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en:data:simul [2018/04/01 09:38]
David Zelený [Data for download]
en:data:simul [2018/04/01 10:58] (current)
David Zelený [Data for download]
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   *simul2 - 2 gradients of different length (5000 a 2000 units), 500 samples, 300 species   *simul2 - 2 gradients of different length (5000 a 2000 units), 500 samples, 300 species
   *simul3 - 2 gradients of the same length (5000 units), 500 samples, 300 species   *simul3 - 2 gradients of the same length (5000 units), 500 samples, 300 species
-  *simul.short - 2 gradients of different length, both rather short (1100 and 800 units), 70 samples, 300 species, samples are distributed evenly along the gradient (distance among samples ​is 100 units) +  *simul.short - 2 gradients of different length, both rather short (1100 and 800 units), 70 samples, 300 species, samples are distributed evenly along the gradient (distances between ​samples ​along each gradient are exactly ​100 units) 
-  *simul.long - 2 gradients of different length, both rather long (5500 and 4000 units), 70 samples, 300 species, samples are distributed evenly along the gradient (distance among samples ​is 100 units)+  *simul.long - 2 gradients of different length, both rather long (5500 and 4000 units), 70 samples, 300 species, samples are distributed evenly along the gradient (distances between ​samples ​along each gradient are exactly ​100 units)
  
 Note: the number of species (e.g. 300) is a parameter set up for simulated models - the number of species in the resulting community matrix does not have to fit to number of simulated species, because some of the less abundant species were not "​sampled"​. Note: the number of species (e.g. 300) is a parameter set up for simulated models - the number of species in the resulting community matrix does not have to fit to number of simulated species, because some of the less abundant species were not "​sampled"​.
  
 +===== Environmental variables =====
 +|< 100% 150px ->|
 +^ Name of variable ​     ^ Description ​                                                                                           ^
 +| gradient ​             | position of the sample along the virtual gradient (for datasets with only one gradient) ​               |
 +| gradient1, gradient2 ​ | position of each sample along the first and second virtual gradient (for datasets with two gradients) ​ |
 +| group                 | classification of samples by modified Twinspan into four groups ​                                       |
 +
 +===== Species attributes ===== 
 +|< 100% 150px ->|
 +| optimum ​                    | position of species optima along the virtual gradient (for datasets with only one virtual gradient) ​              |
 +| niche.width ​                | width of the species niche in units of the virtual gradient (for dataset with only one virtual gradient) ​         |
 +| optimum1, optimum2 ​         | position of species optima along the first and second virtual gradient (for datasets with two virtual gradients) ​ |
 +| niche.width1,​ niche.widht2 ​ | width of the species niche along the first and second virtual gradient (for datasets with two virtual gradients) ​ |
  
  
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 Files containing ''​-spe''​ in the name represent presence-absence matrix of species data, files with ''​-env''​ contain position of simulated sample along virtual gradient (analogy to measured environmental variable), files with ''​-specvalues''​ contain information about position of species optima along the gradient and niche width (both in arbitrary gradient units). ​ Files containing ''​-spe''​ in the name represent presence-absence matrix of species data, files with ''​-env''​ contain position of simulated sample along virtual gradient (analogy to measured environmental variable), files with ''​-specvalues''​ contain information about position of species optima along the gradient and niche width (both in arbitrary gradient units). ​
  
-===== Data for download ===== 
 |< 100% 150px 100px - >| |< 100% 150px 100px - >|
-^ File name                                                                            ^ File type                 ^ Description ​                                                                                                  ​+^ File name                                                                                                           ​^ File type                 ^ Description ​                                                           
-{{https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​vltava.xlsx|vltava.xlsx}} ​       | Excel file                ​| ​Contains species ​× sample ​matrix, ​environmental variables, explanation of species ​abbreviations and metadata ​ | +[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul1-spe.txt|simul1-spe.txt]]                ​| ​tab-delimited txt format ​ | Sample ​× species ​matrix ​(500 samples in rows296 species ​in columns) ​ | 
-{{https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​vltava-spe.txt|vltava-spe.txt}}  ​| tab-delimited txt format ​ | Sample × species matrix (97 samples in rows, 274 species in columns) ​                                         +[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul1-env.txt|simul1-env.txt]] ​               | tab-delimited txt format ​ | Environmental variable matrix (samples in rows, variables in columns) ​ | 
-{{https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​vltava-env.txt|vltava-env.txt}}  ​| tab-delimited txt format ​ | Environmental variable matrix (samples in rows, variables in columns) ​                                        ​+| [[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul1-specvalues.txt|simul1-specvalues.txt]] ​ | tab-delimited txt format ​ | Species attribute matrix (species in rows, attributes in columns) ​     | 
-{{https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​vltava.cep|vltava.cep}}          ​canoco condensed file     | Species ​× sample ​matrix in CANOCO ​format ​                                                                     +| [[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul2-spe.txt|simul2-spe.txt]]                ​| tab-delimited txt format ​ | Sample × species matrix (500 samples in rows, 282 species in columns) ​ 
-{{http://www.davidzeleny.net/anadat-r/lib/exe/fetch.php/data:vltava.r}}              ​| r object file             +[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul2-env.txt|simul2-env.txt]]                ​| tab-delimited txt format ​ | Environmental variable matrix (samples in rows, variables in columns) ​ 
-An R objecta list with seven components ​(see below for detail description)|+[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul2-specvalues.txt|simul2-specvalues.txt]]  ​tab-delimited txt format  ​| Species ​attribute ​matrix ​(species ​in rows, attributes in columns) ​     | 
 +| [[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul3-spe.txt|simul3-spe.txt]] ​               | tab-delimited txt format ​ | Sample × species matrix (500 samples in rows, 279 species in columns)  ​
 +[[https://raw.githubusercontent.com/​zdealveindy/anadat-r/master/data/simul3-env.txt|simul3-env.txt]] ​               | tab-delimited txt format ​ | Environmental variable matrix (samples in rows, variables in columns) ​ | 
 +| [[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/data/​simul3-specvalues.txt|simul3-specvalues.txt]] ​ | tab-delimited txt format ​ | Species attribute matrix (species in rows, attributes in columns) ​     | 
 +| [[https://raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul.short-spe.txt|simul.short-spe.txt]] ​     | tab-delimited txt format ​ | Sample × species matrix (70 samples in rows, 300 species in columns) ​  | 
 +| [[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul.short-env.txt|simul.short-env.txt]] ​     | tab-delimited txt format ​ | Environmental variable matrix (samples in rows, variables in columns)  ​
 +| [[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul.long-spe.txt|simul.long-spe.txt]] ​       | tab-delimited txt format ​ | Sample × species matrix (70 samples in rows300 species in columns) ​  | 
 +| [[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul.long-env.txt|simul.long-env.txt]] ​       | tab-delimited txt format ​ | Environmental variable matrix ​(samples in rows, variables in columns |
  
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul1-spe.csv|simul1-spe.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul1-env.csv|simul1-env.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul1-specvalues.csv|simul1-specvalues.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul2-spe.csv|simul2-spe.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul2-env.csv|simul2-env.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul2-specvalues.csv|simul2-specvalues.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul3-spe.csv|simul3-spe.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul3-env.csv|simul3-env.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul3-specvalues.csv|simul3-specvalues.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul.short-spe.csv|simul.short-spe.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul.short-env.csv|simul.short-env.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul.long-spe.csv|simul.long-spe.csv]] 
-  *[[https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​simul.long-env.csv|simul.long-env.csv]] 
 ===== Script for direct import of data to R ===== ===== Script for direct import of data to R =====
 <code rsplus> <code rsplus>
en/data/simul.1522546690.txt.gz · Last modified: 2018/04/01 09:38 by David Zelený