[R] What is best way to calculate % of time?
Bert Gunter
bgunter@4567 @end|ng |rom gm@||@com
Wed Dec 25 23:39:09 CET 2019
I will not get into your explanation of details that, like John, I find
opaque. Please DO read Hadley's manifesto, as it appears that you need to
organize your data more appropriately.
AFAICS, however, strictly speaking your data cannot answer the question you
have posed. **Strictly speaking** to know the proportion of active time
bats spend feeding, **for each bat** you would need to know when it is
active and when it is feeding during that time. You could then summarize
this for all bats (e.g. take the average or median proportion) in a species
or whatever. As you cannot identify individual bats in your data, you
cannot do this -- i.e. you cannot answer your question.
So the question then becomes: precisely **how** exactly do you propose
using the data you have to determine when a *group* of bats are active and
when they are feeding? How are the groups explicitly identified and how are
their times active and feeding determined? In short, you need to have
information that is something like:
Bat.Group date active.time.start active.time.end feeding.time.start
feeding.time.end
( for a given date and bat group, there may be many multiple entries;
perhaps for a given group, date, and active time start and end, several
feeding time start/stop entries ( I have no idea how bats behave)).
Until you can expicitly explain how your data can generate such
information, I think it will be difficult/impossible to help you.
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Wed, Dec 25, 2019 at 1:52 PM Neotropical bat risk assessments <
neotropical.bats using gmail.com> wrote:
> Tnx John,
> Yep failed to "reply all" my bad.
>
> Yes the mix of "information" on call type and species are in the same
> field. It will be a single mouse click to export only the "buzz" data
> from the master DB as a separate CSV file from the species data. So this
> could be a new DF/data set for R.
> This is due to the legacy issues of how the acoustic data are added to
> the metadata of the bat call recordings.
> Combining date and times does not provide for sampling nights that roll
> over after midnight.
>
> I may need to reread Hadley's Tidy Data manifesto re: data handling ;-).
>
> The location, date and time does provide unique variables.
> Duplicate times mentioned are the "duplicated" values you noted. This
> happens as the actual call files include seconds for a more precise time
> when the recordings were made. Rounding to nearest minute suffices for
> a summary of total minutes spent with "feeding attempts" vs total
> active time.
>
> The data being gathered is reviewed in a purpose build bat acoustic
> software program when reviewing bat call files. The metadata include
> the "Who", "Where" & "When" recorded. What is added to this as the
> acoustic files are reviewed are information on call types and species IDs.
>
> This metadata is exported as a TXT file and imported into a master
> Access DB I developed over the past 15 years to manage "BIG DATA" as
> they say. As a note I currently it have >1.9 million acoustic call
> records store in the relational DB.
>
> The data output/exported from the DB is sufficient to provide wonderful
> temporal activity plots using GGplot2. Original code for this was
> developed with huge assistance from Hadley eons ago and updated to more
> recent R releases and packages by a few others.
>
> The graphics are great to visualize temporal activity but do not provide
> a simple summary of amount of time spent "foraging AKA feeding buzz
> data" vs total activity time for each species.
>
> Perhaps this is /was not a simple question on how to summarize time data
> to derive a % of each category, be it "buzz" or species.
>
> Tnx again,
> Bruce
>
>
> >
> > Hi Bruce,
> > You replied just to me. I have taken the liberty of cc:ing R-help as
> > there lots of more knowledgeable people than me there who may be able
> > to help.
> > In the meantime I remain confused.
> > Here is my impression of the sample data that you supplied. I have
> > combined Date & Time into a single POSIXct variable, dtime. Just paste
> > it into <b>R</b>
> > ##===============================================================##
> > dat2 <- structure(list(Species = structure(c(1L, 1L, 1L, 1L, 1L, 1L,
> > 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
> > 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
> > 3L, 3L), .Label = c("Buzz", "Ptedav", "Ptemes"), class = "factor"),
> > Location = c(7716L, 7716L, 7716L, 7716L, 7716L, 7716L, 7716L, 7717L,
> > 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L,
> > 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L,
> > 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L, 7717L,
> > 7717L, 7717L, 7717L, 7717L), dtime = structure(c(948758700, 948758700,
> > 948758700, 948761220, 948761220, 948761220, 948761220, 962655420,
> > 962655420, 962655420, 962655420, 962656200, 962656200, 962656200,
> > 962656200, 962655240, 962655300, 962655300, 962655300, 962655300,
> > 962655300, 962655420, 962655420, 962655420, 962655480, 962655480,
> > 962655480, 962655480, 962655480, 962666100, 962666460, 962666520,
> > 962666580, 962666700, 962666760, 962666820, 962666880, 962666940,
> > 962667180, 962667300, 962667360, 962667420), class = c("POSIXct",
> > "POSIXt"), tzone = "UTC")), class = "data.frame", row.names = c(NA,
> -42L))
> > ##===============================================================##
> > <b>The 6 letter species codes relate to individual bat species and the
> > Buzz = Feeding buzz that indicates a feeding attempt by a given bat.
> > So the "codes" are both species and information on the call type.</b>
> > But, at the moment you have two variables in the one column, Species:
> > The type of bat and feeding behaviour.
> > <b>The date/time is when the species was recorded and is linked to the
> > location.</b>
> > Okay. Will this give us a unique key?
> > <b>Therefore to run the summary stats I need I will need to remove the
> > duplicate times that are rounded to the minute</b>
> > What duplicate times? Where are they? When are they rounded?
> > I have never used Access. Will it produce a data dictionary? Can it
> > export a small subset of the relevant data to another Access DB, some
> > other DB or in .csv format? At the moment I just cannot visualize what
> > your data layout looks like.
> > Can you point us to any documentation that explains what information
> > in being gathered—preferably in simple–minded English?
> >
> > On Wed, 25 Dec 2019 at 12:08, Neotropical bat risk assessments
> > <neotropical.bats using gmail.com <mailto:neotropical.bats using gmail.com>> wrote:
> >
> > Hi John,
> >
> > Likely TMI but....
> >
> > The example was only to show the data format, clearly not the
> > entire data set. ;-)
> > Analyses will be by locations, dates and species in any case so
> > small subsets.
> >
> > My master relational database has >1.9 million records. These are
> > acoustic data recordings of bats and includes data fro >425 species.
> >
> > The 6 letter species codes relate to individual bat species and
> > the Buzz = Feeding buzz that indicates a feeding attempt by a
> > given bat. So the "codes" are both species and information on the
> > call type.
> >
> > So yes, if a call includes a feeding buzz it is noted as Buzz in
> > addition to the species ID codes..
> > A given 15 second acoustic recording may have up to 5 species
> > recorded and when imported into the relational DB each individual
> > species is parsed into its own record as well as records of call
> > notes e.g. Buzz.
> >
> > The date/time is when the species was recorded and is linked to
> > the location.
> > Although the call data summary below is summarized by *minute* the
> > actual data is recorded by time which includes seconds in addition
> > to minutes.
> > So there could be say 3+ files recorded during the same minute but
> > at different time periods as seconds (0-59) are included.
> >
> > Therefore to run the summary stats I need I will need to remove
> > the duplicate times that are rounded to the minute.
> >
> > Again tnx for taking time to reply.
> >
> > Cheers,
> >
> > Bruce
> >> I am sorry but I am at a loss here.
> >> According to your sample data you have 3 Species : Buzz, Ptedav,
> >> Ptemes, but you say that "Buzz" indicates that the bat is feeding.
> >> What has that to do with feeding?
> >>
> >> Assuming Buzz is feeding activity, are all incidents of feeding
> >> activity a single point in time?
> >>
> >> Likewise the data has multiple entries such as
> >> Ptedav 7717 7/3/2000 20:15
> >> Ptedav 7717 7/3/2000 20:15
> >> Ptedav 7717 7/3/2000 20:15
> >> Ptedav 7717 7/3/2000 20:15
> >>
> >> What does that represent?
> >>
> >>
> >> On Wed, 25 Dec 2019 at 07:29, Neotropical bat risk assessments
> >> <neotropical.bats using gmail.com> <mailto:neotropical.bats using gmail.com>
> wrote:
> >>> Hi all,
> >>>
> >>> It seems R has gotten better/more packages in dealing with time
> data.
> >>>
> >>> I want to create "simple" summaries of time for bat activity.
> >>> Data is all in an Access relational database and exported as a CSV
> file
> >>> with 4 columns in this format:
> >>> Species = a 6 letter code or "Buzz" to indicated when bats are
> feeding
> >>> Location = a 4 digit number
> >>> Date= MMDDYYYY
> >>> Time=HH:MM (24 hr format)
> >>>
> >>> Species Location Date Time
> >>> Buzz 7716 1/25/2000 0:05
> >>> Buzz 7716 1/25/2000 0:05
> >>> Buzz 7716 1/25/2000 0:05
> >>> Buzz 7716 1/25/2000 0:47
> >>> Buzz 7716 1/25/2000 0:47
> >>> Buzz 7716 1/25/2000 0:47
> >>> Buzz 7716 1/25/2000 0:47
> >>> Buzz 7717 7/3/2000 20:17
> >>> Buzz 7717 7/3/2000 20:17
> >>> Buzz 7717 7/3/2000 20:17
> >>> Buzz 7717 7/3/2000 20:17
> >>> Buzz 7717 7/3/2000 20:30
> >>> Buzz 7717 7/3/2000 20:30
> >>> Buzz 7717 7/3/2000 20:30
> >>> Buzz 7717 7/3/2000 20:30
> >>> Ptedav 7717 7/3/2000 20:14
> >>> Ptedav 7717 7/3/2000 20:15
> >>> Ptedav 7717 7/3/2000 20:15
> >>> Ptedav 7717 7/3/2000 20:15
> >>> Ptedav 7717 7/3/2000 20:15
> >>> Ptedav 7717 7/3/2000 20:15
> >>> Ptedav 7717 7/3/2000 20:17
> >>> Ptedav 7717 7/3/2000 20:17
> >>> Ptedav 7717 7/3/2000 20:17
> >>> Ptedav 7717 7/3/2000 20:18
> >>> Ptedav 7717 7/3/2000 20:18
> >>> Ptedav 7717 7/3/2000 20:18
> >>> Ptedav 7717 7/3/2000 20:18
> >>> Ptedav 7717 7/3/2000 20:18
> >>> Ptemes 7717 7/3/2000 23:15
> >>> Ptemes 7717 7/3/2000 23:21
> >>> Ptemes 7717 7/3/2000 23:22
> >>> Ptemes 7717 7/3/2000 23:23
> >>> Ptemes 7717 7/3/2000 23:25
> >>> Ptemes 7717 7/3/2000 23:26
> >>> Ptemes 7717 7/3/2000 23:27
> >>> Ptemes 7717 7/3/2000 23:28
> >>> Ptemes 7717 7/3/2000 23:29
> >>> Ptemes 7717 7/3/2000 23:33
> >>> Ptemes 7717 7/3/2000 23:35
> >>> Ptemes 7717 7/3/2000 23:36
> >>> Ptemes 7717 7/3/2000 23:37
> >>>
> >>> The above is clearly not a complete DF but only a format sample.
> Data
> >>> begins when the first bat was recorded and ends when the last bat
> was
> >>> recorded. So all are times from sunset to sunrise. Dates roll
> over so
> >>> for example one night of data would begin at 18:00 1/1/2000 and end
> >>> 06:00 1/2/2000.
> >>>
> >>> What I need to do is have a summary of Buzz events (feeding) and
> >>> calculate the percentage of total time bats were active and have a
> >>> summary of time feeding buzz was recorded and total bat activity to
> >>> determine what percentage of time was spent with feeding attempts
> over
> >>> the active period.
> >>>
> >>> This by all bats by survey night and by single species by survey
> night.
> >>> Any suggestions welcomed.
> >>>
> >>> Happy holidays all
> >>>
> >>>
> >>> --
> >>> Bruce W. Miller, PhD.
> >>> Neotropical bat risk assessments
> >>> Conservation Fellow - Wildlife Conservation Society
> >>>
> >>> If we lose the bats, we may lose much of the tropical vegetation
> and the lungs of the planet
> >>>
> >>> Using acoustic sampling to identify and map species distributions
> >>> and pioneering acoustic tools for ecology and conservation of bats
> for >25 years.
> >>>
> >>> Key projects include providing free interactive identification
> keys and call fact sheets for the vocal signatures of New World Bats
> >>>
> >>> ______________________________________________
> >>> R-help using r-project.org <mailto:R-help using r-project.org> mailing list
> -- To UNSUBSCRIBE and more, see
> >>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>> PLEASE do read the posting guidehttp://
> www.R-project.org/posting-guide.html
> >>> and provide commented, minimal, self-contained, reproducible code.
> >> --
> >> John Kane
> >> Kingston ON Canada
> >
> >
> > --
> > Bruce W. Miller, PhD.
> > Neotropical bat risk assessments
> > Conservation Fellow - Wildlife Conservation Society
> >
> > If we lose the bats, we may lose much of the tropical vegetation and
> the lungs of the planet
> >
> > Using acoustic sampling to identify and map species distributions
> > and pioneering acoustic tools for ecology and conservation of bats
> for >25 years.
> >
> > Key projects include providing free interactive identification keys
> and call fact sheets for the vocal signatures of New World Bats
> >
> >
> >
> > --
> > John Kane
> > Kingston ON Canada
>
>
> --
> Bruce W. Miller, PhD.
> Neotropical bat risk assessments
> Conservation Fellow - Wildlife Conservation Society
>
> If we lose the bats, we may lose much of the tropical vegetation and the
> lungs of the planet
>
> Using acoustic sampling to identify and map species distributions
> and pioneering acoustic tools for ecology and conservation of bats for >25
> years.
>
> Key projects include providing free interactive identification keys and
> call fact sheets for the vocal signatures of New World Bats
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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