incomp
(Package: poppr) :
Check for samples that are incomparable due to missing data
If two samples share no loci typed in common, they are incomparable and will produce missing data in a distance matrix, which could lead to problems with further analyses. This function finds these samples and returns a matrix of how many other samples these are incomparable with.
● Data Source:
CranContrib
● Keywords:
● Alias: incomp
●
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greycurve
(Package: poppr) :
Display a greyscale gradient adjusted to specific parameters
This function has one purpose. It is for deciding the appropriate scaling for a grey palette to be used for edge weights of a minimum spanning network.
● Data Source:
CranContrib
● Keywords:
● Alias: greycurve
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ia
(Package: poppr) :
Index of Association
Calculate the Index of Association and Standardized Index of Association. Obtain p-values from one-sided permutation tests.
● Data Source:
CranContrib
● Keywords:
● Alias: ia, pair.ia
●
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aboot
(Package: poppr) :
Calculate a dendrogram with bootstrap support using any distance applicable
Calculate a dendrogram with bootstrap support using any distance applicable to genind or genclone objects.
● Data Source:
CranContrib
● Keywords: bootstrap
● Alias: aboot, bootstrap
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is.snpclone
(Package: poppr) :
Check for validity of a genclone or snpclone object
Check for validity of a genclone or snpclone object
● Data Source:
CranContrib
● Keywords:
● Alias: is.clone, is.genclone, is.snpclone
●
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genind2genalex
(Package: poppr) :
Exporting data from genind objects to genalex formatted *.csv files.
genind2genalex will export a genclone or genind object to a *.csv file formatted for use in genalex.
● Data Source:
CranContrib
● Keywords:
● Alias: genind2genalex
●
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as.genclone
(Package: poppr) :
Switch between genind and genclone objects.
as.genclone will create a genclone object from a genind object OR anything that can be passed to the genind initializer.
● Data Source:
CranContrib
● Keywords:
● Alias: as.genclone, as.genclone,genind-method, genclone2genind, genclone2genind,genclone-method
●
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bruvo.dist
(Package: poppr) :
Bruvo's distance for microsatellites
Calculate the average Bruvo's distance over all loci in a population.
● Data Source:
CranContrib
● Keywords:
● Alias: bruvo.dist
●
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diversity_ci
(Package: poppr) :
Perform bootstrap statistics, calculate, and plot confidence intervals.
This function is for calculating bootstrap statistics and their confidence intervals. It is important to note that the calculation of confidence intervals is not perfect (See Details). Please be cautious when interpreting the results.
● Data Source:
CranContrib
● Keywords:
● Alias: diversity_ci
●
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An internal object used for bootstrapping. Not intended for user interaction.
● Data Source:
CranContrib
● Keywords: internal
● Alias: bootgen-class
●
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providing 
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