• setup a default configuration file for stricter linters
• update development dependencies

Functions to work with the on-line side of FAERS

• download a (single) specific FAERS db Quarterly Data Extract (QDE), in the preferred format:

retrieve_qde(
    year = format(Sys.Date(), "%Y"),
    quarter = c("q1", "q2", "q3", "q4"),
    type = c("ascii", "xml")
)

• retrieve the list (only) for the current FAERS db's index/names/ref (on-line):

fetch_remote()

• retrieve the list (only) for the current FAERS db's index/names/ref (on-line):

fetch_local(path = here::here("faers))

• download all the locally missing FAERS dbs, in the preferred format:

update_local(
    path = here::here(faers),
    type = c("ascii", "xml")
)

Functions to read FAERS XML DBs in R

Table-specific read_*()er

Create a suitable function getting the file path in input and return a (list of) tibble(s), correctly formatted (w/ each column in the preferred type). We do not provide a default path for these functions.

• read_xml(path)

NOTE: we use the functions in the {tidyverse} (in particular in the {xml2}), and in the {janitor} packages to implement our read_*() functions.

Table-agnostic read_*()ers

Define a generalized function that can infer the correct type of file and internally call the appropriate read_*() function.

• read_faers(path)

The final answers requested to the user after launching update_local do not follow any explicit question (ending in a question mark) :-)

get this message

Warning message:
`xml_node()` was deprecated in rvest 1.0.0.
Please use `html_element()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated. 
> lifecycle::last_lifecycle_warnings()
[[1]]
<deprecated>
message: `xml_node()` was deprecated in rvest 1.0.0.
Please use `html_element()` instead.
Backtrace:
  1. faers.db::update_local("C:\\Users\\corrado.lanera\\Unit of Biostatistics Epidemiology and Public Health\\FAERS VAERS - FAERS data - FAERS data")
 10. rvest::xml_node(., css = "#accordion")

It could be helpful to set a function set_basepath to set a default base "faers_raw_data" path in the system.

Consider a default to Sys.getenv("FAERS_RAW_PATH"), or similar.

It could be useful to add a progress bar to the update process.

see progressr

• It should be useful to include in the readme the instruction and examples to use the package, in a very simple way.
• It could be important to provide vignettes with complete use-cases scenarios.

add a new coloum in each faers DB, in order to identify which year and quad it is refers.

After the download of all .txt file, the function show this error:
Error in download.file(Url, method = method, ...)
cannot open URL 'https://fis.fda.gov/content/Export/faers_xml_2020q3.zip'.

Functions to read FAERS ASCII DBs in R

Table-specific read_*()ers

For each kind of ASCII file/table, create a suitable function getting the file path in input and return a tibble, correctly formatted (w/ each column in the preferred type). We do not provide a default path for these functions.

• read_demo(path)
• read_drug(path)
• read_reac(path)
• read_outc(path)
• read_rpsr(path)
• read_ther(path)
• read_indi(path)

NOTE: we use the functions in the {tidyverse} (in particular in the {readr}), and in the {janitor} packages to implement our read_*() functions.