{"id":601,"date":"2014-04-21T15:45:55","date_gmt":"2014-04-21T20:45:55","guid":{"rendered":"http:\/\/homepages.uc.edu\/~yaozo\/wordpress\/?p=601"},"modified":"2014-04-21T15:45:55","modified_gmt":"2014-04-21T20:45:55","slug":"oribatid-mite","status":"publish","type":"post","link":"https:\/\/zhuoyao.net\/index.php\/2014\/04\/21\/oribatid-mite\/","title":{"rendered":"Oribatid mite"},"content":{"rendered":"\n\n\n
oribatid<\/td>\nR Documentation<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Oribatid mite<\/h2>\n

Description<\/h3>\n

This data set contains informations about environmental control and spatial structure in ecological communities of Oribatid mites.<\/p>\n

Usage<\/h3>\n
data(oribatid)<\/pre>\n
Format<\/h3>\n
oribatid<\/code>\u00a0is a list containing the following objects :<\/p>\n
\n
fau<\/dt>\n
: a data frame with 70 rows (sites) and 35 columns (Oribatid species)<\/p>\n<\/dd>\n
envir<\/dt>\n
: a data frame with 70 rows (sites) and 5 columns (environmental variables)<\/p>\n<\/dd>\n
xy<\/dt>\n
: a data frame that contains spatial coordinates of the 70 sites<\/p>\n<\/dd>\n<\/dl>\n
Details<\/h3>\n
Variables of\u00a0oribatid$envir<\/code>\u00a0are the following ones :
\nsubstrate: a factor with seven levels that describes the nature of the substratum
\nshrubs: a factor with three levels that describes the absence\/presence of shrubs
\ntopo: a factor with two levels that describes the microtopography
\ndensity: substratum density (g.L^-1<\/i>)
\nwater: water content of the substratum (g.L^-1<\/i>)<\/p>\n
Source<\/h3>\n
Data prepared by P. Legendre\u00a0Pierre.Legendre@umontreal.ca<\/a>\u00a0and
\nD. Borcard\u00a0borcardd@magellan.umontreal.ca<\/a>\u00a0starting from
\nhttp:\/\/www.fas.umontreal.ca\/biol\/casgrain\/fr\/labo\/oribates.html<\/a><\/p>\n
References<\/h3>\n
Borcard, D., and Legendre, P. (1994) Environmental control and spatial structure in ecological communities: an example using Oribatid mites (Acari Oribatei<\/em>).\u00a0Environmental and Ecological Statistics<\/em>,\u00a01<\/b>, 37\u201361.<\/p>\n
Borcard, D., Legendre, P., and Drapeau, P. (1992) Partialling out the spatial component of ecological variation.\u00a0Ecology<\/em>,\u00a073<\/b>, 1045\u20131055.<\/p>\n
See a data description at\u00a0http:\/\/pbil.univ-lyon1.fr\/R\/pps\/pps039.pdf<\/a>\u00a0(in French).<\/p>\n
Examples<\/h3>\n
data(oribatid)\nori.xy <- oribatid$xy[,c(2,1)]\nnames(ori.xy) <- c(\"x\",\"y\")\nplot(ori.xy,pch = 20, cex = 2, asp = 1)\n\nif (require(deldir, quiet = TRUE)) {\n  if (require(spdep, quiet = TRUE)) {\n    plot(deldir(ori.xy), add = TRUE)\n    s.label(ori.xy, add.p = TRUE,\n     neig = nb2neig(knn2nb(knearneigh(as.matrix(ori.xy), 3))),\n     clab = 0)\n    }\n  }\n<\/pre>\n
Results<\/h3>\n
R version 3.0.2 (2013-09-25) -- \"Frisbee Sailing\"\nCopyright (C) 2013 The R Foundation for Statistical Computing\nPlatform: x86_64-unknown-linux-gnu (64-bit)\n\nR is free software and comes with ABSOLUTELY NO WARRANTY.\nYou are welcome to redistribute it under certain conditions.\nType 'license()' or 'licence()' for distribution details.\n\nR is a collaborative project with many contributors.\nType 'contributors()' for more information and\n'citation()' on how to cite R or R packages in publications.\n\nType 'demo()' for some demos, 'help()' for on-line help, or\n'help.start()' for an HTML browser interface to help.\nType 'q()' to quit R.\n\n> library(ade4)\n\nAttaching package: 'ade4'\n\nThe following object is masked from 'package:base':\n\n    within\n\n> png(filename=\"\/home\/oogasawa\/snapshot\/RGM3\/R_CC\/result\/ade4\/oribatid.Rd_%03d_medium.png\", width=480, height=480)\n> ### Name: oribatid\n> ### Title: Oribatid mite\n> ### Aliases: oribatid\n> ### Keywords: datasets\n> \n> ### ** Examples\n> \n> data(oribatid)\n> ori.xy <- oribatid$xy[,c(2,1)]\n> names(ori.xy) <- c(\"x\",\"y\")\n> plot(ori.xy,pch = 20, cex = 2, asp = 1)\n> \n> if (require(deldir, quiet = TRUE)) {\n+   if (require(spdep, quiet = TRUE)) {\n+     plot(deldir(ori.xy), add = TRUE)\n+     s.label(ori.xy, add.p = TRUE,\n+      neig = nb2neig(knn2nb(knearneigh(as.matrix(ori.xy), 3))),\n+      clab = 0)\n+     }\n+   }\ndeldir 0.0-22\nLoading required package: foreign\nLoading required package: grid\nLoading required package: lattice\n\nAttaching package: 'lattice'\n\nThe following object is masked from 'package:boot':\n\n    melanoma\n\nChecking rgeos availability: TRUE\n\nAttaching package: 'spdep'\n\nThe following object is masked from 'package:ade4':\n\n    mstree\n\n\n     PLEASE NOTE:  The components \"delsgs\" and \"summary\" of the \n     object returned by deldir() are now DATA FRAMES rather than \n     matrices (as they were prior to release 0.0-18). \n     See help(\"deldir\").\n \n     PLEASE NOTE: The process that deldir() uses for determining\n     duplicated points has changed from that used in version\n     0.0-9 of this package (and previously). See help(\"deldir\").\n\n> \n> \n> \n> \n> \n> dev.off()\nnull device \n          1 \n>\n<\/pre>\n
 <\/p>\n\n\n\n
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oribatid R Documentation Oribatid mite Description This data set contains informations about environmental control and spatial structure in ecological communities of Oribatid mites. Usage data(oribatid)… <\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[20],"tags":[],"class_list":["post-601","post","type-post","status-publish","format-standard","hentry","category-r"],"_links":{"self":[{"href":"https:\/\/zhuoyao.net\/index.php\/wp-json\/wp\/v2\/posts\/601","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/zhuoyao.net\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/zhuoyao.net\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/zhuoyao.net\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/zhuoyao.net\/index.php\/wp-json\/wp\/v2\/comments?post=601"}],"version-history":[{"count":0,"href":"https:\/\/zhuoyao.net\/index.php\/wp-json\/wp\/v2\/posts\/601\/revisions"}],"wp:attachment":[{"href":"https:\/\/zhuoyao.net\/index.php\/wp-json\/wp\/v2\/media?parent=601"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/zhuoyao.net\/index.php\/wp-json\/wp\/v2\/categories?post=601"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/zhuoyao.net\/index.php\/wp-json\/wp\/v2\/tags?post=601"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}