A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

a - Variable in class sir.util.Unit
Initial number of infected
accept - Variable in class sir.model.EpiState
Acceptance counts for all traditional parameters
acceptProposal(double, double) - Method in class sir.model.EpiState
Based on acceptance probability we find out whether to accept a sample i.e. we accept it with probability min( f(x'|)pi(x') / f(x|)pi(x), 1)
accepted - Variable in class sir.util.Event
Acceptance number, to be used when updating by MCMC
addEscapes(String) - Static method in class sir.estimate.TokenMgrError
Replaces unprintable characters by their espaced (or unicode escaped) equivalents in the given string
addExtraEventsHook(int) - Method in class sir.model.SEIRState
Hook function to add additional events to the events array.
addExtraEventsHook(int) - Method in class sir.model.SEIRwDState
Hook function to add additional events to the events array.
add_escapes(String) - Method in class sir.estimate.ParseException
Used to convert raw characters to their escaped version when these raw version cannot be used as part of an ASCII string literal.
adjustBeginLineColumn(int, int) - Method in class sir.estimate.SimpleCharStream
Method to adjust line and column numbers for the start of a token.
analLog(String) - Method in class sir.model.EpiState
Method to present mean and variance of posterior for each variable contained in the logfile.
areNeighbours(int, int, int, int) - Method in class sir.sim.SimSellke
Determine whether two units are neighbours or not in N_4
array2Params(double[], boolean) - Method in class sir.model.SEIRState
Helper function, given an array of size noOfModelParams assign the values of this vector to the correct names.
array2Params(double[], boolean) - Method in class sir.model.SEIRwDState
Helper function, given an array of size noOfModelParams assign the values of this vector to the correct names.

B

BOOLEAN - Static variable in interface sir.estimate.OptionsFileSpecConstants
 
BeginToken() - Method in class sir.estimate.SimpleCharStream
 
Beta() - Method in class sir.estimate.DataFileSpec
 
BetaN() - Method in class sir.estimate.DataFileSpec
 
Blas_f77 - class sir.optim.Blas_f77.
This class contains Java versions of a number of the LINPACK basic linear algebra subroutines (blas): isamax_f77 daxpy_f77 ddot_f77 dscal_f77 dswap_f77 dnrm2_f77 dcopy_f77 drotg_f77 It also contains utility routines that the translator found useful while translating the FORTRAN code to Java code.
Blas_f77() - Constructor for class sir.optim.Blas_f77
 
BurninProxyListener - class sir.util.BurninProxyListener.
This object serves as a proxy MCMCListener that discards the first burnin events but then truthfully forwards to its subscribers
BurninProxyListener() - Constructor for class sir.util.BurninProxyListener
 
BurninProxyListener(int) - Constructor for class sir.util.BurninProxyListener
 
BurninProxyListener.MyHandle - class sir.util.BurninProxyListener.MyHandle.
 
BurninProxyListener.MyHandle() - Constructor for class sir.util.BurninProxyListener.MyHandle
 
backup(int) - Method in class sir.estimate.SimpleCharStream
 
bakslv_f77(int, double[][], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The bakslv_f77 method solves Ax = b where A is an upper triangular matrix.
beginColumn - Variable in class sir.estimate.Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
beginLine - Variable in class sir.estimate.Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
beta - Variable in class sir.model.EpiState
Infection pressure aka. transmission parameter
betaHaz(Unit, Unit, Event[][]) - Method in class sir.model.SEIRState
Method to compute \lambda_e^j (t-) when the origin of the event is known.
betaHazAll(Unit, Event[][]) - Method in class sir.model.SEIRState
Method to compute \lambda_{all}^j(t-|...) for a specific individual (located in u_j).
betaN - Variable in class sir.model.EpiState
Vaccination effect
betaN_ - Variable in class sir.model.EpiState
 
betaN_ - Static variable in class sir.sim.Score
 
betaN_ - Static variable in class sir.sim.SimSellke
 
betaSurvLn(Unit, double) - Method in class sir.model.SEIRState
Compute log S_j(t), i.e. the survival of an individual located in unit u up to time t, when overall hazard exerted on the individual is \lambda_j(t).
beta_ - Variable in class sir.model.EpiState
 
beta_ - Static variable in class sir.sim.Score
 
beta_ - Static variable in class sir.sim.SimSellke
 
bufpos - Variable in class sir.estimate.SimpleCharStream
 
burninNumber - Variable in class sir.util.BurninProxyListener
 

C

CENSORED - Static variable in interface sir.estimate.DataFileSpecConstants
 
CONSTANT - Static variable in interface sir.estimate.DataFileSpecConstants
 
CONSTANT - Static variable in interface sir.estimate.OptionsFileSpecConstants
 
CeaseTime() - Method in class sir.estimate.DataFileSpec
In case there is any information about it being a transmission experiment
censorTime - Variable in class sir.util.Event
In case an event is censored save the observed time, i.e. censoring time
chlhsn_f77(int, double[][], double, double[], double[]) - Static method in class sir.optim.Uncmin_f77
The chlhsn_f77 method finds "THE L(L-TRANSPOSE) [WRITTEN LL+] DECOMPOSITION OF THE PERTURBED MODEL HESSIAN MATRIX A+MU*I(WHERE MU\0 AND I IS THE IDENTITY MATRIX) WHICH IS SAFELY POSITIVE DEFINITE.
choldc_f77(int, double[][], double, double, double[]) - Static method in class sir.optim.Uncmin_f77
The choldc_f77 method finds "THE PERTURBED L(L-TRANSPOSE) [WRITTEN LL+] DECOMPOSITION OF A+D, WHERE D IS A NON-NEGATIVE DIAGONAL MATRIX ADDED TO A IF NECESSARY TO ALLOW THE CHOLESKY DECOMPOSITION TO CONTINUE."
clone() - Method in class sir.model.SEIRwDState
Clone.
clone() - Method in class sir.util.Event
Clone an event - note array instances are new'ed so the direct mem references are not exactly as before
cloneExposed(double) - Method in class sir.util.Event
Make an exact copy of the event, but change the event to type 'E' and subtract a constant from time.
colaxpy_f77(int, double, double[][], int, int, int) - Static method in class sir.optim.Blas_f77
This method multiplies a constant times a portion of a column of a matrix and adds the product to the corresponding portion of another column of the matrix --- a portion of col2 is replaced by the corresponding portion of a*col1 + col2.
coldot_f77(int, double[][], int, int, int) - Static method in class sir.optim.Blas_f77
This method calculates the dot product of portions of two columns of a matrix.
colisamax_f77(int, double[][], int, int, int) - Static method in class sir.optim.Blas_f77
This method finds the index of the element of a portion of a column of a matrix that has the maximum absolute value.
colnrm2_f77(int, double[][], int, int) - Static method in class sir.optim.Blas_f77
This method calculates the Euclidean norm of a portion of a column of a matrix.
colrot_f77(int, double[][], int, int, double, double) - Static method in class sir.optim.Blas_f77
This method "applies a plane rotation."
colscal_f77(int, double, double[][], int, int) - Static method in class sir.optim.Blas_f77
This method scales a portion of a column of a matrix by a constant.
colswap_f77(int, double[][], int, int) - Static method in class sir.optim.Blas_f77
This method interchanges two columns of a matrix.
colvaxpy_f77(int, double, double[][], double[], int, int) - Static method in class sir.optim.Blas_f77
This method multiplies a constant times a portion of a column of a matrix x[ ][ ] and adds the product to the corresponding portion of a vector y[ ] --- a portion of y[ ] is replaced by the corresponding portion of ax[ ][j] + y[ ].
colvdot_f77(int, double[][], double[], int, int) - Static method in class sir.optim.Blas_f77
This method calculates the dot product of a portion of a column of a matrix and the corresponding portion of a vector.
colvraxpy_f77(int, double, double[], double[][], int, int) - Static method in class sir.optim.Blas_f77
This method multiplies a constant times a portion of a vector y[ ] and adds the product to the corresponding portion of a column of a matrix x[ ][ ] --- a portion of column j of x[ ][ ] is replaced by the corresponding portion of ay[ ] + x[ ][j].
compare(Object, Object) - Method in class sir.util.Event
Comparing based on event time.
compareTo(Object) - Method in class sir.sim.SimSellke.Event
Comparing based on the event time
compareTo(Object) - Method in class sir.sim.SimSellke.Individual
Comparing based on the individuals threshold
curChar - Variable in class sir.estimate.DataFileSpecTokenManager
 
curChar - Variable in class sir.estimate.OptionsFileSpecTokenManager
 
currentToken - Variable in class sir.estimate.ParseException
This is the last token that has been consumed successfully.

D

D - Variable in class sir.model.SEIRwDState
All seroconversion events
D - Variable in class sir.util.Data
Diagnostic Events
DEBUG - Static variable in class sir.estimate.LadyBug
Debugging flag - gives extra printed info
DEFAULT - Static variable in interface sir.estimate.DataFileSpecConstants
 
DEFAULT - Static variable in interface sir.estimate.OptionsFileSpecConstants
 
DIC4(String, PrintStream, int, int, int) - Method in class sir.sim.Score
Compute Deviance Information criterion for the model.
DIC5(String, PrintStream) - Method in class sir.sim.Score
Compute Deviance Information criterion for the model.
DIGIT - Static variable in interface sir.estimate.DataFileSpecConstants
 
DIGIT - Static variable in interface sir.estimate.OptionsFileSpecConstants
 
Data - class sir.util.Data.
Title: LadyBug 2.0 Description: This is Object handles the data reading (i.e. the .data) files.
Data() - Constructor for class sir.util.Data
 
DataFile() - Method in class sir.estimate.DataFileSpec
 
DataFileSpec - class sir.estimate.DataFileSpec.
Used to have plenty of classes here, but for now DataileSpec is all we need It is a JavaCC encoding of the grammar specifying recovery and infection times for each individual individual with such recordings.
DataFileSpec(InputStream) - Constructor for class sir.estimate.DataFileSpec
 
DataFileSpec(Reader) - Constructor for class sir.estimate.DataFileSpec
 
DataFileSpec(DataFileSpecTokenManager) - Constructor for class sir.estimate.DataFileSpec
 
DataFileSpecConstants - interface sir.estimate.DataFileSpecConstants.
 
DataFileSpecTokenManager - class sir.estimate.DataFileSpecTokenManager.
 
DataFileSpecTokenManager(SimpleCharStream) - Constructor for class sir.estimate.DataFileSpecTokenManager
 
DataFileSpecTokenManager(SimpleCharStream, int) - Constructor for class sir.estimate.DataFileSpecTokenManager
 
Diag() - Method in class sir.estimate.DataFileSpec
 
DiagEventTime() - Method in class sir.estimate.DataFileSpec
Diagnosed events can be censored
DiagTimePDF() - Method in class sir.estimate.OptionsFileSpec
Distribution of the seroconversion period, Gamma or Exponential
Distributions - class sir.util.Distributions.
Class extending the set of distributions.
Distributions(PRNG) - Constructor for class sir.util.Distributions
Constructor
Done() - Method in class sir.estimate.SimpleCharStream
 
data - Variable in class sir.estimate.LadyBug
New version - all data related variables are gathered in a Data object
data - Static variable in class sir.model.EpiState
Static link to the data.
data - Static variable in class sir.sim.Score
Data object storing the information read form the .data file
data - Static variable in class sir.sim.SimSellke
Data object storing the information read form the .data file
data - Variable in class sir.util.Unit
Link to data object so it knows a bit about where it is located
daxpy_f77(int, double, double[], int, double[], int) - Static method in class sir.optim.Blas_f77
This method multiplies a constant times a vector and adds the product to another vector --- dy[ ] = da*dx[ ] + dy[ ].
dcopy_f77(int, double[], int, double[], int) - Static method in class sir.optim.Blas_f77
This method copies the vector dx[ ] to the vector dy[ ].
dcopyp_f77(int, double[], double[], int) - Static method in class sir.optim.Blas_f77
This method copies a portion of vector x[ ] to the corresponding portion of vector y[ ].
ddot_f77(int, double[], int, double[], int) - Static method in class sir.optim.Blas_f77
This method calculates the dot product of two vectors.
debugStream - Variable in class sir.estimate.DataFileSpecTokenManager
 
debugStream - Variable in class sir.estimate.OptionsFileSpecTokenManager
 
deltaD - Variable in class sir.model.SEIRwDState
Parameters of the gamma distributed seroconversion time
deltaD_ - Variable in class sir.model.SEIRwDState
Indices in param array
deltaD_ - Static variable in class sir.sim.Score
 
deltaD_ - Static variable in class sir.sim.SimSellke
 
deltaE - Variable in class sir.model.SEIRState
Parameters of the gamma distributed incbuation time
deltaE_ - Variable in class sir.model.SEIRState
Index of inc time parameters in param vector
deltaE_ - Static variable in class sir.sim.Score
 
deltaE_ - Static variable in class sir.sim.SimSellke
 
deltaI - Variable in class sir.model.SEIRState
Parameters of the gamma distributed infectious time
deltaI_ - Variable in class sir.model.SEIRState
Index of inc time parameters in param vector
deltaI_ - Static variable in class sir.sim.Score
 
deltaI_ - Static variable in class sir.sim.SimSellke
 
dfault_f77(int, double[], double[], double[], int[], int[], int[], int[], int[], int[], int[], double[], double[], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The dfault_f77 method sets default values for each input variable to the minimization algorithm.
diagTime - Static variable in class sir.estimate.Options
Distribution of the Seroconversion period: 'E'=exponential, 'G'=gamma, 'N'=none (ignore)
disable_tracing() - Method in class sir.estimate.DataFileSpec
 
disable_tracing() - Method in class sir.estimate.OptionsFileSpec
 
dnrm2_f77(int, double[], int) - Static method in class sir.optim.Blas_f77
This method calculates the Euclidean norm of the vector stored in dx[ ] with storage increment incx.
dnrm2p_f77(int, double[], int) - Static method in class sir.optim.Blas_f77
This method calculates the Euclidean norm of a portion of a vector x[ ].
doString(Object) - Method in class sir.util.MyStrippedListenerWriter
 
dogdrv_f77(int, double[], double[], double[], double[][], double[], double[], double[], Uncmin_methods, double[], double[], double[], double[], int[], boolean[], double[], double[], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The dogdrv_f77 method finds the next Newton iterate (xpls) by the double dogleg method.
dogstp_f77(int, double[], double[][], double[], double[], double, double[], boolean[], boolean[], double[], double[], double[], double[], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The dogstp_f77 method finds the new step by the double dogleg appproach.
drotg_f77(double[]) - Static method in class sir.optim.Blas_f77
This method constructs a Givens plane rotation.
dscal_f77(int, double, double[], int) - Static method in class sir.optim.Blas_f77
This method scales a vector by a constant.
dscalp_f77(int, double, double[], int) - Static method in class sir.optim.Blas_f77
This method scales a portion of a vector by a constant.
dswap_f77(int, double[], int, double[], int) - Static method in class sir.optim.Blas_f77
This method interchanges two vectors.

E

E - Variable in class sir.model.SEIRState
All the exposed states
E - Variable in class sir.util.Data
Exposure times
E0Fixed - Static variable in class sir.estimate.LadyBug
Configuration settings
E1 - Variable in class sir.util.Data
Exposure of first exposed
EOF - Static variable in interface sir.estimate.DataFileSpecConstants
 
EOF - Static variable in interface sir.estimate.OptionsFileSpecConstants
 
EOL - Static variable in interface sir.estimate.DataFileSpecConstants
 
Eaccept - Static variable in class sir.model.SEIRState
 
Eloc() - Method in class sir.model.SEIRState
Count the number of exposures originating from the unit itself.
Enbr() - Method in class sir.model.SEIRState
Count the number of exposures originating from a neighbour.
EpiState - class sir.model.EpiState.
The EpiState is an abstract base class implementing common features of the epidemic model.
EpiState() - Constructor for class sir.model.EpiState
Constructor - initializes structures holding who is parameter and who is fixed among the recovery and infection events.
Event - class sir.util.Event.
Title: SIREstimate Description: Estimation of SIR parameters Copyright: Copyright (c) 2002 Company:
Event(Unit, double[], char) - Constructor for class sir.util.Event
Basic constructor transfering values into the object.
Event(Unit, double[], char, boolean) - Constructor for class sir.util.Event
Constructor with censoring
Event() - Constructor for class sir.util.Event
Empty constructor if we ever need it.
EventTime() - Method in class sir.estimate.DataFileSpec
Event time - either a double or NA with start value We throw on stack in top: startValue, top-1: t
enable_tracing() - Method in class sir.estimate.DataFileSpec
 
enable_tracing() - Method in class sir.estimate.OptionsFileSpec
 
endColumn - Variable in class sir.estimate.Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
endLine - Variable in class sir.estimate.Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
eol - Variable in class sir.estimate.ParseException
The end of line string for this machine.
eta - Variable in class sir.model.EpiState
Neighbour effect
expInfTime - Static variable in class sir.estimate.Options
Is the infectious period exponentially distributed?
expTransformParams - Variable in class sir.model.SEIRState
Are we operating with log transformed parameters in the loglik function.
expectedTokenSequences - Variable in class sir.estimate.ParseException
Each entry in this array is an array of integers.
extraNoOfEventsHook() - Method in class sir.model.SEIRState
Hook function returning how many additional events are put into the events array by subclasses etc.
extraNoOfEventsHook() - Method in class sir.model.SEIRwDState
Hook function returning how many additional events are put into the events array by subclasses etc.
extractLocalTau() - Method in class sir.util.Data
Extract local recovery times for each unit and deduce the number of individuals escaping infection in all units.

F

FLOAT - Static variable in interface sir.estimate.DataFileSpecConstants
 
FLOAT - Static variable in interface sir.estimate.OptionsFileSpecConstants
 
f_to_minimize(double[]) - Method in class sir.model.SEIRState
In case the object is given to a numerical minimizer, this is the function to minimize.
f_to_minimize(double[]) - Method in interface sir.optim.Uncmin_methods
 
f_to_minimizeHook(double[]) - Method in class sir.model.SEIRState
Hook function to move additional parameters in numerical optimizer.
fetchLocalRec(Event[], int) - Method in class sir.util.Unit
Fetch link to all recovery events associated to this unit and once this is found compute the number of individuals from section escaping infection.
finalSize(long[][], TreeSet[][]) - Method in class sir.sim.SimSellke
Show N* for each unit, i.e. number of initial susceptibles affected by the epidemic.
findEvent(char) - Method in class sir.sim.SimSellke.Individual
Return the eventType event for the individual.
firstEvent - Variable in class sir.util.Unit
First event occuring in the unit - usually a 'N' event at time of I_0
firstEventInUnits - Variable in class sir.model.SEIRState
First event in all units - a data structure updated each timegenXYFuncs is called.
firstInfectedUnit - Variable in class sir.util.Data
Pointer to the unit, where the first infection occurs (i.e. a=1)
fixedSeed - Static variable in class sir.estimate.Options
Are we using a random seed value or are we fixing the value to be able to get same results later on?
form - Static variable in class sir.estimate.LadyBug
For formatting of doubles to an output stream.
form - Static variable in class sir.sim.Score
For formatting of doubles to an output stream.
form - Static variable in class sir.sim.SimSellke
For formatting of doubles to an output stream.
forslv_f77(int, double[][], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The forslv_f77 method solves Ax = b where A is a lower triangular matrix.
fromString(String) - Method in class sir.model.EpiState
Take a line from a logfile and assign the parameters.
fstocd_f77(int, double[], Uncmin_methods, double[], double, double[]) - Static method in class sir.optim.Uncmin_f77
The fstocd_f77 method finds a central difference approximation to the gradient of the function to be minimized.
fstofd_f77(int, double[], Uncmin_methods, double[], double[][], double[], double, double[]) - Static method in class sir.optim.Uncmin_f77
This version of the fstofd_f77 method finds a finite difference approximation to the Hessian.
fstofd_f77(int, double[], Uncmin_methods, double[], double[], double[], double) - Static method in class sir.optim.Uncmin_f77
This version of the fstofd_f77 method finds first order finite difference approximations for gradients.

G

GetImage() - Method in class sir.estimate.SimpleCharStream
 
GetSuffix(int) - Method in class sir.estimate.SimpleCharStream
 
gammaCDF(double, double, double) - Method in class sir.util.Distributions
CDF i.e. probability function of a Ga(alpha,beta) distribution
gammaD - Variable in class sir.model.SEIRwDState
Parameters of the gamma distributed seroconversion time
gammaD_ - Variable in class sir.model.SEIRwDState
Indices in param array
gammaD_ - Static variable in class sir.sim.Score
 
gammaD_ - Static variable in class sir.sim.SimSellke
 
gammaDelta2MeanVar() - Method in class sir.model.SEIRwDState
The reverse of @see meanVar2GammaDelta, i.e. y=r(x)
gammaE - Variable in class sir.model.SEIRState
Parameters of the gamma distributed incbuation time
gammaE_ - Variable in class sir.model.SEIRState
Index of inc time parameters in param vector
gammaE_ - Static variable in class sir.sim.Score
 
gammaE_ - Static variable in class sir.sim.SimSellke
 
gammaI - Variable in class sir.model.SEIRState
Parameters of the gamma distributed infectious time
gammaI_ - Variable in class sir.model.SEIRState
Index of inc time parameters in param vector
gammaI_ - Static variable in class sir.sim.Score
 
gammaI_ - Static variable in class sir.sim.SimSellke
 
gammaPDF(double, double, double) - Method in class sir.util.Distributions
Find pdf value at X=x, when X~\Gamma(alpha,beta), i.e.
gammaQuantile(double, double, double) - Method in class sir.util.Distributions
Quantile of a Ga(p,alpha,beta) distribution (i.e. inverse of CDF)
gammaRand(double, double) - Method in class sir.util.Distributions
Sample X ~ Gamma(alpha,beta) , s.t.
gammaSurv(double, double, double) - Method in class sir.util.Distributions
Survival function S(t) of the gamma distribution with parameters a and b
gammaTruncRand(double, double, double) - Method in class sir.util.Distributions
Sample a random number of a left truncated Ga(alpha,beta) distribution using inversion sampling.
genXYFuncs() - Method in class sir.model.EpiState
Generate X, Y as functions of time by bookeeping of events
genXYFuncs() - Method in class sir.model.SEIRState
Generate X, Y, XY, and time by sorting appropriate events.
generate(MCMCState) - Method in class sir.estimate.LadyBug
Generate the next state of the Markov Chain using Gibbs-within-Metropolis.
generateNext(boolean) - Method in class sir.model.EpiState
Generate method for MCMC chain
generateNext() - Method in class sir.model.EpiState
 
generateNext(boolean) - Method in class sir.model.SEIRState
Generate method for MCMC chain Modifcation happen on the instance itself to keep things simple.
generateParseException() - Method in class sir.estimate.DataFileSpec
 
generateParseException() - Method in class sir.estimate.OptionsFileSpec
 
getBeginColumn() - Method in class sir.estimate.SimpleCharStream
 
getBeginLine() - Method in class sir.estimate.SimpleCharStream
 
getBurninNumber() - Method in class sir.util.BurninProxyListener
 
getColumn() - Method in class sir.estimate.SimpleCharStream
Deprecated.  
getData() - Method in class sir.estimate.DataFileSpec
Deliver Data object with data read from file
getEndColumn() - Method in class sir.estimate.SimpleCharStream
 
getEndLine() - Method in class sir.estimate.SimpleCharStream
 
getLine() - Method in class sir.estimate.SimpleCharStream
Deprecated.  
getMessage() - Method in class sir.estimate.ParseException
This method has the standard behavior when this object has been created using the standard constructors.
getMessage() - Method in class sir.estimate.TokenMgrError
You can also modify the body of this method to customize your error messages.
getNextToken() - Method in class sir.estimate.DataFileSpec
 
getNextToken() - Method in class sir.estimate.DataFileSpecTokenManager
 
getNextToken() - Method in class sir.estimate.OptionsFileSpec
 
getNextToken() - Method in class sir.estimate.OptionsFileSpecTokenManager
 
getNoOfCensoredD() - Method in class sir.util.Data
Get the number of unknown diagnosed times by counting number of NA's in the data
getNoOfUnknownD() - Method in class sir.util.Data
Get the number of unknown diagnosed times by counting number of NA's in the data
getNoOfUnknownE() - Method in class sir.util.Data
Get the number of unknown exposure times by counting number of NA's in the data
getNoOfUnknownI() - Method in class sir.util.Data
Get the number of unknown infection times by counting number of NA's in the data
getNoOfUnknownR() - Method in class sir.util.Data
Get the number of unknown recovery times by counting number of NA's in the data
getPRNG() - Method in class sir.util.Distributions
Straight accessor function
getToken(int) - Method in class sir.estimate.DataFileSpec
 
getToken(int) - Method in class sir.estimate.OptionsFileSpec
 
getTotalEvents() - Method in class sir.util.BurninProxyListener
 
getUnknownDIndexes() - Method in class sir.util.Data
Find index of all unknown diagnoed time
getUnknownEIndexes() - Method in class sir.util.Data
Find index of all unknown exposure time
getUnknownIIndexes() - Method in class sir.util.Data
Find index of all unknown infection time
getUnknownRIndexes() - Method in class sir.util.Data
Find index of all unknown recovery times
gotI - Static variable in class sir.estimate.LadyBug
Do we have acces to I time
gradient(double[], double[]) - Method in class sir.model.SEIRState
Gradient function, in case one wants to do numeric optimization of the likelihood.
gradient(double[], double[]) - Method in interface sir.optim.Uncmin_methods
 
grdchk_f77(int, double[], Uncmin_methods, double[], double[], double[], double[], double[], double, double, double[]) - Static method in class sir.optim.Uncmin_f77
The grdchk_f77 method checks the analytic gradient supplied by the user.
gridXY2Index(int, int) - Method in class sir.sim.SimSellke
Function to convert (x,y) coordinate to an index Labelling is (1,1)=1, (2,1)=2

H

heschk_f77(int, double[], Uncmin_methods, double[], double[], double[][], double[], double[], double, double, int[], double[], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The heschk_f77 method checks the analytic Hessian supplied by the user.
hessian(double[], double[][]) - Method in class sir.model.SEIRState
Hessian function, in case one wants to do numeric optimization of the likelihood.
hessian(double[], double[][]) - Method in interface sir.optim.Uncmin_methods
 
hookdr_f77(int, double[], double[], double[], double[][], double[], double[], double[], double[], Uncmin_methods, double[], double[], double[], double[], int[], boolean[], double[], double[], double[], double[], double[], double[], double[], double, int[]) - Static method in class sir.optim.Uncmin_f77
The hookdr_f77 method finds a next Newton iterate (xpls) by the More-Hebdon technique.
hookst_f77(int, double[], double[][], double[], double[], double[], double, double[], double[], double[], double[], double[], boolean[], double[], boolean[], double[], double) - Static method in class sir.optim.Uncmin_f77
The hookst_f77 method finds a new step by the More-Hebdon algorithm.
hsnint_f77(int, double[][], double[], int[]) - Static method in class sir.optim.Uncmin_f77
The hsnint_f77 method provides the initial Hessian when secant updates are being used.

I

I - Variable in class sir.model.EpiState
Array of infection times, I1,...
I - Variable in class sir.util.Data
Infectious times
INTEGER - Static variable in interface sir.estimate.DataFileSpecConstants
 
INTEGER - Static variable in interface sir.estimate.OptionsFileSpecConstants
 
Incu() - Method in class sir.estimate.DataFileSpec
 
IncuTimePDF() - Method in class sir.estimate.OptionsFileSpec
Distribution of the incubation period, Constant, Gamma or Exponential
Inf() - Method in class sir.estimate.DataFileSpec
 
InfTimePDF() - Method in class sir.estimate.OptionsFileSpec
Distribution of the infectious period, Gamma or Exponential
ignoreD - Static variable in class sir.estimate.Options
Ignore any S specified, i.e. all D should be parametric?
ignoreE - Static variable in class sir.estimate.Options
Ignore any E specified, i.e. all E should be parametric?
ignoreI - Static variable in class sir.estimate.Options
Ignore any I specified, i.e. all I should be parametric?
image - Variable in class sir.estimate.Token
The string image of the token.
incu - Variable in class sir.util.Data
Length of incubatoin period
incuTime - Static variable in class sir.estimate.Options
Distribution type for incubation period
incubtime - Variable in class sir.sim.SimSellke.Individual
Individuals length of incubation period
index2GridX(int) - Method in class sir.sim.SimSellke
Function to convert index to a position in the grid.
index2GridX(int) - Method in class sir.util.Data
Function to convert index to a X position in the grid .
index2GridY(int) - Method in class sir.sim.SimSellke
Function to convert index to a position in the grid.
index2GridY(int) - Method in class sir.util.Data
Function to convert a index to a Y grid position Labelling is (1,1)=1, (2,1)=2
inflength - Variable in class sir.sim.SimSellke.Individual
Individuals infection length, if infected
inoculatedIndex - Variable in class sir.util.Data
Index of the inoculated individuals
isCensored - Variable in class sir.util.Event
Is the event censored.
isIValid() - Method in class sir.model.EpiState
Verify whether I is valid wrt. tau, i.e. that the constraints are fulfilled
isNeighbour(Unit) - Method in class sir.util.Unit
Determine whether a unit is a neighbour or not.
isOk() - Method in class sir.util.Data
Function to check that the data found in the data file is ok.
isParametric - Variable in class sir.util.Event
Is the event time parametric, i.e. unknown
isValidHook() - Method in class sir.model.EpiState
Hook function to be used by subclasses
isValidHook() - Method in class sir.model.SEIRState
Hook function to check for a valid state.
isValidHook() - Method in class sir.model.SEIRwDState
Hook function to check for a valid state.
isamax_f77(int, double[], int) - Static method in class sir.optim.Blas_f77
This method finds the index of the element of a vector that has the maximum absolute value.

J

jj_nt - Variable in class sir.estimate.DataFileSpec
 
jj_nt - Variable in class sir.estimate.OptionsFileSpec
 
jjstrLiteralImages - Static variable in class sir.estimate.DataFileSpecTokenManager
 
jjstrLiteralImages - Static variable in class sir.estimate.OptionsFileSpecTokenManager
 
justDiagnostic - Variable in class sir.model.SEIRState
Just a foobar thing - only use diagnostic times in the likelihood

K

kind - Variable in class sir.estimate.Token
An integer that describes the kind of this token.

L

LadyBug - class sir.estimate.LadyBug.
This class implements estimation of the parameters in a SIR epidemic.
LadyBug(PRNG, String) - Constructor for class sir.estimate.LadyBug
Constructor which calls all the necessary sub-routines, s.a. reading of data, registering of listeners and iteration of the MC.
lambda - Variable in class sir.util.Data
 
lastEventInUnits - Variable in class sir.model.SEIRState
Global variable to speed up the lastEventInit method so we do not need to new each time
lastEventInit(boolean) - Method in class sir.model.SEIRState
Prepare the last event data structure.
lastRecDiagTime() - Method in class sir.util.Data
Look in the data and find the last specified rec or diag time
lexStateNames - Static variable in class sir.estimate.DataFileSpecTokenManager
 
lexStateNames - Static variable in class sir.estimate.OptionsFileSpecTokenManager
 
listeners - Variable in class sir.util.BurninProxyListener
 
lltslv_f77(int, double[][], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The lltslv_f77 method solves Ax = b where A has the form L(L transpose) but only the lower triangular part, L, is stored.
lnsrch_f77(int, double[], double[], double[], double[], double[], double[], Uncmin_methods, boolean[], int[], double[], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The lnsrch_f77 method finds a next Newton iterate by line search.
loggammaPDF(double, double, double) - Method in class sir.util.Distributions
My own distribution function on log scale to make sure I got things right.
loglik - Variable in class sir.model.EpiState
LogLikelihood
loglik() - Method in class sir.model.EpiState
Abstract method to calculate the loglikelihood of the state
loglik() - Method in class sir.model.SEIRState
Just a dummy director to the currently used loglik function depending on the currently used parametrisation.
loglikAddIndividualHook(int) - Method in class sir.model.SEIRState
Hook function for adding additional events to the loglikelihood.
loglikAddIndividualHook(int) - Method in class sir.model.SEIRwDState
Hook function for adding additional events to the loglikelihood.
loglikGammaDelta() - Method in class sir.model.SEIRState
Abstract method to calculate the loglikelihood of the state.

M

MCMC() - Method in class sir.estimate.OptionsFileSpec
 
MCMCEst(int, int, int, String) - Method in class sir.estimate.LadyBug
MCMC Estimation method - generates noOfSamples*thinFactor + noOfBurnin samples and estimates beta and gamma based on recovery times alone.
ML(double[][]) - Method in class sir.model.SEIRState
Perform maximum likelihood estimation by numerically maximizing the likelihood equation.
MLEst() - Method in class sir.estimate.LadyBug
Calculate parameters beta and gamma using ML estimation.
MLParamsPrintHook(double[]) - Method in class sir.model.SEIRState
Hook function called inside ML once the results are showns
MLParamsSetup(double[], double[]) - Method in class sir.model.SEIRState
Function to be called when initializing the theta0 and typicalParamSize initialization in the ML method.
MLParamsSetup(double[], double[]) - Method in class sir.model.SEIRwDState
Hook function to be called when initializing the theta0 and typicalParamSize initialization in the ML method.
MLProfiles() - Method in class sir.model.SEIRState
Foo function to be specialized in SEIRWState
MLProfiles() - Method in class sir.model.SEIRwDState
Create Profile Plots of LogLikelihood around the max
MML() - Method in class sir.estimate.OptionsFileSpec
 
MeanVarianceParameters - Variable in class sir.model.SEIRState
Re-parameterization using mean and variance
Method() - Method in class sir.estimate.OptionsFileSpec
 
MethodType() - Method in class sir.estimate.OptionsFileSpec
 
MyStrippedListenerWriter - class sir.util.MyStrippedListenerWriter.
Slightly modified class to enable writing of header to the file
MyStrippedListenerWriter() - Constructor for class sir.util.MyStrippedListenerWriter
 
MyStrippedListenerWriter(String, boolean, boolean) - Constructor for class sir.util.MyStrippedListenerWriter
 
MyStrippedListenerWriter(String, boolean) - Constructor for class sir.util.MyStrippedListenerWriter
 
MyStrippedListenerWriter(String) - Constructor for class sir.util.MyStrippedListenerWriter
 
main(String[]) - Static method in class sir.estimate.DataFileSpec
 
main(String[]) - Static method in class sir.estimate.LadyBug
Main function - start a LadyBug analyserer based on prompt arguments
main(String[]) - Static method in class sir.estimate.OptionsFileSpec
Main class
main(String[]) - Static method in class sir.sim.Score
A sir sampler for command line calling.
main(String[]) - Static method in class sir.sim.SimSellke
A sir sampler for command line calling.
matmat_f77(double[][], double[][], double[][], int, int, int) - Static method in class sir.optim.Blas_f77
This method multiplies an n x p matrix by a p x r matrix.
mattran_f77(double[][], double[][], int, int) - Static method in class sir.optim.Blas_f77
This method obtains the transpose of an n x p matrix.
matvec_f77(double[][], double[], double[], int, int) - Static method in class sir.optim.Blas_f77
This method multiplies an n x p matrix by a p x 1 vector.
mcmc_ERWsigma - Static variable in class sir.estimate.Options
Std. dev of Gaussian proposal distribution for E
mcmc_IRWsigma - Static variable in class sir.estimate.Options
Std. dev of Gaussian proposal distribution for I
mcmc_RRWsigma - Static variable in class sir.estimate.Options
Std. dev of Gaussian proposal distribution for R
mcmc_betaNRWsigma - Static variable in class sir.estimate.Options
 
mcmc_betaRWsigma - Static variable in class sir.estimate.Options
Std. dev of proposal distribution (Gaussian) when suggesting new beta values in the Metropolis Hastings setting.
mcmc_burnin - Static variable in class sir.estimate.Options
Initial number of burnin samples to generate.
mcmc_deltaDRWsigma - Static variable in class sir.estimate.Options
Std. dev of Gaussian proposal distribution for deltaD
mcmc_deltaERWsigma - Static variable in class sir.estimate.Options
Std. dev of Gaussian proposal distribution for deltaE
mcmc_deltaIRWsigma - Static variable in class sir.estimate.Options
Std. dev of Gaussian proposal distribution for deltaI
mcmc_gammaDRWsigma - Static variable in class sir.estimate.Options
Std. dev of Gaussian proposal distribution for gammaD
mcmc_gammaERWsigma - Static variable in class sir.estimate.Options
Std. dev of Gaussian proposal distribution for gammaE
mcmc_gammaIRWsigma - Static variable in class sir.estimate.Options
Std. dev of Gaussian proposal distribution for gammaI
mcmc_samples - Static variable in class sir.estimate.Options
How many samples should the estimation be based on
mcmc_thin - Static variable in class sir.estimate.Options
When generating samples, we only take each thin'th sample - others are thrown away
meanVar - Static variable in class sir.estimate.Options
Should we use a mean/variance representation of all Gamma distribution?
meanVar2GammaDelta() - Method in class sir.model.SEIRwDState
Transform from mean,variance to gammaX,deltaX for all parameters, where this applies.
method - Static variable in class sir.estimate.Options
Which method did we actually pick?
metropolisBeta - Variable in class sir.estimate.LadyBug
Do we want the beta's to be updated using Metropolis sampling.
metropolisGamma - Variable in class sir.estimate.LadyBug
Do we want the gamma's to be updated using Metropolis, i.e.
mml_mcsamples - Static variable in class sir.estimate.Options
Number of samples to use in the Monte Carlo integration approximation of the marginal density
mml_samples - Static variable in class sir.estimate.Options
How many different samples of \bm{I} is the estimation based on.
mml_sumscale - Static variable in class sir.estimate.Options
Scale factor to use when adding the individual monte carlo samples.
mml_theta - Static variable in class sir.estimate.Options
Cut off value for sampling
mml_verboseOptimizer - Static variable in class sir.estimate.Options
Should the optimizer run silent or print extra information?
modelParamNames - Variable in class sir.model.EpiState
The names of all model parameters to be used when printing them
mvmltl_f77(int, double[][], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The mvmltl_f77 method computes y = Lx where L is a lower triangular matrix stored in A.
mvmlts_f77(int, double[][], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The mvmlts_f77 method computes y = Ax where A is a symmetric matrix stored in its lower triangular part.
mvmltu_f77(int, double[][], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The mvmltu_f77 method computes Y = (L transpose)X where L is a lower triangular matrix stored in A (L transpose is taken implicitly).

N

N - Variable in class sir.util.Unit
Initial number of susceptibles
N4 - Variable in class sir.util.Unit
 
N4() - Method in class sir.util.Unit
Return the compass direction neighbours
N4Star - Variable in class sir.util.Unit
Neighbours - precomputed so we don't need to calculate it every time
N4Star() - Method in class sir.util.Unit
Return set of all units belonging to N4Star
NA - Static variable in interface sir.estimate.DataFileSpecConstants
 
NA - Static variable in interface sir.estimate.OptionsFileSpecConstants
 
newSampler() - Static method in class sir.sim.Score
Method to initialize the sampler.
newSampler() - Static method in class sir.sim.SimSellke
Method to initialize the sampler.
newToken(int) - Static method in class sir.estimate.Token
Returns a new Token object, by default.
next - Variable in class sir.estimate.Token
A reference to the next regular (non-special) token from the input stream.
nextEventInSameUnit - Variable in class sir.util.Event
Link to the next event occured in same unit as this event
nextIndividualEvent - Variable in class sir.util.Event
Next event for same individual, i.e. for E it is I, for I it is R.
noOfAffected(long[][], TreeSet[][]) - Method in class sir.sim.SimSellke
Calculate, Z(t), the number of initial susceptibles affected by the epidemic (calced from current state).
noOfBeta - Variable in class sir.util.Data
 
noOfBetaN - Variable in class sir.util.Data
 
noOfIndividuals - Variable in class sir.util.Data
Number of affected individuals, i.e. number of individuals mentioned in the data file
noOfModelParams - Variable in class sir.model.EpiState
Number of model parameters, i.e. no of unknowns when we have full data
noOfUnits - Variable in class sir.util.Data
Various sorts of counters
noOfUnitsX - Variable in class sir.util.Data
Various sorts of counters
noOfUnitsY - Variable in class sir.util.Data
Various sorts of counters
nogen - Variable in class sir.model.EpiState
Boolean telling whether the time wise structure has been created on this object (inits events array)
notify(MCMCEvent) - Method in class sir.util.BurninProxyListener
Function to be called for notification
notify(MCMCEvent) - Method in class sir.util.MyStrippedListenerWriter
 
notifyAll(MCMCEvent) - Method in class sir.util.BurninProxyListener
 
nu - Variable in class sir.util.Data
 
nullUnit - Variable in class sir.util.Data
NullUnit, special void unit to use in case of switch and terminating events

O

Options - class sir.estimate.Options.
Title: Options object.
Options() - Constructor for class sir.estimate.Options
 
Options() - Method in class sir.estimate.OptionsFileSpec
 
OptionsFile() - Method in class sir.estimate.OptionsFileSpec
 
OptionsFileSpec - class sir.estimate.OptionsFileSpec.
Used to have plenty of classes here, but for now OptionsFileSpec is all we need It is a JavaCC encoding of the grammar specifying Recovery Time Files.
OptionsFileSpec(InputStream) - Constructor for class sir.estimate.OptionsFileSpec
 
OptionsFileSpec(Reader) - Constructor for class sir.estimate.OptionsFileSpec
 
OptionsFileSpec(OptionsFileSpecTokenManager) - Constructor for class sir.estimate.OptionsFileSpec
 
OptionsFileSpecConstants - interface sir.estimate.OptionsFileSpecConstants.
 
OptionsFileSpecTokenManager - class sir.estimate.OptionsFileSpecTokenManager.
 
OptionsFileSpecTokenManager(SimpleCharStream) - Constructor for class sir.estimate.OptionsFileSpecTokenManager
 
OptionsFileSpecTokenManager(SimpleCharStream, int) - Constructor for class sir.estimate.OptionsFileSpecTokenManager
 
optchk_f77(int, double[], double[], double[], double[], double[], int[], int[], double, double[], int[], int[], int[], int[], double[], int[]) - Static method in class sir.optim.Uncmin_f77
The optchk_f77 method checks the input for reasonableness.
optdrv_f77(int, double[], Uncmin_methods, double[], double[], int[], int[], int[], int[], int[], int[], int[], double[], double[], double[], double[], double[], double[], double[], int[], double[][], double[], double[], double[], double[], double[], double[], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The optdrv_f77 method is the driver for the nonlinear optimization problem.
optif0_f77(int, double[], Uncmin_methods, double[], double[], double[], int[], double[][], double[]) - Static method in class sir.optim.Uncmin_f77
The optif0_f77 method minimizes a smooth nonlinear function of n variables.
optif9_f77(int, double[], Uncmin_methods, double[], double[], int[], int[], int[], int[], int[], int[], int[], double[], double[], double[], double[], double[], double[], double[], int[], double[][], double[]) - Static method in class sir.optim.Uncmin_f77
The optif9_f77 method minimizes a smooth nonlinear function of n variables.
optstp_f77(int, double[], double[], double[], double[], int[], int[], int[], double[], double[], double[], double[], int[], int[], boolean[], int[]) - Static method in class sir.optim.Uncmin_f77
The optstp_f77 method determines whether the algorithm should terminate due to any of the following: 1) problem solved within user tolerance 2) convergence within user tolerance 3) iteration limit reached 4) divergence or too restrictive maximum step (stepmx) suspected Translated by Steve Verrill, May 12, 1998.
origin - Variable in class sir.util.Event
The unit, where the infection is originating from.

P

ParamStartValue(int) - Method in class sir.estimate.DataFileSpec
 
ParseException - exception sir.estimate.ParseException.
This exception is thrown when parse errors are encountered.
ParseException(Token, int[][], String[]) - Constructor for class sir.estimate.ParseException
This constructor is used by the method "generateParseException" in the generated parser.
ParseException() - Constructor for class sir.estimate.ParseException
The following constructors are for use by you for whatever purpose you can think of.
ParseException(String) - Constructor for class sir.estimate.ParseException
 
params2Array() - Method in class sir.model.EpiState
Helper functions to put all parameters in an array.
params2Array() - Method in class sir.model.SEIRState
Helper functions to put all named parameters in an array.
params2Array() - Method in class sir.model.SEIRwDState
Helper functions to put all parameters in an array.
periodsEV() - Method in class sir.model.SEIRState
Small stats function to compute mean and variance for inf or inc periods of current configuraion
postProcess() - Method in class sir.util.Data
Postprocess data, i.e. make data parametric if requested, setup units, check consistency, etc.
posx - Variable in class sir.util.Event
x position in grid of the unit (quick-access)
posx - Variable in class sir.util.Unit
X-position (i.e. row number) of unit in grid
posy - Variable in class sir.util.Event
y position in grid of the unit (quick-access)
posy - Variable in class sir.util.Unit
Y-position (i.e. column number) of unit in grid
prevEventInSameUnit - Variable in class sir.util.Event
Link to previous event occured in same unit as this event
print(String) - Method in class sir.util.MyStrippedListenerWriter
 
println(String) - Method in class sir.util.MyStrippedListenerWriter
 
prob - Static variable in class sir.estimate.LadyBug
The Pseudo random generator for distributions
prob - Static variable in class sir.model.EpiState
Static link to a random number generator
prob - Static variable in class sir.sim.Score
Distribution object allowing us to sample from various densities etc.
prob - Variable in class sir.util.Unit
Link to a random generator so we got one if we need it

Q

qraux1_f77(int, double[][], int) - Static method in class sir.optim.Uncmin_f77
The qraux1_f77 method interchanges rows i,i+1 of the upper Hessenberg matrix r, columns i to n.
qraux2_f77(int, double[][], int, double, double) - Static method in class sir.optim.Uncmin_f77
The qraux2_f77 method pre-multiplies r by the Jacobi rotation j(i,i+1,a,b).
qrupdt_f77(int, double[][], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The qrupdt_f77 method finds an orthogonal n by n matrix, Q*, and an upper triangular n by n matrix, R*, such that (Q*)(R*) = R+U(V+).

R

R - Variable in class sir.model.EpiState
Array of recovery times, R1,...
R - Variable in class sir.util.Data
Recovery times
ReInit(InputStream) - Method in class sir.estimate.DataFileSpec
 
ReInit(Reader) - Method in class sir.estimate.DataFileSpec
 
ReInit(DataFileSpecTokenManager) - Method in class sir.estimate.DataFileSpec
 
ReInit(SimpleCharStream) - Method in class sir.estimate.DataFileSpecTokenManager
 
ReInit(SimpleCharStream, int) - Method in class sir.estimate.DataFileSpecTokenManager
 
ReInit(InputStream) - Method in class sir.estimate.OptionsFileSpec
 
ReInit(Reader) - Method in class sir.estimate.OptionsFileSpec
 
ReInit(OptionsFileSpecTokenManager) - Method in class sir.estimate.OptionsFileSpec
 
ReInit(SimpleCharStream) - Method in class sir.estimate.OptionsFileSpecTokenManager
 
ReInit(SimpleCharStream, int) - Method in class sir.estimate.OptionsFileSpecTokenManager
 
ReInit(Reader, int, int, int) - Method in class sir.estimate.SimpleCharStream
 
ReInit(Reader, int, int) - Method in class sir.estimate.SimpleCharStream
 
ReInit(Reader) - Method in class sir.estimate.SimpleCharStream
 
ReInit(InputStream, int, int, int) - Method in class sir.estimate.SimpleCharStream
 
ReInit(InputStream) - Method in class sir.estimate.SimpleCharStream
 
ReInit(InputStream, int, int) - Method in class sir.estimate.SimpleCharStream
 
RecTimeList() - Method in class sir.estimate.DataFileSpec
Each individual having events is listed, one per line with format posx posy eventTime eventTime
randomN4Star() - Method in class sir.util.Unit
Sample a unit from N_4^*(u) uniformly
readChar() - Method in class sir.estimate.SimpleCharStream
 
readDataFile(String) - Method in class sir.estimate.LadyBug
Read information about the epidemic from the denoted files.
readDataFile(String) - Static method in class sir.sim.Score
Read the specification from the data file.
readDataFile(String) - Static method in class sir.sim.SimSellke
Read the specification from the data file.
readFromFile - Static variable in class sir.estimate.Options
 
rec - Variable in class sir.util.Unit
Link to all recovery events occuring in this unit
registerListener(MCMCListener) - Method in class sir.util.BurninProxyListener
 
resetTotalEvents() - Method in class sir.util.BurninProxyListener
 
result_f77(int, double[], double[], double[], double[][], double[], int[], int) - Static method in class sir.optim.Uncmin_f77
The result_f77 method prints information.
runs - Static variable in class sir.model.EpiState
Static stuff to keep track of progress

S

SEIRState - class sir.model.SEIRState.
Subclass implementing all functionality for an multivariate SEIR model.
SEIRState() - Constructor for class sir.model.SEIRState
Constructor - new necessary structures
SEIRwDState - class sir.model.SEIRwDState.
Subclass implementing all functionality for an multivariate SEIRwD model.
SEIRwDState() - Constructor for class sir.model.SEIRwDState
Constructor - new necessary structures
SIGNEDFLOAT - Static variable in interface sir.estimate.DataFileSpecConstants
 
SINGLE_LINE_COMMENT - Static variable in interface sir.estimate.DataFileSpecConstants
 
SINGLE_LINE_COMMENT - Static variable in interface sir.estimate.OptionsFileSpecConstants
 
STmembers - Variable in class sir.util.Unit
Number of individuals not affected by the epidemic at time T.
Score - class sir.sim.Score.
New sampler to handle Sellke constructions.
Score() - Constructor for class sir.sim.Score
 
SeedValue() - Method in class sir.estimate.OptionsFileSpec
Are we specifying a fixed seed value?
SimSellke - class sir.sim.SimSellke.
New sampler to handle Sellke constructions.
SimSellke(Distributions, String, PrintStream, String, boolean, boolean, double, boolean) - Constructor for class sir.sim.SimSellke
Constructor - setup the model parameters and initializes the necessary arrays.
SimSellke.Event - class sir.sim.SimSellke.Event.
A class to handle events
SimSellke.Event(SimSellke.Individual, double, char) - Constructor for class sir.sim.SimSellke.Event
Ordinary constructur
SimSellke.Individual - class sir.sim.SimSellke.Individual.
Class to handle each individual in the population.
SimSellke.Individual(int, int) - Constructor for class sir.sim.SimSellke.Individual
Constructor
SimpleCharStream - class sir.estimate.SimpleCharStream.
An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
SimpleCharStream(Reader, int, int, int) - Constructor for class sir.estimate.SimpleCharStream
 
SimpleCharStream(Reader, int, int) - Constructor for class sir.estimate.SimpleCharStream
 
SimpleCharStream(Reader) - Constructor for class sir.estimate.SimpleCharStream
 
SimpleCharStream(InputStream, int, int, int) - Constructor for class sir.estimate.SimpleCharStream
 
SimpleCharStream(InputStream, int, int) - Constructor for class sir.estimate.SimpleCharStream
 
SimpleCharStream(InputStream) - Constructor for class sir.estimate.SimpleCharStream
 
StartValue() - Method in class sir.estimate.DataFileSpec
Start valu of a time
SwitchTo(int) - Method in class sir.estimate.DataFileSpecTokenManager
 
SwitchTo(int) - Method in class sir.estimate.OptionsFileSpecTokenManager
 
sampleOrigins() - Method in class sir.model.SEIRState
Get origins right once we know E(t), I(t), R(t), i.e can't pick an origin where I(t) = 0.
sampleState(boolean) - Method in class sir.model.EpiState
Make a valid instance of the parameters, e.g. to start the MCMC chain with
sampleState(boolean) - Method in class sir.model.SEIRState
Make a valid instance of the parameters to start the MCMC chain with.
sampleStateEventsHook(int, boolean) - Method in class sir.model.SEIRState
Hook function to new any additional events in subclasses.
sampleStateEventsHook(int, boolean) - Method in class sir.model.SEIRwDState
Use hook function to new individual's diagnostic event in case of censoring.
sampleStateParamsHook() - Method in class sir.model.SEIRState
Hook function to initialize any additional parameters introduced in subclasses.
sampleStateParamsHook() - Method in class sir.model.SEIRwDState
Initializing gammaD and deltaD is done using this hook function.
sclmul_f77(int, double, double[], double[]) - Static method in class sir.optim.Uncmin_f77
The sclmul_f77 method multiplies a vector by a scalar.
secfac_f77(int, double[], double[], double[][], double[], double[], double, int[], double, int[], boolean[], double[], double[], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The secfac_f77 method updates the Hessian by the BFGS factored technique.
secunf_f77(int, double[], double[], double[][], double[], double[], double[], double, int[], double, int[], boolean[], double[], double[], double[]) - Static method in class sir.optim.Uncmin_f77
The secunf_f77 method updates the Hessian by the BFGS unfactored approach.
seed - Static variable in class sir.estimate.Options
Seed value for the random generator (if required)
serotime - Variable in class sir.sim.SimSellke.Individual
Time from exposure to seroconversion
setBurninNumber(int) - Method in class sir.util.BurninProxyListener
 
setData(Data) - Static method in class sir.model.EpiState
Set reference to the data
setDebugStream(PrintStream) - Method in class sir.estimate.DataFileSpecTokenManager
 
setDebugStream(PrintStream) - Method in class sir.estimate.OptionsFileSpecTokenManager
 
setLocalLinks(Data, Distributions) - Method in class sir.util.Unit
 
setPRNG(PRNG) - Method in class sir.util.Distributions
 
setProb(Distributions) - Static method in class sir.model.EpiState
 
setupUnitArrays(Vector) - Method in class sir.util.Data
Check, that all cells in the grid layout obtained from the units are specified Convert units vector to a 2D array, and setup up unit related parameters
showStats(String) - Method in class sir.model.EpiState
Show statistics once we are done.
showStats(int) - Method in class sir.model.SEIRState
 
sign_f77(double, double) - Static method in class sir.optim.Blas_f77
This method implements the FORTRAN sign (not sin) function.
sir.estimate - package sir.estimate
Contains the LadyBug program and all file I/O.
sir.model - package sir.model
Provides a class hierarchy for the epidemic models.
sir.optim - package sir.optim
Wraps the Fortran converted LINPACK optimizing function.
sir.sim - package sir.sim
Provides classes to simulate from multivariate SEIR models.
sir.util - package sir.util
Provides utility classes, e.g. the event, data, etc.
slowButSafe - Static variable in class sir.estimate.Options
Internal option
sndofd_f77(int, double[], Uncmin_methods, double[], double[][], double[], double, double[], double[]) - Static method in class sir.optim.Uncmin_f77
The sndofd_f77 method finds second order forward finite difference approximations to the Hessian.
specialConstructor - Variable in class sir.estimate.ParseException
This variable determines which constructor was used to create this object and thereby affects the semantics of the "getMessage" method (see below).
specialToken - Variable in class sir.estimate.Token
This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
startT - Variable in class sir.util.Event
Start value if unknown and we don't want to sample blindly we can provide a start value
startVal - Variable in class sir.util.Data
 
state(TreeSet[][], TreeSet[][], TreeSet[][], TreeSet[][]) - Method in class sir.sim.SimSellke
Show current X(t) and Y(t) for all units
staticFlag - Static variable in class sir.estimate.SimpleCharStream
 

T

T - Variable in class sir.util.Data
End of observation
Token - class sir.estimate.Token.
Describes the input token stream.
Token() - Constructor for class sir.estimate.Token
 
TokenMgrError - error sir.estimate.TokenMgrError.
 
TokenMgrError() - Constructor for class sir.estimate.TokenMgrError
 
TokenMgrError(String, int) - Constructor for class sir.estimate.TokenMgrError
 
TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for class sir.estimate.TokenMgrError
 
Ttime - Variable in class sir.util.Data
Time, where experiment has ceased.
t - Variable in class sir.util.Event
Time of event
theta - Variable in class sir.model.EpiState
Dual representation of params by array
threshold - Variable in class sir.sim.SimSellke.Individual
The individual's threshold before becoming exposed
toHeader() - Method in class sir.model.EpiState
What to write to the header of the log
toHeaderHook() - Method in class sir.model.EpiState
 
toHeaderHook() - Method in class sir.model.SEIRState
Hook function for header writing
toHeaderHook() - Method in class sir.model.SEIRwDState
Hook function for header writing
toString() - Method in class sir.estimate.Options
Standard DEBUG routine.
toString() - Method in class sir.estimate.Token
Returns the image.
toString() - Method in class sir.model.EpiState
Debug/Information as usual.
toString(double) - Method in class sir.sim.SimSellke.Event
Just show it on the screen, pos, time (corrected for origoTime) and type
toString() - Method in class sir.sim.SimSellke.Event
Standard toString nothing fancy here.
toString(double) - Method in class sir.sim.SimSellke.Individual
Method to write all event times of an individual to the log file
toString() - Method in class sir.util.Data
Usual debug method to display all on screen
toString() - Method in class sir.util.Event
For debug purposes
toString() - Method in class sir.util.Unit
Debug Method
toStringDiagnostic() - Method in class sir.model.SEIRState
Show how state params relate to data
toStringDiagnostic() - Method in class sir.model.SEIRwDState
Function to display how parameters relate to data.
toStringEvents() - Method in class sir.model.EpiState
Show X(t) and Y(t) as functions
toStringEvents2() - Method in class sir.model.SEIRwDState
This version shows only time of exposure and the length of the infectious time
toStringEvents3() - Method in class sir.model.SEIRwDState
Show all stats
toStringHook() - Method in class sir.model.EpiState
 
toStringHook() - Method in class sir.model.SEIRState
Hook function for SEIR specific output
toStringHook() - Method in class sir.model.SEIRwDState
Hook function calling the super before adding SEIRwD specifc things
toStringLong() - Method in class sir.model.EpiState
Current State information is shown on screen in long format
toStringLong() - Method in class sir.model.SEIRState
Current State information is shown on screen in long format
token - Variable in class sir.estimate.DataFileSpec
 
token - Variable in class sir.estimate.OptionsFileSpec
 
tokenImage - Static variable in interface sir.estimate.DataFileSpecConstants
 
tokenImage - Static variable in interface sir.estimate.OptionsFileSpecConstants
 
tokenImage - Variable in class sir.estimate.ParseException
This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
token_source - Variable in class sir.estimate.DataFileSpec
 
token_source - Variable in class sir.estimate.OptionsFileSpec
 
totalEvents - Variable in class sir.util.BurninProxyListener
 
tregup_f77(int, double[], double[], double[], double[][], Uncmin_methods, double[], double[], boolean[], double[], double[], double[], int[], double[], double[], double[], double[], boolean[], int, double[]) - Static method in class sir.optim.Uncmin_f77
The tregup_f77 method decides whether to accept xpls = x + sc as the next iterate and update the trust region dlt.
type - Variable in class sir.sim.SimSellke.Event
Event type
type - Variable in class sir.util.Event
Even type: S,E,I,R,T

U

Uncmin_f77 - class sir.optim.Uncmin_f77.
This class contains Java translations of the UNCMIN unconstrained optimization routines.
Uncmin_f77() - Constructor for class sir.optim.Uncmin_f77
 
Uncmin_methods - interface sir.optim.Uncmin_methods.
 
Unit() - Method in class sir.estimate.DataFileSpec
 
Unit - class sir.util.Unit.
Title: LadyBug Description: Estimation of SIR parameters Copyright: Copyright (c) 2002 Company:
Unit(int, int, int, int, boolean) - Constructor for class sir.util.Unit
Constructor
UnitList() - Method in class sir.estimate.DataFileSpec
 
uniformRand() - Method in class sir.util.Distributions
Overwrite the uniformRand method so we use the better PRNG!
unit - Variable in class sir.util.Event
Link to unit, corresponds to x,y position
units - Variable in class sir.util.Data
 
unregisterListener(MCMCListenerHandle) - Method in class sir.util.BurninProxyListener
 
updateBeta() - Method in class sir.model.SEIRState
Gibbs updating of beta - we know the full conditional (see paper) This version handles the multiple unit setup.
updateBetaN() - Method in class sir.model.SEIRState
Gibbs updating of betaN - we know the full conditional (see paper) This is a new version correcting an mistake of the conditioning on o_j.
updateD() - Method in class sir.model.SEIRwDState
Method to update the D.
updateDeltaD() - Method in class sir.model.SEIRwDState
Gibbs updating of deltaD - we know the full conditional (see paper)
updateDeltaE() - Method in class sir.model.SEIRState
Gibbs updating of deltaI - we know the full conditional (see paper)
updateDeltaI() - Method in class sir.model.SEIRState
Gibbs updating of deltaI - we know the full conditional (see paper)
updateE() - Method in class sir.model.SEIRState
Update E using full conditionals.
updateE() - Method in class sir.model.SEIRwDState
Update E using full conditionals.
updateEPropagate() - Method in class sir.model.SEIRwDState
Update E using full conditionals.
updateGammaD() - Method in class sir.model.SEIRwDState
Update gammaD using Metropolis Hastings.
updateGammaE() - Method in class sir.model.SEIRState
Update gammaE using Metropolis Hastings.
updateGammaI() - Method in class sir.model.SEIRState
Update gammaI using Metropolis Hastings.
updateHook(boolean) - Method in class sir.model.SEIRState
Hook method to update additional parameters using MCMC.
updateHook(boolean) - Method in class sir.model.SEIRwDState
Hook method to update additional parameters using MCMC, i.e. deltaD and gammaD
updateI() - Method in class sir.model.SEIRState
Update I using Metropolis Hastings.
updateMetroHastings(double[], int, double) - Method in class sir.model.SEIRState
Random Walk Metropolis-Hastings updating of a parameter with gamma prior distribution.
updateO() - Method in class sir.model.SEIRState
Update the o vector using Gibbs Sampling.
updateR() - Method in class sir.model.SEIRState
Update R using Metropolis Hastings.
useOrigins - Variable in class sir.model.SEIRState
Are we using exposure origins in the loglik calculations.

V

VERBOSE - Static variable in class sir.optim.Uncmin_f77
 
Vaccinated() - Method in class sir.estimate.DataFileSpec
 
vacc - Variable in class sir.util.Unit
Are animals in this unit vaccinated?

W

who - Variable in class sir.sim.SimSellke.Event
Location of the event, i.e. the individual
writeDataHeader(PrintStream) - Method in class sir.sim.SimSellke
Function writes the header of the .data file based on the current parameter values.
writeHeader(String) - Method in class sir.util.MyStrippedListenerWriter
Method to write the header of the log file, i.e. column names and stuff
writeLogFiles(String) - Method in class sir.sim.SimSellke
Write the corresponding events into the logfiles
writeResultHeader() - Method in class sir.sim.SimSellke
Stupid function to write header of final size results

X

X - Variable in class sir.util.Event
Number of susceptibles in unit posx,posy at time t
x - Variable in class sir.sim.SimSellke.Individual
Location of the individual

Y

Y - Variable in class sir.util.Event
Number of infected in unit posx,posy at time t
Yintegrate(Unit, double) - Method in class sir.model.EpiState
Calculate int_{i_0}^t Y_u(t) dt for a unit u and regime r.
y - Variable in class sir.sim.SimSellke.Individual
Location of the individual

Z

Z - Variable in class sir.util.Event
Number of exposed in unit posy,posy at time t

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