[FLR-list] Plotting FLSR object

Thu Jan 28 16:07:25 CET 2016

Hi,

The issue has been a change in the latest version of ggplot2 that broke 
some of our code. Fixed now in ggplotFL in github, will upload an 
updated package to the repository later today.

If you can compile packages, you can test it using devtools to install 
from github

library(devtools)

install_github('flr/ggplotFL')

library(ggplotFL)

data(nsher)

plot(nsher)

Thanks both for reporting it

Best,

Iago

On 28/01/16 15:54, Marc Taylor wrote:
> Hi all,
>
> I was curious for an answer to this as well. I thought I would chime in
> with an example where the same happens for me.
>
> The plot of the FLSR object works until one loads the FLBRP package:
>
> ###########
> library(FLCore)
> data("ple4")
> ple4_sr <- as.FLSR(ple4)
> model(ple4_sr) <- "ricker"
> ple4_sr <- fmle(ple4_sr)
> plot(ple4_sr) # works
>
> library(FLBRP)
> plot(ple4_sr) # works no longer
> ############
>
> Cheers,
> Marc
>
> Dr. Marc Taylor
> Marine Lebende Resourcen / Marine Living Resources
> Thünen-Institut für Seefischerei / Thünen Institute of Sea Fisheries
> Palmaille 9
> 22767 Hamburg, Germany
>
> Tel:  +49 40 38905-143
> Mail:marc.taylor at ti.bund.de
> Web:www.ti.bund.de
>
> On 1/28/2016 3:43 PM, Iago MOSQUEIRA (JRC) wrote:
>> Hi,
>>
>> It works here with the same versions.
>>
>> Can you try
>>
>> - on a clean session loading ggplotFL and running it
>> - clean session, load ggplot2, then ggplotFL, then run
>>
>> and report the results?
>>
>> There could also be some method conflict withj some of the other pkgs
>> in your session.
>>
>> Cheers,
>>
>>
>> Iago
>>
>> On 26/01/16 13:18, Piera Carpi wrote:
>>> Hi all,
>>> I’m trying to plot a FLSR object, but whenever I do:
>>>
>>> sr <- fmle(as.FLSR(stk, model=“ricker”))
>>> plot(sr)
>>>
>>> I obtain the following output, and no plots at all:
>>>
>>> TableGrob (3 x 2) "arrange": 6 grobs
>>>    z     cells    name           grob
>>> 1 1 (1-1,1-1) arrange gtable[layout]
>>> 2 2 (1-1,2-2) arrange gtable[layout]
>>> 3 3 (2-2,1-1) arrange gtable[layout]
>>> 4 4 (2-2,2-2) arrange gtable[layout]
>>> 5 5 (3-3,1-1) arrange gtable[layout]
>>> 6 6 (3-3,2-2) arrange gtable[layout]
>>>
>>>
>>> Below info on my R session:
>>>
>>>
>>> R version 3.2.2 (2015-08-14)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>> Running under: Ubuntu 14.04.3 LTS
>>>
>>> locale:
>>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>   LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> 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_0.1.16            FLSAM_1.0 FLBRP_2.5.20140822
>>>   plyr_1.8.3            ggplotFL_2.5.20141027
>>>   [6] reshape2_1.4.1        gridExtra_2.0.0       ggplot2_1.0.1
>>> FLa4a_0.300.2         copula_0.999-13
>>> [11] triangle_0.8          mgcv_1.8-7            nlme_3.1-121
>>>   FLXSA_2.5.20140808    FLAssess_2.5.20130716
>>> [16] FLash_2.5.2           FLCore_2.5.20150513   MASS_7.3-43
>>> lattice_0.20-33       RevoUtilsMath_3.2.2
>>>
>>> loaded via a namespace (and not attached):
>>>   [1] Rcpp_0.12.1      tools_3.2.2      digest_0.6.8 gtable_0.1.2
>>>    pspline_1.0-17   Matrix_1.2-2     yaml_2.1.13
>>>   [8] mvtnorm_1.0-3    proto_0.3-10     knitr_1.11 stringr_1.0.0
>>>   stats4_3.2.2     ADGofTest_0.3    rmarkdown_0.7
>>> [15] magrittr_1.5     htmltools_0.2.6  scales_0.3.0 stabledist_0.7-0
>>> colorspace_1.2-6 labeling_0.3     stringi_0.5-5
>>> [22] gsl_1.9-10       munsell_0.4.2”
>>>
>>>
>>> Any idea why?
>>>
>>> Thanks in advance!
>>>
>>> Piera
>>>
>>>
>>>
>>>
>>> ----------------------------------
>>> Piera Carpi, Ph.D.
>>> Istituto di Scienze del Mare (CNR-ISMAR)
>>> Sezione Pesca Marittima-Ancona
>>> Largo Fiera della Pesca
>>> 60125, Ancona - ITALY
>>> Tel: 071-2078858
>>> Fax: 071-55313
>>> e-mail: piera.carpi at an.ismar.cnr.it <mailto:piera.carpi at an.ismar.cnr.it>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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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-- 
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