[R-sig-Geo] Incorrect month order in zApply function
Ben Tupper
btupper at bigelow.org
Sat Jul 30 14:51:43 CEST 2016
Hi Vijay,
Whoops! I think you misunderstood my message - I didn't think I was pointing out a mistake on your part. My 'uhoh' was pointing out surprising behavior on the part of zApply.
If I use my earlier edited example and remove the "name=" argument to zApply, the results still make my forehead get all wrinkled up as the month labels don't align with the results.
library(raster)
# Create date sequence
idx <- seq(as.Date("1996/1/1"), as.Date("1996/12/31"), by = "day")
mon_num <- as.numeric(format(idx, "%m"))
# Create raster stack and assign dates
r <- raster(ncol=5, nrow=5)
s <- stack(
lapply(1:length(idx),
function(x) setValues(r, rep(mon_num[x],ncell(r)))
)
)
s <- setZ(s, idx)
# Calculate monthly average
x <- zApply(s, by=months, fun = mean)
x
#class : RasterBrick
#dimensions : 5, 5, 25, 12 (nrow, ncol, ncell, nlayers)
#resolution : 72, 36 (x, y)
#extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
#coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
#data source : in memory
#names : April, August, December, February, January, July, June, March, May, November, October, September
#min values : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
#max values : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
# : April, August, December, February, January, July, June, March, May, November, October, September
So, what the heck does the "by=" do if not group the layers by month? I can't see why you need to define your own aggregation m() to get it to work (and I am impressed that you did get it to work.)
Cheers,
Ben
> On Jul 29, 2016, at 10:27 PM, Vijay Lulla <vijaylulla at gmail.com> wrote:
>
> Ben,
> You're right about a mistake in my code but it is not use of ordered function. It is that I shouldn't have used the name argument. Following your example this is what I get:
>
> > m <- function(x) ordered(months(x), labels=month.name <http://month.name/>)
> > x1 <- zApply(s, by=m, mean) # no name argument.
> > x1
> # class : RasterBrick
> # dimensions : 5, 5, 25, 12 (nrow, ncol, ncell, nlayers)
> # resolution : 72, 36 (x, y)
> # extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
> # coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> # data source : in memory
> # names : January, February, March, April, May, June, July, August, September, October, November, December
> # min values : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
> # max values : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
> # : January, February, March, April, May, June, July, August, September, October, November, December
>
> Thanks for pointing out the mistake,
> Vijay.
>
>
> On Fri, Jul 29, 2016 at 7:17 PM, Ben Tupper <btupper at bigelow.org <mailto:btupper at bigelow.org>> wrote:
> Hi,
>
> I reworked your example a bit so that it encompasses just one year, and the value of each layer is the month number for the Z index. Sure enough, the mean month number values look like they are mismatched relative to the layer name. Example below - sorry about line-wrapping. Uhoh.
>
> Cheers,
> Ben
>
> library(raster)
>
> # Create date sequence
> idx <- seq(as.Date("1996/1/1"), as.Date("1996/12/31"), by = "day")
>
> mon_num <- as.numeric(format(idx, "%m"))
>
> # Create raster stack and assign dates
> r <- raster(ncol=5, nrow=5)
> s <- stack(
> lapply(1:length(idx),
> function(x) setValues(r, rep(mon_num[x],ncell(r)))
> )
> )
> s <- setZ(s, idx)
>
> # Calculate monthly average
> x <- zApply(s, by=months, mean, name=month.abb[])
>
> x
> # class : RasterBrick
> # dimensions : 5, 5, 25, 12 (nrow, ncol, ncell, nlayers)
> # resolution : 72, 36 (x, y)
> # extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
> # coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> # data source : in memory
> # names : April, August, December, February, January, July, June, March, May, November, October, September
> # min values : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
> # max values : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
>
>
> > sessionInfo()
> R version 3.3.1 (2016-06-21)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.11.6 (El Capitan)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] raster_2.5-8 sp_1.2-3
>
> loaded via a namespace (and not attached):
> [1] rgdal_1.1-10 Rcpp_0.12.6 grid_3.3.1 lattice_0.20-33
>
>
> > On Jul 29, 2016, at 3:20 PM, Thiago V. dos Santos via R-sig-Geo <r-sig-geo at r-project.org <mailto:r-sig-geo at r-project.org>> wrote:
> >
> > Thanks everyone for their suggestions.
> >
> > Reordering the output of zApply would be a WRONG solution, because the layers are already ordered from Jan to Dec.
> >
> > It is just the NAMES that are misaligned, which can cause a bit of confusion.
> >
> > I already contacted Robert about this issue and we should see a solution soon.
> > Greetings,
> > -- Thiago V. dos Santos
> >
> > PhD student
> > Land and Atmospheric Science
> > University of Minnesota
> >
> >
> >
> > On Friday, July 29, 2016 2:09 PM, Kay Kilpatrick <kkilpatrick at rsmas.miami.edu <mailto:kkilpatrick at rsmas.miami.edu>> wrote:
> > Hi
> >
> > The various Apply functions always return the output in simple
> > alphabetical order when the factor label is a character, regardless of
> > the order of the factor in the calling argument.
> >
> > Ben had a correct solution --- simply reorder the output from Zapply.
> >
> > Alternatively you could use a numeric representation for the month label
> > using by = as.numeric(months(x). The output would then be in increasing
> > numeric order from 1 -12.
> >
> > I do not believe Vijay's suggestion is proper. It does not reorder the
> > output --- instead it changes the label of a given monthly mean eg. The
> > value for Jan. would then be labeled as Apr.
> >
> > k
> >
> > On 7/28/16 10:52 PM, Thiago V. dos Santos via R-sig-Geo wrote:
> >> Dear all,
> >>
> >> I am using the raster package to calculate monthly averages of climatic variables.
> >>
> >> Essentially, this is the function I use:
> >>
> >> library(raster)
> >>
> >> # Create date sequence
> >> idx <- seq(as.Date("1996/1/1"), as.Date("2010/12/31"), by = "day")
> >>
> >> # Create raster stack and assign dates
> >> r <- raster(ncol=5, nrow=5)
> >> s <- stack(lapply(1:length(idx), function(x) setValues(r, runif(ncell(r)))))
> >> s <- setZ(s, idx)
> >>
> >> # Calculate monthly average
> >> x <- zApply(s, by=months, mean, name=month.abb[])
> >>
> >> names(x)
> >> [1] "April" "August" "December" "February" "January" "July" "June"
> >> [8] "March" "May" "November" "October" "September"
> >> getZ(x)
> >> [1] "April" "August" "December" "February" "January" "July" "June"
> >> [8] "March" "May" "November" "October" "September"
> >>
> >>
> >> The problem here is the output of both names(x) and getZ(x). It looks like a random month order is returned (even though I provide the labels), which makes me confused about the results.
> >>
> >>
> >> By performing the same calculation in a different software and comparing the results, I came to realize that the order of months for the results by raster should, in fact, be Jan-Feb-Mar-Apr-May-Jun-Jul-Aug-Sep-Oct-Nov-Dec
> >>
> >> How can I control the way raster delivers the object names after using zApply, in order to sort the months in the "natural" order?
> >>
> >> Greetings, -- Thiago V. dos Santos
> >>
> >> PhD student
> >> Land and Atmospheric Science
> >> University of Minnesota
> >>
> >> _______________________________________________
> >> R-sig-Geo mailing list
> >> R-sig-Geo at r-project.org <mailto:R-sig-Geo at r-project.org>
> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dgeo&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=VXzrzLaooo912e5bVVEO_z5cHQXu_22lipAXBkfCXjM&m=tzdb3kN3Nxjo7NbPkPVqtF269bJen1bf3AzSHEwd7CA&s=zuokuoKIDT6cOaBD2J6ePy1klmf1J3-f3BynP_G5I-g&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dgeo&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=VXzrzLaooo912e5bVVEO_z5cHQXu_22lipAXBkfCXjM&m=tzdb3kN3Nxjo7NbPkPVqtF269bJen1bf3AzSHEwd7CA&s=zuokuoKIDT6cOaBD2J6ePy1klmf1J3-f3BynP_G5I-g&e=>
> >
> >
> > --
> > Katherine (Kay) Kilpatrick
> > University of Miami/RSMAS
> > Ocean Science Department
> > Satellite Remote Sensing Laboratory
> > MSC 231
> > 4600 Rickenbacker Cswy
> > Miami, Fl
> > ph: 305-962-3069 <tel:305-962-3069>
> > kkilpatrick at rsmas.miami.edu <mailto:kkilpatrick at rsmas.miami.edu>
> >
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo <https://stat.ethz.ch/mailman/listinfo/r-sig-geo>
> >
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>
>
>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org <http://www.bigelow.org/>
>
> Report Gulf of Maine jellyfish sightings to jellyfish at bigelow.org <mailto:jellyfish at bigelow.org> or tweet them to #MaineJellies -- include date, time, and location, as well as any descriptive information such as size or type. Learn more at https://www.bigelow.org/research/srs/nick-record/nick-record-laboratory/mainejellies/ <https://www.bigelow.org/research/srs/nick-record/nick-record-laboratory/mainejellies/>
>
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>
Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org
Report Gulf of Maine jellyfish sightings to jellyfish at bigelow.org or tweet them to #MaineJellies -- include date, time, and location, as well as any descriptive information such as size or type. Learn more at https://www.bigelow.org/research/srs/nick-record/nick-record-laboratory/mainejellies/
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