Raquel Rangel de Meireles Guimarães
2010-Dec-23 01:17 UTC
[R] Running sweave automatically using cygwin
Hi all,
Hope someone could help me.
I am trying to run automatically the conversion of an Rwn file to a tex
file.
I am using windows 7, and cygwin.
I tried to run automatically the Sweave.sh script, in its the most
recent version available at R webpage:
http://cran.r-project.org/contrib/extra/scripts/Sweave.sh
Unfortunately, I got this error message:
==========================
Raquel at Dell-Raquel-PC ~
$ cd /cygdrive/c/Users/Raquel/Desktop/test_max_planck/test-raquel
Raquel at Dell-Raquel-PC
/cygdrive/c/Users/Raquel/Desktop/test_max_planck/test-raquel
$ chmod +x Sweave.sh
Raquel at Dell-Raquel-PC
/cygdrive/c/Users/Raquel/Desktop/test_max_planck/test-raquel
$ ./Sweave.sh test-raquel.Rnw
Run Sweave and postprocess with LaTeX directly from the command line
./Sweave.sh: line 657: R: command not found
An error occured after the use of 'R'!
Quiting.
========================================
I don't know what is the problem. Could you please help me? Below you
find my Rnw code and the data for running sweave.
Best regards,
Raquel
=======================================Rnw file
\documentclass[12pt,oneside,a4paper]{article}
\usepackage[latin1]{inputenc}
\usepackage[brazil]{babel}
\usepackage{amsthm,amsfonts,bm}
\usepackage{graphicx}
\usepackage[T1]{fontenc}
\usepackage{ae}
\usepackage[alf,bibjustif,recuo=1cm]{abntcite} %bibliografia da ABNT
\usepackage{setspace}
\usepackage[charter]{mathdesign}
\usepackage{graphicx}
\usepackage{Sweave}
\bibliographystyle{abnt-alf}
\onehalfspacing
\setlength\parskip{0.5cm} % espa?amento entre par?grafos
\title{MP 187: Statistical Models with missing values \\Final Test}
\author{Raquel Rangel de Meireles Guimar?es}
\date{December, 2010}
\begin{document}
\maketitle
<<echo=false,results=hide>> if (require(xtable) == FALSE)
stop("Pacote xtable() necess?rio para rodar essa an?lise.")
options(digits=3)
@
In this test we were required to analyse data from IQ scores of 250
subjects, repeated after one month. A large part of the sample dropped
the second visit.
Using only the complete cases, estimate the parameters of the regression
line:
<<>>
setwd("C:\\Users\\Raquel\\Desktop\\test_max_planck")
data<-read.table("IQ.txt")
attach(data)
@
I start here with a scatterplot of the two variables. It is easy to see
from the figure \ref{fig:scatter} that we have a censored
\begin{figure}[ht!]
\centering
<<echo=false,fig=true>> plot(data$IQ1,data$IQ2)
@
\caption{Scatterplot of the two measurements of the IQ score, in the
first and second visit.}
\label{fig:scatter}
\end{figure}
\end{document}
====================================
Data file: IQ.txt
"IQ1" "IQ2"
"1" 114.71 NA
"2" 112.84 NA
"3" 184.88 NA
"4" 120.03 NA
"5" 67 85.28
"6" 75.12 64.24
"7" 104.87 NA
"8" 73.07 67.34
"9" 100.7 NA
"10" 129.79 NA
"11" 11.83 109.91
"12" 139.52 NA
"13" 130.74 NA
"14" 111.92 NA
"15" 83.45 106.15
"16" 80.33 19.14
"17" 80.85 146.93
"18" 65.63 89.09
"19" 152.95 NA
"20" 9.84 104.58
"21" 112.47 NA
"22" 92.14 NA
"23" 151.66 NA
"24" 168.06 NA
"25" 34.6 47.21
"26" 120.65 NA
"27" 112.47 NA
"28" 80.5 109.71
"29" 58.46 52.5
"30" 112.97 NA
"31" 75.95 55.53
"32" 58.59 123.95
"33" 147.19 NA
"34" 38.98 90.26
"35" 115.18 NA
"36" 98.93 NA
"37" 113.2 NA
"38" 144.42 NA
"39" 145.52 NA
"40" 134.97 NA
"41" 98.61 NA
"42" 98.23 NA
"43" 166.18 NA
"44" 43.75 95.76
"45" 77.07 99.5
"46" 112.2 NA
"47" -0.03 13.23
"48" 102.19 NA
"49" 70.98 74.52
"50" 80.48 26.61
"51" 102.87 NA
"52" 94.22 NA
"53" 60.33 52.95
"54" 54.09 95.25
"55" 60.81 87.87
"56" 106.98 NA
"57" 71.18 112.27
"58" 80.95 53
"59" 122.56 NA
"60" 74.22 41.55
"61" 109.73 NA
"62" 142.66 NA
"63" 95.39 NA
"64" 97.68 NA
"65" 114.37 NA
"66" 114.02 NA
"67" 87.39 NA
"68" 183.12 NA
"69" 88.39 NA
"70" 57.81 99.84
"71" 133.65 NA
"72" 78.16 30.84
"73" 80.52 82.42
"74" 107.02 NA
"75" 85.35 NA
"76" 84.35 NA
"77" 92.62 NA
"78" 45.62 100.89
"79" 79.53 102.13
"80" 85.11 NA
"81" 108.72 NA
"82" 95.55 NA
"83" 57.17 52.48
"84" 106.16 NA
"85" 72.3 109.69
"86" 88.13 NA
"87" 117.57 NA
"88" 86.59 NA
"89" 65.56 71.14
"90" 97.76 NA
"91" 81.91 85.55
"92" 65.58 78.26
"93" 109.13 NA
"94" 92.55 NA
"95" 112.54 NA
"96" 66.77 106.92
"97" 106.69 NA
"98" 43.65 56.27
"99" 13.29 14.43
"100" 108.6 NA
"101" 111.95 NA
"102" 62.04 25.49
"103" 113.79 NA
"104" 125.43 NA
"105" 68.13 85.19
"106" 112.13 NA
"107" 21.61 83.67
"108" 49.13 132.66
"109" 104.61 NA
"110" 105.9 NA
"111" 107.7 NA
"112" 157.83 NA
"113" 20.3 41.49
"114" 43.87 -7.62
"115" 130.19 NA
"116" 137.28 NA
"117" 62.99 128.23
"118" 97.71 NA
"119" 103.46 NA
"120" 90.81 NA
"121" 40.89 51
"122" 146.28 NA
"123" 136.18 NA
"124" 111.93 NA
"125" 84.19 51.3
"126" 105.01 NA
"127" 78.28 44.44
"128" 74.54 67.52
"129" 80.92 152.09
"130" 151.56 NA
"131" 30.4 147.39
"132" 62.99 97.48
"133" 111.86 NA
"134" 81.48 27.73
"135" 146.15 NA
"136" 67.1 102.68
"137" 143.29 NA
"138" 96.46 NA
"139" 68.32 111.41
"140" 99.3 NA
"141" 84.19 NA
"142" 81.72 125.93
"143" 96.15 NA
"144" 108.72 NA
"145" 90.13 NA
"146" 122.81 NA
"147" 105.8 NA
"148" 62.01 74.33
"149" 119.9 NA
"150" 106.85 NA
"151" 122.73 NA
"152" 165.65 NA
"153" 102.62 NA
"154" 104.4 NA
"155" 164.31 NA
"156" 131.4 NA
"157" 63.49 55.07
"158" 101.66 NA
"159" 78 112.99
"160" 123.43 NA
"161" 57.85 89.96
"162" 122.07 NA
"163" 73.16 96.74
"164" 82.56 80.55
"165" 83.13 127.28
"166" 96.86 NA
"167" 71 105.9
"168" 87.04 NA
"169" 111.32 NA
"170" 81.98 109.89
"171" 66.82 49.2
"172" 47.69 69.14
"173" 125.36 NA
"174" 102.1 NA
"175" 135.84 NA
"176" 113.58 NA
"177" 58.7 44.42
"178" 103.84 NA
"179" 136.15 NA
"180" 71.53 78.96
"181" 114.4 NA
"182" 123.94 NA
"183" 149.28 NA
"184" 137.63 NA
"185" 77.12 89.17
"186" 96.78 NA
"187" 124.7 NA
"188" 36.6 87.75
"189" 119.91 NA
"190" 98.61 NA
"191" 68.51 64.39
"192" 114.2 NA
"193" 14.52 103.93
"194" 140.32 NA
"195" 41.35 89.9
"196" 105.18 NA
"197" 51.7 46.25
"198" 128.1 NA
"199" 86.58 NA
"200" 105.8 NA
"201" 156.95 NA
"202" 116.36 NA
"203" 105.48 NA
"204" 31.71 78.27
"205" 99.88 NA
"206" 99.88 NA
"207" 44.45 61.91
"208" 124.56 NA
"209" 92.08 NA
"210" 174.38 NA
"211" 75.18 28.15
"212" 137.6 NA
"213" 133.73 NA
"214" 70.77 116
"215" 55.07 95.08
"216" 106.5 NA
"217" 122.68 NA
"218" 34.61 99.65
"219" 53.79 46.15
"220" 157.05 NA
"221" 36.79 109.09
"222" 97.73 NA
"223" 10.11 104.35
"224" 87.95 NA
"225" 72.36 163.16
"226" 57.72 113.36
"227" 62.33 26.95
"228" 122.27 NA
"229" 49.03 78.68
"230" 92.04 NA
"231" 69.14 137.36
"232" 29.93 138.28
"233" 60.21 128.74
"234" 124.81 NA
"235" 121.18 NA
"236" 106.76 NA
"237" 116.47 NA
"238" 59.32 86.54
"239" 95.38 NA
"240" 103.09 NA
"241" 80.5 77.09
"242" 56.99 76.54
"243" 45.43 53.26
"244" 114.7 NA
"245" 50.22 144.81
"246" 107.48 NA
"247" 165.26 NA
"248" 67.44 72.73
"249" 89.46 NA
"250" 88.88 NA
======================================
--
Raquel Rangel de Meireles Guimar?es
Doutoranda em Demografia
raquel at cedeplar.ufmg.br
http://ufmg.academia.edu/RaquelGuimaraes
Cedeplar - Centro de Desenvolvimento e Planejamento Regional
Faculdade de Ci?ncias Econ?micas, UFMG (http://www.cedeplar.ufmg.br)
On 23.12.2010 02:17, Raquel Rangel de Meireles Guimar?es wrote:> Hi all, > > Hope someone could help me. > > I am trying to run automatically the conversion of an Rwn file to a tex > file. > > I am using windows 7, and cygwin. > > I tried to run automatically the Sweave.sh script, in its the most > recent version available at R webpage: > > http://cran.r-project.org/contrib/extra/scripts/Sweave.sh > > Unfortunately, I got this error message: > > ==========================> > Raquel at Dell-Raquel-PC ~ > $ cd /cygdrive/c/Users/Raquel/Desktop/test_max_planck/test-raquel > > Raquel at Dell-Raquel-PC > /cygdrive/c/Users/Raquel/Desktop/test_max_planck/test-raquel > $ chmod +x Sweave.sh > > Raquel at Dell-Raquel-PC > /cygdrive/c/Users/Raquel/Desktop/test_max_planck/test-raquel > $ ./Sweave.sh test-raquel.Rnw > > Run Sweave and postprocess with LaTeX directly from the command line > > ./Sweave.sh: line 657: R: command not foundThen R is not in your PATH, obviously. On the other hand, why don't you simply use R CMD Sweave yourFIle.Rnw from your favorite shell (for which you need R in the PATH environment variable as well). Best, Uwe Ligges> An error occured after the use of 'R'! > Quiting. > > ========================================> > I don't know what is the problem. Could you please help me? Below you > find my Rnw code and the data for running sweave. > > Best regards, > > Raquel > > =======================================> Rnw file > > \documentclass[12pt,oneside,a4paper]{article} > \usepackage[latin1]{inputenc} > \usepackage[brazil]{babel} > \usepackage{amsthm,amsfonts,bm} > \usepackage{graphicx} > \usepackage[T1]{fontenc} > \usepackage{ae} > \usepackage[alf,bibjustif,recuo=1cm]{abntcite} %bibliografia da ABNT > \usepackage{setspace} > \usepackage[charter]{mathdesign} > \usepackage{graphicx} > \usepackage{Sweave} > > \bibliographystyle{abnt-alf} > > \onehalfspacing > \setlength\parskip{0.5cm} % espa?amento entre par?grafos > > \title{MP 187: Statistical Models with missing values \\Final Test} > \author{Raquel Rangel de Meireles Guimar?es} > \date{December, 2010} > > \begin{document} > > \maketitle > > <<echo=false,results=hide>>> if (require(xtable) == FALSE) > stop("Pacote xtable() necess?rio para rodar essa an?lise.") > options(digits=3) > @ > > > In this test we were required to analyse data from IQ scores of 250 > subjects, repeated after one month. A large part of the sample dropped > the second visit. > > Using only the complete cases, estimate the parameters of the regression > line: > > <<>>> setwd("C:\\Users\\Raquel\\Desktop\\test_max_planck") > data<-read.table("IQ.txt") > attach(data) > @ > > > I start here with a scatterplot of the two variables. It is easy to see > from the figure \ref{fig:scatter} that we have a censored > > \begin{figure}[ht!] > \centering > <<echo=false,fig=true>>> plot(data$IQ1,data$IQ2) > @ > \caption{Scatterplot of the two measurements of the IQ score, in the > first and second visit.} > \label{fig:scatter} > \end{figure} > > \end{document} > > ====================================> > Data file: IQ.txt > > "IQ1" "IQ2" > "1" 114.71 NA > "2" 112.84 NA > "3" 184.88 NA > "4" 120.03 NA > "5" 67 85.28 > "6" 75.12 64.24 > "7" 104.87 NA > "8" 73.07 67.34 > "9" 100.7 NA > "10" 129.79 NA > "11" 11.83 109.91 > "12" 139.52 NA > "13" 130.74 NA > "14" 111.92 NA > "15" 83.45 106.15 > "16" 80.33 19.14 > "17" 80.85 146.93 > "18" 65.63 89.09 > "19" 152.95 NA > "20" 9.84 104.58 > "21" 112.47 NA > "22" 92.14 NA > "23" 151.66 NA > "24" 168.06 NA > "25" 34.6 47.21 > "26" 120.65 NA > "27" 112.47 NA > "28" 80.5 109.71 > "29" 58.46 52.5 > "30" 112.97 NA > "31" 75.95 55.53 > "32" 58.59 123.95 > "33" 147.19 NA > "34" 38.98 90.26 > "35" 115.18 NA > "36" 98.93 NA > "37" 113.2 NA > "38" 144.42 NA > "39" 145.52 NA > "40" 134.97 NA > "41" 98.61 NA > "42" 98.23 NA > "43" 166.18 NA > "44" 43.75 95.76 > "45" 77.07 99.5 > "46" 112.2 NA > "47" -0.03 13.23 > "48" 102.19 NA > "49" 70.98 74.52 > "50" 80.48 26.61 > "51" 102.87 NA > "52" 94.22 NA > "53" 60.33 52.95 > "54" 54.09 95.25 > "55" 60.81 87.87 > "56" 106.98 NA > "57" 71.18 112.27 > "58" 80.95 53 > "59" 122.56 NA > "60" 74.22 41.55 > "61" 109.73 NA > "62" 142.66 NA > "63" 95.39 NA > "64" 97.68 NA > "65" 114.37 NA > "66" 114.02 NA > "67" 87.39 NA > "68" 183.12 NA > "69" 88.39 NA > "70" 57.81 99.84 > "71" 133.65 NA > "72" 78.16 30.84 > "73" 80.52 82.42 > "74" 107.02 NA > "75" 85.35 NA > "76" 84.35 NA > "77" 92.62 NA > "78" 45.62 100.89 > "79" 79.53 102.13 > "80" 85.11 NA > "81" 108.72 NA > "82" 95.55 NA > "83" 57.17 52.48 > "84" 106.16 NA > "85" 72.3 109.69 > "86" 88.13 NA > "87" 117.57 NA > "88" 86.59 NA > "89" 65.56 71.14 > "90" 97.76 NA > "91" 81.91 85.55 > "92" 65.58 78.26 > "93" 109.13 NA > "94" 92.55 NA > "95" 112.54 NA > "96" 66.77 106.92 > "97" 106.69 NA > "98" 43.65 56.27 > "99" 13.29 14.43 > "100" 108.6 NA > "101" 111.95 NA > "102" 62.04 25.49 > "103" 113.79 NA > "104" 125.43 NA > "105" 68.13 85.19 > "106" 112.13 NA > "107" 21.61 83.67 > "108" 49.13 132.66 > "109" 104.61 NA > "110" 105.9 NA > "111" 107.7 NA > "112" 157.83 NA > "113" 20.3 41.49 > "114" 43.87 -7.62 > "115" 130.19 NA > "116" 137.28 NA > "117" 62.99 128.23 > "118" 97.71 NA > "119" 103.46 NA > "120" 90.81 NA > "121" 40.89 51 > "122" 146.28 NA > "123" 136.18 NA > "124" 111.93 NA > "125" 84.19 51.3 > "126" 105.01 NA > "127" 78.28 44.44 > "128" 74.54 67.52 > "129" 80.92 152.09 > "130" 151.56 NA > "131" 30.4 147.39 > "132" 62.99 97.48 > "133" 111.86 NA > "134" 81.48 27.73 > "135" 146.15 NA > "136" 67.1 102.68 > "137" 143.29 NA > "138" 96.46 NA > "139" 68.32 111.41 > "140" 99.3 NA > "141" 84.19 NA > "142" 81.72 125.93 > "143" 96.15 NA > "144" 108.72 NA > "145" 90.13 NA > "146" 122.81 NA > "147" 105.8 NA > "148" 62.01 74.33 > "149" 119.9 NA > "150" 106.85 NA > "151" 122.73 NA > "152" 165.65 NA > "153" 102.62 NA > "154" 104.4 NA > "155" 164.31 NA > "156" 131.4 NA > "157" 63.49 55.07 > "158" 101.66 NA > "159" 78 112.99 > "160" 123.43 NA > "161" 57.85 89.96 > "162" 122.07 NA > "163" 73.16 96.74 > "164" 82.56 80.55 > "165" 83.13 127.28 > "166" 96.86 NA > "167" 71 105.9 > "168" 87.04 NA > "169" 111.32 NA > "170" 81.98 109.89 > "171" 66.82 49.2 > "172" 47.69 69.14 > "173" 125.36 NA > "174" 102.1 NA > "175" 135.84 NA > "176" 113.58 NA > "177" 58.7 44.42 > "178" 103.84 NA > "179" 136.15 NA > "180" 71.53 78.96 > "181" 114.4 NA > "182" 123.94 NA > "183" 149.28 NA > "184" 137.63 NA > "185" 77.12 89.17 > "186" 96.78 NA > "187" 124.7 NA > "188" 36.6 87.75 > "189" 119.91 NA > "190" 98.61 NA > "191" 68.51 64.39 > "192" 114.2 NA > "193" 14.52 103.93 > "194" 140.32 NA > "195" 41.35 89.9 > "196" 105.18 NA > "197" 51.7 46.25 > "198" 128.1 NA > "199" 86.58 NA > "200" 105.8 NA > "201" 156.95 NA > "202" 116.36 NA > "203" 105.48 NA > "204" 31.71 78.27 > "205" 99.88 NA > "206" 99.88 NA > "207" 44.45 61.91 > "208" 124.56 NA > "209" 92.08 NA > "210" 174.38 NA > "211" 75.18 28.15 > "212" 137.6 NA > "213" 133.73 NA > "214" 70.77 116 > "215" 55.07 95.08 > "216" 106.5 NA > "217" 122.68 NA > "218" 34.61 99.65 > "219" 53.79 46.15 > "220" 157.05 NA > "221" 36.79 109.09 > "222" 97.73 NA > "223" 10.11 104.35 > "224" 87.95 NA > "225" 72.36 163.16 > "226" 57.72 113.36 > "227" 62.33 26.95 > "228" 122.27 NA > "229" 49.03 78.68 > "230" 92.04 NA > "231" 69.14 137.36 > "232" 29.93 138.28 > "233" 60.21 128.74 > "234" 124.81 NA > "235" 121.18 NA > "236" 106.76 NA > "237" 116.47 NA > "238" 59.32 86.54 > "239" 95.38 NA > "240" 103.09 NA > "241" 80.5 77.09 > "242" 56.99 76.54 > "243" 45.43 53.26 > "244" 114.7 NA > "245" 50.22 144.81 > "246" 107.48 NA > "247" 165.26 NA > "248" 67.44 72.73 > "249" 89.46 NA > "250" 88.88 NA > > ======================================>