coala (version 0.7.2)

sumstat_class: Base Class for Summary Statistics

Description

Base Class for Summary Statistics

Base Class for Summary Statistics

Super class

coala::coalmodelpart -> sumstat

Methods

Public methods

• sumstat_class$new()

• sumstat_class$calculate()

• sumstat_class$check()

• sumstat_class$get_name()

• sumstat_class$requires_files()

• sumstat_class$requires_segsites()

• sumstat_class$requires_trees()

• sumstat_class$print()

• sumstat_class$transform()

• sumstat_class$clone()

---

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.

Details

If you want to create additional summary statistics for coala, create R6 classes that inherit from this object.