check_strat not working

[afredston]

When I run the check_strat example provided in the documentation ?check_strat, I get an error:

> neus.check <- check_strat(neus[,c("year"):=list(as.integer(year))], "neus")
Error in is.finite(y) : default method not implemented for type 'list'

Thanks for looking into this!

[rBatt]

I think this has been fixed. The problem was, apparently, some change to data.table.

Previously, doing something like

a <- data.table(ref=sample(LETTERS, 20, replace=TRUE), goat=rnorm(20))
a[,1:length(unique(ref))]

would return something like

[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14

i.e., a sequence of integers beginning at 1 and increasing to the maximum number of unique values in the column ref. Now, however, it returns something like this:

ref

1: M
2: V
3: X
4: F
5: K
6: K
7: S
8: A
9: T
10: N
11: C
12: I
13: K
14: C
15: U
16: L
17: A
18: G
19: F
20: M

I'm not entirely sure what it's getting at, here. The fix is to simply wrap the j statement (the stuff after the first comma) in ():

a[,(1:length(unique(ref)))]

@afredstonhermann --- if it works for you now, I can assume the fix was good and I'll close the issue. Thanks for calling this to my attention, and for helping me test!

[afredston]

Thanks @rBatt! Happy to test the function, but I can't get devtools::install_github("rBatt/trawlData") to run. I get basically the same error on the NCEAS server and on my local machine (except the path name to the package, of course):

Error in load(zfile, envir = envir) : 
  bad restore file magic number (file may be corrupted) -- no data loaded
ERROR: lazydata failed for package ‘trawlData’
* removing ‘/home/fredstonhermann/R/x86_64-pc-linux-gnu-library/3.4/trawlData’

Any ideas for what might be the issue? Sorry this bug refuses to die...

[rBatt]

yeah, you'll have to do another `git pull` or possibly `git lfs pull` to get the most recent version of the repo, then open up Terminal (on Mac), navigate to the directory of the repo, and do a `devtools::install()`

…

On Tue, Jun 26, 2018 at 9:24 AM Alexa Fredston-Hermann < ***@***.***> wrote: Thanks @rBatt <https://github.com/rBatt>! Happy to test the function, but I can't get devtools::install_github("rBatt/trawlData") to run. I get basically the same error on the NCEAS server and on my local machine (except the path name to the package, of course): Error in load(zfile, envir = envir) : bad restore file magic number (file may be corrupted) -- no data loaded ERROR: lazydata failed for package ‘trawlData’ * removing ‘/home/fredstonhermann/R/x86_64-pc-linux-gnu-library/3.4/trawlData’ Any ideas for what might be the issue? Sorry this bug refuses to die... — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#78 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFXrfxJA5_8hGPssxqJV74qUG2qx2C77ks5uAjXzgaJpZM4U0AtT> .

-- Ryan D. Batt, Ph.D. Aquatic Ecologist Postdoctoral Fellow, National Academy of Sciences, US EPA Website: batt.limnology.wisc.edu Pronouns: he/ him

[afredston]

OK, took a minute to figure that out on the server, but it works perfectly now--and isn't even that slow ;) Thank you!