GeoDetector_2015_Example(DiseaseDataset).zip_Geodetector_数据挖掘

<html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta charset="utf-8"> <meta name="generator" content="pdf2htmlEX"> <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1"> <link rel="stylesheet" href="https://static.pudn.com/base/css/base.min.css"> <link rel="stylesheet" href="https://static.pudn.com/base/css/fancy.min.css"> <link rel="stylesheet" href="https://static.pudn.com/prod/directory_preview_static/622bc0ac3d2fbb00079afe89/raw.css"> <script src="https://static.pudn.com/base/js/compatibility.min.js"></script> <script src="https://static.pudn.com/base/js/pdf2htmlEX.min.js"></script> <script> try{ pdf2htmlEX.defaultViewer = new pdf2htmlEX.Viewer({}); }catch(e){} </script> <title></title> </head> <body> <div id="sidebar" style="display: none"> <div id="outline"> </div> </div> <div id="pf1" class="pf w0 h0" data-page-no="1"><div class="pc pc1 w0 h0"><img class="bi x0 y0 w1 h1" alt="" src="https://static.pudn.com/prod/directory_preview_static/622bc0ac3d2fbb00079afe89/bg1.jpg"><div class="t m0 x1 h2 y1 ff1 fs0 fc0 sc0 ls0 ws0">Sweave User Manual</div><div class="t m0 x2 h3 y2 ff2 fs1 fc0 sc0 ls0 ws0">Friedrich Leisch and R-core</div><div class="t m0 x3 h3 y3 ff2 fs1 fc0 sc0 ls0 ws0">August 14, 2015</div><div class="t m0 x4 h4 y4 ff3 fs2 fc0 sc0 ls0 ws0">1 Introduction</div><div class="t m0 x4 h5 y5 ff4 fs3 fc0 sc0 ls0 ws0">Sweave provides a ﬂexible framework for mixing text and R code for automatic document</div><div class="t m0 x4 h5 y6 ff4 fs3 fc0 sc0 ls0 ws0">generation. A single source ﬁle contains both documentation text and R code, which are then</div><div class="t m0 x4 h5 y7 ff6 fs3 fc0 sc0 ls0 ws0">woven into a ﬁnal document containing</div><div class="t m0 x5 h5 y8 ff7 fs3 fc0 sc0 ls0 ws0">• the documentation text together with</div><div class="t m0 x5 h5 y9 ff7 fs3 fc0 sc0 ls0 ws0">• the R code and/or</div><div class="t m0 x5 h5 ya ff7 fs3 fc0 sc0 ls0 ws0">• the output of the code (text, graphs)</div><div class="t m0 x4 h5 yb ff4 fs3 fc0 sc0 ls0 ws0">This allows the re-generation of a report if the input data change and documents the code to</div><div class="t m0 x4 h5 yc ff4 fs3 fc0 sc0 ls0 ws0">reproduce the analysis in the same ﬁle that contains the report. The R code of the complete</div><div class="t m0 x4 h5 yd ff4 fs3 fc0 sc0 ls0 ws0">analysis is embedded into a L</div><div class="t m0 x6 h6 ye ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 x7 h5 yd ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 x1 h5 yf ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 x8 h5 yd ff4 fs3 fc0 sc0 ls0 ws0">X document</div><div class="t m0 x9 h6 y10 ff8 fs4 fc0 sc0 ls0 ws0">1</div><div class="t m0 xa h5 yd ff4 fs3 fc0 sc0 ls0 ws0">using the noweb syntax (Ramsey, 1998) which is</div><div class="t m0 x4 h5 y11 ff4 fs3 fc0 sc0 ls0 ws0">usually used for literate programming Knuth (1984). Hence, the full power of L</div><div class="t m0 xb h6 y12 ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 xc h5 y11 ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 xd h5 y13 ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 xe h5 y11 ff4 fs3 fc0 sc0 ls0 ws0">X (for high-</div><div class="t m0 x4 h5 y14 ff4 fs3 fc0 sc0 ls0 ws0">quality typesetting) and R (for data analysis) can be used simultaneously. See Leisch (2002)</div><div class="t m0 x4 h5 y15 ff4 fs3 fc0 sc0 ls0 ws0">and references therein for more general thoughts on dynamic report generation and pointers to</div><div class="t m0 x4 h5 y16 ff4 fs3 fc0 sc0 ls0 ws0">other systems.</div><div class="t m0 x5 h5 y17 ff4 fs3 fc0 sc0 ls0 ws0">Sweave uses a modular concept using diﬀerent drivers for the actual translations. Obviously</div><div class="t m0 x4 h5 y18 ff4 fs3 fc0 sc0 ls0 ws0">diﬀerent drivers are needed for diﬀerent text markup languages (L</div><div class="t m0 xf h6 y19 ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 x10 h5 y18 ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 x11 h5 y1a ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 x12 h5 y18 ff4 fs3 fc0 sc0 ls0 ws0">X, HTML, . . . ). Several</div><div class="t m0 x4 h5 y1b ff4 fs3 fc0 sc0 ls0 ws0">packages on CRAN provide support for other word processing systems (see Appendix A).</div><div class="t m0 x4 h4 y1c ff3 fs2 fc0 sc0 ls0 ws0">2 Noweb ﬁles</div><div class="t m0 x4 h5 y1d ff9 fs3 fc0 sc0 ls0 ws0">noweb (Ramsey, 1998) is a simple literate-programming tool which allows combining program</div><div class="t m0 x4 h5 y1e ff4 fs3 fc0 sc0 ls0 ws0">source code and the corresponding documentation into a single ﬁle. A noweb ﬁle is a simple</div><div class="t m0 x4 h5 y1f ff4 fs3 fc0 sc0 ls0 ws0">text ﬁle which consists of a sequence of code and documentation segments, called chunks:</div><div class="t m0 x4 h5 y20 ffa fs3 fc0 sc0 ls0 ws0">Documentation chunks start with a line that has an at sign (@) as ﬁrst character, followed</div><div class="t m0 x13 h5 y21 ff4 fs3 fc0 sc0 ls0 ws0">by a space or newline character. The rest of this line is a comment and ignored. Typically</div><div class="t m0 x13 h5 y22 ff4 fs3 fc0 sc0 ls0 ws0">documentation chunks will contain text in a markup language like L</div><div class="t m0 x14 h6 y23 ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 x15 h5 y22 ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 x16 h5 y24 ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 x17 h5 y22 ff4 fs3 fc0 sc0 ls0 ws0">X. The chunk</div><div class="t m0 x13 h5 y25 ff4 fs3 fc0 sc0 ls0 ws0">continues until a new code or documentation chunk is started: note that Sweave does not</div><div class="t m0 x13 h5 y26 ff4 fs3 fc0 sc0 ls0 ws0">interpret the contents of documentation chunks, and so will identify chunk indicators even</div><div class="t m0 x13 h5 y27 ff4 fs3 fc0 sc0 ls0 ws0">inside L</div><div class="t m0 x18 h6 y28 ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 x19 h5 y27 ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 x1a h5 y29 ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 x1b h5 y27 ff4 fs3 fc0 sc0 ls0 ws0">X verbatim environments.</div><div class="t m0 x4 h5 y2a ffa fs3 fc0 sc0 ls0 ws0">Code chunks start with <<options>>= at the beginning of a line; again the rest of the line is</div><div class="t m0 x13 h5 y2b ff4 fs3 fc0 sc0 ls0 ws0">a comment and ignored.</div><div class="t m0 x4 h5 y2c ff4 fs3 fc0 sc0 ls0 ws0">The default for the ﬁrst chunk is documentation.</div><div class="t m0 x5 h5 y2d ff4 fs3 fc0 sc0 ls0 ws0">In the simplest usage of noweb, the options (if present) of the code chunks give the names</div><div class="t m0 x4 h5 y2e ff4 fs3 fc0 sc0 ls0 ws0">of source code ﬁles, and the tool notangle can be used to extract the code chunks from the</div><div class="t m0 x1c h7 y2f ffb fs5 fc0 sc0 ls0 ws0">1</div><div class="t m0 x5 h8 y30 ffc fs6 fc1 sc0 ls0 ws0">http://www.ctan.org</div><div class="t m0 x1d h5 y31 ff4 fs3 fc0 sc0 ls0 ws0">1</div><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a></div><div class="pi" data-data='{"ctm":[1.611850,0.000000,0.000000,1.611850,0.000000,0.000000]}'></div></div> </body> </html>

<div id="pf2" class="pf w0 h0" data-page-no="2"><div class="pc pc2 w0 h0"><img class="bi x0 y0 w1 h1" alt="" src="https://static.pudn.com/prod/directory_preview_static/622bc0ac3d2fbb00079afe89/bg2.jpg"><div class="t m0 x4 h5 y32 ff9 fs3 fc0 sc0 ls0 ws0">noweb ﬁle. Multiple code chunks can have the same name, the corresponding code chunks are</div><div class="t m0 x4 h5 y33 ff4 fs3 fc0 sc0 ls0 ws0">the concatenated when the source code is extracted. noweb has some additional mechanisms</div><div class="t m0 x4 h5 y34 ff4 fs3 fc0 sc0 ls0 ws0">to cross-reference code chunks (the [[...]] operator, etc.), Sweave does currently not use nor</div><div class="t m0 x4 h5 y35 ff4 fs3 fc0 sc0 ls0 ws0">support these features, so they are not described here.</div><div class="t m0 x4 h4 y36 ff3 fs2 fc0 sc0 ls0 ws0">3 Sweave ﬁles</div><div class="t m0 x4 h9 y37 ff3 fs1 fc0 sc0 ls0 ws0">3.1 A simple example</div><div class="t m0 x4 h5 y38 ff4 fs3 fc0 sc0 ls0 ws0">Sweave source ﬁles are noweb ﬁles with some additional syntax that allows some additional</div><div class="t m0 x4 h5 y39 ff4 fs3 fc0 sc0 ls0 ws0">control over the ﬁnal output. Traditional noweb ﬁles have the extension ‘.nw’, which is also</div><div class="t m0 x4 h5 y3a ff4 fs3 fc0 sc0 ls0 ws0">ﬁne for Sweave ﬁles (and fully supported by the software). Additionally, Sweave currently</div><div class="t m0 x4 h5 y3b ff4 fs3 fc0 sc0 ls0 ws0">recognizes ﬁles with extensions ‘.rnw’, ‘.Rnw’, ‘.snw’ and ‘.Snw’ to directly indicate a noweb ﬁle</div><div class="t m0 x4 h5 y3c ff4 fs3 fc0 sc0 ls0 ws0">with Sweave extensions. We will use ‘.Rnw’ throughout this document.</div><div class="t m0 x5 h5 y3d ff4 fs3 fc0 sc0 ls0 ws0">A minimal Sweave ﬁle is shown in Figure 1, which contains two code chunks embedded in a</div><div class="t m0 x4 h5 y3e ff4 fs3 fc0 sc0 ls0 ws0">simple L</div><div class="t m0 x1e h6 y3f ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 x1f h5 y3e ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 x20 h5 y40 ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 x21 h5 y3e ff4 fs3 fc0 sc0 ls0 ws0">X document. Running</div><div class="t m0 x4 ha y41 ffd fs3 fc0 sc0 ls0 ws0">> rnwfile <- system.file("Sweave", "example-1.Rnw", package = "utils")</div><div class="t m0 x4 ha y42 ffd fs3 fc0 sc0 ls0 ws0">> Sweave(rnwfile)</div><div class="t m0 x4 ha y43 ff9 fs3 fc0 sc0 ls0 ws0">Writing to file example-1.tex</div><div class="t m0 x4 ha y44 ff9 fs3 fc0 sc0 ls0 ws0">Processing code chunks with options ...</div><div class="t m0 x22 ha y45 ff9 fs3 fc0 sc0 ls0 ws0">1 : echo keep.source term verbatim (example-1.Rnw:13)</div><div class="t m0 x22 ha y46 ff9 fs3 fc0 sc0 ls0 ws0">2 : keep.source term verbatim pdf (example-1.Rnw:23)</div><div class="t m0 x4 ha y47 ff9 fs3 fc0 sc0 ls0 ws0">You can now run (pdf)latex on 'example-1.tex'</div><div class="t m0 x4 h5 y48 ff4 fs3 fc0 sc0 ls0 ws0">translates this into the L</div><div class="t m0 x23 h6 y49 ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 x24 h5 y48 ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 x25 h5 y4a ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 x26 h5 y48 ff4 fs3 fc0 sc0 ls0 ws0">X document shown in Figures 2 and 3. The latter can also be created</div><div class="t m0 x4 h5 y4b ff4 fs3 fc0 sc0 ls0 ws0">directly from within R using</div><div class="t m0 x4 ha y4c ffd fs3 fc0 sc0 ls0 ws0">> tools::texi2pdf("example-1.tex")</div><div class="t m0 x5 h5 y4d ff4 fs3 fc0 sc0 ls0 ws0">The ﬁrst diﬀerence between ‘example-1.Rnw’ and ‘example-1.tex’ is that the L</div><div class="t m0 x27 h6 y4e ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 x28 h5 y4d ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 x29 h5 y4f ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 x2a h5 y4d ff4 fs3 fc0 sc0 ls0 ws0">X style</div><div class="t m0 x4 h5 y50 ff4 fs3 fc0 sc0 ls0 ws0">ﬁle ‘Sweave.sty’ is automatically loaded, which provides environments for typesetting R input</div><div class="t m0 x4 h5 y51 ff4 fs3 fc0 sc0 ls0 ws0">and output (the L</div><div class="t m0 x2b h6 y52 ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 x2c h5 y51 ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 x2d h5 y53 ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 x2e h5 y51 ff4 fs3 fc0 sc0 ls0 ws0">X environments Sinput and Soutput). Otherwise, the documentation</div><div class="t m0 x4 h5 y54 ff4 fs3 fc0 sc0 ls0 ws0">chunks are copied without any modiﬁcation from ‘example-1.Rnw’ to ‘example-1.tex’.</div><div class="t m0 x5 h5 y55 ff4 fs3 fc0 sc0 ls0 ws0">The real work of Sweave is done on the code chunks: The ﬁrst code chunk has no name, hence</div><div class="t m0 x4 h5 y56 ff4 fs3 fc0 sc0 ls0 ws0">the default behavior of Sweave is used, which transfers both the R commands and their respective</div><div class="t m0 x4 h5 y57 ff4 fs3 fc0 sc0 ls0 ws0">output to the L</div><div class="t m0 x2f h6 y58 ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 x30 h5 y57 ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 x31 h5 y59 ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 x2b h5 y57 ff4 fs3 fc0 sc0 ls0 ws0">X ﬁle, embedded in Sinput and Soutput environments, respectively.</div><div class="t m0 x5 h5 y5a ff4 fs3 fc0 sc0 ls0 ws0">The second code chunk shows one of the Sweave extension to the noweb syntax: Code chunk</div><div class="t m0 x4 h5 y5b ff4 fs3 fc0 sc0 ls0 ws0">names can be used to pass options to Sweave which control the ﬁnal output.</div><div class="t m0 x5 h5 y5c ff7 fs3 fc0 sc0 ls0 ws0">• The chunk is marked as a ﬁgure chunk (fig=TRUE) such that Sweave creates (by de-</div><div class="t m0 x13 h5 y5d ff4 fs3 fc0 sc0 ls0 ws0">fault) a PDF ﬁle of the plot created by the commands in the chunk. Furthermore, a</div><div class="t m0 x13 h5 y5e ff9 fs3 fc0 sc0 ls0 ws0">\includegraphics{example-1-002} statement is inserted into the L</div><div class="t m0 x32 h6 y5f ff8 fs4 fc0 sc0 ls0 ws0">A</div><div class="t m0 x33 h5 y5e ff4 fs3 fc0 sc0 ls0 ws0">T</div><div class="t m0 x34 h5 y60 ff4 fs3 fc0 sc0 ls0 ws0">E</div><div class="t m0 x35 h5 y5e ff4 fs3 fc0 sc0 ls0 ws0">X ﬁle (details on</div><div class="t m0 x13 h5 y61 ff4 fs3 fc0 sc0 ls0 ws0">the choice of ﬁle names for ﬁgures follow later in this manual).</div><div class="t m0 x5 h5 y62 ff7 fs3 fc0 sc0 ls0 ws0">• Option echo=FALSE indicates that the R input should not be included in the ﬁnal document</div><div class="t m0 x13 h5 y63 ff4 fs3 fc0 sc0 ls0 ws0">(no Sinput environment).</div><div class="t m0 x4 h9 y64 ff3 fs1 fc0 sc0 ls0 ws0">3.2 Sweave options</div><div class="t m0 x4 h5 y65 ff4 fs3 fc0 sc0 ls0 ws0">Options control how code chunks and their output (text, ﬁgures) are transferred from the ‘.Rnw’</div><div class="t m0 x4 h5 y66 ff4 fs3 fc0 sc0 ls0 ws0">ﬁle to the ‘.tex’ ﬁle. All options have the form key=value, where value can be a number,</div><div class="t m0 x1d h5 y31 ff4 fs3 fc0 sc0 ls0 ws0">2</div><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a><a class="l" rel='nofollow' onclick='return false;'><div class="d m1"></div></a></div><div class="pi" data-data='{"ctm":[1.611850,0.000000,0.000000,1.611850,0.000000,0.000000]}'></div></div>

<div id="pf3" class="pf w0 h0" data-page-no="3"><div class="pc pc3 w0 h0"><img class="bi x0 y0 w1 h1" alt="" src="https://static.pudn.com/prod/directory_preview_static/622bc0ac3d2fbb00079afe89/bg3.jpg"><div class="t m0 x36 hb y67 fff fs7 fc0 sc0 ls0 ws0">\ docu men tcl ass [ a4pa per ]{ article }</div><div class="t m0 x36 hb y68 fff fs7 fc0 sc0 ls0 ws0">\ title { Sweave Examp le 1}</div><div class="t m0 x36 hb y69 fff fs7 fc0 sc0 ls0 ws0">\ au thor { Fr iedrich Leisc h }</div><div class="t m0 x36 hb y6a fff fs7 fc0 sc0 ls0 ws0">\ begin { document }</div><div class="t m0 x36 hb y6b fff fs7 fc0 sc0 ls0 ws0">\ ma ketitle</div><div class="t m0 x36 hb y6c fff fs7 fc0 sc0 ls0 ws0">In this exa mple we embed parts of the exam ples from the</div><div class="t m0 x36 hb y6d fff fs7 fc0 sc0 ls0 ws0">\ te xttt { kruskal . test } help page into a \ LaTeX {} doc umen t :</div><div class="t m0 x36 hb y6e fff fs7 fc0 sc0 ls0 ws0"><< >>=</div><div class="t m0 x36 hb y6f fff fs7 fc0 sc0 ls0 ws0">data ( airquality , package =" datas ets ")</div><div class="t m0 x36 hb y70 fff fs7 fc0 sc0 ls0 ws0">libra ry (" stats ")</div><div class="t m0 x36 hb y71 fff fs7 fc0 sc0 ls0 ws0">krusk al . test ( Ozone ~ Month , data = ai rqu alit y )</div><div class="t m0 x36 hb y72 fff fs7 fc0 sc0 ls0 ws0">@</div><div class="t m0 x36 hb y73 fff fs7 fc0 sc0 ls0 ws0">which shows that the lo cati on para mete r of the Ozone</div><div class="t m0 x36 hb y74 fff fs7 fc0 sc0 ls0 ws0">dis tri but ion vari es s ign ifi cantl y from month to month . Finally we</div><div class="t m0 x36 hb y75 fff fs7 fc0 sc0 ls0 ws0">inclu de a boxp lot of the data :</div><div class="t m0 x36 hb y76 fff fs7 fc0 sc0 ls0 ws0">\ begin { center }</div><div class="t m0 x36 hb y77 fff fs7 fc0 sc0 ls0 ws0"><< fig =TRUE , echo = FALSE > >=</div><div class="t m0 x36 hb y78 fff fs7 fc0 sc0 ls0 ws0">libra ry (" graphi cs ")</div><div class="t m0 x36 hb y79 fff fs7 fc0 sc0 ls0 ws0">boxpl ot ( Ozone ~ Month , data = a irqu ali ty )</div><div class="t m0 x36 hb y7a fff fs7 fc0 sc0 ls0 ws0">@</div><div class="t m0 x36 hb y7b fff fs7 fc0 sc0 ls0 ws0">\ end { center }</div><div class="t m0 x36 hb y7c fff fs7 fc0 sc0 ls0 ws0">\ end { docum ent }</div><div class="t m0 x37 h5 y7d ff4 fs3 fc0 sc0 ls0 ws0">Figure 1: A minimal Sweave ﬁle: ‘example-1.Rnw’.</div><div class="t m0 x1d h5 y31 ff4 fs3 fc0 sc0 ls0 ws0">3</div></div><div class="pi" data-data='{"ctm":[1.611850,0.000000,0.000000,1.611850,0.000000,0.000000]}'></div></div>