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fix `as.incfreq()` warnings, clarify documentation and add tests #66

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stragu wants to merge 3 commits into JohnsonHsieh:master from stragu:master

stragu commented Aug 14, 2021

as.incfreq() would throw a warning when the presence-absence data was only 0s or only 1s.

For example, try the following in the current release:

test_df0 <- data.frame(col1 = rep.int(0, 10))
library(iNEXT)
as.incfreq(test_df0)

This PR fixes the following:

Make it so warning is not shown when only either 1 or 0 is present
Clarify warnings and documentation
Use warning() instead of warnings() for the vector warning (assumed to be a typo)
Add tests for as.infreq()

I am not particularly familiar with the package, so wanted to also ask:

Is the current behaviour for NAs correct? (As in, keeps the NA, and returns NAs as row sums)
What should happen if there are negative values in the matrix or dataframe? Currently, they are not convert to 1s in line 374.

stragu added 3 commits

August 14, 2021 18:16


          fix warning for only 0s or only 1s; clarify warning and docs

f75554b


          use warning() instead of warnings()

b787d30


          add tests for as.incfreq()

bf32d2b

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