Difference between revisions of "Diversity index"
From Testiwiki
(→Answer: seems to work. A new example) |
(→Answer: something wrong with qD) |
||
Line 18: | Line 18: | ||
qD <- function(pi, q){ | qD <- function(pi, q){ | ||
+ | print(pi) | ||
+ | print(q) | ||
+ | print(q) | ||
pi <- pi/sum(pi) | pi <- pi/sum(pi) | ||
out <- rep(NA, length(q)) | out <- rep(NA, length(q)) | ||
Line 83: | Line 86: | ||
out <- qDa(qDj, wj$wj, q) | out <- qDa(qDj, wj$wj, q) | ||
out2 <- qD(pi, q) | out2 <- qD(pi, q) | ||
− | + | qt <- gsub("999", "∞", q) | |
− | outlabel <- c(paste("Alpha diversity with q=", | + | outlabel <- c(paste("Alpha diversity with q=", qt, sep=""), paste("Gamma diversity with q=", qt, sep="")) |
− | outsymbol <- c(paste( | + | outsymbol <- c(paste(qt, "Da", sep=""), paste(qt, "D", sep="")) |
out <- data.frame(Name = c(outlabel, "Richness", "Shannon index", | out <- data.frame(Name = c(outlabel, "Richness", "Shannon index", | ||
Line 96: | Line 99: | ||
return(out) | return(out) | ||
} | } | ||
+ | library(OpasnetBaseUtils) | ||
+ | data <- c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20) | ||
+ | diversity(amount=data, species = 1:20, transect = c(rep(1, 10), rep(2, 10)), q = c(0, 1, 2)) | ||
</rcode> | </rcode> | ||
Line 101: | Line 107: | ||
'''Example 1 to use function | '''Example 1 to use function | ||
− | <rcode include="page:Diversity_index|name:answer" variables=" | + | <rcode include="page:Diversity_index|name:answer|page:OpasnetBaseUtils|name:generic" variables=" |
name:data|description:Give your data in R format or leave empty for example data| | name:data|description:Give your data in R format or leave empty for example data| | ||
name:individual|description:Is your data individual data or group abundancies?|type:selection|options:TRUE;Individual;FALSE;Group|default:TRUE | name:individual|description:Is your data individual data or group abundancies?|type:selection|options:TRUE;Individual;FALSE;Group|default:TRUE | ||
Line 108: | Line 114: | ||
if(is.null(data)) {data <- c(1,4,6,9,3,4,5,6,5,4,3,3,5,5,7,5,5,4,3,4,5,6,8,9,5,4,5,4,3,3,4,9,6,6,4,5,3,2,1,1,2,3,4,3,2,3,4,5,6,7,7)} | if(is.null(data)) {data <- c(1,4,6,9,3,4,5,6,5,4,3,3,5,5,7,5,5,4,3,4,5,6,8,9,5,4,5,4,3,3,4,9,6,6,4,5,3,2,1,1,2,3,4,3,2,3,4,5,6,7,7)} | ||
data | data | ||
− | if(individual==TRUE) out <- diversity(species = data) else out <- diversity(amount = data) | + | diversity(data) |
+ | if(individual==TRUE) out <- diversity(species = data, q = 1) else out <- diversity(amount = data, q = 1) | ||
print(xtable(out), type = 'html') | print(xtable(out), type = 'html') | ||
</rcode> | </rcode> | ||
Line 129: | Line 136: | ||
out <- diversity(amount, species, transect, q) | out <- diversity(amount, species, transect, q) | ||
print(xtable(out), type = 'html') | print(xtable(out), type = 'html') | ||
+ | |||
</rcode> | </rcode> |
Revision as of 18:51, 8 January 2012
This page is a method.
The page identifier is Op_en5455 |
---|
Moderator:Jouni (see all) |
This page is a stub. You may improve it into a full page, and then a rating bar will appear here. |
Upload data
|
Question
How to calculate diversity indices?
Answer
Upload your data to Opasnet Base. Use the function diversity to calculate the most common indices.
Actual function diversity
Example 1 to use function
Example 2
The data should be given in R format as a list of values in parenthesis, beginning with c:
c(3,5,3,5,2,1,3,3,4,2) or equivalently c(0.1,0.2,0.4,0.1,0.2)
where the values are either
- identifiers of the species 1,2,3... in which the individuals belong (one entry per individual), or
- abundancies of species, i.e. proportions of individuals belonging to each species among the whole population (one entry per species).
Rationale
Diversity indices are thoroughly described in Wikipedia.
See also
References
Related files
<mfanonymousfilelist></mfanonymousfilelist>