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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 development version of amregtest from GitHub with:

# install.packages("devtools")
devtools::install_github("torstax/amregtest")

Usage

library(allelematch)
library(amregtest)

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

artRun()

##     About to test installed version of allelematch:  <<<2.5.5>>>
## FAILED  WARNINGS  SKIPPED  OK      FILE
## ------------------------------------------------------------------------ 
## 0       0         0        74      test-allelematch_1-amDataset.R
## 0       0         0        10      test-allelematch_1-amDataset_negative.R
## 0       0         0        30      test-allelematch_2-amMatrix.R
## 0       0         0        20      test-allelematch_2-amMatrix_negative.R
## 0       0         0        362     test-allelematch_3-amPairwise.R
## 0       0         0        39      test-allelematch_3-amPairwise_negative.R
## 0       1         0        19      test-allelematch_3-amPairwise_print.R
## 0       0         0        1344    test-allelematch_4-amCluster.R
## 0       1         0        19      test-allelematch_4-amCluster_print.R
## 0       0         0        22      test-allelematch_5-amAlleleFreq.R
## 0       0         0        768     test-allelematch_6-amUnique.R
## 0       0         0        42      test-allelematch_6-amUnique_negative.R
## 0       1         0        21      test-allelematch_6-amUnique_print.R
## 0       0         0        13      test-allelematch_7-amUniqueProfile.R
## 0       0         0        16      test-amExample1.R
## 0       0         0        14      test-amExample2.R
## 0       0         0        14      test-amExample3.R
## 0       0         0        14      test-amExample4.R
## 0       0         0        4       test-art_api.R
## 0       0         0        8       test-ggData.R
## ------------------------------------------------------------------------ 
## 0       3         0        2853    TOTAL
##     Done testing installed version of allelematch:  <<<2.5.5>>>

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

artRun(filter = "amExample2|amExample4")

##     About to test installed version of allelematch:  <<<2.5.5>>>
## FAILED  WARNINGS  SKIPPED  OK      FILE
## ------------------------------------------------------------------------ 
## 0       0         1        7       test-amExample2.R
## 0       0         1        9       test-amExample4.R
## ------------------------------------------------------------------------ 
## 0       0         2        16      TOTAL
##     Done testing installed version of allelematch:  <<<2.5.5>>>

List all available tests without running them:

artList()

## 
## Tests in files under "C:/Users/Torva/AppData/Local/Temp/RtmpEf1k0b/temp_libpath53f819d62beb/amregtest/tests/testthat/":
## 
## Tests by functions in allelematch:
##  [1] "allelematch_1-amDataset"          
##  [2] "allelematch_1-amDataset_negative" 
##  [3] "allelematch_2-amMatrix"           
##  [4] "allelematch_2-amMatrix_negative"  
##  [5] "allelematch_3-amPairwise"         
##  [6] "allelematch_3-amPairwise_negative"
##  [7] "allelematch_3-amPairwise_print"   
##  [8] "allelematch_4-amCluster"          
##  [9] "allelematch_4-amCluster_print"    
## [10] "allelematch_5-amAlleleFreq"       
## [11] "allelematch_6-amUnique"           
## [12] "allelematch_6-amUnique_negative"  
## [13] "allelematch_6-amUnique_print"     
## [14] "allelematch_7-amUniqueProfile"    
## 
## Reproduction of the examples in 'allelematchSuppDoc.pdf':
## [1] "amExample1" "amExample2" "amExample3" "amExample4"
## 
## Other:
## [1] "art_api" "ggData"

Check the installed versions of allelematch and amregtest:

artVersion()

## 
##     Version of package 'amregtest' is 1.0.10
##     Installed (and thus tested) version of package 'allelematch' is: 2.5.5

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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