sumstat_class {coala} | R Documentation |
Base Class for Summary Statistics
Description
Base Class for Summary Statistics
Base Class for Summary Statistics
Details
If you want to create additional summary statistics for coala, create R6 classes that inherit from this object.
Super class
coala::coalmodelpart
-> sumstat
Methods
Public methods
Method new()
Initialization of $sumstat
Usage
sumstat_class$new(name, transformation)
Arguments
name
the name to be used for this statistic
transformation
transformation to be used for this statistic
Returns
NULL
Method calculate()
This function must be overwritten in the derived class
Usage
sumstat_class$calculate(seg_sites, trees, files, model)
Arguments
seg_sites
seg_sites object containing the segregating sites
trees
trees
files
files
model
demographic model
Returns
NULL
Method check()
Optional functions that checks if a model is compatible with the stat.
In a derived class this can be overwritten by a function that throws an informative error if the model is incompatible with the statistic The function is executed before the statistic is added to the model.
Usage
sumstat_class$check(model)
Arguments
model
demographic model
Returns
invisible TRUE
Method get_name()
function to read the private attribute name
Usage
sumstat_class$get_name()
Returns
name of the statistic
Method requires_files()
function to check whether files are required by this statsitic
Usage
sumstat_class$requires_files()
Returns
req_files, which is TRUE or FALSE and indicates whether files are required by this statsitic
Method requires_segsites()
function to check whether segregating sites are required by this statsitic
Usage
sumstat_class$requires_segsites()
Returns
req_segsites, which is TRUE or FALSE and indicates whether segregating sites are required by this statsiti
Method requires_trees()
function to check whether trees are required by this statsitic
Usage
sumstat_class$requires_trees()
Returns
req_trees, which is TRUE or FALSE and indicates whether trees are required by this statsitic
Method print()
function to print the class of the statistic
Usage
sumstat_class$print()
Method transform()
Transformation that is applied to the statistic
Usage
sumstat_class$transform(x)
Arguments
x
untransformed value
Returns
transformed value
Method clone()
The objects of this class are cloneable with this method.
Usage
sumstat_class$clone(deep = FALSE)
Arguments
deep
Whether to make a deep clone.