tests/README.md

In BioCor: Functional similarities

Tests and Coverage

15 septiembre, 2018 12:21:00

• Coverage
• Unit Tests

This output is created by covrpage.

Coverage

Coverage summary is created using the covr package.

| Object | Coverage (%) | |:----------------------------------------------|:------------:| | BioCor | 87.25 | | R/geneSim.R | 53.19 | | R/mgeneSim.R | 53.70 | | R/pathSim.R | 69.23 | | R/mpathSim.R | 86.49 | | R/combineScores.R | 86.55 | | R/mclusterSim.R | 91.38 | | R/clusterSim.R | 95.00 | | R/clusterGeneSim.R | 98.55 | | R/AintoB.R | 100.00 | | R/auxiliar.R | 100.00 | | R/combineSources.R | 100.00 | | R/conversions.R | 100.00 | | R/diceSim.R | 100.00 | | R/mclusterGeneSim.R | 100.00 | | R/similarities.R | 100.00 | | R/weighted.R | 100.00 | | R/zzz.R | 100.00 |

Unit Tests

Unit Test summary is created using the testthat package.

| | file | n| time| error| failed| skipped| warning| |------------------------|:---------------------------------------------------------|----:|------:|------:|-------:|--------:|--------:| | test_AintoB.R | test_AintoB.R | 6| 0.314| 0| 0| 0| 0| | test_auxiliar.R | test_auxiliar.R | 16| 0.040| 0| 0| 0| 0| | test_clusterGeneSim.R | test_clusterGeneSim.R | 49| 0.202| 0| 0| 0| 0| | test_clusterSim.R | test_clusterSim.R | 57| 0.200| 0| 0| 0| 0| | test_combineScores.R | test_combineScores.R | 62| 0.104| 0| 0| 0| 0| | test_combineSources.R | test_combineSources.R | 5| 0.009| 0| 0| 0| 0| | test_conversions.R | test_conversions.R | 7| 0.010| 0| 0| 0| 0| | test_diceSim.R | test_diceSim.R | 7| 0.010| 0| 0| 0| 0| | test_geneSim.R | test_geneSim.R | 23| 0.083| 0| 0| 0| 0| | test_mpathSim.R | test_mpathSim.R | 25| 0.057| 0| 0| 0| 0| | test_pathSim.R | test_pathSim.R | 6| 0.011| 0| 0| 0| 0| | test_similarities.R | test_similarities.R | 18| 0.028| 0| 0| 0| 0| | test_weighted.R | test_weighted.R | 14| 0.017| 0| 0| 0| 0|

Show Detailed Test Results

| file | context | test | status | n| time| |:-----------------------------------------------------------------|:------------------------------|:--------------------------------------------------|:-------|----:|------:| | test_AintoB.R | Testing AintoB functions | AintoB | PASS | 6| 0.314| | test_auxiliar.R | Testing auxiliar functions | seq2mat puts a combination to the right place | PASS | 5| 0.013| | test_auxiliar.R | Testing auxiliar functions | combinadic | PASS | 3| 0.006| | test_auxiliar.R | Testing auxiliar functions | duplicateIndices | PASS | 3| 0.006| | test_auxiliar.R | Testing auxiliar functions | removeDup | PASS | 4| 0.012| | test_auxiliar.R | Testing auxiliar functions | inverseList | PASS | 1| 0.003| | test_clusterGeneSim.R | Testing clusterGeneSim | clusterGeneSim | PASS | 13| 0.081| | test_clusterGeneSim.R | Testing clusterGeneSim | mclusterGeneSim | PASS | 9| 0.040| | test_clusterGeneSim.R | Testing clusterGeneSim | clusterGeneSim GeneSetCollection | PASS | 16| 0.045| | test_clusterGeneSim.R | Testing clusterGeneSim | mclusterGeneSim GeneSetCollection | PASS | 11| 0.036| | test_clusterSim.R | Testing clusterSim | clusterSim | PASS | 13| 0.056| | test_clusterSim.R | Testing clusterSim | mclusterSim | PASS | 16| 0.069| | test_clusterSim.R | Testing clusterSim | clusterSim | PASS | 14| 0.036| | test_clusterSim.R | Testing clusterSim | mclusterSim | PASS | 14| 0.039| | test_combineScores.R | Testing combineScores | combineScores | PASS | 42| 0.063| | test_combineScores.R | Testing combineScores | combineScoresPar | PASS | 1| 0.003| | test_combineScores.R | Testing combineScores | combineScoresPar equivalent to combineScores | PASS | 12| 0.025| | test_combineScores.R | Testing combineScores | reciprocal | PASS | 5| 0.009| | test_combineScores.R | Testing combineScores | BMA | PASS | 1| 0.002| | test_combineScores.R | Testing combineScores | rcmax | PASS | 1| 0.002| | test_combineSources.R | Testing combineSources | combineSources | PASS | 5| 0.009| | test_conversions.R | Testing conversions functions | Conversions | PASS | 7| 0.010| | test_diceSim.R | Testing diceSim | diceSim | PASS | 7| 0.010| | test_geneSim.R | Testing geneSim | geneSim | PASS | 11| 0.036| | test_geneSim.R | Testing geneSim | mgeneSim | PASS | 12| 0.047| | test_mpathSim.R | Testing mpathSim | mpathSim | PASS | 7| 0.014| | test_mpathSim.R | Testing mpathSim | pathSims_matrix | PASS | 3| 0.005| | test_mpathSim.R | Testing mpathSim | mpathSim for GeneSetCollections and list is equal | PASS | 10| 0.032| | test_mpathSim.R | Testing mpathSim | mpathSim for GeneSetCollections | PASS | 5| 0.006| | test_pathSim.R | Testing pathSim | pathSim | PASS | 6| 0.011| | test_similarities.R | Testing Similarities function | addSimilarities | PASS | 9| 0.013| | test_similarities.R | Testing Similarities function | similarities | PASS | 9| 0.015| | test_weighted.R | Testing weighted functions | weighted.sum | PASS | 8| 0.010| | test_weighted.R | Testing weighted functions | weighted.prod | PASS | 6| 0.007|

Session Info

| Field | Value | |:---------|:------------------------------| | Version | R version 3.5.1 (2018-07-02) | | Platform | x86_64-pc-linux-gnu (64-bit) | | Running | Ubuntu 18.04.1 LTS | | Language | en_US | | Timezone | Europe/Madrid |

| Package | Version | |:---------|:--------| | testthat | 2.0.0 | | covr | 3.1.0 | | covrpage | 0.0.55 |

BioCor documentation built on Nov. 8, 2020, 4:56 p.m.