[FLR-list] Plotting FLSR object

Piera Carpi piera.carpi at an.ismar.cnr.it
Sun Jan 31 02:26:47 CET 2016 

Thank you Iago: it is working now! 

Best,

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



> On 28 Jan 2016, at 22:02, Iago MOSQUEIRA (JRC) <iago.mosqueira at jrc.ec.europa.eu> wrote:
> 
> 
> 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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>> 
> 
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