[FLR-list] Plotting FLSR object

Iago MOSQUEIRA (JRC) iago.mosqueira at jrc.ec.europa.eu
Thu Jan 28 22:02:41 CET 2016


Dear all,

The corrected packages are now available on the repository for R 3.2

Best,


Iago

On 28/01/16 16:07, Iago MOSQUEIRA (JRC) wrote:
> 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>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>
>>
>>
>>
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