tests/testthat/test-02_convert_lengths.R

In Delta-Stewardship-Council/deltafish: Accesses an Integrated Fish Count and Length Dataset from the San Francisco Delta

cat("testing convert_lengths\n")
require(dplyr)
# lengths are converted correctly
con <- open_database()
surv <- open_survey(con)
fish <- open_fish(con, quiet = TRUE) %>%
  mutate(Row = paste(SampleID, Taxa, Notes_catch, Length))
length_conv <- open_length_conv(con)

df_converted_s <- fish %>%
  dplyr::inner_join(surv %>%
    filter(Source == "Suisun")) %>%
  convert_lengths()

df_unconverted_s <- fish %>%
  dplyr::inner_join(surv %>%
    filter(Source == "Suisun"))

df_converted_compare_s <- df_unconverted_s %>%
  select(Taxa, Length, Source, Row) %>%
  dplyr::left_join(length_conv, by = c("Taxa" = "Species")) %>%
  dplyr::mutate(Length_un = ifelse(is.na(Slope), Length, Length * Slope +
    Intercept)) %>%
  dplyr::left_join(
    df_converted_s %>%
      dplyr::select(Row, Length_con = Length),
    by = c("Row")
  ) %>%
  dplyr::select(Length_con, Length_un) %>%
  mutate(missmatch = Length_con - Length_un) %>%
  filter(!(missmatch == 0 |
    (is.na(Length_con) & is.na(Length_un))))

test_that("convert_lengths errors if taxa not in data", {
  expect_error(convert_lengths(df_unconverted_s %>%
    select(-Taxa)))
})

test_that("input data without Suisun is returned with a warning", {
  expect_warning(
    df_converted_fmwt <- fish %>%
      dplyr::inner_join(surv %>%
        filter(Source == "FMWT")) %>%
      convert_lengths()
  )
})

test_that("lengths are converted correctly", {
  num_row <- df_converted_compare_s %>%
    summarize(n = n()) %>%
    collect_data()
  expect_equal(num_row$n, 0)
})

# Converting lengths does not change the number of rows or columns or the total catch

df_converted_col <- df_converted_s %>%
  select(Count) %>%
  dplyr::summarise(N = n(), Count_sum = sum(Count, na.rm = T)) %>%
  collect_data()

df_unconverted_col <- df_unconverted_s %>%
  select(Count) %>%
  dplyr::summarise(N = n(), Count_sum = sum(Count, na.rm = T)) %>%
  collect_data()

test_that("Converting lengths does not change the number of rows or columns or the total catch", {
  expect_equal(df_converted_col$N, df_unconverted_col$N)
  expect_setequal(colnames(df_converted_s), colnames(df_unconverted_s))
  expect_equal(
    df_converted_col$Count_sum,
    df_unconverted_col$Count_sum
  )
})

# Converting lengths does not induce lengths <= 0

df_less_0 <- df_converted_s %>%
  dplyr::filter(Length <= 0) %>%
  select(Count) %>%
  collect_data()

test_that("Converting lengths does not induce lengths <= 0", {
  expect_equal(nrow(df_less_0), 0)
})

# Converting lengths does not affect non-Suisun data

df_converted_compare <- fish %>%
  select(SampleID, Taxa, Length) %>%
  mutate(Length_o = Length) %>%
  dplyr::inner_join(surv %>%
    select(Source, SampleID)) %>%
  convert_lengths() %>%
  filter(Source != "Suisun") %>%
  dplyr::select(Length_con = Length, Length = Length_o) %>%
  mutate(missmatch = Length_con - Length) %>%
  filter(!(missmatch == 0 |
    (is.na(Length_con) & is.na(Length))))

test_that("Converting lengths does not affect non-Suisun data", {
  num_row <- df_converted_compare %>%
    summarize(n = n()) %>%
    collect_data()
  expect_equal(num_row$n, 0)
})

test_that("convert_lengths fails when the required column colnames are not included", {
  expect_error(
    convert_lengths(data.frame(Taxa = "a", length = 1)),
    "Input data must have Taxa and Length column names",
    fixed = TRUE
  )
})

test_that("convert_lengths works without 'Source' column", {
  df_converted_nosource <- open_fish(con, quiet = TRUE) %>%
    filter(Taxa %in% "Alosa sapidissima") %>%
    convert_lengths() %>%
    head() %>%
    collect_data()

  expect_true(!"Source" %in% colnames(df_converted_nosource))
  expect_gt(nrow(df_converted_nosource), 0)
})
close_database(con)
rm(list = ls())
gc()
cat("finished testing convert_lengths\n")