tests/testthat/test_utility_functions.R

In zachcp/phylogeo: Mapping of Phyloseq Information

################################################################################
# Use testthat to test phyloseq data objects for the presence of Lat/Long
################################################################################
library("phylogeo")
library("testthat")
library("dplyr")
context("Utility Functions")

# Test the following funcitons
# check_physeq <- function(physeq){
# create_basemap <-function(region, df, latcol, loncol){
# check_NA <- function(df, col){
# coerce_numeric <- function(df, col)
# dist_to_edge_table = function(Dist, dname = "dist")
# degree_to_radian <- function(degree)
# radian_to_degree <- function(radian)


test_that("phyloseq objects are converted to phylogeo objects", {
    data(mountainsoil)
    data(batmicrobiome)
    data(epoxomicin_KS)

    phy1 <- phylogeo(mountainsoil)
    phy2 <- phylogeo(batmicrobiome)
    phy3 <- phylogeo(epoxomicin_KS)

    expect_equal(phy1@latitude, "LATITUDE")
    expect_equal(phy1@longitude, "LONGITUDE")
    expect_equal(phy2@latitude, "LATITUDE")
    expect_equal(phy2@longitude, "LONGITUDE")
    expect_equal(phy3@latitude, "Latitude")
    expect_equal(phy3@longitude, "Longitude")

    # remove lat.long column and be sure it trips an error
    df <- data.frame(sample_data(mountainsoil))
    dflat <- df %>% dplyr::select(-LATITUDE)
    dflon <- df %>% dplyr::select(-LONGITUDE)
    bat_lat <- mountainsoil
    sample_data(bat_lat) <- dflat
    expect_error(phylogeo(bat_lat))
    bat_lon <- mountainsoil
    sample_data(bat_lon) <- dflon
    expect_error(phylogeo(bat_lon))
})


test_that("jittering works and uses the seed correctly", {
  df <- data.frame(x= c(1,2,3,4,5), y=c(3,4,5,6,7))
  df_j1 <- jitter_df(df, "x","y",3,4,123)
  df_j2 <- jitter_df(df, "x","y",3,4,123)
  expect_is(df_j1 , "data.frame")
  expect_is(df_j2 , "data.frame")
  #jittered dfs with same seed should be equal
  expect_equal(df_j1, df_j2)
})

test_that("checknames trips an error when its supposed to",{
  df <- data.frame(col1=c(1,2,3),
                   col2=c(1,2,3))

  expect_output(check_names("col1", df),"")
  expect_output(check_names("col2", df),"")
  expect_error(check_names("col3", df))
})

test_that("coerce_latlon_columns can handle columns that are factors and convert 'None' to NA", {
  #col2 has "NONE"
  df1 <- data.frame(col1=c(1,2,3,4,1,2,3),
                   col2=c(1,2,3,"None",1,2,3))
  #col2 is a factor with "None"
  df2 <- data.frame(col1=c(1,2,3,4,1,2,3),
                   col2=as.factor(c(1,2,3,"None",1,2,3)))
  expect_is(df2$col2, "factor")

  #check that the none is removed  values
  testdf <- coerce_latlon_columns(df1, "col2")
  expect_equal(testdf$col2, c(1,2,3,NA,1,2,3))
  testdf <- coerce_latlon_columns(df2, "col2")
  expect_equal(testdf$col2, c(1,2,3,NA,1,2,3))
})