Fix/non atomic values #108
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KatherineKayMRG
approved these changes
Feb 19, 2022
kyleam
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to metrumresearchgroup/pmforest
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Mar 18, 2022
yspec 0.5.2 now errors for miscoded values. From its NEWS:
ys_load() will now detect if values / decode are mis-coded as a
list of lists; all items in values and decode must be atomic
This leads to two pmforest test failures with errors like this:
Error (test-base-plot.R:6:1): (code run outside of `test_that()`)
Error: invalid column data
In file: analysis3.yml
column: BLQ
- values field includes non-atomic data ...
- yaml code possibly used brackets [ ] when braces { } were
intended
[...]
7. yspec:::.stop("invalid ", context, " data\n", file, "\n", err)
at yspec/R/load_spec.R:139:2
Adjust the BLQ value to have the correct coding (see
<metrumresearchgroup/yspec#108>).
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Summary
Basically, when values are coded like this:
values: [ male: 1, female: 2]yaml returns a list of lists; the correct coding is
values: {male: 1, female: 2}This PR implements a check for
valuesto make sure they are atomic and generates an error when not.