tests/testthat/test-fitRF.R

In TheoreticalEcosystemEcology/alienR: Comparative analysis of interaction inference methods

# Set seed
set.seed(43)

#######################
# Generate bogus adjMat
#######################
bipart <- matrix(rbinom(n = 20, prob = 0.6, size = 1),
                 nrow = 5, ncol = 4)

# Add row an column names
rownames(bipart) <- letters[1:5]
colnames(bipart) <- LETTERS[1:4]

##########################
# Generate bogus traitFrom
##########################
# Convert TraitF to data.frame 
TraitFDF <- data.frame(tr1 = rnorm(5),
                       tr2 = rnorm(5),
                       tr3 = as.factor(c("red", "red",
                                         "blue", "green",
                                         "green")))

rownames(TraitFDF) <- letters[1:5]

########################
# Generate bogus traitTo
########################
# Convert TraitT to data.frame 
TraitTDF <- data.frame(Tr1 = rnorm(4),
                       Tr2 = as.factor(c("red", "red",
                                         "blue","blue")),
                       Tr3 = rnorm(4))

rownames(TraitTDF) <- LETTERS[1:4]

#################
# Build alienData
#################
AllData <- alienData(adjMat = bipart,
                     traitFrom = TraitFDF,
                     traitTo = TraitTDF)

#########################
# Test randomForest model
#########################
# Function
fitRFComplexRes <- fitRF(data = AllData,
                         formula = ~ tr1 + tr2 + tr3 + Tr1 + Tr2 + Tr3,
                         ntree = 500,
                         nodesize = 3)


fitRFSimpleRes <- fitRF(data = AllData,
                        formula = ~ -1 + tr1,
                        ntree = 500,
                        nodesize = 3)

# Trick to compare the result obtained from fit
fitRFComplexResMat <- matrix(NA, nrow = 5, ncol = 4)
fitRFComplexResMat[,1:4] <- fitRFComplexRes[,1:4]

fitRFSimpleResMat <- matrix(NA, nrow = 5, ncol = 4)
fitRFSimpleResMat[,1:4] <- fitRFSimpleRes[,1:4]

# Test
test_that("fitRF expected output",
  expect_false(isTRUE(all.equal(fitRFSimpleResMat,
                                fitRFComplexResMat))))