DiversityCurveclass {alakazam}  R Documentation 
S4 class defining a diversity curve
Description
DiversityCurve
defines diversity (D
) scores over multiple diversity
orders (Q
).
Usage
## S4 method for signature 'DiversityCurve'
print(x)
## S4 method for signature 'DiversityCurve,missing'
plot(x, y, ...)
## S4 method for signature 'DiversityCurve,numeric'
plot(x, y, ...)
Arguments
x 
DiversityCurve object 
y 
diversity order to plot (q). 
... 
arguments to pass to plotDiversityCurve or plotDiversityTest. 
Slots
diversity
data.frame defining the diversity curve with the following columns:

group
: group label. 
q
: diversity order. 
d
: mean diversity index over all bootstrap realizations. 
d_sd
: standard deviation of the diversity index over all bootstrap realizations. 
d_lower
: diversity lower confidence inverval bound. 
d_upper
: diversity upper confidence interval bound. 
e
: evenness index calculated asD
divided byD
atQ=0
. 
e_lower
: evenness lower confidence inverval bound. 
e_upper
: eveness upper confidence interval bound.

tests
data.frame describing the significance test results with columns:

test
: string listing the two groups tested. 
delta_mean
: mean of theD
bootstrap delta distribution for the test. 
delta_sd
: standard deviation of theD
bootstrap delta distribution for the test. 
pvalue
: pvalue for the test.

group_by
string specifying the name of the grouping column in diversity calculation.
groups
vector specifying the names of unique groups in group column in diversity calculation.
method
string specifying the type of diversity calculated.
q
vector of diversity hill diversity indices used for computing diversity.
n
numeric vector indication the number of sequences sampled in each group.
ci
confidence interval defining the upper and lower bounds (a value between 0 and 1).