Clean Data Export

[lukeloken]

Is it possible to create a 'clean' function that removes the flagged observations.

Suggestions:
Add an argument "which" that can either be "ALL" or a list of rules with the default being ALL.
Add an argument that simply deletes the whole row.

clean(flaggedobject, which=ALL, replace=NA)
clean(flaggedobject, which=c(1,2,4), replace=99999)
clean(flaggedobject, which=ALL, deleterow=TRUE)

[jordansread]

Cool, thanks @lukeloken. Great ideas.

[jordansread]

the one change I might suggest is:

clean(flaggedobject, which='ALL', replace=NA) # to replace w/ NA
clean(flaggedobject, which='ALL', replace=NULL) # to delete row

and the ability to do this:

clean(object, which, ..., replace) #as the function arguments, which would support this:
clean(object, 'x > 9999', 'persist(x) > 10', 'MAD(x) > 3', replace=NA)

Thoughts @lukeloken and @aappling-usgs ?

[lukeloken]

I like the replace=Null option.

Do you want the ability to 'clean' an unflagged object?

clean(object, 'x > 9999', 'persist(x) > 10', replace=NA)

Or is it more straightforward to run two commands?

flagged <- flag(object, 'x > 9999', 'persist(x) > 10')
cleaned <- clean(flagged, which=ALL, replace=NA) 

[jordansread]

I like that option personally, because then I can use sensorQC to really rapidly clean a vector or data.frame with one line. The key is having it be a good thing for powerusers but not get in the way of a more normal workflow.

[lukeloken]

I like having both options, but I don't know how difficult this is to code.

[jordansread]

oh yeah, for sure, I was thinking both.

[lukeloken]

I'm have another question for you Jordan: How you would recommend removing a single observation that is clearly an outlier if there are also NA values. I think the MAD function does not work properly if there are NA values also in the series.

  dates <- seq(as.POSIXct('1999-01-01'),by=1,length.out=16)
  values1 <- c(runif(10,2,4),10000, runif(5,2,4))
  values2 <- c(runif(10,2,4),10000, NA, runif(4,2,4))
  data.in1 <- data.frame("DateTime"=dates,"sensor.obs"=values1)
  data.in2 <- data.frame("DateTime"=dates,"sensor.obs"=values2)
  flag(data.in1, "is.na(x)", 'MAD(x) > 3')
  flag(data.in2, "is.na(x)", 'MAD(x) > 3')

The two {flag} commands do not treat the 10000 observation the same.

[jordansread]

whoops, that is a bug. Good catch! #37

Also note that you can do:

values1 <- c(runif(10,2,4),10000, runif(5,2,4))
values2 <- c(runif(10,2,4),10000, NA, runif(4,2,4))
flag(values1, "is.na(x)", 'MAD(x) > 3')
flag(values2, "is.na(x)", 'MAD(x) > 3')

for really simple quick qaqc

[jordansread]

@lukeloken you should be able to try this after doing another devtools::install_github('usgs-r/sensorQC')

check out the readme for the pattern: https://github.com/USGS-R/sensorQC/blob/master/README.md

Can you let me if that is what you expected? (note that I changed 'ALL' to 'all' as an argument just to be consistent with other packages that is used in)

[lukeloken]

Jordan, I think this works great. The only comment I have is in regard to the output of {clean}. Is there any reason to keep the structure of this a list rather than unlisting it to a data.frame class? This would save a line of code after processing.

[jordansread]

I think I need to think on that...
In the meantime, clean(bla bla)$sensor should get you a data.frame, right?