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en:monte_carlo_r [2017/10/11 20:36]
127.0.0.1 external edit
en:monte_carlo_r [2019/02/10 16:04]
David Zelený [R functions]
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-====== ​Constrained ordination ​====== +====== ​Ordination analysis ​====== 
-===== Monte Carlo permutation test =====+===== Monte Carlo permutation test (constrained ordination) ​===== 
 [[{|width: 7em; background-color:​ white; color: navy}monte_carlo|Theory]] [[{|width: 7em; background-color:​ white; color: navy}monte_carlo|Theory]]
 [[{|width: 7em; background-color:​ light; color: firebrick}monte_carlo_R|**R functions**]] [[{|width: 7em; background-color:​ light; color: firebrick}monte_carlo_R|**R functions**]]
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 [[{|width: 7em; background-color:​ white; color: navy}monte_carlo_exercise|Exercise {{::​lock-icon.png?​nolink|}}]] [[{|width: 7em; background-color:​ white; color: navy}monte_carlo_exercise|Exercise {{::​lock-icon.png?​nolink|}}]]
  
-==== R functions ==== + 
-  * **''​anova.cca''​** (library ''​vegan''​) - tests the significance of the variation in species composition explained by explanatory variables in constrained ordination (RDA, CCA), using Monte Carlo permutation test. It can test the significance of  +
-    * the global model (default setting), i.e. all variables included in the analysis; +
-    * only the first constrained axis (adding argument ''​first = TRUE''​);​ +
-    * individual axes (''​by = "​axis"''​),​ sequentially from the first to the last (this is done by using samples scores on the //n//-th axis as explanatory variables, while using scores of the axis 1, 2, ... //n// as covariables);​ +
-    * individual terms (explanatory variables) added sequentially in the order in which they appear in the formula or data frame (''​by = "​terms"'';​ note that this variation depends on the order of variables in which they enter the model); +
-    * variation explained by individual explanatory variables after removing variation of all other variables in the model (''​by = "​margin"'';​ here the variation does not depend on the order of variables in the model).+
en/monte_carlo_r.txt · Last modified: 2019/02/10 16:04 by David Zelený