Run Bayesian Transmission MCMC

Usage

runMCMC(
  data,
  modelParameters,
  nsims,
  nburn = 100L,
  outputparam = TRUE,
  outputfinal = FALSE,
  verbose = FALSE
)

Arguments

data: Data frame with columns, in order: facility, unit, time, patient, and event type.
modelParameters: List of model parameters, see LogNormalModelParams().
nsims: Number of MCMC samples to collect after burn-in.
nburn: Number of burn-in iterations.
outputparam: Whether to output parameter values at each iteration.
outputfinal: Whether to output the final model state.
verbose: Print progress messages.

Value

A list with the following elements:

Parameters the MCMC chain of model parameters (if outputparam=TRUE)
LogLikelihood the log likelihood of the model at each iteration (if outputparam=TRUE)
MCMCParameters the MCMC parameters used
ModelParameters the model parameters used
ModelName the name of the model
nstates the number of states in the model
waic1 the WAIC1 estimate
waic2 the WAIC2 estimate
and optionally (if outputfinal=TRUE) FinalModel the final model state.

Examples

  # Minimal example: create parameters and run a very short MCMC
  params <- LinearAbxModel(nstates = 2)
  data(simulated.data_sorted, package = "bayestransmission")
  results <- runMCMC(
    data = simulated.data_sorted,
    modelParameters = params,
    nsims = 3,
    nburn = 0,
    outputparam = TRUE,
    outputfinal = FALSE,
    verbose = FALSE
  )
  str(results)
#> List of 6
#>  $ Parameters     :List of 3
#>   ..$ :List of 6
#>   .. ..$ Insitu          : Named num [1:2] 0.99593 0.00407
#>   .. .. ..- attr(*, "names")= chr [1:2] "Insit.P(unc)" "Insit.P(col)"
#>   .. ..$ SurveillanceTest: Named num [1:4] 1.00e-10 2.26e-01 1.00e-10 1.00
#>   .. .. ..- attr(*, "names")= chr [1:4] "ATest.P(+|unc-)" "ATest.P(+|col-)" "ATest.P(+|unc+)" "ATest.P(+|col+)"
#>   .. ..$ ClinicalTest    : Named num [1:4] 0.5 0.5 1 1
#>   .. .. ..- attr(*, "names")= chr [1:4] "RTest.P(+|unc)" "RTest.P(+|col)" "RTest.rateUnc" "RTest.rateCol"
#>   .. ..$ OutCol          : Named num [1:2] 0.05 0.01
#>   .. .. ..- attr(*, "names")= chr [1:2] "Out.acq" "Out.clr"
#>   .. ..$ InCol           : Named num [1:10] 0.000892 1 1 1 1 ...
#>   .. .. ..- attr(*, "names")= chr [1:10] "LABX.base" "LABX.time" "LABX.mass.mx" "LABX.freq.mx" ...
#>   .. ..$ Abx             : Named num [1:2] 1 1
#>   .. .. ..- attr(*, "names")= chr [1:2] "Abx.rateUnc" "Abx.rateCol"
#>   ..$ :List of 6
#>   .. ..$ Insitu          : Named num [1:2] 0.99896 0.00104
#>   .. .. ..- attr(*, "names")= chr [1:2] "Insit.P(unc)" "Insit.P(col)"
#>   .. ..$ SurveillanceTest: Named num [1:4] 1.00e-10 2.39e-01 1.00e-10 7.39e-01
#>   .. .. ..- attr(*, "names")= chr [1:4] "ATest.P(+|unc-)" "ATest.P(+|col-)" "ATest.P(+|unc+)" "ATest.P(+|col+)"
#>   .. ..$ ClinicalTest    : Named num [1:4] 0.5 0.5 1 1
#>   .. .. ..- attr(*, "names")= chr [1:4] "RTest.P(+|unc)" "RTest.P(+|col)" "RTest.rateUnc" "RTest.rateCol"
#>   .. ..$ OutCol          : Named num [1:2] 0.00705 0.00723
#>   .. .. ..- attr(*, "names")= chr [1:2] "Out.acq" "Out.clr"
#>   .. ..$ InCol           : Named num [1:10] 0.000907 1 1 1 1 ...
#>   .. .. ..- attr(*, "names")= chr [1:10] "LABX.base" "LABX.time" "LABX.mass.mx" "LABX.freq.mx" ...
#>   .. ..$ Abx             : Named num [1:2] 1 1
#>   .. .. ..- attr(*, "names")= chr [1:2] "Abx.rateUnc" "Abx.rateCol"
#>   ..$ :List of 6
#>   .. ..$ Insitu          : Named num [1:2] 0.668 0.332
#>   .. .. ..- attr(*, "names")= chr [1:2] "Insit.P(unc)" "Insit.P(col)"
#>   .. ..$ SurveillanceTest: Named num [1:4] 1.00e-10 3.83e-01 1.00e-10 6.71e-01
#>   .. .. ..- attr(*, "names")= chr [1:4] "ATest.P(+|unc-)" "ATest.P(+|col-)" "ATest.P(+|unc+)" "ATest.P(+|col+)"
#>   .. ..$ ClinicalTest    : Named num [1:4] 0.5 0.5 1 1
#>   .. .. ..- attr(*, "names")= chr [1:4] "RTest.P(+|unc)" "RTest.P(+|col)" "RTest.rateUnc" "RTest.rateCol"
#>   .. ..$ OutCol          : Named num [1:2] 0.00705 0.00723
#>   .. .. ..- attr(*, "names")= chr [1:2] "Out.acq" "Out.clr"
#>   .. ..$ InCol           : Named num [1:10] 0.000909 1 1 1 1 ...
#>   .. .. ..- attr(*, "names")= chr [1:10] "LABX.base" "LABX.time" "LABX.mass.mx" "LABX.freq.mx" ...
#>   .. ..$ Abx             : Named num [1:2] 1 1
#>   .. .. ..- attr(*, "names")= chr [1:2] "Abx.rateUnc" "Abx.rateCol"
#>  $ LogLikelihood  : num [1:3] -16088 -15270 -14472
#>  $ MCMCParameters :List of 4
#>   ..$ nsims      : num 3
#>   ..$ nburn      : num 0
#>   ..$ outputparam: logi TRUE
#>   ..$ outputfinal: logi FALSE
#>  $ ModelParameters:List of 12
#>   ..$ modname         : chr "LinearAbxModel"
#>   ..$ nstates         : int 2
#>   ..$ nmetro          : int 1
#>   ..$ forward         : logi TRUE
#>   ..$ cheat           : logi FALSE
#>   ..$ Insitu          :List of 3
#>   .. ..$ probs : num [1:3] 0.9 0 0.1
#>   .. ..$ priors: num [1:3] 0.9 1 0.1
#>   .. ..$ doit  : logi [1:3] TRUE FALSE TRUE
#>   ..$ SurveillanceTest:List of 3
#>   .. ..$ colonized  :List of 4
#>   .. .. ..$ init  : num 0.8
#>   .. .. ..$ update: logi TRUE
#>   .. .. ..$ prior : num 0.8
#>   .. .. ..$ weight: num 1
#>   .. .. ..- attr(*, "class")= chr "Param"
#>   .. ..$ uncolonized:List of 4
#>   .. .. ..$ init  : num 1e-10
#>   .. .. ..$ update: logi FALSE
#>   .. .. ..$ prior : num 1e-10
#>   .. .. ..$ weight: num 0
#>   .. .. ..- attr(*, "class")= chr "Param"
#>   .. ..$ latent     :List of 4
#>   .. .. ..$ init  : num 0
#>   .. .. ..$ update: logi FALSE
#>   .. .. ..$ prior : num 0
#>   .. .. ..$ weight: num 0
#>   .. .. ..- attr(*, "class")= chr "Param"
#>   ..$ ClinicalTest    :List of 3
#>   .. ..$ uncolonized:List of 2
#>   .. .. ..$ param:List of 4
#>   .. .. .. ..$ init  : num 0.5
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 0.5
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ rate :List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. ..$ colonized  :List of 2
#>   .. .. ..$ param:List of 4
#>   .. .. .. ..$ init  : num 0.5
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 0.5
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ rate :List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. ..$ latent     :List of 2
#>   .. .. ..$ param:List of 4
#>   .. .. .. ..$ init  : num 0
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 0
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ rate :List of 4
#>   .. .. .. ..$ init  : num 0
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 0
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   ..$ OutCol          :List of 3
#>   .. ..$ acquisition:List of 4
#>   .. .. ..$ init  : num 0.05
#>   .. .. ..$ update: logi TRUE
#>   .. .. ..$ prior : num 0.05
#>   .. .. ..$ weight: num 1
#>   .. .. ..- attr(*, "class")= chr "Param"
#>   .. ..$ clearance  :List of 4
#>   .. .. ..$ init  : num 0.01
#>   .. .. ..$ update: logi TRUE
#>   .. .. ..$ prior : num 0.01
#>   .. .. ..$ weight: num 1
#>   .. .. ..- attr(*, "class")= chr "Param"
#>   .. ..$ progression:List of 4
#>   .. .. ..$ init  : num 0
#>   .. .. ..$ update: logi FALSE
#>   .. .. ..$ prior : num 0
#>   .. .. ..$ weight: num 0
#>   .. .. ..- attr(*, "class")= chr "Param"
#>   ..$ InCol           :List of 3
#>   .. ..$ acquisition:List of 7
#>   .. .. ..$ base     :List of 4
#>   .. .. .. ..$ init  : num 0.001
#>   .. .. .. ..$ update: logi TRUE
#>   .. .. .. ..$ prior : num 0.001
#>   .. .. .. ..$ weight: num 1
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ time     :List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ mass     :List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi TRUE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 1
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ freq     :List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi TRUE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 1
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ col_abx  :List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ suss_abx :List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ suss_ever:List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. ..$ progression:List of 3
#>   .. .. ..$ rate    :List of 4
#>   .. .. .. ..$ init  : num 0.01
#>   .. .. .. ..$ update: logi TRUE
#>   .. .. .. ..$ prior : num 0.01
#>   .. .. .. ..$ weight: num 1
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ abx     :List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ ever_abx:List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. ..$ clearance  :List of 3
#>   .. .. ..$ rate    :List of 4
#>   .. .. .. ..$ init  : num 0.01
#>   .. .. .. ..$ update: logi TRUE
#>   .. .. .. ..$ prior : num 0.01
#>   .. .. .. ..$ weight: num 1
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ abx     :List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   .. .. ..$ ever_abx:List of 4
#>   .. .. .. ..$ init  : num 1
#>   .. .. .. ..$ update: logi FALSE
#>   .. .. .. ..$ prior : num 1
#>   .. .. .. ..$ weight: num 0
#>   .. .. .. ..- attr(*, "class")= chr "Param"
#>   ..$ Abx             :List of 3
#>   .. ..$ onoff: logi FALSE
#>   .. ..$ delay: num 0
#>   .. ..$ life : num 1
#>   ..$ AbxRate         :List of 3
#>   .. ..$ uncolonized:List of 4
#>   .. .. ..$ init  : num 1
#>   .. .. ..$ update: logi FALSE
#>   .. .. ..$ prior : num 1
#>   .. .. ..$ weight: num 0
#>   .. .. ..- attr(*, "class")= chr "Param"
#>   .. ..$ colonized  :List of 4
#>   .. .. ..$ init  : num 1
#>   .. .. ..$ update: logi FALSE
#>   .. .. ..$ prior : num 1
#>   .. .. ..$ weight: num 0
#>   .. .. ..- attr(*, "class")= chr "Param"
#>   .. ..$ latent     :List of 4
#>   .. .. ..$ init  : num 0
#>   .. .. ..$ update: logi FALSE
#>   .. .. ..$ prior : num 0
#>   .. .. ..$ weight: num 0
#>   .. .. ..- attr(*, "class")= chr "Param"
#>  $ waic1          : num 0.422
#>  $ waic2          : num 0.486

Run Bayesian Transmission MCMC

Usage

Arguments

Value

See also

Examples