Adding new covariates - HopkinsIDD/cholera-mapping-pipeline GitHub Wiki

This page refers to adding new covariates in the old pipeline.

The first step to adding a covariate

Config entry should look like this:

dist_to_lakes:
  name: distance_to_lakes
  description: Distance to closest lake
  alias: dist_lakes
  abbr: dl
  dir: lake_dist/lake_dist_5km_raster.tif
  type: static
  time_aggregator: ~ 
  space_aggregator: average
  transform: ~
  unit: km

• name : Name of the covariate. Can be used to access covariate from pipeline.
• description : High level description of covariate. Unused by pipeline.
• alias : Short name of covariate. Can be used to access covariate from pipeline.
• abbr : Really short name for covariate. Used to create filenames for pipeline results using this covariate.
• dir : Path to single geotiff file. Called because it is a directory for temporal files.
• type : always "static"
• time_aggregator : always "~"
• space_aggregator : function to use to aggregate the data of this type across space. Used by the pipeline to aggregate different spatial scales
• transform : function to use to transform the data. Used by the pipeline to transform the data after aggregation (I think)
• unit : Units associated with this data. Unused by the pipeline

pop:
  name: population
  description: population in each gridcell
  alias: pop
  abbr: p
  dir: pop/
  type: temporal
  time_aggregator: average
  res_time: 1 years
  space_aggregator: sum
  transform: ~
  unit: number

• name : Name of the covariate. Can be used to access covariate from pipeline.
• description : High level description of covariate. Unused by pipeline.
• alias : Short name of covariate. Can be used to access covariate from pipeline.
• abbr : Really short name for covariate. Used to create filenames for pipeline results using this covariate.
• dir : Directory containing the netcdf files. Historically, we have used 1 netcdf file per time slice. I am not sure if this is required.
• type : always "temporal"
• time_aggregator : function to use to aggregate data of this type across time. Used by pipeline for aggregating to different time scales.
• res_time : The time resolution of the flat files. Used by pipeline for determining gridsize in time.
• space_aggregator : function to use to aggregate the data of this type across space. Used by the pipeline to aggregate different spatial scales
• transform : function to use to transform the data. Used by the pipeline to transform the data after aggregation (I think)
• unit : Units associated with this data. Unused by the pipeline

Most of the data sets we use are not originally netcdf4 (.nc) files. In order to convert, please use the taxdat::write_netcdf function.