tests/testthat/test_severalCycles.R

In bgctw/RespChamberProc: Processing Data from Respiration Chambers

#require(testthat)
context("severalCycles")

fName <- system.file(
  "genData/SMANIE_Chamber1_26032015.zip", package = "RespChamberProc")
if (nzchar(fName)) { 
  ds0 <- readDat(
    unz(fName, filename = unzip(fName, list = TRUE)[1,"Name"] ),tz = "UTC")
  ds <- ds0 %>% 
    filter(UQ(sym("TIMESTAMP")) < as.POSIXct("2015-03-26 06:29:12", tz = "UTC"))
  ds$Pa <- ds$AirPres * 100  # convert hPa to Pa
  ds$CO2_dry <- corrConcDilution(ds, colConc = "CO2_LI840", colVapour = "H2O_LI840")
  ds$H2O_dry <- corrConcDilution(ds, colConc = "H2O_LI840", colVapour = "H2O_LI840")
  ds$VPD <- calcVPD( ds$SurTemp, ds$Pa, ds$H2O_LI840)
  #
  dsChunked <- subsetContiguous(ds, colTime = "TIMESTAMP", colIndex = "Collar") 
  test_that("subsetContiguous",{
        expect_true( nrow(dsChunked) > 1 )    
        expect_true( nrow(dsChunked) < nrow(ds) )
        expect_true( all( names(ds) %in% names(dsChunked)) )
        expect_true( all( "iChunk" %in% names(dsChunked)) )
        expect_true( length(unique(dsChunked$iChunk)) > 1 )
        expect_true( all( is.finite(dsChunked$CO2_dry) ))
      })
  #
  chamberVol = 0.6*0.6*0.6    # chamber was a cube of 0.6m length
  surfaceArea = 0.6*0.6
  nChunk <- length(unique(dsChunked$iChunk))
  # pretend more chunks in volume dataset as in dsChunke
  chamberVolByChunk <- data.frame( 
    iChunk = c(as.character(unique(dsChunked$iChunk)), "unknownChunk")
    , volume = chamberVol * c(0.9, 1.1, 1))
  resChunks <- calcClosedChamberFluxForChunks(
    dsChunked, colTemp = "T_LI840"
    # linear and saturating shape
    ,fRegress = c(lin = regressFluxLinear, tanh = regressFluxTanh)  
    ,debugInfo = list(omitEstimateLeverage = TRUE)  # faster
    ,volumesByChunk = chamberVolByChunk
    ,area = surfaceArea)
  
  test_that("calcClosedChamberFluxForChunks", {
        expect_true( nrow(resChunks) > 1 )    
        expect_true( all( c("flux","sdFlux") %in% names(resChunks)) )
        expect_true( all( "iChunk" %in% names(resChunks)) )
        expect_true( all( table(resChunks$iChunk) == 1) )
        resChunks1 <- calcClosedChamberFluxForChunks(
          dsChunked, colTemp = "T_LI840"
          # linear and saturating shape
          , fRegress = c(lin = regressFluxLinear, tanh = regressFluxTanh)  
          , debugInfo = list(omitEstimateLeverage = TRUE)  # faster
          , volume = chamberVol
          , area = surfaceArea)
        # using a smaller volume in chunk-varying volume
        expect_true( resChunks$flux[1] < resChunks1$flux[1] )  
        # using a larger volume in chunk-varying volume
        expect_true( resChunks$flux[2] > resChunks1$flux[1] )  
      })
  
  test_that("calcClosedChamberFluxForChunks with error on volumes",{
        chamberVolByChunkWrongColumnName <- slice(chamberVolByChunk, 2L);
        expect_error(
        resChunks2 <- calcClosedChamberFluxForChunks(
          dsChunked, colTemp = "T_LI840"
          , fRegress = c(lin = regressFluxLinear, tanh = regressFluxTanh)  
          , debugInfo = list(omitEstimateLeverage = TRUE)  # faster
          , volumesByChunk = chamberVolByChunkWrongColumnName
          , area = surfaceArea)
        )
      })
  
  test_that("calcClosedChamberFluxForChunks with error on volume column names",{
        chamberVolByChunkWrongColumnName <- structure(
          chamberVolByChunk, names = c("iChunk","Vol"))
        expect_error(
            resChunks2 <- calcClosedChamberFluxForChunks(
              dsChunked, colTemp = "T_LI840"
              ,fRegress = c(lin = regressFluxLinear, tanh = regressFluxTanh)  
              ,debugInfo = list(omitEstimateLeverage = TRUE)  # faster
              ,volumesByChunk = chamberVolByChunkWrongColumnName
              ,area = surfaceArea)
        )
      })
  
  test_that("calcClosedChamberFluxForChunks with error on volume as vector",{
    chamberVolVector <- chamberVolByChunk$volume
    expect_error(
      resChunks2 <- calcClosedChamberFluxForChunks(
        dsChunked, colTemp = "T_LI840"
        ,fRegress = c(lin = regressFluxLinear, tanh = regressFluxTanh)  
        ,debugInfo = list(omitEstimateLeverage = TRUE)  # faster
        ,volumesByChunk = chamberVolVector
        ,area = surfaceArea)
    )
  })
  
  #
  suppressMessages(
    dsPlots <- plotCampaignConcSeries( dsChunked, resChunks, isVerbose = FALSE)
    )
  #dsPlots <- plotCampaignConcSeries(dsChunked, resChunks1, isVerbose = FALSE)
  #dsPlots$plot[[1]]
  test_that("plotCampaignConcSeries",{
        expect_true( nrow(dsPlots) > 0 )    
        expect_true( all( c("iPage","plot") %in% names(dsPlots)) )
        expect_true( inherits( dsPlots$plot[[1]],"ggplot") )
      })
  #print(dsPlots$plot[[1]])
  #dsPlots %>% rowwise() %>% do({print(.$plot); data.frame()})

} # if nzchar(fname)