v2.7, further small corrections from r8808
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v2.7, integrated JS's paper-welfare-v2.6_jg-2.docx r8808
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v2.6, JG deletions from paper-welfare-v2.6_jg-1.docx
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v2.6: fix typo
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v2.6: reverted to r8804, r8805 is for comparison and control
- `svn merge -r HEAD:8804 .`
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v2.5: Jarl's comments and changes, from file paper-welfare-v2.5_jarl-1.docx
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v2.6, deleted challenges, now we have expectations from the architecture; this version is distributed to coauthors
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v2.6: ref fixed
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v2.6: fitted in JG paper-welfare-v2.5_jarl.docx
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v2.5: small wording changes
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Coded together, added simple individual energetics.
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v2.5: did model predictions and digital twin, refs reformated for appl. anim. behav. sci.
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small edits
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Coded together, also with Agnes. Added autocorrelated environment.
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small edits
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v2.5: started to edit model predictions
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v2.5: responded on consciousness part, pasted JG predictions
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v2.5: JG's fixes from the next portion (before last predictions) + further small changes
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v2.5: incorporated comments and changes from Jarl and Sigrunn
- paper-welfare-v2.4 jg (002).docx
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Deleted old files
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fixed the test program, HEDTOOLS are not needed any more
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GUI plotting now makes use of global parameters
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added modified benchmark for qsort
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Coded together, added step function.
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Coded together, added step function in environment.
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(rate2int) is a better name
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I commented the code out
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(each_n_s) is a time rate conversion function
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adapted food transport cycle to approximately 4 h
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tolerance is increased so far
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report time interval between succeeding food items
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use `Global_Food_Input_Rate` parameter (with recalc to "every 6 second")
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tolerance is higher for better agreement with experimental resolution
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basic parameters agreed with Ivar
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parametrized argument for higher readability
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calculate evacuation time in (check_disappear)
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documented public interfaces for fish and environment objects
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merge r8772 destination dir and move macro
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use destination dir option for `a2x` and use mv macro (forgotten)
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(schedule) method for food items added target_value for arbitrary scheduling, e.g. based on appetite (for testing)
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tidied up code
added environments
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web: typo
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web: add tar.gz archive with sources for direct download
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web: configure letsencrypt ssl certificates, automatically with default certbot. No redirection http to https
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web: switch to gum theme, it works better with mobile clients
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comments only
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schedule food is now type-bound (schedule), moved to ENVIRON module
- build and test ok
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collapse feed provision function
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impure explicitly declared
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use indicator from (schedule_feed)
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pointer-based feed scheduler (schedule_feed) and simplistic appetite-based decision procedure (decide_eat)
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Added forward only model version for experiments where one can change both parasite expoitation rate and food availiability, while switching between several optimalisation tables.
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Updated to also include runpve to run model forward only with differeing parasite virulence and food availiability.
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disable test condition for feed, back to r8755
- `svn merge -r HEAD:8755 .`
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another complex feed provision condition for test simulation
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add counter for waste feed, test simulation
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rename (ingest) method to (do_ingest), may need a separate method for decision to ingest
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small changes for readability of test code
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From our first coding session together on the new model.
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testing fractional smulations
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long integer for time steps
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enable generate doxygen output in RFT, pdflatex makefile seems broken in new versions
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web: smaller pic
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web: add pic
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web: fix install script
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web: static contents tag not needed, breaks pictures
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web: links to ahamodel.uib.no must be relative all
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web: crontab entries fix
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update install script for ubuntu 18 LTS (rebuilt from 19.0)
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web: use relative links for portrability
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web: fix paths for crontab, ubuntu-based AHAWEB
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web: point to all plugins
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web: adapted scripts for new ubuntu-based AHAWEB
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web: adapted scripts to new ubuntu-based AHAWEB
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web: switch config to pelican 4.0.1 on new ubuntu-based AHAWEB
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deleted outdated binary
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Minor change
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Fixed bug in figure B and edited x-axis title on FigureF.
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comment only
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(test_run) now uses probabilistic ingestion depending on appetite factor
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added BASE_RANDOM from HEDTOOLS but substituted non-portable (RANDOM_SEED_INIT) with simple non-parallel version
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Added unit to Fultons condition factor in Figure A.
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depth loop added
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minor changes - but why does zooplankton size not affect survival rates?
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deleted confusing comment
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better name
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debug code, cryptic assignment error in (fish_ingest_food_item) fixed
- the assignment ln 371 `this%food_items_eaten(1) = loc_new_food_item`
did not pass all data components even though both are same type
due to assignment (=) overloading in downstream FOOD_ITEM class
- assignment overloading was deleted in r8720
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better variable names, avoid assignment overloading
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overloading `assignment (+)` is dangerous as can propagate over higher-order derived types, use (copy) method safer
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debug code
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debug code
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larger array limit
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(step): procedure to update stomach and food items at each time step
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added comments
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constructors with default values
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(zero) normally destructs food item
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(food_item_eaten_set_zero_init_state): arbitrary parameters for constructor
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example table widget from dislin doc
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doxygen comments, some fixes
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appetite function and computing backend: (appetite_func) (fish_appetite_factor_stomach)
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(appetite_stomach): calculate appetite factor
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delete obsolete code
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(food_volume): calculate total food volume in stomach
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fix comment
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minor fix texts
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better doxygen comments
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only doxygen comments
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better doxygen descriptions
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cleaner logistic parameters in (food_item_volume)
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delete obsolete proc
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(save_stomach_transport_data): save stomach transport data for a single food item into csv file
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add CSV_IO
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fix logistic formula in (food_item_volume), must have been increment over dry volume
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use (food_item_volume) in (do_plot_stomach_transport_global) for plotting
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obsolete code deleted
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better comments in (food_item_volume)
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stomach transport grid parameters more realistic
- food goes out fully during apprx. 10 h (36000 s)
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small change
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use (logistic) backend
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(logistic) is logistic function
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old type-bound function obsolete
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backend function (food_item_volume) is done
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(food_item_volume) is the calculation backend for single food item
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Added light grey dashed lines to figure 4 to assist the reader.
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doxygen comments searate for two parameters
- but they are identical
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water uptake pattern is logistic growth fnction, additional global parameters
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Fixed minor bug in figure F
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Changed y-axis lable of figure Fa (survival.plot) and make the y-axis start on 0 like in the other plots that make up this figure.
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(water_uptake) must be function
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ingestion_delay is a property pf food item rather than fish
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Renamed Lifetime Mortality Risk to Accumulated Mortality Risk in figure C to reflect the terms used in the stochastic paper.
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(time_update) method for FOOD_ITEM_EATEN class
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(volume_stomach) method more logical in FOOD_ITEM_EATEN class, also no need in time in stomach argument
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FISH class name better for highest order object, base is more logical name FISH_SKEL
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water uptake moved to THE_FISH FOOD_ITEM_EATEN class
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(init_ingest) uses `class` as input, generic better
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reorder as in standard `assignment_sub(out,in)`
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better use `=` assignment operator overloaded for FOOD_ITEM class
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added rudimentary init constructor for FISH object
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reformat white space only
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adapt to arrays, redeclared elemental; optional arguments for zero states
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FOOD_ITEM object (init) method now accepts optional missing
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flere sma endringer i bussen
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building objects
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better use fixed array of foor items
- simple fixed stack object
- no aliasing unlike linked list
- use heap arrays
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started implementing food and fish stomach objects
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better name
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doxygen: two entries were collapsed, confusion
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better comments
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