context("irs")

# find system info
on_solaris <- Sys.info()[["sysname"]] == "SunOS"
if (on_solaris) {
  test_that("on solaris", {
    expect_true(on_solaris)
  })
} else {
  
  
  # set reproducible seed (as there are random components here)
  set.seed(5)
  
  test_local <- FALSE # FALSE for CRAN
  
  #################################################
  ########### NE_LAKES DATA TESTS
  #################################################
  
  #--------------------------------------
  #-------- Class Inheritance
  #--------------------------------------
  
  test_that("algorithm executes", {
    n_base <- 50
    irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "equal")
    # class inheritance
    expect_s3_class(irs_output, "sp_design")
  })
  
  #--------------------------------------
  #-------- Work with sp_frame
  #--------------------------------------
  
  test_that("algorithm executes", {
    n_base <- 50
    irs_output <- irs(sp_frame(NE_Lakes), n_base = n_base, seltype = "equal")
    # class inheritance
    expect_s3_class(irs_output, "sp_design")
  })
  
  if (test_local) {
    #--------------------------------------
    #-------- Regular
    #--------------------------------------
    
    # number of irs columns added
    col_irs_add <- 9
    
    # number of NE_Lakes columns
    col_data <- NCOL(NE_Lakes)
    
    # number of irs columns plus NE_Lakes columns
    col_out <- col_irs_add + col_data
    
    # unstratified, equal probability
    test_that("algorithm executes", {
      n_base <- 50
      irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "equal")
      # see if function ran without error
      expect_true(exists("irs_output"))
      # no legacy sites
      expect_equal(NROW(irs_output$sites_legacy), 0)
      # base sample size of 50
      expect_equal(NROW(irs_output$sites_base), n_base)
      # no rho replacement sites
      expect_equal(NROW(irs_output$sites_over), 0)
      # no nn replacement sites
      expect_equal(NROW(irs_output$sites_near), 0)
      # no legacy sites
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      # base sample size columns should equal extra columns plus original columns
      expect_equal(NCOL(irs_output$sites_base), col_out)
      # no rho replacement sites
      expect_equal(NCOL(irs_output$sites_over), 1)
      # no nn replacement sites
      expect_equal(NCOL(irs_output$sites_near), 1)
      # class inheritance
      expect_s3_class(irs_output, "sp_design")
    })
    
    # stratified, equal probability
    test_that("algorithm executes", {
      n_base <- c(low = 20, high = 30)
      irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "equal", stratum_var = "ELEV_CAT")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "low", , drop = FALSE]),
        n_base[["low"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "high", , drop = FALSE]),
        n_base[["high"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # unstratified, unequal probability
    test_that("algorithm executes", {
      n_base <- 50
      caty_n <- c(small = 24, large = 26)
      irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "unequal", caty_var = "AREA_CAT", caty_n = caty_n)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # stratified, unequal probability
    test_that("algorithm executes", {
      n_base <- c(low = 20, high = 30)
      caty_n <- list(low = c(small = 10, large = 10), high = c(small = 10, large = 20))
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "unequal", stratum_var = "ELEV_CAT",
                        caty_var = "AREA_CAT", caty_n = caty_n
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "low", , drop = FALSE]),
        n_base[["low"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "high", , drop = FALSE]),
        n_base[["high"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # stratified, unequal probability (with repeated caty_n)
    test_that("algorithm executes", {
      n_base <- c(low = 25, high = 25)
      caty_n <- c(small = 12.5, large = 12.5)
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "unequal", stratum_var = "ELEV_CAT",
                        caty_var = "AREA_CAT", caty_n = caty_n
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "low", , drop = FALSE]),
        n_base[["low"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "high", , drop = FALSE]),
        n_base[["high"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # stratified, unequal probability (with different caty_n)
    test_that("algorithm executes", {
      n_base <- c(low = 25, high = 25)
      caty_n <- list(low = c(small = 10, large = 15), high = c(small = 12, large = 13))
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "unequal", stratum_var = "ELEV_CAT",
                        caty_var = "AREA_CAT", caty_n = caty_n
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "low", , drop = FALSE]),
        n_base[["low"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "high", , drop = FALSE]),
        n_base[["high"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # unstratified, proportional (to size) probability
    test_that("algorithm executes", {
      n_base <- 50
      irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "proportional", aux_var = "AREA")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out + 1)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # stratified, proportional probability
    test_that("algorithm executes", {
      n_base <- c(low = 20, high = 30)
      irs_output <- irs(NE_Lakes, n_base = n_base, stratum_var = "ELEV_CAT", aux_var = "AREA")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "low", , drop = FALSE]),
        n_base[["low"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "high", , drop = FALSE]),
        n_base[["high"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out + 1)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    test_that("A warning (in message form) is produced", {
      n_base <- c(low = 20, high = 30)
      expect_message(expect_error(irs(NE_Lakes, n_base = n_base, stratum_var = "XYZ")))
      
    })
    
    #--------------------------------------
    #-------- Legacy
    #--------------------------------------
    
    # legacy sites, unstratified, equal probability
    test_that("algorithm executes", {
      n_base <- 50
      n_legacy <- NROW(NE_Lakes_Legacy)
      irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "equal", legacy_sites = NE_Lakes_Legacy)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), n_legacy)
      expect_equal(NROW(irs_output$sites_base), n_base - n_legacy)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), col_out)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # legacy sites, stratified, equal probability
    test_that("algorithm executes", {
      n_base <- c(low = 20, high = 30)
      n_legacy <- NROW(NE_Lakes_Legacy)
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "equal",
                        stratum_var = "ELEV_CAT", legacy_sites = NE_Lakes_Legacy,
                        legacy_stratum_var = "ELEV_CAT"
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), n_legacy)
      n_legacy_low <- sum(irs_output$sites_legacy$stratum == "low")
      n_legacy_high <- sum(irs_output$sites_legacy$stratum == "high")
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "low", , drop = FALSE]),
        n_base[["low"]] - n_legacy_low
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "high", , drop = FALSE]),
        n_base[["high"]] - n_legacy_high
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base) - n_legacy)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), col_out)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # legacy sites, unequal probability
    test_that("algorithm executes", {
      n_base <- 50
      caty_n <- c(small = 24, large = 26)
      n_legacy <- NROW(NE_Lakes_Legacy)
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "unequal",
                        caty_var = "AREA_CAT", caty_n = caty_n, legacy_sites = NE_Lakes_Legacy,
                        legacy_caty_var = "AREA_CAT"
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), n_legacy)
      expect_equal(NROW(irs_output$sites_base), n_base - n_legacy)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), col_out)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # legacy sites, proportional probability
    test_that("algorithm executes", {
      n_base <- 50
      n_legacy <- NROW(NE_Lakes_Legacy)
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "proportional",
                        aux_var = "AREA", legacy_sites = NE_Lakes_Legacy,
                        legacy_aux_var = "AREA"
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), n_legacy)
      expect_equal(NROW(irs_output$sites_base), n_base - n_legacy)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), col_out + 1)
      expect_equal(NCOL(irs_output$sites_base), col_out + 1)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # legacy sites, unstratified, equal probability -- old method
    test_that("algorithm executes", {
      n_base <- 50
      n_legacy <- NROW(NE_Lakes_Legacy)
      NE_Lakes$LEGACY <- NA
      NE_Lakes_Legacy$LEGACY <- paste0("LEGACY-SITES-", 1:5)
      NE_Lakes_bind <- rbind(NE_Lakes_Legacy, NE_Lakes)
      irs_output <- irs(NE_Lakes_bind, n_base = n_base, seltype = "equal", legacy_var = "LEGACY")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), n_legacy)
      expect_equal(NROW(irs_output$sites_base), n_base - n_legacy)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), col_out + 1) # as legacy variable added
      expect_equal(NCOL(irs_output$sites_base), col_out + 1) # as legacy variable added
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    #--------------------------------------
    #-------- Minimum Distance
    #--------------------------------------
    
    # minimum distance, unstratified, equal probability
    test_that("algorithm executes", {
      library(sf)
      n_base <- 50
      mindis <- 1600
      irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "equal", mindis = mindis)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
      dist_mx <- as.vector(st_distance(irs_output$sites_base))
      expect_true(min(dist_mx[dist_mx > 0]) > mindis)
    })
    
    #--------------------------------------
    #-------- RHO replacement
    #--------------------------------------
    
    # rho replacement sites, unstratified, equal probability
    test_that("algorithm executes", {
      n_base <- 50
      n_over <- 5
      irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "equal", n_over = n_over)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), n_over)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), col_out)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # rho replacement sites, stratified, equal probability
    test_that("algorithm executes", {
      n_base <- c(low = 20, high = 30)
      n_over <- list(low = 2, high = 3)
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "equal",
                        stratum_var = "ELEV_CAT", n_over = n_over
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "low", , drop = FALSE]),
        n_base[["low"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "high", , drop = FALSE]),
        n_base[["high"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(
        NROW(irs_output$sites_over[irs_output$sites_over$stratum == "low", , drop = FALSE]),
        n_over[["low"]]
      )
      expect_equal(
        NROW(irs_output$sites_over[irs_output$sites_over$stratum == "high", , drop = FALSE]),
        n_over[["high"]]
      )
      expect_equal(NROW(irs_output$sites_over), sum(unlist(n_over)))
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), col_out)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # rho replacement sites, unstratified, unequal probability
    test_that("algorithm executes", {
      n_base <- 50
      caty_n <- c(small = 24, large = 26)
      n_over <- 10
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "unequal",
                        caty_var = "AREA_CAT", caty_n = caty_n, n_over = n_over
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), n_over)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), col_out)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # rho replacement sites, unstratified, proportional probability
    test_that("algorithm executes", {
      n_base <- 50
      caty_n <- c(small = 24, large = 26)
      n_over <- 10
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "proportional",
                        aux_var = "AREA", n_over = n_over
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), n_over)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out + 1)
      expect_equal(NCOL(irs_output$sites_over), col_out + 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # stratification and n_over
    test_that("algorithm executes", {
      n_base <- c(low = 5, high = 6)
      stratum_var <- "ELEV_CAT"
      caty_n <- list(low = c(small = 2, large = 3), high = c(small = 3, large = 3))
      caty_var <- "AREA_CAT"
      n_over <- c(low = 4, high = 3)
      irs_output <- irs(NE_Lakes, n_base, stratum_var, caty_n = caty_n, caty_var = caty_var, n_over = n_over)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), sum(n_over))
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), col_out)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    #--------------------------------------
    #-------- NN replacement
    #--------------------------------------
    
    # nn replacement sites, unstratified, equal probability
    test_that("algorithm executes", {
      n_base <- 50
      n_near <- 2
      irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "equal", n_near = n_near)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), n_base * n_near)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), col_out)
    })
    
    # nn replacement sites, stratified, equal probability
    test_that("algorithm executes", {
      n_base <- c(low = 20, high = 30)
      n_near <- 2
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "equal",
                        stratum_var = "ELEV_CAT", n_near = n_near
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "low", , drop = FALSE]),
        n_base[["low"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "high", , drop = FALSE]),
        n_base[["high"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), n_near * sum(n_base))
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), col_out)
    })
    
    # nn replacement sites, unstratified, unequal probability
    test_that("algorithm executes", {
      n_base <- 50
      caty_n <- c(small = 24, large = 26)
      n_near <- 2
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "unequal",
                        caty_var = "AREA_CAT", caty_n = caty_n, n_near = n_near
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), n_base * n_near)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), col_out)
    })
    
    # nn replacement sites, unstratified, proportional probability
    test_that("algorithm executes", {
      n_base <- 50
      caty_n <- c(small = 24, large = 26)
      n_near <- 2
      irs_output <- irs(NE_Lakes,
                        n_base = n_base, seltype = "proportional",
                        aux_var = "AREA", n_near = n_near
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), n_base * n_near)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out + 1)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), col_out + 1)
    })
    
    # stratification and n_near
    test_that("algorithm executes", {
      n_base <- c(low = 5, high = 6)
      stratum_var <- "ELEV_CAT"
      n_near <- c(low = 2, high = 1)
      irs_output <- irs(NE_Lakes, n_base, stratum_var, n_near = n_near)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), sum(n_base * n_near))
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), col_out)
    })
    
    #--------------------------------------
    #-------- RHO and NN replacement
    #--------------------------------------
    
    # both replacement sites, unstratified
    test_that("algorithm executes", {
      n_base <- 50
      n_over <- 5
      n_near <- 2
      irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "equal", n_over = n_over, n_near = n_near)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), n_over)
      expect_equal(NROW(irs_output$sites_near), (n_base + n_over) * n_near)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), col_out)
      expect_equal(NCOL(irs_output$sites_near), col_out)
    })
    
    #--------------------------------------
    #-------- Bad name replacement
    #--------------------------------------
    
    test_that("algorithm executes", {
      n_legacy <- NROW(NE_Lakes_Legacy)
      n_base <- 50
      n_over <- 5
      n_near <- 2
      NE_Lakes$siteID <- seq_len(nrow(NE_Lakes))
      irs_output <- irs(NE_Lakes, n_base = n_base, seltype = "equal", legacy_sites = NE_Lakes_Legacy, n_over = n_over, n_near = n_near)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), n_legacy)
      expect_equal(NROW(irs_output$sites_base), n_base - n_legacy)
      expect_equal(NROW(irs_output$sites_over), n_over)
      # used to be n_base - n_legacy + n_over but made legacy sites have nn sites
      expect_equal(NROW(irs_output$sites_near), (n_base + n_over) * n_near)
      expect_equal(NCOL(irs_output$sites_legacy), col_out + 1)
      expect_equal(NCOL(irs_output$sites_base), col_out + 1)
      expect_equal(NCOL(irs_output$sites_over), col_out + 1)
      expect_equal(NCOL(irs_output$sites_near), col_out + 1)
    })
    
    #--------------------------------------
    #-------- Projected CRS
    #--------------------------------------
    
    # unstratified, equal probability
    test_that("algorithm executes", {
      n_base <- 50
      irs_output <- irs(st_transform(NE_Lakes, 4326), n_base = n_base, seltype = "equal", projcrs_check = FALSE)
      # see if function ran without error
      expect_true(exists("irs_output"))
      # no legacy sites
      expect_equal(NROW(irs_output$sites_legacy), 0)
      # base sample size of 50
      expect_equal(NROW(irs_output$sites_base), n_base)
      # no rho replacement sites
      expect_equal(NROW(irs_output$sites_over), 0)
      # no nn replacement sites
      expect_equal(NROW(irs_output$sites_near), 0)
      # no legacy sites
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      # base sample size columns should equal extra columns plus original columns
      expect_equal(NCOL(irs_output$sites_base), col_out)
      # no rho replacement sites
      expect_equal(NCOL(irs_output$sites_over), 1)
      # no nn replacement sites
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    #################################################
    ########### Illinois_River DATA TESTS
    #################################################
    
    # number of irs columns added
    col_irs_add <- 9
    
    # number of Illinois_River columns
    col_data <- NCOL(Illinois_River)
    
    # number of irs columns plus Illinois_River columns
    col_out <- col_irs_add + col_data
    
    #--------------------------------------
    #-------- Regular
    #--------------------------------------
    
    # unstratified, equal probability
    test_that("algorithm executes", {
      n_base <- 50
      irs_output <- irs(Illinois_River, n_base = n_base, seltype = "equal")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # unstratified, large sample size
    test_that("algorithm executes", {
      n_base <- 500
      irs_output <- irs(Illinois_River, n_base = n_base, seltype = "equal")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # unstratified, large sample size, replacement sites
    test_that("algorithm executes", {
      n_base <- 50
      n_over <- 200
      irs_output <- irs(Illinois_River, n_base = n_base, n_over = n_over, seltype = "equal")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), n_over)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), col_out)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # stratified, equal probability
    test_that("algorithm executes", {
      n_base <- c(Oklahoma = 20, Arkansas = 30)
      irs_output <- irs(Illinois_River, n_base = n_base, seltype = "equal", stratum_var = "STATE_NAME")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "Oklahoma", , drop = FALSE]),
        n_base[["Oklahoma"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "Arkansas", , drop = FALSE]),
        n_base[["Arkansas"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # stratified, equal probability
    test_that("algorithm executes", {
      n_base <- c(Oklahoma = 200, Arkansas = 300)
      irs_output <- irs(Illinois_River, n_base = n_base, seltype = "equal", stratum_var = "STATE_NAME")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "Oklahoma", , drop = FALSE]),
        n_base[["Oklahoma"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "Arkansas", , drop = FALSE]),
        n_base[["Arkansas"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # stratified, equal probability
    test_that("algorithm executes", {
      n_base <- c(Oklahoma = 20, Arkansas = 30)
      n_over <- list(Oklahoma = 200, Arkansas = 300)
      irs_output <- irs(Illinois_River, n_base = n_base, seltype = "equal", stratum_var = "STATE_NAME", n_over = n_over)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "Oklahoma", , drop = FALSE]),
        n_base[["Oklahoma"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "Arkansas", , drop = FALSE]),
        n_base[["Arkansas"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), sum(unlist(n_over)))
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), col_out)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    #--------------------------------------
    #-------- Legacy
    #--------------------------------------
    
    # legacy sites, unstratified, equal probability
    test_that("algorithm executes", {
      n_base <- 50
      n_legacy <- nrow(Illinois_River_Legacy)
      irs_output <- irs(Illinois_River, n_base = n_base, seltype = "equal", legacy_sites = Illinois_River_Legacy)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), n_legacy)
      expect_equal(NROW(irs_output$sites_base), n_base - n_legacy)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), col_out)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # legacy sites, stratified, equal probability
    test_that("algorithm executes", {
      n_base <- c(Oklahoma = 20, Arkansas = 30)
      n_legacy <- nrow(Illinois_River_Legacy)
      irs_output <- irs(Illinois_River,
                        n_base = n_base, seltype = "equal",
                        stratum_var = "STATE_NAME", legacy_sites = Illinois_River_Legacy,
                        legacy_stratum_var = "STATE_NAME"
      )
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), n_legacy)
      n_legacy_Oklahoma <- sum(irs_output$sites_legacy$stratum == "Oklahoma")
      n_legacy_Arkansas <- sum(irs_output$sites_legacy$stratum == "Arkansas")
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "Oklahoma", , drop = FALSE]),
        n_base[["Oklahoma"]] - n_legacy_Oklahoma
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "Arkansas", , drop = FALSE]),
        n_base[["Arkansas"]] - n_legacy_Arkansas
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base) - n_legacy)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), col_out)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    #################################################
    ########### Lake_Ontario DATA TESTS
    #################################################
    
    # number of irs columns added
    col_irs_add <- 9
    
    # number of Lake_Ontario columns
    col_data <- NCOL(Lake_Ontario)
    
    # number of irs columns plus Lake_Ontario columns
    col_out <- col_irs_add + col_data
    
    #--------------------------------------
    #-------- Regular
    #--------------------------------------
    
    # unstratified, equal probability
    test_that("algorithm executes", {
      n_base <- 50
      irs_output <- irs(Lake_Ontario, n_base = n_base, seltype = "equal")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # unstratified, large sample size
    test_that("algorithm executes", {
      n_base <- 500
      irs_output <- irs(Lake_Ontario, n_base = n_base, seltype = "equal")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # unstratified, large sample size, replacement sites
    test_that("algorithm executes", {
      n_base <- 50
      n_over <- 200
      irs_output <- irs(Lake_Ontario, n_base = n_base, n_over = n_over, seltype = "equal")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(NROW(irs_output$sites_base), n_base)
      expect_equal(NROW(irs_output$sites_over), n_over)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), col_out)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # stratified, equal probability
    test_that("algorithm executes", {
      n_base <- c(CAN = 20, USA = 30)
      irs_output <- irs(Lake_Ontario, n_base = n_base, seltype = "equal", stratum_var = "COUNTRY")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "CAN", , drop = FALSE]),
        n_base[["CAN"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "USA", , drop = FALSE]),
        n_base[["USA"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # stratified, large sample size
    test_that("algorithm executes", {
      n_base <- c(CAN = 200, USA = 300)
      irs_output <- irs(Lake_Ontario, n_base = n_base, seltype = "equal", stratum_var = "COUNTRY")
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "CAN", , drop = FALSE]),
        n_base[["CAN"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "USA", , drop = FALSE]),
        n_base[["USA"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), 0)
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), 1)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
    
    # replacement sites
    test_that("algorithm executes", {
      n_base <- c(CAN = 200, USA = 300)
      n_over <- list(CAN = 100, USA = 100)
      irs_output <- irs(Lake_Ontario, n_base = n_base, seltype = "equal", stratum_var = "COUNTRY", n_over = n_over)
      expect_true(exists("irs_output"))
      expect_equal(NROW(irs_output$sites_legacy), 0)
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "CAN", , drop = FALSE]),
        n_base[["CAN"]]
      )
      expect_equal(
        NROW(irs_output$sites_base[irs_output$sites_base$stratum == "USA", , drop = FALSE]),
        n_base[["USA"]]
      )
      expect_equal(NROW(irs_output$sites_base), sum(n_base))
      expect_equal(NROW(irs_output$sites_over), sum(unlist(n_over)))
      expect_equal(NROW(irs_output$sites_near), 0)
      expect_equal(NCOL(irs_output$sites_legacy), 1)
      expect_equal(NCOL(irs_output$sites_base), col_out)
      expect_equal(NCOL(irs_output$sites_over), col_out)
      expect_equal(NCOL(irs_output$sites_near), 1)
    })
  }
}