tests/testthat/test-data-summary.R

In chromer: Interface to Chromosome Counts Database API

context("Testing data processing and summary")

test_that("data processing and summary", {

    skip_if_offline()    # offline or on CRAN
    skip_if(ccdb_down()) # ccdb.tau.ac.il is down

    cp <- chrom_counts("Castilleja", "genus")
    sum_res <- summarize_counts(cp)

    parse_counts <- chromer:::parse_counts
    get_counts_n <- chromer:::get_counts_n


    # Summary returns correct object"
    expect_that(sum_res, is_a("data.frame"))
    expect_equal(ncol(sum_res), 5)

    coln <- c("resolved_binomial", "count_type", "count",
              "inferred_n", "num_records")
    expect_equal(colnames(sum_res), coln)

    sp_cnt <- unique(cp$resolved_binomial)
    sp_sum <- sum_res$resolved_binomial
    expect_true(all(sp_sum %in% sp_cnt))

    expect_true(all(is.numeric(sum_res$count)))
    expect_true(all(is.numeric(sum_res$num_records)))

    ##############################


    # Only takes a chrom.counts object
    tmp <- cp
    attr(tmp, "class") <- "data.frame"
    expect_error(summarize_counts(tmp))

    ##############################

    # Parsing works properly
    tmp <- c(1,2,3)
    expect_equal(parse_counts(as.character(tmp)), tmp)
    tmp2 <- c(0,1,2,3)
    expect_equal(parse_counts(as.character(tmp2)), tmp)

    tmp3 <- c(1, 2, "3-4", "c.5", "6/7")
    expect_equal(parse_counts(tmp3), seq_len(7))

})