[FLR-list] incompatible units of measurements in FLQuant objects: f + NA

[Luis Ridao]

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
>>
>>
>>
>> _______________________________________________
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>>
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