AML functions by module
**** Kernel functions *****
Abs
AllPos
Angle
Append
Arithmetic operators
Array
At
Boolean operators
Ceil
Comparison operators
Constants
Date operators
Delete
Display
DisplayAllNames
DisplayAllUserNames
Echo
EchoOn / EchoOff
EDist
Filter
Flatten
Floor
Foreach
Head
Identity
If-Then-Else
InsertAt
Inter
Invert
List
Mathematical functions
Max
Min
Mod
Norm
Plot, NewPlot
Pos
Prod
ProdSeries
RemoveAt
Rint
Save
Select
Series
Set
SetMinus
Size
Sort
SProd
SubArray
Sum
Switch
Tail
ToArray
ToInt
ToList
ToReal
ToSet
ToString
Trigonometric functions
Truncate
Union
VProd
**** MTG functions *****
Activate
Active
AlgHeight
AlgOrder
AlgRank
Alpha
Ancestors
Axis
Beta
BottomCoord
BottomDiameter
Class
ClassScale
Complex
ComponentRoots
Components
Coord
DateSample
Defined
Descendants
DressingData
EdgeType
Extremities
Father
Feature
FirstDefinedFeature
Height
Index
LastDefinedFeature
Length
Location
MatchingExtract
MTG
MTGRoot
NextDate
Order
Path
PDir
PlantFrame
Plot
Predecessor
PreviousDate
Rank
RelBottomCoord
RelTopCoord
Root
Scale
SDir
Sons
Successor
TopCoord
TopDiameter
TreeMatching
Trunk
VirtualPattern
VtxList
**** STAT functions *****
Cluster
Clustering
Compare (distributions)
Compare (vectors)
Compare (sequences)
Compare (Markovian models of sequences)
Compare (Markovian models)
ComparisonTest
Compound
ComputeCorrelation
ComputePartialAutoCorrelation
ComputeRankCorrelation
ComputeSelfTransition
ComputeStateSequences
ComputeWhiteNoiseAutoCorrelation
ContingencyTable
Convolution
Cumulate
Difference
Display
Distribution
Estimate (distributions)
Estimate (renewal process)
Estimate (Markovian models)
Estimate ('top' parameters)
ExtractData
ExtractDistribution
ExtractHistogram
ExtractVectors
Fit
HiddenMarkov
HiddenSemiMarkov
Histogram
IndexExtract
LengthSelect
Load
Markov
Merge
MergeVariable
Mixture
ModelSelectionTest
MovingAverage
NbEventSelect
Plot, NewPlot
RecurrenceTimeSequences
Regression
RemoveApicalInternodes
RemoveRun
Renewal
Reverse
Save
SegmentationExtract
SelectIndividual
SelectVariable
SemiMarkov
Sequences
Shift
Simulate (distributions)
Simulate (renewal process)
Simulate (Markovian models)
Simulate ('top' parameters)
Symmetrize
TimeEvents
TimeScaling
TimeSelect
ToDistribution
ToHistogram
TopParameters
Tops
Transcode
TransformPosition
ValueSelect
VariableScaling
VarianceAnalysis
VectorDistance
Vectors
Site Map
PART I AMAPmod
1
Introduction
2
Installation
2.1
Mininum system requirements
2.2
Getting the software
2.3
Test the executable
2.4
File access convention
3
AMAPmod: an overview
3.1
Introduction
3.2
AMAPmod system overview
3.2.1
Plant architecture databases
3.2.2
Coding individuals
3.2.3
Exploration: a simple example
3.2.4
The AMAPmod querying language: AML
3.2.5
Types of extracted data
3.2.6
Statsitical exploration and model building
3.3
Illustration
3.3.1
Biological context and data collection
3.3.2
3D visualisation of real plants
3.3.3
Extraction of data samples
3.3.4
Extraction and analysis of biological sequences
4
The AML language
4.1
Starting an AMAPmod session
4.2
AML
4.3
Data structures
4.3.1
Simple types
4.3.2
Array
4.3.3
Sets
4.3.4
Lists
4.4
Iterators
4.5
Functions
4.6
Comments
4.7
Access to shell commands
4.8
Input and Output
5
The MTG module
5.1
AML primitives related to MTGs
6
The STAT module
6.1
L'organisaion du module STAT
6.1.1
Application lois et combinaisons de lois
6.1.2
Application processus de renouvellement
6.1.3
Application modèle Markoviens
6.1.4
Application analyse des cimes
6.2
Les fonctions AML du module STAT
6.2.1
Les fonctions d'entrées/sorties
6.2.2
Les fonctiions de manipulation des données
6.2.3
Les fonctions algorithmiques
PART II REFERENCE MANUAL
1
The Kernel module of AML
1.1
Alphabetic list
1.2
Sort by type
2
The MTG module of AML
2.1
Alphabetic list
2.2
Sort by type
3
The STAT module of AML
3.1
Alphabetic list
3.2
Sort by categorie
3.4
Sort by type
4
File syntax
4.1
General conventions
4.2
MTGs
4.2.1
Coding files
4.2.2
Les fichiers de codages
4.2.3
Example of coding strategies in different classical situations
4.2
Dressing Files (.drf)
4.2.1
Definition of basis geometric models associated with plant components
4.2.2
Definition of virtual elements
4.2.3
Definition of defaults parameters
4.2.4
Example of dressing file
4.3
Curve Files (.crv)
4.5
Geom Files
4.5.1
Overview
4.5.1
File format syntax
4.5.1
Geoms format reference
4.6
Glance configuration file(.cfg)
4.7
STAT
4.7.1
type COMPOUND
4.7.2
type COMVOLUTION
4.7.3
type DISTRIBUTION, type RENEWAL
4.7.4
type HIDDEN_MARKOV
4.7.5
type HIDDEN_SEMI_MARKOV
4.7.6
type HISTOGRAM
4.7.7
type MARKOV
4.7.8
type MIXTURE
4.7.9
type SEMI_MARKOV
4.7.10
type SEQUENCES
4.7.11
type TIME_EVENTS
4.7.12
type TOPS
4.7.13
type TOPS_PARAMETERS
4.7.14
type VECTOR_DISTANCE
4.7.15
type VECTORS
Appendice A
File example
Appendice B
Bibliography
Appendice C
Copyright
Index