This function reads in the output files from sim_trajectory_CSV
and splits them into smaller files. The files are output by patch, with the
appropriate patch numbers for mosquitoes or humans, and specific stages are
aggregated by a given metric.
split_aggregate_CSV_decoupled(
read_dir,
write_dir = read_dir,
spn_P,
tmax,
dt,
human_states,
sum_fem = FALSE,
rem_file = FALSE,
verbose = TRUE,
erlang = FALSE
)Writes output to files in write_dir
Directory where output was written to
Directory to write output to. Default is read_dir
Places object, see details
The final time to end simulation
The time-step at which to return output (not the time-step of the sampling algorithm)
human state distribution
if TRUE, in addition to FS, FE, FI output by node and repetition, output an
additional file F which sums over infection states (S,E,I). Does nothing if the
simulation did not include epi dynamics.
Remove original output? Default is FALSE
Chatty? Default is TRUE
erlang distributed states
Given the read_dir, this function assumes the follow file structure:
read_dir
repetition 1
M.csv
FS.csv
...
repetition 2
M.csv
FS.csv
...
repetition 3
...
This function expects the write_dir to be empty, and it sets up the
same file structure as the read_dir. For a 2-node simulation, the output
will be organized similar to:
write_dir
repetition 1
M_0001.csv
M_0002.csv
FS_0001.csv
FS_0001.csv
...
repetition 2
M_0001.csv
M_0002.csv
FS_0001.csv
FS_0001.csv
...
repetition 3
...
The places (spn_P) object is generated from one of the following:
spn_P_lifecycle_node, spn_P_lifecycle_network,
spn_P_epiSIS_node, spn_P_epiSIS_network,
spn_P_epiSEIR_node, or spn_P_epiSEIR_network.
tmax, dt define the last sampling
time, and each sampling time in-between.
For more details about using this function to process CSV output see:
vignette("data-analysis", package = "MGDrivE2")