Diversity index: Difference between revisions
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####### qD calculates true diversity for abundance pi with exponent q. | ####### qD calculates true diversity for abundance pi with exponent q. | ||
qD <- function(pi, q = q){ | qD <- function(pi, q = q.div){ # q.div is the q used by the diversity function. | ||
pi <- pi/sum(pi) | pi <- pi/sum(pi) | ||
out <- rep(NA, length(q)) | out <- rep(NA, length(q)) | ||
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return(out) | return(out) | ||
} | } | ||
###### qDa calculates alpha diversity using gamma diversities of each transect. | ###### qDa calculates alpha diversity using gamma diversities of each transect. | ||
qDa <- function(divj, wj = 1, q){ | qDa <- function(divj, wj = 1, q = q.div){ | ||
q. <- rep(q, each = length(wj)) | q. <- rep(q, each = length(wj)) | ||
out <- ifelse(q. == 1, exp(sum(wj * log(divj))), (sum(wj * divj^(1-q.)))^(1/(1 - q.))) | out <- ifelse(q. == 1, exp(sum(wj * log(divj))), (sum(wj * divj^(1-q.)))^(1/(1 - q.))) | ||
minqDj <- tapply(out, q., min) | minqDj <- tapply(out, q., min) | ||
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## species: an identifier for a species | ## species: an identifier for a species | ||
## transect: an identifier for a transect | ## transect: an identifier for a transect | ||
## q: exponent for the diversity calculation | ## q.div: exponent for the diversity calculation | ||
diversity <- function(amount = rep(1,length(species)), species = 1:length(amount), transect = 1, q = 0){ | diversity <- function(amount = rep(1,length(species)), species = 1:length(amount), transect = 1, q.div = 0){ | ||
pij <- as.data.frame(as.table(tapply(amount, data.frame(Transect = transect, Species = species), sum))) | pij <- as.data.frame(as.table(tapply(amount, data.frame(Transect = transect, Species = species), sum))) | ||
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out <- tapply(out$pij, out$Transect, qD) | out <- tapply(out$pij, out$Transect, qD) | ||
qDj <- rep(NA, nrow(wj)*length(q)) | qDj <- rep(NA, nrow(wj)*length(q.div)) | ||
for(i in 1:nrow(wj)){ | for(i in 1:nrow(wj)){ | ||
for(j in 1:length(q)){ | for(j in 1:length(q.div)){ | ||
qDj[i + (j - 1) * nrow(wj)] <- out[[i]][j] | qDj[i + (j - 1) * nrow(wj)] <- out[[i]][j] | ||
} | } | ||
} | } | ||
out <- qDa(qDj, wj$wj, q) | out <- qDa(qDj, wj$wj, q.div) | ||
out2 <- qD(pi, q) | out2 <- qD(pi, q.div) | ||
qt <- gsub("999", "∞", q) | qt <- gsub("999", "∞", q.div) | ||
outlabel <- c(paste("Alpha diversity with q=", qt, sep=""), paste("Gamma diversity with q=", qt, sep="")) | outlabel <- c(paste("Alpha diversity with q=", qt, sep=""), paste("Gamma diversity with q=", qt, sep="")) | ||
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<rcode include="page:OpasnetBaseUtils|name:generic|page:Diversity_index|name:answer" variables=" | <rcode include="page:OpasnetBaseUtils|name:generic|page:Diversity_index|name:answer" variables=" | ||
name:wikidata|description:Select your data|type:selection|options:'5/54/Tigre-data.csv';Tigre|default:'5/54/Tigre-data.csv'| | name:wikidata|description:Select your data|type:selection|options:'5/54/Tigre-data.csv';Tigre|default:'5/54/Tigre-data.csv'| | ||
name: | name:q.wiki|description:Which q values you want to calculate.|type:checkbox|options:0;0;1;1;2;2;3;3;999;∞|default:0;1;2;999 | ||
"> | "> | ||
library(OpasnetBaseUtils) | library(OpasnetBaseUtils) | ||
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amount <- data$Individuals | amount <- data$Individuals | ||
transect <- data$Transect | transect <- data$Transect | ||
q.wiki | |||
out <- diversity(amount, species, transect, | out <- diversity(amount, species, transect, q.wiki) | ||
print(xtable(out), type = 'html') | print(xtable(out), type = 'html') | ||
Revision as of 22:26, 8 January 2012
| Moderator:Jouni (see all) |
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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
Examples
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>