.c:(.text+0x45): undefined reference to `Rf_mkString' | |||
embed.c:(.text+0x52): undefined reference to `Rf_install' | |||
embed.c:(.text+0x5d): undefined reference to `Rf_lang2' | |||
embed.c:(.text+0x6d): undefined reference to `Rf_protect' | |||
embed.c:(.text+0x74): undefined reference to `R_GlobalEnv' | |||
embed.c:(.text+0x87): undefined reference to `R_tryEval' | |||
embed.c:(.text+0x91): undefined reference to `Rf_unprotect' | |||
embed.c:(.text+0x9b): undefined reference to `Rf_ScalarLogical' | |||
embed.c:(.text+0xa8): undefined reference to `Rf_install' | |||
embed.c:(.text+0xb3): undefined reference to `Rf_lang2' | |||
embed.c:(.text+0xc3): undefined reference to `Rf_protect' | |||
embed.c:(.text+0xcd): undefined reference to `Rf_install' | |||
embed.c:(.text+0xdc): undefined reference to `CDR' | |||
embed.c:(.text+0xe7): undefined reference to `SET_TAG' | |||
embed.c:(.text+0xee): undefined reference to `R_GlobalEnv' | |||
embed.c:(.text+0x102): undefined reference to `R_tryEval' | |||
embed.c:(.text+0x10c): undefined reference to `Rf_unprotect' | |||
embed.c:(.text+0x116): undefined reference to `Rf_mkString' | |||
embed.c:(.text+0x123): undefined reference to `Rf_install' | |||
embed.c:(.text+0x12e): undefined reference to `Rf_lang2' | |||
embed.c:(.text+0x13e): undefined reference to `Rf_protect' | |||
embed.c:(.text+0x145): undefined reference to `R_GlobalEnv' | |||
embed.c:(.text+0x158): undefined reference to `R_tryEval' | |||
embed.c:(.text+0x162): undefined reference to `Rf_unprotect' | |||
collect2: ld returned 1 exit status | |||
</pre> | </pre> | ||
Revision as of 10:17, 2 November 2012
Install rgdal package on ubuntu
sudo apt-get install libgdal1-dev libproj-dev
R
> install.packages("rgdal")
Embedding R
Reference http://bioconductor.org/help/course-materials/2012/Seattle-Oct-2012/AdvancedR.pdf
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ export R_HOME=/home/mli/Downloads/R-2.15.2
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/mli/Downloa ds/R-2.15.2/lib
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ g++ embed.c -I/home/mli/Downloads/R-2.15.2/include -L/hom e/mli/Downloads/R-2.15.2/lib -lR -rpath/home/mli/Downloads/R-2.15.2
g++: error: unrecognized option ‘-rpath/home/mli/Downloads/R-2.15.2’
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ g++ embed.c -I/home/mli/Downloads/R-2.15.2/include -L/hom e/mli/Downloads/R-2.15.2/lib -lR
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ R CMD ./a.out
WARNING: ignoring environment value of R_HOME
R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
ns> require(stats); require(graphics)
ns> ns(women$height, df = 5)
1 2 3 4 5
[1,] 0.000000e+00 0.000000e+00 0.00000000 0.00000000 0.0000000000
[2,] 7.592323e-03 0.000000e+00 -0.08670223 0.26010669 -0.1734044626
[3,] 6.073858e-02 0.000000e+00 -0.15030440 0.45091320 -0.3006088020
[4,] 2.047498e-01 6.073858e-05 -0.16778345 0.50335034 -0.3355668952
[5,] 4.334305e-01 1.311953e-02 -0.13244035 0.39732106 -0.2648807067
[6,] 6.256681e-01 8.084305e-02 -0.07399720 0.22199159 -0.1479943948
[7,] 6.477162e-01 2.468416e-01 -0.02616007 0.07993794 -0.0532919575
[8,] 4.791667e-01 4.791667e-01 0.01406302 0.02031093 -0.0135406187
[9,] 2.468416e-01 6.477162e-01 0.09733619 0.02286023 -0.0152401533
[10,] 8.084305e-02 6.256681e-01 0.27076826 0.06324188 -0.0405213106
[11,] 1.311953e-02 4.334305e-01 0.48059836 0.12526031 -0.0524087186
[12,] 6.073858e-05 2.047498e-01 0.59541597 0.19899261 0.0007809246
[13,] 0.000000e+00 6.073858e-02 0.50097182 0.27551020 0.1627793975
[14,] 0.000000e+00 7.592323e-03 0.22461127 0.35204082 0.4157555879
[15,] 0.000000e+00 0.000000e+00 -0.14285714 0.42857143 0.7142857143
attr(,"degree")
[1] 3
attr(,"knots")
20% 40% 60% 80%
60.8 63.6 66.4 69.2
attr(,"Boundary.knots")
[1] 58 72
attr(,"intercept")
[1] FALSE
attr(,"class")
[1] "ns" "basis" "matrix"
ns> summary(fm1 <- lm(weight ~ ns(height, df = 5), data = women))
Call:
lm(formula = weight ~ ns(height, df = 5), data = women)
Residuals:
Min 1Q Median 3Q Max
-0.38333 -0.12585 0.07083 0.15401 0.30426
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 114.7447 0.2338 490.88 < 2e-16 ***
ns(height, df = 5)1 15.9474 0.3699 43.12 9.69e-12 ***
ns(height, df = 5)2 25.1695 0.4323 58.23 6.55e-13 ***
ns(height, df = 5)3 33.2582 0.3541 93.93 8.91e-15 ***
ns(height, df = 5)4 50.7894 0.6062 83.78 2.49e-14 ***
ns(height, df = 5)5 45.0363 0.2784 161.75 < 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.2645 on 9 degrees of freedom
Multiple R-squared: 0.9998, Adjusted R-squared: 0.9997
F-statistic: 9609 on 5 and 9 DF, p-value: < 2.2e-16
ns> ## example of safe prediction
ns> plot(women, xlab = "Height (in)", ylab = "Weight (lb)")
ns> ht <- seq(57, 73, length.out = 200)
ns> lines(ht, predict(fm1, data.frame(height=ht)))
ns> ## Don't show:
ns> ## Consistency:
ns> x <- c(1:3,5:6)
ns> stopifnot(identical(ns(x), ns(x, df = 1)),
ns+ identical(ns(x, df=2), ns(x, df=2, knots=NULL)),# not true till 2.15.2
ns+ !is.null(kk <- attr(ns(x), "knots")),# not true till 1.5.1
ns+ length(kk) == 0)
ns> ## End Don't show
ns>
ns>
ns>
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ R
WARNING: ignoring environment value of R_HOME
R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(splines)
> example("ns")
ns> require(stats); require(graphics)
ns> ns(women$height, df = 5)
1 2 3 4 5
[1,] 0.000000e+00 0.000000e+00 0.00000000 0.00000000 0.0000000000
[2,] 7.592323e-03 0.000000e+00 -0.08670223 0.26010669 -0.1734044626
[3,] 6.073858e-02 0.000000e+00 -0.15030440 0.45091320 -0.3006088020
[4,] 2.047498e-01 6.073858e-05 -0.16778345 0.50335034 -0.3355668952
[5,] 4.334305e-01 1.311953e-02 -0.13244035 0.39732106 -0.2648807067
[6,] 6.256681e-01 8.084305e-02 -0.07399720 0.22199159 -0.1479943948
[7,] 6.477162e-01 2.468416e-01 -0.02616007 0.07993794 -0.0532919575
[8,] 4.791667e-01 4.791667e-01 0.01406302 0.02031093 -0.0135406187
[9,] 2.468416e-01 6.477162e-01 0.09733619 0.02286023 -0.0152401533
[10,] 8.084305e-02 6.256681e-01 0.27076826 0.06324188 -0.0405213106
[11,] 1.311953e-02 4.334305e-01 0.48059836 0.12526031 -0.0524087186
[12,] 6.073858e-05 2.047498e-01 0.59541597 0.19899261 0.0007809246
[13,] 0.000000e+00 6.073858e-02 0.50097182 0.27551020 0.1627793975
[14,] 0.000000e+00 7.592323e-03 0.22461127 0.35204082 0.4157555879
[15,] 0.000000e+00 0.000000e+00 -0.14285714 0.42857143 0.7142857143
attr(,"degree")
[1] 3
attr(,"knots")
20% 40% 60% 80%
60.8 63.6 66.4 69.2
attr(,"Boundary.knots")
[1] 58 72
attr(,"intercept")
[1] FALSE
attr(,"class")
[1] "ns" "basis" "matrix"
ns> summary(fm1 <- lm(weight ~ ns(height, df = 5), data = women))
Call:
lm(formula = weight ~ ns(height, df = 5), data = women)
Residuals:
Min 1Q Median 3Q Max
-0.38333 -0.12585 0.07083 0.15401 0.30426
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 114.7447 0.2338 490.88 < 2e-16 ***
ns(height, df = 5)1 15.9474 0.3699 43.12 9.69e-12 ***
ns(height, df = 5)2 25.1695 0.4323 58.23 6.55e-13 ***
ns(height, df = 5)3 33.2582 0.3541 93.93 8.91e-15 ***
ns(height, df = 5)4 50.7894 0.6062 83.78 2.49e-14 ***
ns(height, df = 5)5 45.0363 0.2784 161.75 < 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.2645 on 9 degrees of freedom
Multiple R-squared: 0.9998, Adjusted R-squared: 0.9997
F-statistic: 9609 on 5 and 9 DF, p-value: < 2.2e-16
ns> ## example of safe prediction
ns> plot(women, xlab = "Height (in)", ylab = "Weight (lb)")
ns> ht <- seq(57, 73, length.out = 200)
ns> lines(ht, predict(fm1, data.frame(height=ht)))
ns> ## Don't show:
ns> ## Consistency:
ns> x <- c(1:3,5:6)
ns> stopifnot(identical(ns(x), ns(x, df = 1)),
ns+ identical(ns(x, df=2), ns(x, df=2, knots=NULL)),# not true till 2.15.2
ns+ !is.null(kk <- attr(ns(x), "knots")),# not true till 1.5.1
ns+ length(kk) == 0)
ns> ## End Don't show
ns>
ns>
ns>
Note that if I follow the instruction to put embed.c at the end of g++ command, I will get an error.
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ g++ -I/home/mli/Downloads/R-2.15.2/include -L/home/mli/Downloads/R-2.15.2/lib -lR embed.c /tmp/cc7Vum5j.o: In function `main': embed.c:(.text+0x1c): undefined reference to `Rf_initEmbeddedR' embed.c:(.text+0x2b): undefined reference to `Rf_endEmbeddedR' /tmp/cc7Vum5j.o: In function `doSplinesExample()': embed.c:(.text+0x45): undefined reference to `Rf_mkString' embed.c:(.text+0x52): undefined reference to `Rf_install' embed.c:(.text+0x5d): undefined reference to `Rf_lang2' embed.c:(.text+0x6d): undefined reference to `Rf_protect' embed.c:(.text+0x74): undefined reference to `R_GlobalEnv' embed.c:(.text+0x87): undefined reference to `R_tryEval' embed.c:(.text+0x91): undefined reference to `Rf_unprotect' embed.c:(.text+0x9b): undefined reference to `Rf_ScalarLogical' embed.c:(.text+0xa8): undefined reference to `Rf_install' embed.c:(.text+0xb3): undefined reference to `Rf_lang2' embed.c:(.text+0xc3): undefined reference to `Rf_protect' embed.c:(.text+0xcd): undefined reference to `Rf_install' embed.c:(.text+0xdc): undefined reference to `CDR' embed.c:(.text+0xe7): undefined reference to `SET_TAG' embed.c:(.text+0xee): undefined reference to `R_GlobalEnv' embed.c:(.text+0x102): undefined reference to `R_tryEval' embed.c:(.text+0x10c): undefined reference to `Rf_unprotect' embed.c:(.text+0x116): undefined reference to `Rf_mkString' embed.c:(.text+0x123): undefined reference to `Rf_install' embed.c:(.text+0x12e): undefined reference to `Rf_lang2' embed.c:(.text+0x13e): undefined reference to `Rf_protect' embed.c:(.text+0x145): undefined reference to `R_GlobalEnv' embed.c:(.text+0x158): undefined reference to `R_tryEval' embed.c:(.text+0x162): undefined reference to `Rf_unprotect' collect2: ld returned 1 exit status