amregtest

“amregtest” stands for “allelematch regression test”. allelematch is an R package for identifying and removing duplicate multilocus genotypes from microsatellite data sets. amregtest verifies that allelematch remains backwards compatible across versions.

By decoupling the regression test suite from the main allelematch source code and its specific testthat dependencies, amregtest allows you to run regression tests against any version of allelematch without modifying the package under test.

Installation

You can install the released version from CRAN with:

# Install remotes if you don't have it
install.packages("remotes")

# Install amregtest with tests included
remotes::install_cran(
  "amregtest", 
  type = "source", 
  INSTALL_opts = "--install-tests"
)

Usage

library(allelematch)
library(amregtest)

Run the full regression test suite against your currently installed version of allelematch (takes a few minutes):

artRun()

To run only tests whose names match a Perl regular expression:

artRun(filter = "amExample2|amExample4")

    About to test installed version of allelematch:  <<<3.0.0>>>
✔ | F W  S  OK | Context
✔ |         14 | amExample2 [4.6s]
✔ |         14 | amExample4 [5.8s]

══ Results ═══════════════════════════════════════════════
Duration: 10.4 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 28 ]
    Done testing installed version of allelematch:  <<<3.0.0>>>

List all available tests without running them:

artList()

## 
## Tests in files under "C:/Users/Torva/AppData/Local/Temp/RtmpiKfJ30/temp_libpath9ec641c4c61/amregtest/tests/testthat/":
## 
## Tests by functions in allelematch:
##  [1] "allelematch_0-package"            
##  [2] "allelematch_1-amDataset"          
##  [3] "allelematch_1-amDataset_negative" 
##  [4] "allelematch_2-amMatrix"           
##  [5] "allelematch_2-amMatrix_negative"  
##  [6] "allelematch_3-amPairwise"         
##  [7] "allelematch_3-amPairwise_negative"
##  [8] "allelematch_3-amPairwise_print"   
##  [9] "allelematch_4-amCluster-amMini"   
## [10] "allelematch_4-amCluster-Ex1"      
## [11] "allelematch_4-amCluster-Ex2"      
## [12] "allelematch_4-amCluster-Ex3"      
## [13] "allelematch_4-amCluster-Ex4"      
## [14] "allelematch_4-amCluster-Ex5"      
## [15] "allelematch_4-amCluster"          
## [16] "allelematch_4-amCluster_print"    
## [17] "allelematch_5-amAlleleFreq"       
## [18] "allelematch_6-amUnique"           
## [19] "allelematch_6-amUnique_negative"  
## [20] "allelematch_6-amUnique_print"     
## [21] "allelematch_7-amUniqueProfile"    
## 
## Reproduction of the examples in 'allelematchSuppDoc.pdf':
## [1] "amExample1" "amExample2" "amExample3" "amExample4"
## 
## Other:
## [1] "ggData"

Check the installed versions of allelematch and amregtest:

artVersion()

## 
##     Installed version of package 'amregtest'   is: 1.3.2      (Built 21:20)
##     Installed version of package 'allelematch' is: 3.0.0      (Built 13:24)