TODO

general

Fisnish integrating transport

see ticket#124

Integrate sudoe areas (GEREM) in river dataset

see ticket#123

Test parallel processing for caret problems with transport

see ticket #121

Remaining ticket#120

finish testing model validation

Create a variable mixing distance sea and dam

integrate distance to gibraltar

integrate other metrics

change type of fishing for GT6

ALberto Aguirre Belén Muñoz Carlos Antunes Carlos Fernandez Francisco Hervella Iker Azpiroz Isabel Domingos Josu Iñaki Elso Huarte Lluis Zamora

com 1163 50 30 0 4595 1298 41 11 0 oth 41 891 50 91 651 0 912 46 139

Lucía García Florez Nacho Ferrando Belloch Rafael Miranda Ferreiro

com 200 0 5375 oth 10 182 265

invert distance from gibraltar in the med to avoid independence between alt and mediterranean silver_eel$dist_from_gibraltar_km[silver_eel$codesea=="M"]<- -silver_eel$dist_from_gibraltar_km[silver_eel$codesea=="M"]

delta

Find best fit => nearly there model structure OK

Try to integrate separate fit for Rhin and Meuse (without excluding them altogether as transported)

Try model using only transported areas.

Check high collinearity for gam using additional height...

Compare results for different height

Run model with altitude or altituderemain

finalize model choice

finalize model graphs => cedric

fit with distance to gibraltar

test cumulated surface downstream

gamma

Find best fit => nearly there model structure OK

Try to integrate separate fit for Rhin and Meuse (without excluding them altogether as transported)

Try model using only transported areas.

finalize model choice

finalize model graphs => Maria

Delta.gamma predictions

Adapt prediction scripts

predict data

write database

integrate new variables in prediction by merging

create maps

caret

Create function for delta model validation

Create function for gamma model validation

Data selection

The selection in multinomial must exclude transport stations or use the transport as a factor in the model, or use two separate models for transport and other. Apply same filters ... Correct current setting to adapt from gamma model using 20 000 observations.

Model fit

• check that no two dimensional plots are done if the response is not bi-dimensional
• model fit
• test using delta gamma density predictions in multinomial
• test using riverwidtm or logriverwithm
• test using s(riverwidtm)
• test model using only delta prediction ? => not the best model
• try to center and reduce variables ...
• produce graph for model fit
• test distance from gibraltar

Predictions

• use the model predictions to predict the whole size structure delta* gamma * mutlinomial_p

Data validation

• import all data
• check all data adapting Laurents checks
• Calculate Durif stage
• Prediction number stage per stations

Integrate delta gamma and multinomial predictions (redo) correct problem with distance from gibraltar med (wrong basins) get the code from data integration remove transport as in data integration

Model calibration

• sex ratio

Model predictions

graphs of model predictions

There has been double checking of size data, could we integrate that in multinomial ?

multinomial model

By running algorythm from the source, cumulate the silver eel per size and total and write the results to the database

these along with the basin selection should come later on in the script (better to load everything and filter after)

dbeel@datadbeel$ef_wetted_area <- Hmisc::impute(dbeel@datadbeel$ef_wetted_area, mean) # 2582 values imputed to 515.4054 summary(dbeel@datadbeel$ef_wetted_area) # 15.7% values imputed ele$densCSwarning <- is.imputed(ele$ef_wetted_area)

The task in in Trello also, excel file table_obstacles_SUDOANG_E2.1 Use the comments on the side of the table to complete the translate name table Close the Trello.

Clean up the Rmarkdown script of fitting_dam_models.Rmd. Create all the outputs for the variables for the paper. Create a summary of all available data for dams and eels along with some maps Describe the structure of data integration to build the dam database (how to create the cumulated values) (Or another working paper) model conceptuel GT2 Describe the hypothesis tested and the models built to test the hypothesis Discuss the results - check bibliography for existing refs (at least swedish example and japan and perhaps model tested in new zealand) Discuss the data needs : have a date for dam and pass construction Consider advice for eel transport and how to integrate those Exchange with Laurent and Hilaire for further ideas.

transfer everyhting (database included) to linux Make trac run transfer subversion create connections....

• Synthesize answers
• Send to CB, HD, LB, MK and ED

Check why some dams heights are larger than 2* altitude on map

View(frsppt[frsppt$transport=="possible",]) line 1327

model validation

run caret using the best model structure to obtain the results. (low priority) the script is ready, this is for the paper, moved from ticket#118