Zebulun Arendsee

Missing children of Bacteria

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Session Info ```r Session info ------------------------------------------------------------------ setting value version R version 3.4.3 (2017-11-30) system x86_64, linux-gnu ui X11 language (EN) collate en_US.UTF-8 tz America/Chicago date 2018-02-03 Packages ---------------------------------------------------------------------- package *...

`downsteam` misses descendents of ambiguous clades

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This call ```R taxize::downstream('Brassicaceae', db='ncbi', downto='genus') ``` loses all descendents of the clade 'Brassicaceae incertae sedis'. I believe this clade gets filtered out as ambiguous when `children` is called on...

A long chain of functions, such as: ``` R u >% u %>>% u %>>% u %>>% u %>>% u %>>% u %>>% u %>>% u %>>% u %>>% u...

Very long chains of operations hit the C stack limit and crash. For example: ``` R u >% u %>>% u %>>% u %>>% u %>>% u %>>% u %>>%...

'.' breaks when function call is unbraced

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In `magrittr` you can do this: ```R "a" %>% paste("b", .) ``` But this breaks in `rmonad`: ```R "a" %>>% paste("b", .) ``` While this does work: ```R "a" %>>%...

These all record the same history: ```R foo >% sqrt } bar >% sqrt %>>% sqrt %>>% bar 16 %>>% sqrt %>>% bar 4 %>>% bar ``` This, for example,...

In the expression ``` > "a" %__% "b" %__% "c" %>% get_value() [[1]] [1] "a" [[2]] [1] "c" ``` The second node in the chain is missing. For longer chains,...

How should `rmonad` handle mutable data? For example, if an environment is stored in `rmonad`, say as the head node in an `Rmonad` object, and then the environment is altered...

In the pipeline: ```R "a" %v>% paste("b") %>% funnel("c" %v>% paste("d")) %*>% paste %>% plot(label='value') ``` `funnel` creates an extra node whose purpose seems only to merge the inputs to...

Given the pipeline: ```R "a" %v>% paste("b") %>% funnel("c" %v>% paste("d")) %*>% paste %>% plot(label='value') ``` I can easily cache the nodes wrapping `"a"`, `"c"`, and `"a b c d"`....