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en:data:mite [2013/12/05 15:21]
David Zelený [Description of the dataset (from Borcard et al. 2011)]
en:data:mite [2019/02/06 14:00] (current)
David Zelený
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 ===== Source of data ===== ===== Source of data =====
-Used as example dataset in Borcard et al. (2011); first used in Borcard et al. (1992). +Used as example dataset in Borcard et al. (2011, 2018); the dataset was first used in Borcard et al. (1992), and details are in Borcard & Legendre (1994).  
-===== Description of the dataset (from Borcard et al. 2011) =====+===== Description of the dataset ​===== 
 +<wrap lo>(from Borcard et al. 2011)</​wrap>​
 [{{  :​obrazky:​oribatida.png|Oribatida (source: [[http://​en.wikipedia.org/​wiki/​Oribatida|Wikipedia]])}}] [{{  :​obrazky:​oribatida.png|Oribatida (source: [[http://​en.wikipedia.org/​wiki/​Oribatida|Wikipedia]])}}]
 Oribatid mites (Acari: Oribatida) are a very diversified group of small (0.2–1.2 mm) soil-dwelling,​ mostly microphytophagous and detritivorous arthropods. A well aerated soil or a complex substrate like Sphagnum mosses present in bogs and wet forests can harbour up to several hundred thousand (10<​sup>​5</​sup>​) individuals per square metre. Local assemblages are sometimes composed of over a hundred species, including many rare ones. This diversity makes oribatid mites an interesting target group to study community–environment relationships at very local scales. Oribatid mites (Acari: Oribatida) are a very diversified group of small (0.2–1.2 mm) soil-dwelling,​ mostly microphytophagous and detritivorous arthropods. A well aerated soil or a complex substrate like Sphagnum mosses present in bogs and wet forests can harbour up to several hundred thousand (10<​sup>​5</​sup>​) individuals per square metre. Local assemblages are sometimes composed of over a hundred species, including many rare ones. This diversity makes oribatid mites an interesting target group to study community–environment relationships at very local scales.
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 |SubsDens|Substrate density (dry matter) [g dm<​sup>​-3</​sup>​] ​ | |SubsDens|Substrate density (dry matter) [g dm<​sup>​-3</​sup>​] ​ |
 |WatrCont|Water content [g dm<​sup>​-3</​sup>​] ​ | |WatrCont|Water content [g dm<​sup>​-3</​sup>​] ​ |
-|Substrate|Substrate [7 unordered classes] ​ |+|Substrate|Substrate [7 unordered classes; 6 substrate types + interface category]  |
 |Shrub|Shrubs [3 ordered classes] ​ | |Shrub|Shrubs [3 ordered classes] ​ |
 |Topo|Microtopography [Blanket - Hummock] ​ | |Topo|Microtopography [Blanket - Hummock] ​ |
 +
 +<​imgcaption mites_map|Map of the studied samples, distribution of substratum types, shrub cover and mircotopography (Figs. 1 and 2 from Borcard & Legendre 1994).>​{{:​obrazky:​mites_map_borcard-legendre1994.jpg?​direct|}}</​imgcaption>​
 +
 ===== R script for direct import of data to R ===== ===== R script for direct import of data to R =====
 <code rsplus> <code rsplus>
-mite <- read.delim ('http://www.sci.muni.cz/botany/​zeleny/​wiki/​anadat-r/​data-download/​mite.txt'​) +mite <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/​data/​mite.txt'​) 
-mite.env <- read.delim ('http://www.sci.muni.cz/botany/​zeleny/​wiki/​anadat-r/​data-download/​mite_env.txt'​) +mite.env <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/​data/​mite_env.txt'​) 
-mite.xy <- read.delim ('http://www.sci.muni.cz/​botany/​zeleny/wiki/​anadat-r/​data-download/​mite_xy.txt'​)+mite.xy <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/​data/​mite_xy.txt'​) 
 + 
 </​code>​ </​code>​
  
-or - data are in ''​vegan'' ​package:+or - data are in ''​vegan'' ​or in ''​ade4''​ packages:
 <code rsplus> <code rsplus>
 # install.packages ('​vegan'​) ​ # install vegan if not installed yet on your computer # install.packages ('​vegan'​) ​ # install vegan if not installed yet on your computer
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 data (mite) data (mite)
 data (mite.env) data (mite.env)
 +
 +# install.packages ('​ade4'​) # install ade4 if not installed yet on your computer
 +library (ade4)
 +data (oribatid) ​ # a list containing three components, check ?oribatid for details
 + 
 </​code>​ </​code>​
 ===== References ===== ===== References =====
   *Borcard, D., Legendre, P. & Drapeau, P. (1992) Partialling out the spatial component of ecological variation. //Ecology// 73: 1045-1055.   *Borcard, D., Legendre, P. & Drapeau, P. (1992) Partialling out the spatial component of ecological variation. //Ecology// 73: 1045-1055.
 +  *Borcard, D. & Legendre, P. (1994) Environmental control and spatial structure in ecological communities:​ an example using oribatid mites (Acari, Oribatei). //​Environmental and Ecological Statistics//​ 1: 37-61.
   *Borcard, D., Gillet, F. & Legendre, P. (2011) Numerical Ecology with R. Springer, UseR! Edition.   *Borcard, D., Gillet, F. & Legendre, P. (2011) Numerical Ecology with R. Springer, UseR! Edition.
en/data/mite.1386228094.txt.gz · Last modified: 2017/10/11 20:36 (external edit)