bioarch package

Submodules

bioarch.age module

class bioarch.age.AgeCategory[source]

Bases: enum.Enum

An enumeration.

ADULT = 6
MIDDLE = 3
MIDDLE_OLD = 4
OLD = 5
UNKNOWN = 0
YOUNG = 1
YOUNG_ADULT = 2
as_quad()[source]
dtype = <function AgeCategory.dtype>[source]
parse = <function AgeCategory.parse>[source]
class bioarch.age.EstimatedAge(category: str, ranged: Optional[str])[source]

Bases: object

docstring for EstimatedAge

MAX_AGE = 100
static empty()[source]
to_pd_data_frame(index)[source]

bioarch.individual module

class bioarch.individual.AgeSexStature(osteological_sex: bioarch.individual.OsteologicalSex, age: bioarch.age.EstimatedAge, femur: bioarch.individual.LongBoneMeasurement, humerus: bioarch.individual.LongBoneMeasurement, tibia: bioarch.individual.LongBoneMeasurement, stature: Optional[str], body_mass: Optional[str])[source]

Bases: object

docstring for AgeSexStature

age
body_mass
static empty()[source]
femur
humerus
osteological_sex
stature
tibia
to_pd_data_frame(index)[source]
class bioarch.individual.BurialInfo(site_name: str, site_id: str)[source]

Bases: object

docstring for BurialInfo

to_pd_series(prefix='')[source]
class bioarch.individual.Individual(_id: str, site: bioarch.individual.BurialInfo, age_sex_stature: bioarch.individual.AgeSexStature, mouth: bioarch.mouth.Mouth, occupational_markers: bioarch.occupational_markers.OccupationalMarkers, joints: bioarch.joints.Joints, trauma: bioarch.trauma.Trauma, context: bioarch.context.Context)[source]

Bases: object

docstring for Individual

to_pd_data_frame()[source]
class bioarch.individual.LongBoneMeasurement(_max: Optional[float], bi: Optional[float], head: Optional[float], distal: Optional[float])[source]

Bases: object

docstring for LongBoneMeasurement

static empty()[source]
static empty_lr()[source]
to_pd_series(prefix='')[source]
class bioarch.individual.OsteologicalSex(pelvic: Optional[bioarch.sex.Sex], cranium: Optional[bioarch.sex.Sex], combined: Optional[bioarch.sex.Sex])[source]

Bases: object

docstring for OsteologicalSex

static empty()[source]
to_pd_data_frame(index)[source]

bioarch.left_right module

class bioarch.left_right.LeftRight(left: Optional[T], right: Optional[T])[source]

Bases: typing.Generic

Wrapper around measurements taken on both the left and right sides. This augments the two measurements by adding a meta-measurement with the “avg”/”best” combination of both.

avg() → Optional[T][source]

meta-measurement with the “avg”/”best” combination of both.

left
right
bioarch.left_right.best_effort_avg(left: Optional[T], right: Optional[T]) → Optional[T][source]

bioarch.mouth module

class bioarch.mouth.Mouth(teeth: List[bioarch.mouth.Tooth])[source]

Bases: object

Object to hold the 32 teeth

static empty()[source]
to_pd_series(prefix='')[source]
class bioarch.mouth.Tooth[source]

Bases: object

docstring for Tooth

abcess

‘NA’, ‘0’, ‘1’

calculus

‘NA’, ‘0’, ‘1’, ‘2’, ‘3’

cavities

‘NA’, ‘0’, ‘1’

eh

‘NA’, ‘0’, ‘1’

static empty()[source]
to_pd_series(prefix='')[source]
tooth

‘NA’, ‘0’, ‘1’, ‘A’, ‘B1’, ‘B2’, ‘C’, ‘D’, ‘E’, ‘F’, ‘G’, ‘H’, ‘I’

bioarch.occupational_markers module

class bioarch.occupational_markers.EnthesialMarker(value: Union[int, float], is_s: bool = False, is_oe: bool = False)[source]

Bases: object

docstring for EnthesialMarker

as_num() → float[source]
static avg(left: Optional[EnthesialMarker], right: Optional[EnthesialMarker]) → Optional[bioarch.occupational_markers.EnthesialMarker][source]
static parse(value: Any) → Optional[bioarch.occupational_markers.EnthesialMarker][source]
class bioarch.occupational_markers.OccupationalMarkers(c_trapezius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_o_deltiod: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_o_pectoralis_major: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_costoclaviclar_lig: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_subcalvius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_conoid_lig: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_trapezoid_lig: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], s_pectoralis_minor: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], s_levator_scapulae: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], s_triceps_long_head: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], s_trapezius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_subscapularis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_teres_major: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_latissimus_dorsi: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_pectoralis_major: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_deltoid: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_coracobrachialis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_supraspinatus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_infraspinatus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_teres_minor: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_o_extensor: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_o_flexor: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], u_brachialis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], u_o_pronator_quadrataus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], u_triceps_brachii: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], u_anconeus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], u_o_supinator: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], r_biceps_brachii: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], r_supinator: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], r_pronator_teres: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], r_pronator_quadratus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], r_brachoradialis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_gluteus_minimus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_gluteus_medius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_piriformus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_obturator_internus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_obturator_externus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_quadratis_femoris: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_ilioposas: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_gluteus_maximus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_pectineus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_vastus_medialis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_vastus_lateralis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_adductor_magnus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_gastrocnemius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_plantaris: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_popliteus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_tensor_fascia_latae: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_quadriceps: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_sartorius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_gracilis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_semitendinosus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_o_tibialus_anterior: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_biceps_femoris: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_semimembranosus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_popliteus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_o_soleus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_o_tibialis_posterior: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_o_flexor_digitorium: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_biceps_femoris: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_extensor_muscles: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_flexor_muscles: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_peroneus_longus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_peronus_brevis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_soleus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], p_quadriceps: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_achilles: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker])[source]

Bases: object

docstring for OccupationalMarkers

static empty() → bioarch.occupational_markers.OccupationalMarkers[source]
to_pd_data_frame(index) → pandas.core.series.Series[source]

bioarch.sex module

class bioarch.sex.Sex[source]

Bases: enum.Enum

An enumeration.

FEMALE = 0
FEMALE_ASSUMED = 20
FEMALE_LIKELY = 10
MALE = 100
MALE_ASSUMED = 80
MALE_LIKELY = 90
UNKNOWN = 50
as_bin()[source]
dtype = <function Sex.dtype>[source]
parse = <function Sex.parse>[source]

Module contents

class bioarch.AgeCategory[source]

Bases: enum.Enum

An enumeration.

ADULT = 6
MIDDLE = 3
MIDDLE_OLD = 4
OLD = 5
UNKNOWN = 0
YOUNG = 1
YOUNG_ADULT = 2
as_quad()[source]
dtype = <function AgeCategory.dtype>[source]
parse = <function AgeCategory.parse>[source]
class bioarch.EstimatedAge(category: str, ranged: Optional[str])[source]

Bases: object

docstring for EstimatedAge

MAX_AGE = 100
static empty()[source]
to_pd_data_frame(index)[source]
class bioarch.BodyPosition[source]

Bases: enum.Enum

An enumeration.

CROUCHED = 2
CROUCHED_LEFT_SIDE = 3
CROUCHED_RIGHT_SIDE = 4
STOMACH = 5
SUPINE = 0
SUPINE_FLEXED_LEGS = 1
dtype = <function BodyPosition.dtype>[source]
parse = <function BodyPosition.parse>[source]
class bioarch.CompassBearing[source]

Bases: enum.Enum

An enumeration.

EAST = 2
NORTH = 0
NORTH_EAST = 1
NORTH_WEST = 7
SOUTH = 4
SOUTH_EAST = 3
SOUTH_WEST = 5
WEST = 6
dtype = <function CompassBearing.dtype>[source]
parse = <function CompassBearing.parse>[source]
to_short_code()[source]
class bioarch.Context(body_position: Optional[bioarch.context.BodyPosition], body_orientation: Optional[bioarch.context.CompassBearing], disturbed: Optional[bioarch.context.Present], decapitation: Optional[bioarch.context.Present], double_grave: Optional[bioarch.context.Present], stone_layer: Optional[bioarch.context.Present], grave_goods: Dict[str, Optional[Any]])[source]

Bases: object

docstring for Context

static empty()[source]
static group(value)[source]
to_pd_data_frame(index)[source]
class bioarch.Present[source]

Bases: enum.Enum

An enumeration.

NOT_PRESENT = 0
PRESENT = 1
dtype = <function Present.dtype>[source]
parse = <function Present.parse>[source]
class bioarch.AgeSexStature(osteological_sex: bioarch.individual.OsteologicalSex, age: bioarch.age.EstimatedAge, femur: bioarch.individual.LongBoneMeasurement, humerus: bioarch.individual.LongBoneMeasurement, tibia: bioarch.individual.LongBoneMeasurement, stature: Optional[str], body_mass: Optional[str])[source]

Bases: object

docstring for AgeSexStature

age
body_mass
static empty()[source]
femur
humerus
osteological_sex
stature
tibia
to_pd_data_frame(index)[source]
class bioarch.BurialInfo(site_name: str, site_id: str)[source]

Bases: object

docstring for BurialInfo

to_pd_series(prefix='')[source]
class bioarch.Individual(_id: str, site: bioarch.individual.BurialInfo, age_sex_stature: bioarch.individual.AgeSexStature, mouth: bioarch.mouth.Mouth, occupational_markers: bioarch.occupational_markers.OccupationalMarkers, joints: bioarch.joints.Joints, trauma: bioarch.trauma.Trauma, context: bioarch.context.Context)[source]

Bases: object

docstring for Individual

to_pd_data_frame()[source]
class bioarch.LongBoneMeasurement(_max: Optional[float], bi: Optional[float], head: Optional[float], distal: Optional[float])[source]

Bases: object

docstring for LongBoneMeasurement

static empty()[source]
static empty_lr()[source]
to_pd_series(prefix='')[source]
class bioarch.OsteologicalSex(pelvic: Optional[bioarch.sex.Sex], cranium: Optional[bioarch.sex.Sex], combined: Optional[bioarch.sex.Sex])[source]

Bases: object

docstring for OsteologicalSex

static empty()[source]
to_pd_data_frame(index)[source]
class bioarch.JointCondition[source]

Bases: enum.Enum

1 - slight/mild 2 - medium 3 - extreme 4 - fused 5 - SCHMORALS NODES 6 - FRACTURE

EXTREAM = 3
FRACTURE = 6
FUSED = 4
MEDIUM = 2
MILD = 1
NORMAL = 0
SCHMORALS_NODES = 5
avg = <function JointCondition.avg>[source]
dtype = <function JointCondition.dtype>[source]
parse = <function JointCondition.parse>[source]
class bioarch.Joints(shoulder: bioarch.left_right.LeftRight[bioarch.joints.JointCondition][bioarch.joints.JointCondition], elbow: bioarch.left_right.LeftRight[bioarch.joints.JointCondition][bioarch.joints.JointCondition], wrist: bioarch.left_right.LeftRight[bioarch.joints.JointCondition][bioarch.joints.JointCondition], hip: bioarch.left_right.LeftRight[bioarch.joints.JointCondition][bioarch.joints.JointCondition], knee: bioarch.left_right.LeftRight[bioarch.joints.JointCondition][bioarch.joints.JointCondition], ankle: bioarch.left_right.LeftRight[bioarch.joints.JointCondition][bioarch.joints.JointCondition], sacro_illiac: bioarch.joints.JointCondition, c1_3: bioarch.joints.JointCondition, c4_7: bioarch.joints.JointCondition, t1_4: bioarch.joints.JointCondition, t5_8: bioarch.joints.JointCondition, t9_12: bioarch.joints.JointCondition, l1_5: bioarch.joints.JointCondition)[source]

Bases: object

docstring for Joints

static empty()[source]
to_pd_data_frame(index)[source]
class bioarch.EnthesialMarker(value: Union[int, float], is_s: bool = False, is_oe: bool = False)[source]

Bases: object

docstring for EnthesialMarker

as_num() → float[source]
static avg(left: Optional[EnthesialMarker], right: Optional[EnthesialMarker]) → Optional[bioarch.occupational_markers.EnthesialMarker][source]
static parse(value: Any) → Optional[bioarch.occupational_markers.EnthesialMarker][source]
class bioarch.OccupationalMarkers(c_trapezius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_o_deltiod: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_o_pectoralis_major: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_costoclaviclar_lig: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_subcalvius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_conoid_lig: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_trapezoid_lig: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], s_pectoralis_minor: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], s_levator_scapulae: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], s_triceps_long_head: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], s_trapezius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_subscapularis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_teres_major: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_latissimus_dorsi: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_pectoralis_major: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_deltoid: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_coracobrachialis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_supraspinatus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_infraspinatus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_teres_minor: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_o_extensor: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], h_o_flexor: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], u_brachialis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], u_o_pronator_quadrataus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], u_triceps_brachii: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], u_anconeus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], u_o_supinator: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], r_biceps_brachii: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], r_supinator: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], r_pronator_teres: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], r_pronator_quadratus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], r_brachoradialis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_gluteus_minimus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_gluteus_medius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_piriformus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_obturator_internus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_obturator_externus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_quadratis_femoris: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_ilioposas: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_gluteus_maximus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_pectineus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_vastus_medialis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_vastus_lateralis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_adductor_magnus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_gastrocnemius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_plantaris: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_popliteus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_tensor_fascia_latae: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_quadriceps: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_sartorius: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_gracilis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_semitendinosus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_o_tibialus_anterior: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_biceps_femoris: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_semimembranosus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_popliteus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_o_soleus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_o_tibialis_posterior: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], t_o_flexor_digitorium: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_biceps_femoris: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_extensor_muscles: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_flexor_muscles: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_peroneus_longus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_peronus_brevis: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], f_o_soleus: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], p_quadriceps: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker], c_achilles: bioarch.left_right.LeftRight[bioarch.occupational_markers.EnthesialMarker][bioarch.occupational_markers.EnthesialMarker])[source]

Bases: object

docstring for OccupationalMarkers

static empty() → bioarch.occupational_markers.OccupationalMarkers[source]
to_pd_data_frame(index) → pandas.core.series.Series[source]
class bioarch.LeftRight(left: Optional[T], right: Optional[T])[source]

Bases: typing.Generic

Wrapper around measurements taken on both the left and right sides. This augments the two measurements by adding a meta-measurement with the “avg”/”best” combination of both.

avg() → Optional[T][source]

meta-measurement with the “avg”/”best” combination of both.

left
right
class bioarch.Mouth(teeth: List[bioarch.mouth.Tooth])[source]

Bases: object

Object to hold the 32 teeth

static empty()[source]
to_pd_series(prefix='')[source]
class bioarch.Tooth[source]

Bases: object

docstring for Tooth

abcess

‘NA’, ‘0’, ‘1’

calculus

‘NA’, ‘0’, ‘1’, ‘2’, ‘3’

cavities

‘NA’, ‘0’, ‘1’

eh

‘NA’, ‘0’, ‘1’

static empty()[source]
to_pd_series(prefix='')[source]
tooth

‘NA’, ‘0’, ‘1’, ‘A’, ‘B1’, ‘B2’, ‘C’, ‘D’, ‘E’, ‘F’, ‘G’, ‘H’, ‘I’

class bioarch.Sex[source]

Bases: enum.Enum

An enumeration.

FEMALE = 0
FEMALE_ASSUMED = 20
FEMALE_LIKELY = 10
MALE = 100
MALE_ASSUMED = 80
MALE_LIKELY = 90
UNKNOWN = 50
as_bin()[source]
dtype = <function Sex.dtype>[source]
parse = <function Sex.parse>[source]
class bioarch.Trauma(facial_bones: bioarch.trauma.TraumaCategory, clavicle: bioarch.left_right.LeftRight[bioarch.trauma.TraumaCategory][bioarch.trauma.TraumaCategory], scapula: bioarch.left_right.LeftRight[bioarch.trauma.TraumaCategory][bioarch.trauma.TraumaCategory], humerus: bioarch.left_right.LeftRight[bioarch.trauma.TraumaCategory][bioarch.trauma.TraumaCategory], ulna: bioarch.left_right.LeftRight[bioarch.trauma.TraumaCategory][bioarch.trauma.TraumaCategory], radius: bioarch.left_right.LeftRight[bioarch.trauma.TraumaCategory][bioarch.trauma.TraumaCategory], femur: bioarch.left_right.LeftRight[bioarch.trauma.TraumaCategory][bioarch.trauma.TraumaCategory], tibia: bioarch.left_right.LeftRight[bioarch.trauma.TraumaCategory][bioarch.trauma.TraumaCategory], fibula: bioarch.left_right.LeftRight[bioarch.trauma.TraumaCategory][bioarch.trauma.TraumaCategory], ribs: bioarch.trauma.TraumaCategory, vertabrae: bioarch.trauma.TraumaCategory)[source]

Bases: object

docstring for Trauma

static empty()[source]
to_pd_data_frame(index)[source]
class bioarch.TraumaCategory[source]

Bases: enum.Enum

An enumeration.

BLUNT_FORCE_TRAUMA = 6
BONY_GROWTH = 10
CRIBA = 5
FRACTURE = 3
FUSED = 11
INFECTION = 2
NORMAL = 1
NOT_PRESENT = -1
OSTEOCHONDRITIS_DESSICANS = 12
PARTIAL_BONE = 0.5
SHARP_FORCE_TRAUMA = 7
TREPONATION = 8
UNFUSED = 9
UNHEALED_FRACTURE = 4
avg = <function TraumaCategory.avg>[source]
dtype = <function TraumaCategory.dtype>[source]
parse = <function TraumaCategory.parse>[source]