tests/testthat/test-filterData.R

In federicomarini/bettr: A Better Way To Explore What Is Best

test_that("filterData works", {
    df <- data.frame(Method = rep(c("A", "B", "C"), each = 3),
                     Metric = rep(c("m1", "m2", "m3"), 3),
                     Value = runif(n = 9, min = 0, max = 3)) |>
        tidyr::spread(key = Metric, value = Value)
    metrics <- setdiff(colnames(df), "Method")
    metricInfo <- data.frame(Metric = c("m1", "m2", "m3"), num = c(1, 1, 2),
                             lets3 = c("m", "n", "o"))
    idInfo <- data.frame(Method = c("A", "B", "C"), lets = c("a", "b", "b"),
                         lets2 = c("d", "d", "e"))
    
    ## No filtering
    keepIds <- c("A", "B", "C")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("d", "e"))
    keepMetrics <- c("m1", "m2", "m3")
    keepMetricsBy <- list(num = c(1, 2), lets3 = c("m", "n", "o"))
    fd <- .filterData(df = df, idInfo = idInfo, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = metricInfo, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(3, 4))
    expect_named(fd, c("Method", "m1", "m2", "m3"))
    expect_equal(fd$Method, c("A", "B", "C"))
    expect_equal(fd$m1, df$m1)
    
    ## Method filtering
    keepIds <- c("A", "C")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("d", "e"))
    keepMetrics <- c("m1", "m2", "m3")
    keepMetricsBy <- list(num = c(1, 2), lets3 = c("m", "n", "o"))
    fd <- .filterData(df = df, idInfo = idInfo, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = metricInfo, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(2, 4))
    expect_named(fd, c("Method", "m1", "m2", "m3"))
    expect_equal(fd$Method, c("A", "C"))
    expect_equal(fd$m1, df$m1[c(1, 3)])

    ## Method filtering by annotation
    keepIds <- c("A", "C")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("d"))
    keepMetrics <- c("m1", "m2", "m3")
    keepMetricsBy <- list(num = c(1, 2), lets3 = c("m", "n", "o"))
    fd <- .filterData(df = df, idInfo = idInfo, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = metricInfo, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(1, 4))
    expect_named(fd, c("Method", "m1", "m2", "m3"))
    expect_equal(fd$Method, c("A"))
    expect_equal(fd$m1, df$m1[c(1)])

    ## Method filtering
    keepIds <- c("A", "C")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("e"))
    keepMetrics <- c("m1", "m2", "m3")
    keepMetricsBy <- list(num = c(1, 2), lets3 = c("m", "n", "o"))
    fd <- .filterData(df = df, idInfo = idInfo, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = metricInfo, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(1, 4))
    expect_named(fd, c("Method", "m1", "m2", "m3"))
    expect_equal(fd$Method, c("C"))
    expect_equal(fd$m1, df$m1[c(3)])
    
    ## Method filtering
    keepIds <- c("A", "B", "C")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("e"))
    keepMetrics <- c("m1", "m2", "m3")
    keepMetricsBy <- list(num = c(1, 2), lets3 = c("m", "n", "o"))
    fd <- .filterData(df = df, idInfo = idInfo, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = metricInfo, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(1, 4))
    expect_named(fd, c("Method", "m1", "m2", "m3"))
    expect_equal(fd$Method, c("C"))
    expect_equal(fd$m1, df$m1[c(3)])
    
    ## Metric filtering
    keepIds <- c("A", "B", "C")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("d", "e"))
    keepMetrics <- c("m2", "m3")
    keepMetricsBy <- list(num = c(1, 2), lets3 = c("m", "n", "o"))
    fd <- .filterData(df = df, idInfo = idInfo, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = metricInfo, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(3, 3))
    expect_named(fd, c("Method", "m2", "m3"))
    expect_equal(fd$Method, c("A", "B", "C"))
    expect_equal(fd$m2, df$m2)
    
    ## Metric filtering by annotation
    keepIds <- c("A", "B", "C")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("d", "e"))
    keepMetrics <- c("m2", "m3")
    keepMetricsBy <- list(num = c(2), lets3 = c("m", "n", "o"))
    fd <- .filterData(df = df, idInfo = idInfo, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = metricInfo, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(3, 2))
    expect_named(fd, c("Method", "m3"))
    expect_equal(fd$Method, c("A", "B", "C"))
    expect_equal(fd$m3, df$m3)
    
    ## Method and metric filtering
    keepIds <- c("A", "B")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("d", "e"))
    keepMetrics <- c("m2", "m3")
    keepMetricsBy <- list(num = c(2), lets3 = c("m", "n"))
    fd <- .filterData(df = df, idInfo = idInfo, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = metricInfo, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(2, 1))
    expect_named(fd, c("Method"))
    expect_equal(fd$Method, c("A", "B"))
    
    ## Method and metric filtering
    keepIds <- c("A", "B")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("d", "e"))
    keepMetrics <- c("m2", "m3")
    keepMetricsBy <- list(num = c(1), lets3 = c("m", "n"))
    fd <- .filterData(df = df, idInfo = idInfo, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = metricInfo, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(2, 2))
    expect_named(fd, c("Method", "m2"))
    expect_equal(fd$Method, c("A", "B"))
    
    ## Method and metric filtering, no idInfo
    keepIds <- c("A", "B")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("d", "e"))
    keepMetrics <- c("m2", "m3")
    keepMetricsBy <- list(num = c(1), lets3 = c("m", "n"))
    fd <- .filterData(df = df, idInfo = NULL, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = metricInfo, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(2, 2))
    expect_named(fd, c("Method", "m2"))
    expect_equal(fd$Method, c("A", "B"))
    
    ## Method and metric filtering, no metricInfo
    keepIds <- c("A", "B")
    keepIdsBy <- list(lets = c("a", "b"), lets2 = c("d", "e"))
    keepMetrics <- c("m2", "m3")
    keepMetricsBy <- list(num = c(1), lets3 = c("m", "n"))
    fd <- .filterData(df = df, idInfo = NULL, idCol = "Method", 
                      keepIds = keepIds, keepIdsBy = keepIdsBy, 
                      metricInfo = NULL, metricCol = "Metric",
                      keepMetrics = keepMetrics, keepMetricsBy = keepMetricsBy, 
                      metrics = metrics)
    expect_s3_class(fd, "data.frame")
    expect_equal(dim(fd), c(2, 3))
    expect_named(fd, c("Method", "m2", "m3"))
    expect_equal(fd$Method, c("A", "B"))

})