WeightedGenomicEstimatedBreedingValueMatrix

class pybrops.model.wgebvmat.WeightedGenomicEstimatedBreedingValueMatrix.WeightedGenomicEstimatedBreedingValueMatrix

Bases: BreedingValueMatrix

An abstract class for storing weighted genomic estimated breeding value matrices.

The purpose of this abstract interface is to provide functionality for:

1. Estimation of wGEBVs from a genomic model.

Methods

adjoin	Add additional elements to the end of the Matrix along an axis.
adjoin_taxa	Add additional elements to the end of the Matrix along the taxa axis.
adjoin_trait	Add additional elements to the end of the Matrix along the trait axis.
append	Append values to the Matrix.
append_taxa	Append values to the Matrix along the taxa axis.
append_trait	Append values to the TraitMatrix along the trait axis.
concat	Concatenate matrices together along an axis.
concat_taxa	Concatenate list of Matrix together along the taxa axis.
concat_trait	Concatenate list of Matrix together along the trait axis.
copy	Make a shallow copy of the Matrix.
deepcopy	Make a deep copy of the Matrix.
delete	Delete sub-arrays along an axis.
delete_taxa	Delete sub-arrays along the taxa axis.
delete_trait	Delete sub-arrays along the trait axis.
from_algmod	Estimate Weighted Genomic Estimated Breeding Values (wGEBVs) from an AdditiveLinearGenomicModel.
from_csv	Read a BreedingValueMatrix from a CSV file.
from_hdf5	Read a BreedingValueMatrix from an HDF5 file.
from_pandas	Read a BreedingValueMatrix from a pandas.DataFrame.
group	Sort the GroupableMatrix along an axis, then populate grouping indices.
group_taxa	Sort the Matrix along the taxa axis, then populate grouping indices for the taxa axis.
incorp	Incorporate values along the given axis before the given indices.
incorp_taxa	Incorporate values along the taxa axis before the given indices.
incorp_trait	Incorporate values along the trait axis before the given indices.
insert	Insert values along the given axis before the given indices.
insert_taxa	Insert values along the taxa axis before the given indices.
insert_trait	Insert values along the trait axis before the given indices.
is_grouped	Determine whether the Matrix has been sorted and grouped.
is_grouped_taxa	Determine whether the Matrix has been sorted and grouped along the taxa axis.
lexsort	Perform an indirect stable sort using a sequence of keys.
lexsort_taxa	Perform an indirect stable sort using a sequence of keys along the taxa axis.
lexsort_trait	Perform an indirect stable sort using a sequence of keys along the trait axis.
remove	Remove sub-arrays along an axis.
remove_taxa	Remove sub-arrays along the taxa axis.
remove_trait	Remove sub-arrays along the trait axis.
reorder	Reorder elements of the Matrix using an array of indices.
reorder_taxa	Reorder elements of the Matrix along the taxa axis using an array of indices.
reorder_trait	Reorder elements of the Matrix along the trait axis using an array of indices.
select	Select certain values from the matrix.
select_taxa	Select certain values from the Matrix along the taxa axis.
select_trait	Select certain values from the Matrix along the trait axis.
sort	Sort slements of the Matrix using a sequence of keys.
sort_taxa	Sort slements of the Matrix along the taxa axis using a sequence of keys.
sort_trait	Sort slements of the Matrix along the trait axis using a sequence of keys.
targmax	Return indices of the maximum values along the trait axis.
targmin	Return indices of the minimum values along the trait axis.
tmax	Return the maximum along the trait axis.
tmean	Return the mean along the trait axis.
tmin	Return the minimum along the trait axis.
to_csv	Write an object to a CSV file.
to_hdf5	Write an object to an HDF5 file.
to_pandas	Export an object to a pandas.DataFrame.
trange	Return the range along the trait axis.
tstd	Return the standard deviation along the trait axis.
tvar	Return the variance along the trait axis.
ungroup	Ungroup the GroupableMatrix along an axis by removing grouping metadata.
ungroup_taxa	Ungroup the TaxaMatrix along the taxa axis by removing taxa group metadata.
unscale	Transform values within the BreedingValueMatrix back to their unscaled and de-centered values.

Attributes

location	Mean of the phenotype values used to calculate breeding values.
mat	Pointer to raw matrix object.
mat_ndim	Number of dimensions of the raw matrix.
mat_shape	Shape of the raw matrix.
ntaxa	Number of taxa.
ntrait	Number of traits.
scale	Standard deviation of the phenotype values used to calculate breeding values.
taxa	Taxa label.
taxa_axis	Axis along which taxa are stored.
taxa_grp	Taxa group label.
taxa_grp_len	Taxa group length.
taxa_grp_name	Taxa group name.
taxa_grp_spix	Taxa group stop index.
taxa_grp_stix	Taxa group start index.
trait	Trait label.
trait_axis	Axis along which traits are stored.

abstract __add__(value)

Elementwise add matrices

Parameters:

value (object) – Object which to add.

Returns:

out – An object resulting from the addition.

Return type:

object

abstract __mul__(value)

Elementwise multiply matrices

Parameters:

value (object) – Object which to multiply.

Returns:

out – An object resulting from the multiplication.

Return type:

object

abstract adjoin(values, axis, **kwargs)

Add additional elements to the end of the Matrix along an axis.

Parameters:

• values (Matrix or numpy.ndarray) – Values are appended to append to the Matrix.

• axis (int) – The axis along which values are adjoined.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A copy of mat with values appended to axis. Note that adjoin does not occur in-place: a new Matrix is allocated and filled.

Return type:

Matrix

abstract adjoin_taxa(values, taxa, taxa_grp, **kwargs)

Add additional elements to the end of the Matrix along the taxa axis.

Parameters:

• values (Matrix, numpy.ndarray) – Values are appended to adjoin to the Matrix.

• taxa (numpy.ndarray) – Taxa names to adjoin to the Matrix.

• taxa_grp (numpy.ndarray) – Taxa groups to adjoin to the Matrix.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A copy of TaxaMatrix with values appended to axis. Note that adjoin does not occur in-place: a new TaxaMatrix is allocated and filled.

Return type:

TaxaMatrix

abstract adjoin_trait(values, trait, **kwargs)

Add additional elements to the end of the Matrix along the trait axis.

Parameters:

• values (Matrix, numpy.ndarray) – Values are appended to adjoin to the Matrix.

• trait (numpy.ndarray) – Trait names to adjoin to the TraitMatrix.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A copy of the TraitMatrix with values appended to axis. Note that adjoin does not occur in-place: a new TraitMatrix is allocated and filled.

Return type:

TraitMatrix

abstract append(values, axis, **kwargs)

Append values to the Matrix.

Parameters:

• values (Matrix, numpy.ndarray) – Values are appended to append to the matrix.

• axis (int) – The axis along which values are appended.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract append_taxa(values, taxa, taxa_grp, **kwargs)

Append values to the Matrix along the taxa axis.

Parameters:

• values (Matrix, numpy.ndarray) – Values are appended to append to the matrix.

• taxa (numpy.ndarray) – Taxa names to append to the Matrix.

• taxa_grp (numpy.ndarray) – Taxa groups to append to the Matrix.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract append_trait(values, trait, **kwargs)

Append values to the TraitMatrix along the trait axis.

Parameters:

• values (Matrix, numpy.ndarray) – Values are appended to append to the TraitMatrix.

• trait (numpy.ndarray) – Trait names to append to the TraitMatrix.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract classmethod concat(mats, axis, **kwargs)

Concatenate matrices together along an axis.

Parameters:

• mats (Sequence of Matrix) – List of Matrix to concatenate. The matrices must have the same shape, except in the dimension corresponding to axis.

• axis (int) – The axis along which the arrays will be joined.

• kwargs (dict) – Additional keyword arguments

Returns:

out – The concatenated matrix. Note that concat does not occur in-place: a new Matrix is allocated and filled.

Return type:

Matrix

abstract classmethod concat_taxa(mats, **kwargs)

Concatenate list of Matrix together along the taxa axis.

Parameters:

• mats (Sequence of Matrix) – List of Matrix to concatenate. The matrices must have the same shape, except in the dimension corresponding to axis.

• kwargs (dict) – Additional keyword arguments

Returns:

out – The concatenated TaxaMatrix. Note that concat does not occur in-place: a new TaxaMatrix is allocated and filled.

Return type:

TaxaMatrix

abstract classmethod concat_trait(mats, **kwargs)

Concatenate list of Matrix together along the trait axis.

Parameters:

• mats (Sequence of TraitMatrix) – List of TraitMatrix to concatenate. The matrices must have the same shape, except in the dimension corresponding to axis.

• kwargs (dict) – Additional keyword arguments

Returns:

out – The concatenated TraitMatrix. Note that concat does not occur in-place: a new TraitMatrix is allocated and filled.

Return type:

TraitMatrix

abstract copy()

Make a shallow copy of the Matrix.

Returns:

out – A shallow copy of the original Matrix.

Return type:

Matrix

abstract deepcopy(memo)

Make a deep copy of the Matrix.

Parameters:

memo (dict) – Dictionary of memo metadata.

Returns:

out – A deep copy of the original Matrix.

Return type:

Matrix

abstract delete(obj, axis, **kwargs)

Delete sub-arrays along an axis.

Parameters:

• obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.

• axis (int) – The axis along which to delete the subarray defined by obj.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A Matrix with deleted elements. Note that concat does not occur in-place: a new Matrix is allocated and filled.

Return type:

Matrix

abstract delete_taxa(obj, **kwargs)

Delete sub-arrays along the taxa axis.

Parameters:

• obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A TaxaMatrix with deleted elements. Note that concat does not occur in-place: a new TaxaMatrix is allocated and filled.

Return type:

TaxaMatrix

abstract delete_trait(obj, **kwargs)

Delete sub-arrays along the trait axis.

Parameters:

• obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A TraitMatrix with deleted elements. Note that concat does not occur in-place: a new TraitMatrix is allocated and filled.

Return type:

TraitMatrix

abstract classmethod from_algmod(algmod, gmat, **kwargs)

Estimate Weighted Genomic Estimated Breeding Values (wGEBVs) from an AdditiveLinearGenomicModel.

Parameters:

• algmod (AdditiveLinearGenomicModel) – An AdditiveLinearGenomicModel with which to estimate wGEBVs.

• gmat (GenotypeMatrix) – Genotypes for which to estimate wGEBVs.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A WeightedGenomicEstimatedBreedingValueMatrix object containing wGEBVs.

Return type:

WeightedGenomicEstimatedBreedingValueMatrix

abstract classmethod from_csv(filename, **kwargs)

Read a BreedingValueMatrix from a CSV file.

Parameters:

• filename (str) – CSV file name from which to read.

• kwargs (dict) – Additional keyword arguments to use for dictating importing from a CSV.

Returns:

out – A BreedingValueMatrix read from a CSV file.

Return type:

BreedingValueMatrix

abstract classmethod from_hdf5(filename, groupname)

Read a BreedingValueMatrix from an HDF5 file.

Parameters:

• filename (str, Path, h5py.File) – If str or Path, an HDF5 file name from which to read. File is closed after reading. If h5py.File, an opened HDF5 file from which to read. File is not closed after reading.

• groupname (str, None) – If str, HDF5 group name under which object data is stored. If None, object is read from base HDF5 group.

Returns:

out – A BreedingValueMatrix read from an HDF5 file.

Return type:

BreedingValueMatrix

abstract classmethod from_pandas(df, **kwargs)

Read a BreedingValueMatrix from a pandas.DataFrame.

Parameters:

• df (pandas.DataFrame) – Pandas dataframe from which to read.

• kwargs (dict) – Additional keyword arguments to use for dictating importing from a pandas.DataFrame.

Returns:

out – A BreedingValueMatrix read from a pandas.DataFrame.

Return type:

BreedingValueMatrix

abstract group(axis, **kwargs)

Sort the GroupableMatrix along an axis, then populate grouping indices.

Parameters:

• axis (int) – The axis along which values are grouped.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract group_taxa(**kwargs)

Sort the Matrix along the taxa axis, then populate grouping indices for the taxa axis.

Parameters:

kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract incorp(obj, values, axis, **kwargs)

Incorporate values along the given axis before the given indices.

Parameters:

• obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is incorporated.

• values (numpy.ndarray) – Values to incorporate into the matrix.

• axis (int) – The axis along which values are incorporated.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract incorp_taxa(obj, values, taxa, taxa_grp, **kwargs)

Incorporate values along the taxa axis before the given indices.

Parameters:

• obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is incorporated.

• values (Matrix, numpy.ndarray) – Values to incorporate into the matrix.

• taxa (numpy.ndarray) – Taxa names to incorporate into the Matrix.

• taxa_grp (numpy.ndarray) – Taxa groups to incorporate into the Matrix.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract incorp_trait(obj, values, trait, **kwargs)

Incorporate values along the trait axis before the given indices.

Parameters:

• obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is incorporated.

• values (Matrix, numpy.ndarray) – Values to incorporate into the matrix.

• trait (numpy.ndarray) – Trait names to incorporate into the Matrix.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract insert(obj, values, axis, **kwargs)

Insert values along the given axis before the given indices.

Parameters:

• obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is inserted.

• values (ArrayLike) – Values to insert into the matrix.

• axis (int) – The axis along which values are inserted.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A Matrix with values inserted. Note that insert does not occur in-place: a new Matrix is allocated and filled.

Return type:

Matrix

abstract insert_taxa(obj, values, taxa, taxa_grp, **kwargs)

Insert values along the taxa axis before the given indices.

Parameters:

• obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is inserted.

• values (Matrix, numpy.ndarray) – Values to insert into the matrix.

• taxa (numpy.ndarray) – Taxa names to insert into the Matrix.

• taxa_grp (numpy.ndarray) – Taxa groups to insert into the Matrix.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A TaxaMatrix with values inserted. Note that insert does not occur in-place: a new TaxaMatrix is allocated and filled.

Return type:

TaxaMatrix

abstract insert_trait(obj, values, trait, **kwargs)

Insert values along the trait axis before the given indices.

Parameters:

• obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is inserted.

• values (Matrix, numpy.ndarray) – Values to insert into the matrix.

• trait (numpy.ndarray) – Trait names to insert into the TraitMatrix.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A TraitMatrix with values inserted. Note that insert does not occur in-place: a new TraitMatrix is allocated and filled.

Return type:

TraitMatrix

abstract is_grouped(axis, **kwargs)

Determine whether the Matrix has been sorted and grouped.

Parameters:

• axis (int) – Axis along which to determine whether elements have been sorted and grouped.

• kwargs (dict) – Additional keyword arguments.

Returns:

grouped – True or False indicating whether the Matrix has been sorted and grouped.

Return type:

bool

abstract is_grouped_taxa(**kwargs)

Determine whether the Matrix has been sorted and grouped along the taxa axis.

Parameters:

kwargs (dict) – Additional keyword arguments.

Returns:

grouped – True or False indicating whether the Matrix has been sorted and grouped.

Return type:

bool

abstract lexsort(keys, axis, **kwargs)

Perform an indirect stable sort using a sequence of keys.

Parameters:

• keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.

• axis (int) – Axis to be indirectly sorted.

• kwargs (dict) – Additional keyword arguments.

Returns:

indices – Array of indices that sort the keys along the specified axis.

Return type:

A (N,) ndarray of ints

abstract lexsort_taxa(keys, **kwargs)

Perform an indirect stable sort using a sequence of keys along the taxa axis.

Parameters:

• keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.

• kwargs (dict) – Additional keyword arguments.

Returns:

indices – Array of indices that sort the keys along the specified axis.

Return type:

A (N,) ndarray of ints

abstract lexsort_trait(keys, **kwargs)

Perform an indirect stable sort using a sequence of keys along the trait axis.

Parameters:

• keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.

• kwargs (dict) – Additional keyword arguments.

Returns:

indices – Array of indices that sort the keys along the specified axis.

Return type:

A (N,) ndarray of ints

abstract property location: object

Mean of the phenotype values used to calculate breeding values.

abstract property mat: object

Pointer to raw matrix object.

abstract property mat_ndim: int

Number of dimensions of the raw matrix.

abstract property mat_shape: tuple

Shape of the raw matrix.

abstract property ntaxa: int

Number of taxa.

abstract property ntrait: int

Number of traits.

abstract remove(obj, axis, **kwargs)

Remove sub-arrays along an axis.

Parameters:

• obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.

• axis (int) – The axis along which to remove the subarray defined by obj.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract remove_taxa(obj, **kwargs)

Remove sub-arrays along the taxa axis.

Parameters:

• obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract remove_trait(obj, **kwargs)

Remove sub-arrays along the trait axis.

Parameters:

• obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract reorder(indices, axis, **kwargs)

Reorder elements of the Matrix using an array of indices. Note this modifies the Matrix in-place.

Parameters:

• indices (A (N,) ndarray of ints, Sequence of ints) – Array of indices that reorder the matrix along the specified axis.

• axis (int) – Axis to be reordered.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract reorder_taxa(indices, **kwargs)

Reorder elements of the Matrix along the taxa axis using an array of indices. Note this modifies the Matrix in-place.

Parameters:

• indices (A (N,) ndarray of ints) – Array of indices that reorder the matrix along the specified axis.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract reorder_trait(indices, **kwargs)

Reorder elements of the Matrix along the trait axis using an array of indices. Note this modifies the Matrix in-place.

Parameters:

• indices (A (N,) ndarray of ints, Sequence of ints) – Array of indices that reorder the matrix along the specified axis.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract property scale: object

Standard deviation of the phenotype values used to calculate breeding values.

abstract select(indices, axis, **kwargs)

Select certain values from the matrix.

Parameters:

• indices (ArrayLike (Nj, ...)) – The indices of the values to select.

• axis (int) – The axis along which values are selected.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – The output matrix with values selected. Note that select does not occur in-place: a new Matrix is allocated and filled.

Return type:

Matrix

abstract select_taxa(indices, **kwargs)

Select certain values from the Matrix along the taxa axis.

Parameters:

• indices (array_like (Nj, ...)) – The indices of the values to select.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – The output TaxaMatrix with values selected. Note that select does not occur in-place: a new TaxaMatrix is allocated and filled.

Return type:

TaxaMatrix

abstract select_trait(indices, **kwargs)

Select certain values from the Matrix along the trait axis.

Parameters:

• indices (ArrayLike (Nj, ...)) – The indices of the values to select.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – The output TraitMatrix with values selected. Note that select does not occur in-place: a new TraitMatrix is allocated and filled.

Return type:

TraitMatrix

abstract sort(keys, axis, **kwargs)

Sort slements of the Matrix using a sequence of keys. Note this modifies the Matrix in-place.

Parameters:

• keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.

• axis (int) – Axis to be indirectly sorted.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract sort_taxa(keys, **kwargs)

Sort slements of the Matrix along the taxa axis using a sequence of keys. Note this modifies the Matrix in-place.

Parameters:

• keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract sort_trait(keys, **kwargs)

Sort slements of the Matrix along the trait axis using a sequence of keys. Note this modifies the Matrix in-place.

Parameters:

• keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract targmax()

Return indices of the maximum values along the trait axis.

Returns:

out – An index array of shape (t,) containing indices of maximum values along the trait axis.

Where:

• t is the number of traits.

Return type:

numpy.ndarray

abstract targmin()

Return indices of the minimum values along the trait axis.

Returns:

out – An index array of shape (t,) containing indices of minimum values along the trait axis.

Where:

• t is the number of traits.

Return type:

numpy.ndarray

abstract property taxa: object

Taxa label.

abstract property taxa_axis: int

Axis along which taxa are stored.

abstract property taxa_grp: object

Taxa group label.

abstract property taxa_grp_len: object

Taxa group length.

abstract property taxa_grp_name: object

Taxa group name.

abstract property taxa_grp_spix: object

Taxa group stop index.

abstract property taxa_grp_stix: object

Taxa group start index.

abstract tmax(unscale)

Return the maximum along the trait axis.

Parameters:

unscale (bool) – whether to transform results to their unscaled values.

Returns:

out – An array of shape (t,) containing maximum values along the trait axis.

Where:

• t is the number of traits.

Return type:

numpy.ndarray

abstract tmean(unscale)

Return the mean along the trait axis.

Parameters:

unscale (bool) – whether to transform results to their unscaled values.

Returns:

out – An array of shape (t,) containing maximum values along the trait axis.

Where:

• t is the number of traits.

Return type:

numpy.ndarray

abstract tmin(unscale)

Return the minimum along the trait axis.

Parameters:

unscale (bool) – whether to transform results to their unscaled values.

Returns:

out – An index array of shape (t,) containing minimum values along the trait axis.

Where:

• t is the number of traits.

Return type:

numpy.ndarray

abstract to_csv(filename, **kwargs)

Write an object to a CSV file.

Parameters:

• filename (str) – CSV file name to which to write.

• kwargs (dict) – Additional keyword arguments to use for dictating export to a CSV.

Return type:

None

abstract to_hdf5(filename, groupname, overwrite)

Write an object to an HDF5 file.

Parameters:

• filename (str, Path, h5py.File) – If str, an HDF5 file name to which to write. If Path, an HDF5 file path to which to write. If h5py.File, an opened HDF5 file to which to write.

• groupname (str, None) – If str, an HDF5 group name under which object data is stored. If None, object is written to the base HDF5 group.

• overwrite (bool) – Whether to overwrite values in an HDF5 file if a field already exists.

Return type:

None

abstract to_pandas(**kwargs)

Export an object to a pandas.DataFrame.

Parameters:

kwargs (dict) – Additional keyword arguments to use for dictating export to a pandas.DataFrame.

Returns:

out – An output dataframe.

Return type:

pandas.DataFrame

abstract property trait: object

Trait label.

abstract property trait_axis: int

Axis along which traits are stored.

abstract trange(unscale)

Return the range along the trait axis.

Parameters:

unscale (bool) – whether to transform results to their unscaled values.

Returns:

out – An array of shape (t,) containing variance values along the trait axis.

Where:

• t is the number of traits.

Return type:

numpy.ndarray

abstract tstd(unscale)

Return the standard deviation along the trait axis.

Parameters:

unscale (bool) – whether to transform results to their unscaled values.

Returns:

out – An array of shape (t,) containing standard deviation values along the trait axis.

Where:

• t is the number of traits.

Return type:

numpy.ndarray

abstract tvar(unscale)

Return the variance along the trait axis.

Parameters:

unscale (bool) – whether to transform results to their unscaled values.

Returns:

out – An array of shape (t,) containing variance values along the trait axis.

Where:

• t is the number of traits.

Return type:

numpy.ndarray

abstract ungroup(axis, **kwargs)

Ungroup the GroupableMatrix along an axis by removing grouping metadata.

Parameters:

• axis (int) – The axis along which values should be ungrouped.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract ungroup_taxa(**kwargs)

Ungroup the TaxaMatrix along the taxa axis by removing taxa group metadata.

Parameters:

kwargs (dict) – Additional keyword arguments.

Return type:

None

abstract unscale()

Transform values within the BreedingValueMatrix back to their unscaled and de-centered values.

Returns:

out – An array of shape (n,t) containing unscaled and de-centered values.

Where:

• n is the number of taxa.

• t is the number of traits.

Return type:

numpy.ndarray