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Read a variable list out of a SAS job

Source: R/sas_blocks.R
sas_variable_block.Rd

The SAS jobs this package's callers reproduce specify their variables as blocks in the .sas: a phase name on its own line, then comma-separated names, terminated by a bare ;.

Reading them rather than transcribing them is the point. A transcribed list drifts from the job it claims to reproduce, and nothing catches it.

Usage

sas_variable_block(lines, marker, after = NULL, what = "block")

Arguments

lines

Character vector: the .sas file, as from readLines().

marker

Regular expression matching the line that opens the block, e.g. "^\\s*early\\s*$".

after

Optional regular expression. When given, the search starts at the first line matching it, so a block can be located inside one particular macro rather than the first one in the file.

what

Character label for the block, used in error messages.

Value

A character vector of unique variable names, lowercased, in the order they appear in the block.

Details

Comment handling is the whole difficulty, and getting it wrong is silent in both directions. Measured on a real screen (bh.dead_s3_JR.sas):

  • Stripping /*...*/ line by line leaves banner comments intact, because /***** Patient Variables *****/ contains * and so does not match a [^*]* body. The banner text then glues onto the first name on the next line and that name vanishes: female, afib_pr, plvidd and size were all lost this way.

  • A /* ... */ spanning two lines is never stripped at all, so a commented-out variable is read as live: avet_con entered a screen that way.

Collapsing the block first and stripping lazily handles both, and that is what this function does.

Three name forms are normalised. name=value appears where a job carries starting or converged estimates; only the name is taken, because a job's converged values are its answer for its own study and must not be inherited by a copy of it. name/I marks a variable forced into the model, and the suffix is an option on the name rather than part of it. Names are lowercased, because SAS variable names are case-insensitive and read_clinical_data lowercases them.

See also

sas_path, covariate_audit

Examples

sas <- c("%macro final;", "  early", "    age, ln_age, /* dropped */",
         "    bsa=0.31", "  ;", "%mend;")
sas_variable_block(sas, "^\\s*early\\s*$", after = "^\\s*%macro\\s+final")
#> [1] "age"    "ln_age" "bsa"