- eqnfile
The (relative or full) path to the file that specifies the MPT
model (standard .eqn syntax). Note that category labels must start with a
letter (different to multiTree) and match the column names of data
.
Alternatively, the EQN-equations can be provided within R as a character
value (cf. readEQN
). Note that the first line of an .eqn-file
is reserved for comments and always ignored.
- data
The (relative or full) path to the .csv file with the data (comma
separated; category labels in first row). Alternatively: a data frame or
matrix (rows=individuals, columns = individual category frequencies,
category labels as column names)
- restrictions
Specifies which parameters should be (a) constant (e.g.,
"a=b=.5"
) or (b) constrained to be identical (e.g., "Do=Dn"
)
or (c) treated as fixed effects (i.e., identical for all participants;
"a=b=FE"
). Either given as the path to a text file with restrictions
per row or as a list of restrictions, e.g., list("D1=D2","g=0.5")
.
Note that numbers in .eqn-equations (e.g., d*(1-g)*.50
) are directly
interpreted as equality constraints.
- covData
Data that contains covariates, for which correlations with
individual MPT parameters will be sampled. Either the path to a .csv file
(comma-separated: rows=individuals in the same order as data
; first
row must contain covariate labels). Alternatively: a data frame or matrix
(rows=individuals, columns = variables; covariate labels as column names).
Note that in betaMPT
, correlations are computed for discrete
variables that are coded numerically (in traitMPT
, this can be
suppressed by using predType="f"
)
- corProbit
whether to use probit-transformed MPT parameters to compute
correlations (probit-values of +Inf
are truncated to
max(5,max(probit))
; similarly for -Inf
). Default for
beta-MPT: MPT parameters are used on the probability scale [0,1].
- n.iter
Number of iterations per chain (including burnin samples). See
run.jags
for details.
- n.burnin
Number of samples for burnin (samples will not be stored and
removed from n.iter)
- n.thin
Thinning rate.
- n.chains
number of MCMC chains (sampled in parallel).
- ppp
number of samples to compute posterior predictive p-value (see
posteriorPredictive
)
- shape
shape parameter(s) of Gamma-hyperdistribution for the
hierarchical beta-parameters \(\alpha_s\) and \(\beta_s\) (can be a
named vector to provide different hyperpriors for each parameter)
- rate
rate parameter(s) of Gamma-hyperdistribution
- parEstFile
Name of the file to with the estimates should be stored
(e.g., "parEstFile.txt")
- posteriorFile
path to RData-file where to save the model including
MCMC posterior samples (an object named fittedModel
; e.g.,
posteriorFile="mcmc.RData"
)
- cores
number of CPUs to be used