tests/testthat/test_fluxEstimates.R

In bgctw/RespChamberProc: Processing Data from Respiration Chambers

#require(testthat)
context("fluxEstimates")

#data(chamberLoggerEx1s, package = "RespChamberProc")	
#   does not work with RCMDCheck and testthat
ds <- chamberLoggerEx1s[-(1:16),]
conc <- ds$CO2_dry <- corrConcDilution(ds)
times <- ds$TIMESTAMP
times0 <- as.numeric(times) - as.numeric(times[1])


.tmp.f <- function(){
}

test_that("default example flux Estimates runs",{
			#trace(calcClosedChamberFlux, recover)		#untrace(calcClosedChamberFlux)
			#resFit <- calcClosedChamberFlux(ds, debugInfo = list(tLagFixed = 0))
			resFit <- calcClosedChamberFlux(ds, useFixedTLag = 0)
			#plotResp(ds, resFit)
		})

test_that("no flux with random data",{
  concR <- 390 + rnorm(length(times), sd = 0.3)
  #plot( concR ~ times )
  ds <- data.frame(
    CO2_dry = concR, TIMESTAMP = times, TA_Avg = 20, Pa = 101*1000)
  #trace(calcClosedChamberFlux, recover)		#untrace(calcClosedChamberFlux)
  res <- calcClosedChamberFlux(ds)
  expect_true( abs(res$flux) - 2*res$sdFlux < 0 )	# not significantly different from 0
  expect_that( length(coefficients(res$model[[1]])), equals(2) )	# fitted a linear model
})

test_that("detect special case of numericall equal fluxes",{
  # https://github.com/bgctw/RespChamberProc/issues/2
  timesR <- 0:81
  concR <- rep(88.01, length(timesR))
  concR[3] <- NA    # test dealing with NA
  #plot( concR ~ timesR )
  ds <- data.frame(
    CO2_dry = concR, TIMESTAMP = timesR, TA_Avg = 20, Pa = 101*1000)
  #trace(calcClosedChamberFlux, recover)		#untrace(calcClosedChamberFlux)
  expect_warning(
    res <- calcClosedChamberFlux(ds)
  )
  expect_true( is.na(res$flux) )
})			
			
test_that("detect special case no finite concentrations",{
  timesR <- 0:81
  concR <- rep(NA_real_, length(timesR))
  #plot( concR ~ timesR )
  ds <- data.frame(
    CO2_dry = concR, TIMESTAMP = timesR, TA_Avg = 20, Pa = 101*1000)
  #trace(calcClosedChamberFlux, recover)		#untrace(calcClosedChamberFlux)
  expect_warning(
    res <- calcClosedChamberFlux(ds)
  )
  expect_true( is.na(res$flux) )
})