UsingTfRecords_Tutorial.R

#!/usr/bin/env Rscript
{
  # clear workspace
  rm(list=ls())

  ################################
  # Image confounding tutorial using causalimages
  # and tfrecords for faster results
  ################################

  # remote install latest version of the package if needed
  # devtools::install_github(repo = "cjerzak/causalimages-software/causalimages")

  # local install for development team
  # install.packages("~/Documents/causalimages-software/causalimages",repos = NULL, type = "source",force = F)

  # build backend you haven't ready:
  # causalimages::BuildBackend()

  # load in package
  library( causalimages  )

  # load in tutorial data
  data(  CausalImagesTutorialData )

  # example acquire image function (loading from memory)
  # in general, you'll want to write a function that returns images
  # that saved disk associated with keys
  acquireImageFromMemory <- function(keys){
    # here, the function input keys
    # refers to the unit-associated image keys
    m_ <- FullImageArray[match(keys, KeysOfImages),,,]

    # if keys == 1, add the batch dimension so output dims are always consistent
    # (here in image case, dims are batch by height by width by channel)
    if(length(keys) == 1){
      m_ <- array(m_,dim = c(1L,dim(m_)[1],dim(m_)[2],dim(m_)[3]))
    }

    # uncomment for a test with different image dimensions
    #if(length(keys) == 1){ m_ <- abind::abind(m_,m_,m_,along = 3L) }; if(length(keys) > 1){ m_ <- abind::abind(m_,m_,m_,.along = 4L) }
    return( m_ )
  }

  dim( acquireImageFromMemory(KeysOfImages[1]) )
  dim( acquireImageFromMemory(KeysOfImages[1:2]) )

  # drop first column
  X <- X[,-1]

  # mean imputation for simplicity
  X <- apply(X,2,function(zer){
    zer[is.na(zer)] <- mean( zer,na.rm = T )
    return( zer )
  })

  # select observation subset to make tutorial analyses run faster
  # select 50 treatment and 50 control observations
  set.seed(1.)
  take_indices <- unlist( tapply(1:length(obsW),obsW,function(zer){sample(zer, 50)}) )

  # !!! important note !!!
  # when using tf recordings, it is essential that the data inputs be pre-shuffled like is done here.
  # you can use a seed for reproducing the shuffle (so the tfrecord is correctly indexed and you don't need to re-make it)
  # tf records read data quasi-sequentially, so systematic patterns in the data ordering
  # reduce performance

  # uncomment for a larger n analysis
  #take_indices <- 1:length( obsY )

  # set tfrecord save location (safest using absolute path)
  tfrecord_loc <- "~/Downloads/ExampleRecord.tfrecord"

  # tfrecord_loc <- "ExampleRecord.tfrecord"

  # you may use relative paths like this:
  # tfrecord_loc <- "./Downloads/test1/test2/test3/ExampleRecord.tfrecord"

  # or absolute paths like this:
  # tfrecord_loc <- "~/Downloads/test1/test2/test3/ExampleRecord.tfrecord"

  # write a tf records repository
  causalimages::WriteTfRecord(  file = tfrecord_loc,
                  uniqueImageKeys = unique( KeysOfObservations[ take_indices ] ),
                  acquireImageFxn = acquireImageFromMemory )

  # perform causal inference with image and tabular confounding -- toy example for illustration purposes
  ImageConfoundingAnalysis <- causalimages::AnalyzeImageConfounding(
    obsW = obsW[ take_indices ],
    obsY = obsY[ take_indices ],
    X = X[ take_indices,apply(X[ take_indices,],2,sd)>0],
    long = LongLat$geo_long[ take_indices ],
    lat = LongLat$geo_lat[ take_indices ],
    imageKeysOfUnits = KeysOfObservations[ take_indices ],
    file = tfrecord_loc, # point to tfrecords file

    nSGD = 200L,
    plotBands = c(1,2,3),
    figuresTag = "TutorialExample",
    figuresPath = "~/Downloads/TFRecordTutorial" # figures saved here (use absolute file paths)
  )

  # ATE estimate (image confounder adjusted)
  ImageConfoundingAnalysis$tauHat_propensityHajek

  # ATE se estimate (image confounder adjusted)
  ImageConfoundingAnalysis$tauHat_propensityHajek_se

  # see figuresPath for image analysis output
  print("Done with TfRecords tutorial!")
}