missing value handling in avtable and avtable_import

[smgogarten]

Currently, NA values in a data.frame written to AnVIL with avtable_import results in the string "NA" appearing in the AnVIL data table, regardless of data type. Reading the same data table back into R with avtable results in NA for numeric columns, but the character string "NA" for character columns.

It would be helpful to control how missing values are read and written, as in the na argument to read_delim and write_delim in the readr package.

[mtmorgan]

Can you try

BiocManager::install("Bioconductor/AnVIL", ref = "issue-75-avtable-NA")

Examples include

## round-trip "" and NA_character_ from R to AnVIL and back
tbl0 <- tibble(
    issue75 = letters[1:4],
    x = c("a", "", NA, "d"),
    i = c(1:2, NA, 3L),
    r = as.numeric(i),
)
avtable_import(tbl0)
avtable("issue75", na = "NA")

## preserve "", NA_character_, and "NA" (sodium? North America?)
tbl0 <- tibble(
    issue75 = letters[1:4],
    x = c("a", "", NA, "NA"),
    i = c(1:2, NA, 3L),
    r = as.numeric(i),
)
avtable_import(tbl0, na = "__MISSING_VALUE__")
avtable("issue75", na = "__MISSING_VALUE__")

This follows the {readr} defaults, and change the default behavior of AnVIL (which wasn't very helpful anyway)

[smgogarten]

This is great, thank you!