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Compute accuracy metrics of taxonomic assignation using a mock (known) community for one rank

Source: R/compare_taxo.R
tc_metrics_mock_vec.Rd

lifecycle-experimental

Compute numerous metrics comparing the computed taxonomic assignation to a true assignation.

Note that to compute all metrics, one need to insert fake taxa (by shuffling sequences and/or by adding external sequences). The user must fake taxa using functions add_external_seq_pq(), add_shuffle_seq_pq()) before taxonomic assignation.

Usage

tc_metrics_mock_vec(
  physeq,
  taxonomic_rank,
  true_values,
  fake_taxa = TRUE,
  fake_pattern = c("^fake_", "^external_"),
  verbose = TRUE
)

Arguments

physeq

(required) A phyloseq-class object obtained using the phyloseq package.

taxonomic_rank

(required) Name (or number) of a taxonomic rank to count.

true_values

(required) A vector with the true taxonomic assignation

fake_taxa

(logical, default TRUE) If TRUE, the fake_pattern vector is used to identify fake taxa, i.e. taxa who are not in the reference database (see add_external_seq_pq()) or taxa with fake sequences (see add_shuffle_seq_pq()).

fake_pattern

(character vector, default c("^fake_", "^external_")) A vector of patterns used to identify the fake taxa using a regex search in their name.

verbose

(logical, default TRUE) If TRUE, print informative messages.

Value

A list of metrics (see the confusion matrix article on wikipedia):

  • TP (number of true positive)

  • FP (number of false positive)

  • FN (number of false negative)

  • FDR (false discovery rate) = FP / (FP + TP)

  • TPR (true positive rate, also named recall or sensitivity)

  • PPV (positive predictive value, also named precision) = TP / (TP + FP)

  • F1_score (F1 score) = 2 * TP / (2 * TP + FP + FN)

If fake taxa are present and fake_taxa is true, other metrics are computed:

  • TN (number of true negative)

  • ACC (Accuracy) = (TP + TN) / (TP + TN + FP + FN)

  • MCC (Matthews correlation coefficient) = (TP * TN - FP * FN) / sqrt((TP + FP) * (TP + FN) * (FP + TN) * (TN + FN))

See also

tc_metrics_mock(), add_external_seq_pq(), add_shuffle_seq_pq())

Author

Adrien Taudière