Index


a | c | d | e | g | h | i | l | m | n | o | p | r | s | w

A

Acknowledgments
ancestor loss coefficient

C

column delimiter
computational details
ancestral inbreeding
effective ancestor number
effective founder number
founder genome equivalents
computational details (continued)
generation coefficients
inbreeding and related measures
partial inbreeding
pedigree completeness
configuration file
configuration files

D

databases
new input sources
new output destinations
Dict4Ini
Disclaimer

E

environment variables
PATH
PYTHONPATH
example programs

G

GEDCOM files
GENES files
graphics
graphics (continued)
drawing line graphs
drawing pedigrees
visualizing relationship matrices

H

how do I
basic tasks
load a pedigree
load comma-delimited pedigree
load multiple pedigrees
load tab-delimited pedigree
renumber a pedigree
turn off output
calculate genetic variation
coefficients of inbreeding
contribute a HOWTO
databases and reports
load a pedigree
how do I (continued)
databases and reports (continued)
update pedigree table
miscellaneous
export NRM to a file
export NRM to Octave
load a GEDCOM pedigree
load a pedigree from a string
save to GEDCOM pedigree
pedigrees as graphs
graph to file
graph to pedigree
pedigree from graph file
pedigree to graph

I

ID mapping
input
databases
GEDCOM files
GENES files
graph objects
integrity checks
text files
text streams
installation
extensions
installation (continued)
installation from source
installation on Cygwin
installation on Linux
installation on Windows
environment variables
Python Enthought Edition
testing the installation
interacting with PyPedal
interactively
programmatically
internal reports

L

license
logging

M

measures of genetic variation

N

new features
contributing code
defining the problem
module template
function prototype
new features (continued)
module template (continued)
header
imports
solving the problem
numerator relationship matrix
decomposition
direct inverses

O

objects
options
list
output
databases
output (continued)
GEDCOM files
GENES files
graph objects
text files
text streams

P

PATH (environment variable)
pedigree files
pedigree format codes
list
pedigree simulation
pedsource, [Link], [Link]
program structure
PyGraphviz
pypedal (extension module)
PyPedal objects
AMatrix objects
Animal objects
LightAnimal
NewAnimal
SimAnimal
Metadata objects
Pedigree objects
PYTHONPATH (environment variable)

R

renumbering pedigrees
animal identification
reordering and renumbering
report generation
report generation (continued)
creating custom internal reports
creating custom printed reports
three generation pedigrees

S

savegedcom

W

working with pedigrees
inbreeding and relationships
working with pedigrees (continued)
matings
relatives
2
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