performance-analytics: Assessing classifier performance

In MLInterfaces: Uniform interfaces to R machine learning procedures for data in Bioconductor containers

Description

Methods to calculate the number of true positives (tp), true negatives (tn), false negatives (fn), false positive (fp), accuracy (acc), precision, recall (same as sensitivity), specificity, F1 and macroF1 scores.

Each method also accepts an naAs0 argument definiting if NAs should be replaced by 0 (default is FALSE).

Methods

Methods tp, tn, fp, fn, F1, acc and specificity:

signature(obj = "table")

Methods recall (sensitivity), precision and macroF1:

signature(obj = "classifierOutput", type = "character")

signature(obj = "classifierOutput", type = "missing")

signature(obj = "classifierOutput", type = "numeric")

signature(obj = "table")

Examples

## the confusion matrix
cm <- table(iris$Species, sample(iris$Species))
tp(cm)
tn(cm)
fp(cm)
fn(cm)
acc(cm)
precision(cm)
recall(cm)
F1(cm)
macroF1(cm)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: cluster
Warning message:
replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces' 
    setosa versicolor  virginica 
        14         11         12 
    setosa versicolor  virginica 
        64         61         62 
    setosa versicolor  virginica 
        36         39         38 
    setosa versicolor  virginica 
        36         39         38 
[1] 0.2466667
    setosa versicolor  virginica 
      0.28       0.22       0.24 
    setosa versicolor  virginica 
      0.28       0.22       0.24 
    setosa versicolor  virginica 
      0.28       0.22       0.24 
[1] 0
Warning message:
system call failed: Cannot allocate memory 

MLInterfaces documentation built on Nov. 8, 2020, 8:14 p.m.