README.md
In NFA/alsr: Reading of ALS result reports into dataframe

alsr - Import laboratory reports from ALS Scandinavia AB easy

Two types of reports are supported. They are in this package internally referred to as v1 and v2. The reports in v1 were used until sometime in 2020 when v2 format was introduced. They differ somewhat in layout and structure.

Reports from subcontractors are currently not supported.

Use a package that can install from Github. For example remotes.

install.packages("remotes")

Then you can install alsr using:

remotes::install_github("NFA/alsr")

Parsing a PDF report:

> library(alsr)
> data <- read_ALS("report.pdf")
i ALS V1 report.
i Parsing tables.
√ Parsed 3 table(s) from report.pdf.

> data
# ALS Report (V1)
# Filename: report.pdf
# Order ID: L2022374
# Arrived: 2020-10-26
# Issued: 2020-11-11
# Project: 1773270
# Analyses: M2-VB
# Samples: N15-Sludge, N15-C-Cake and N15-T-Cake
# Number of tables: 3

Objects are represented using the S4 class structure. Each sample analyzed is parsed into a separate table. The tables are stored in the tables slot as a list of data frames. The tables slot can be accessed using the @ operator.

> data@tables
# prints out the list of tables
> data@tables[[1]]
# prints out the first table

Alternatively, the helper function reports may be used to return all tables (samples) put together into one single data frame.

> reports(data)
# prints out all tables in one

If you want to read all the PDFs in a certain directory the following little function may be of use:

read_all_ALS <- function(path) {
   als_files <- dir(path, pattern = "*.pdf", full.names = TRUE)

   als_objects <- lapply(als_files, alsr::read_ALS)
   als_tables <- lapply(als_objects, alsr::reports)

   do.call("rbind", als_tables)
}

When a result for a parameter is below the reporting limit the numerical part of the result is parsed into the Result column and the BQL (below quantification limit) column is set to TRUE. For example, a result <1, the number 1 is parsed into Result, and BQL set to TRUE.

If the report is an replacement for an earlier report the replacement slot is set to true. However, there is no further logic to discard the previous report, this you will have to curate manually.