start of simpler rewrite
finished fitmodel, testFitmodel and example

fitmodel now has also a “theta.names” argument with parameter names.

several variable and function names have been changed using replace in
all files.
I will check that everything work as I go in different files.

fitmodel.r is clean and the example works.

the package almost passes the check, 2 warnings due to undocumented
functions.
fix typos in documentation of fitmodel
fix typo

replace gamma by nu for consistency with other functions
SEITL and SEIT2L constructor + inst/tests

note that incidence is now computed in the simulate function as it
makes more sense and simplify the coding of logLikePoint and
generateObservation
More consistent documentation
rename TdC dataset
rewrite functions for simplified fitmodel

all functions in files:
logLikelihood.r
smc.r
function to print named vectors

useful for warnings, message and stop
two tests

test simulation and likelihood computation for both SEITL and SEIT2L
and both deter and sto
mcmc rewrited with simplified fitmodel
minor edits

renamed targetPosterior as posteriorDensity
make faster tests by reducing length of data
minor edits

renamed SEITL_createModelTdC as SEIT2L_createFitmodel since TDC dataset
is not in fitmodel anymore
rename simulateTraj -> simulate
rename generateObservation -> generateObs
use more stable ode integrator
double brackets for likelihood calculation