[FLR-list] incompatible units of measurements in FLQuant objects: f + NA
Havstovan FAMRI
luridao at gmail.com
Mon Jan 26 15:18:07 CET 2015
I will try that Iago
thanks for your help
Best,
Luis
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
Luis Ridao Cruz
Faroe Marine Research Institute
Nóatún 1, P.O. Box 3051
FO-110 Tórshavn
Faroe Islands
Tel : (+298) 353900
Fax: : (+298) 353901
e-mail: luisr at hav.fo
luridao at gmail.com
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
On Mon, Jan 26, 2015 at 1:46 PM, Iago MOSQUEIRA (JRC) <
iago.mosqueira at jrc.ec.europa.eu> wrote:
>
> Hi,
>
> That message in the call to max comes from calling it with an empty vector
>
> > max()
> [1] -Inf
> Warning message:
> In max() : no non-missing arguments to max; returning -Inf
>
> so something inside SRplot is passing an empty vector, called ssb, to max.
>
> You will have to ask the author of the msy package, or try debug(SRplot)
> and see if you can see where ssb is calculated/extracted.
>
>
> Iago
>
> On 26/01/15 14:09, Havstovan FAMRI wrote:
> > hey,
> >
> > "FIT" is a list and it seems that function calls ssb and rec work:
> >
> >> SRplot(FIT)
> > Error in split.default(X, group) : first argument must be a vector
> > In addition: Warning messages:
> > 1: In max(ssb) : no non-missing arguments to max; returning -Inf
> > 2: In max(ssb) : no non-missing arguments to max; returning -Inf
> > 3: In max(rec * 1.5) : no non-missing arguments to max; returning -Inf
> >
> >> class(FIT)
> > [1] "list"
> >
> >> ssb(stock)
> > An object of class "FLQuant"
> > , , unit = unique, season = all, area = unique
> >
> > .....
> > .....
> > age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008
> > 2009 2010 2011 2012
> > all 78536 81162 83683 80683 96734 112908 127358 126181 120553
> 104484
> > 92801 67499 54354 55251
> >
> > units: t
> >
> >> rec(stock)
> >
> > ....
> > ....
> > year
> > age 1991 1992 1993 1994 1995 1996 1997 1998
> > 1999 2000 2001 2002 2003 2004 2005
> > 3 24969.8 19552.4 23778.3 16873.2 38969.7 24308.2 33472.0
> 12741.5
> > 58789.8 35781.1 87950.1 105894.1 64469.1 53818.0 69512.3
> > year
> > age 2006 2007 2008 2009 2010 2011 2012
> > 3 21688.7 18407.1 32493.3 13606.6 27986.9 73259.1 28990.8
> >
> > Trying to figuring out what function:
> >
> > FIT <- eqsr_fit(stock,
> > + nsamp = 1000,
> > + id.sr = "stock",
> > + models = c("segreg"),
> > + method = "Buckland")
> >
> > is doing.
> >
> > Best,
> > Luis
> >
> >
> >
> > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
> > Luis Ridao Cruz
> > Faroe Marine Research Institute
> > Nóatún 1, P.O. Box 3051
> > FO-110 Tórshavn
> > Faroe Islands
> > Tel : (+298) 353900
> > Fax: : (+298) 353901
> > e-mail: luisr at hav.fo
> > luridao at gmail.com
> > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
> >
> >
> > On Mon, Jan 26, 2015 at 12:22 PM, Iago MOSQUEIRA (JRC) <
> > iago.mosqueira at jrc.ec.europa.eu> wrote:
> >
> >>
> >> Hi,
> >>
> >> That warning by lattice has nothing to do with the units. It shows up
> >> every now and then, I will investigate it further.
> >>
> >>>> SRplot(FIT)
> >>> Error in split.default(X, group) : first argument must be a vector
> >>> In addition: Warning messages:
> >>> 1: In max(ssb) : no non-missing arguments to max; returning -Inf
> >>> 2: In max(ssb) : no non-missing arguments to max; returning -Inf
> >>> 3: In max(rec * 1.5) : no non-missing arguments to max; returning -Inf
> >>
> >> I don't know that package, but my guess is something is not right in the
> >> calculation of ssb and rec. Look at ssb(stock). What type f object is
> FIT?
> >>
> >> Cheers,
> >>
> >>
> >> Iago
> >>
> >>
> >> On 26/01/15 11:27, Luis Ridao wrote:
> >>>
> >>> I have changed the FLStock units to ('ple4' units):
> >>> $catch
> >>> [1] "t"
> >>>
> >>> $catch.n
> >>> [1] "10^3"
> >>>
> >>> $catch.wt
> >>> [1] "kg"
> >>>
> >>> $discards
> >>> [1] "t"
> >>>
> >>> $discards.n
> >>> [1] "10^3"
> >>>
> >>> $discards.wt
> >>> [1] "kg"
> >>>
> >>> $landings
> >>> [1] "t"
> >>>
> >>> $landings.n
> >>> [1] "10^3"
> >>>
> >>> $landings.wt
> >>> [1] "kg"
> >>>
> >>> $stock
> >>> [1] "t"
> >>>
> >>> $stock.n
> >>> [1] "10^3"
> >>>
> >>> $stock.wt
> >>> [1] "kg"
> >>>
> >>> $m
> >>> [1] "m"
> >>>
> >>> $mat
> >>> [1] "NA"
> >>>
> >>> $harvest
> >>> [1] "f"
> >>>
> >>> $harvest.spwn
> >>> [1] "NA"
> >>>
> >>> $m.spwn
> >>> [1] "NA"
> >>>
> >>> The plot function does the plotting but it stills issues a warning:
> >>>
> >>>> plot(stock)
> >>> Warning message:
> >>> In `[<-.factor`(`*tmp*`, ri, value = c(3, 3, 3, 3, 3, 3, 3, 3, 3, :
> >>> invalid factor level, NA generated
> >>>
> >>>
> >>> which it might trigger the error when calling the SRplot function
> >>> in "msy" package:
> >>>
> >>>> SRplot(FIT)
> >>> Error in split.default(X, group) : first argument must be a vector
> >>> In addition: Warning messages:
> >>> 1: In max(ssb) : no non-missing arguments to max; returning -Inf
> >>> 2: In max(ssb) : no non-missing arguments to max; returning -Inf
> >>> 3: In max(rec * 1.5) : no non-missing arguments to max; returning -Inf
> >>>
> >>> I'm just trying to make sure that the error does not come from the FLR
> >>> objects
> >>> which "msy" package makes use of.
> >>>
> >>> Best,
> >>> Luis
> >>>
> >>>
> >>> On 01/23/2015 03:20 PM, Iago Mosqueira wrote:
> >>>> Hi,
> >>>>
> >>>> The FLQuant arithmetic tries now to do something about combinations of
> >>>> units, but as you saw only issues warnings when it fails. To get it to
> >>>> work, you need to use the standard units names, which are
> >>>>
> >>>> 't' instead of 'tonnes'
> >>>>
> >>>> '1000' instead of 'thousands'
> >>>>
> >>>> For example
> >>>>
> >>>> kg * 1000 = t
> >>>>
> >>>>> FLQuant(1, units='kg') * FLQuant(10, units='1000')
> >>>> An object of class "FLQuant"
> >>>> , , unit = unique, season = all, area = unique
> >>>>
> >>>> year
> >>>> quant 1
> >>>> all 10
> >>>>
> >>>> units: t
> >>>> The warning has been taken away in recent versions, so try
> re-installing
> >>>> from the repository.
> >>>>
> >>>> Let us know how it goes.
> >>>>
> >>>> Best,
> >>>>
> >>>>
> >>>> Iago
> >>>>
> >>>> On 23/01/15 16:13, Havstovan FAMRI wrote:
> >>>>> Hi all,
> >>>>>
> >>>>> Trying to work with a FLStock object.
> >>>>> When doing a basic call like:
> >>>>>
> >>>>>> plot(stock)
> >>>>> Warning messages:
> >>>>> 1: In FLCore:::uom(op, units(e1), units(e2)) :
> >>>>> incompatible units of measurements in FLQuant objects: f + NA
> >>>>> 2: In `[<-.factor`(`*tmp*`, ri, value = c(3, 3, 3, 3, 3, 3, 3, 3,
> 3, :
> >>>>> invalid factor level, NA generated
> >>>>>
> >>>>> I get the graph but the warning propagates forward to other function
> >>>>> calls
> >>>>> like
> >>>>>
> >>>>> eqsr_fit(stock,.....) in packaǵe "msy":
> >>>>>
> >>>>>> eqsr_fit(stock,
> >>>>> + nsamp = 1000,
> >>>>> + id.sr = "mystock",
> >>>>> + models = c("segreg"),
> >>>>> + method = "Buckland")
> >>>>>
> >>>>> Warning message:
> >>>>> In FLCore:::uom(op, units(e1), units(e2)) :
> >>>>> incompatible units of measurements in FLQuant objects: f + NA
> >>>>>
> >>>>> The units in the "stock" object are:
> >>>>>
> >>>>>> units(stock)
> >>>>> $catch
> >>>>> [1] "tonnes"
> >>>>>
> >>>>> $catch.n
> >>>>> [1] "thousands"
> >>>>>
> >>>>> $catch.wt
> >>>>> [1] "kg"
> >>>>>
> >>>>> $discards
> >>>>> [1] "tonnes"
> >>>>>
> >>>>> $discards.n
> >>>>> [1] "thousands"
> >>>>>
> >>>>> $discards.wt
> >>>>> [1] "kg"
> >>>>>
> >>>>> $landings
> >>>>> [1] "tonnes"
> >>>>>
> >>>>> $landings.n
> >>>>> [1] "thousands"
> >>>>>
> >>>>> $landings.wt
> >>>>> [1] "kg"
> >>>>>
> >>>>> $stock
> >>>>> [1] "tonnes"
> >>>>>
> >>>>> $stock.n
> >>>>> [1] "NA"
> >>>>>
> >>>>> $stock.wt
> >>>>> [1] "kg"
> >>>>>
> >>>>> $m
> >>>>> [1] "NA"
> >>>>>
> >>>>> $mat
> >>>>> [1] "NA"
> >>>>>
> >>>>> $harvest
> >>>>> [1] "f"
> >>>>>
> >>>>> $harvest.spwn
> >>>>> [1] "NA"
> >>>>>
> >>>>>
> >>>>> I'm using:
> >>>>>
> >>>>> R version 3.0.2 (2013-09-25)
> >>>>> Platform: x86_64-pc-linux-gnu (64-bit) UBUNTU
> >>>>>
> >>>>> and FLCore version FLCore_2.5.20140213
> >>>>>
> >>>>>
> >>>>> Thanks in advance
> >>>>>
> >>>>> #######################################################
> >>>>> The full sessionInfo() is below:
> >>>>> #######################################################
> >>>>>
> >>>>>> sessionInfo()
> >>>>> R version 3.0.2 (2013-09-25)
> >>>>> Platform: x86_64-pc-linux-gnu (64-bit)
> >>>>>
> >>>>> locale:
> >>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> >>>>> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> >>>>> LC_MONETARY=en_US.UTF-8
> >>>>> [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
> >>>>> LC_ADDRESS=C LC_TELEPHONE=C
> >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >>>>>
> >>>>> attached base packages:
> >>>>> [1] grid stats graphics grDevices utils datasets
> methods
> >>>>> base
> >>>>>
> >>>>> other attached packages:
> >>>>> [1] msy_0.1.12 stringr_0.6.2 R2admb_0.7.10
> >>>>> gridExtra_0.9.1 ggplot2_1.0.0 reshape2_1.2.2
> >>>>> [7] scam_1.1-8 mgcv_1.7-28 nlme_3.1-113
> >>>>> devtools_1.5 FLCore_2.5.20140213 MASS_7.3-29
> >>>>> [13] lattice_0.20-29 xtable_1.7-1 plyr_1.8.1
> >>>>>
> >>>>> loaded via a namespace (and not attached):
> >>>>> [1] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4
> >>>>> evaluate_0.5.5 formatR_0.10 gtable_0.1.2 httr_0.4
> >>>>> [8] knitr_1.6 labeling_0.2 Matrix_1.1-2
> >>>>> memoise_0.2.1
> >>>>> munsell_0.4.2 parallel_3.0.2 proto_0.3-10
> >>>>> [15] RColorBrewer_1.0-5 Rcpp_0.11.0 RCurl_1.95-4.3
> >>>>> scales_0.2.3
> >>>>> splines_3.0.2 stats4_3.0.2 tools_3.0.2
> >>>>> [22] whisker_0.3-2
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> flr-list mailing list
> >>>>> flr-list at flr-project.org
> >>>>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list
> >>>>>
> >>>> _______________________________________________
> >>>> flr-list mailing list
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> >>>
> >>> _______________________________________________
> >>> flr-list mailing list
> >>> flr-list at flr-project.org
> >>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list
> >>
> >>
> >> --
> >> Dr Iago Mosqueira
> >>
> >> European Commission – Joint Research Center
> >> Institute for the Protection and Security of the Citizen (IPSC)
> >> Maritime Affairs Unit G03
> >> TP 051, Via Enrico Fermi 2749
> >> I-21027 Ispra (VA), Italy
> >>
> >> Office : +39 0332 785413
> >> Fax: +39 0332 789658
> >>
> >> iago.mosqueira at jrc.ec.europa.eu
> >>
> >> http://fishreg.jrc.ec.europa.eu/home
> >>
> >> _______________________________________________
> >> flr-list mailing list
> >> flr-list at flr-project.org
> >> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list
> >>
> >
> >
> >
> > _______________________________________________
> > flr-list mailing list
> > flr-list at flr-project.org
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list
> >
>
>
> --
> Dr Iago Mosqueira
>
> European Commission – Joint Research Center
> Institute for the Protection and Security of the Citizen (IPSC)
> Maritime Affairs Unit G03
> TP 051, Via Enrico Fermi 2749
> I-21027 Ispra (VA), Italy
>
> Office : +39 0332 785413
> Fax: +39 0332 789658
>
> iago.mosqueira at jrc.ec.europa.eu
>
> http://fishreg.jrc.ec.europa.eu/home
>
> _______________________________________________
> flr-list mailing list
> flr-list at flr-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list
>
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