The goal of marcr is to collect various functions that may be useful in other projects. It’s a personal “misc” package.
You can install the released version of marcr from Github with:
remotes::install_github("marcmtk/marcr")This is a basic example which shows you how to solve a common problem:
library(marcr)
read_cobas_rst("data-raw/invalid.rst")
#> # A tibble: 1 x 27
#> AnalysisDateTime `Approved By` Assay `Ctrl Exp` Details `Device S/N`
#> <dttm> <chr> <chr> <chr> <chr> <chr>
#> 1 2019-01-01 23:44:00 <NA> Liat~ <NA> "" M1-E-17163
#> # ... with 21 more variables: `Failure Code` <chr>, MacAddress <chr>,
#> # Operator <chr>, OrderingPhysician <chr>, Patient <chr>, `Report
#> # Results` <chr>, `Run No.` <chr>, `Run Status` <chr>, `Sample
#> # ID` <chr>, SampleType <chr>, `SW Ver` <chr>, `Time/Date` <chr>, `Tube
#> # Exp` <date>, `Tube Lot` <chr>, `Tube S/N` <chr>, Use <chr>,
#> # infl_a <lgl>, infl_b <lgl>, rsv <lgl>, invalid <lgl>, warning <lgl>
read_biotyper_out("data-raw/biotyper_1.astm")
#> # A tibble: 350 x 11
#> organism organism_id score spot_number guess_number clinical_name sample
#> <chr> <chr> <dbl> <chr> <chr> <chr> <chr>
#> 1 Meyeroz~ 4929 1.45 1 1 Candida guil~ 10041~
#> 2 Lactoba~ 1603 1.39 1 2 Lactobacillu~ 10041~
#> 3 Prevote~ 28127 1.38 1 3 Prevotella b~ 10041~
#> 4 Pseudom~ 75612 1.36 1 4 Pseudomonas ~ 10041~
#> 5 Lactoba~ 33962 1.30 1 5 Lactobacillu~ 10041~
#> 6 Strepto~ 1923 1.30 1 6 Streptomyces~ 10041~
#> 7 Candida~ 49331 1.26 1 7 Candida para~ 10041~
#> 8 Burkhol~ 292 1.25 1 8 Burkholderia~ 10041~
#> 9 Lactoba~ 259059 1.25 1 9 Lactobacillu~ 10041~
#> 10 Lactoba~ 47770 1.23 1 10 Lactobacillu~ 10041~
#> # ... with 340 more rows, and 4 more variables: isolate <int>,
#> # spot_location <chr>, time <dttm>, instrument_id <chr>
random_timestamp(1)
#> [1] "2016-05-01T16:19:42.543"