An interactive mock of a project scaffolded by init_polis_pipeline() — expand the folders and click a script to open it (several can be open at once; the 01_data / 03_outputs folders are structure only and don’t open).
Exactly what init_polis_pipeline("emro_polis", regions = "EMRO", renv = TRUE) produces: the .Rprofile manifest defines the data-directory roots once and builds cfg from them, so the two 02_scripts/ and the cleaners all share the same paths. See Scaffolding a pipeline project for the step-by-step version.
Explorer
emro_polis
01_data
1a_shapefiles
raw
who_polio_global_gdb.gdb
processed
spatial_global_adm0.qs2
spatial_global_adm1.qs2
spatial_global_adm2.qs2
1b_population
worldpop
raw
all/global_pop_2020.tif
u5/global_total_00_04_2020.tif
u15/global_total_00_14_2020.tif
processed
global_worldpop_total_pop.qs2
global_worldpop_u5_pop.qs2
global_worldpop_u15_pop.qs2
polis_pop
raw
raw_population.qs2
processed
cleaned denominators
1c_polis
raw
raw_afp.qs2
raw_es.qs2
raw_hum_spec.qs2
raw_activity.qs2
raw_sub_activity.qs2
raw_im.qs2
raw_lqas.qs2
processed
data
polished_afp.qs2
polished_es.qs2
polished_virus.qs2
polished_detections.qs2
polished_indicators.qs2
polished_pop_adm2.qs2
checks
checks_afp.xlsx
checks_es.xlsx
checks_pop.xlsx
cache
regenerable cache
1d_vaccination
raw
coverage inputs (optional)
processed
derived tables
02_scripts
03_outputs
plots
figures (.png / .pdf)
tables
exported summaries (.csv / .xlsx)