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Classes | |
| class | AquaMaps |
Variable Documentation
| const Scalar BOTTOM_LOWER_LIMIT[7] |
Definition at line 129 of file aquamaps.hh.
Referenced by AquaMaps::_calculateEnvelopes().
| const Scalar BOTTOM_UPPER_LIMIT[7] |
Definition at line 145 of file aquamaps.hh.
Referenced by AquaMaps::_calculateEnvelopes().
| const Scalar DEPTH_LIMIT = 200.0 |
Declaration of AquaMaps Algorithm.
- Date
- 2006-08-07
- Id:
- aquamaps.hh 5928 2014-03-17 21:22:24Z rdg
LICENSE INFORMATION
Copyright(c) 2006 by CRIA - Centro de Referência em Informação Ambiental
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details:
http://www.gnu.org/copyleft/gpl.html Notes
This algorithm requires access to a SQLite database (aquamaps.db) which contains depth range information about marine species.
The original database comes from the Incofish projet (http://www.incofish.org/). It is an Access database with the main tables: HCAF (env data), HSPEC (probabilities), HSPEN (species data).
To export data to the SQLite database it is necessary to create a query in the Access database using this SQL statement:
SELECT HSPEN.SpeciesID, SpeciesOccursum.genus+' '+SpeciesOccursum.species AS name, hspen.pelagic, Speciesaddinfo.Provider, hspen.depthmin, hspen.depthprefmin, hspen.depthprefmax, hspen.depthmax, hspen.tempmin, hspen.tempmax, hspen.tempprefmin, hspen.tempprefmax, hspen.salinitymin, hspen.salinitymax, hspen.salinityprefmin, hspen.salinityprefmax, hspen.primprodmin, hspen.primprodmax, hspen.primprodprefmin, hspen.primprodprefmax, hspen.iceconmin, hspen.iceconmax, hspen.iceconprefmin, hspen.iceconprefmax, hspen.landdistmin, hspen.landdistmax, hspen.landdistprefmin, hspen.landdistprefmax FROM (hspen INNER JOIN SpeciesOccursum ON HSPEN.SpeciesID=SpeciesOccursum.SPECIESID) LEFT JOIN Speciesaddinfo ON HSPEN.SpeciesID=Speciesaddinfo.SpeciesID WHERE hspen.depthmin Is Not Null And Speciesaddinfo.Provider = "MM" UNION SELECT HSPEN.SpeciesID, SpeciesOccursum.genus+' '+SpeciesOccursum.species AS name, hspen.pelagic, Speciesaddinfo.Provider, hspen.depthmin, hspen.depthprefmin, hspen.depthprefmax, hspen.depthmax, Null AS tempmin, Null AS tempmax, Null AS tempprefmin, Null AS tempprefmax, Null AS salinitymin, Null AS salinitymax, Null AS salinityprefmin, Null AS salinityprefmax, Null AS primprodmin, Null AS primprodmax, Null AS primprodprefmin, Null AS primprodprefmax, Null AS iceconmin, Null AS iceconmax, Null AS iceconprefmin, Null AS iceconprefmax, Null AS landdistmin, Null AS landdistmax, Null AS landdistprefmin, Null AS landdistprefmax FROM (hspen INNER JOIN SpeciesOccursum ON HSPEN.SpeciesID=SpeciesOccursum.SPECIESID) LEFT JOIN Speciesaddinfo ON HSPEN.SpeciesID=Speciesaddinfo.SpeciesID WHERE hspen.depthmin Is Not Null And Speciesaddinfo.Provider <> "MM";
The result of this query must be exported to a csv file in US-ASCII, without header, separated by TABs, without text qualifier and using "." as the decimal separator.
To create and import data to a SQLite database, use:
sqlite3 aquamaps.db sqlite> CREATE TABLE spinfo (id TEXT, species TEXT, pelagic INTEGER, provider TEXT, depthmin REAL, depthprefmin REAL, depthprefmax REAL, depthmax REAL, tempmin REAL, tempmax REAL, tempprefmin REAL, tempprefmax REAL, salinitymin REAL, salinitymax REAL, salinityprefmin REAL, salinityprefmax REAL, primprodmin REAL, primprodmax REAL, primprodprefmin REAL, primprodprefmax REAL, iceconmin REAL, iceconmax REAL, iceconprefmin REAL, iceconprefmax REAL, landdistmin REAL, landdistmax REAL, landdistprefmin REAL, landdistprefmax REAL); sqlite> .separator sqlite> .import location_of_csv_file spinfo sqlite> CREATE INDEX idx_species ON spinfo(species); sqlite> .q
In case you are wondering why this algorithm requires all 9 layers to be specified (instead of letting the user specify a smaller set only with bottom layers or surface layers) the reason is that users may not know whether to choose bottom or surface layers. In this case, if the species has depth ranges in the local database, then the algorithm will be able to decide what subset of layers to use.
Definition at line 83 of file aquamaps.hh.
Referenced by AquaMaps::_calculateEnvelopes().
| const int DISTANCE_TO_LAND = 3 |
Definition at line 174 of file aquamaps.hh.
Referenced by AquaMaps::_hasExpertRange(), and AquaMaps::initialize().
| const int ICE_CONCENTRATION = 2 |
Definition at line 173 of file aquamaps.hh.
Referenced by AquaMaps::_hasExpertRange(), AquaMaps::_readSpeciesData(), and AquaMaps::initialize().
| const Scalar INNER_SIZE[7] |
Definition at line 153 of file aquamaps.hh.
| const int MAXDEPTH = 0 |
Definition at line 171 of file aquamaps.hh.
Referenced by AquaMaps::_calculateEnvelopes(), AquaMaps::_readSpeciesData(), AquaMaps::getValue(), and AquaMaps::initialize().
| const Scalar MAXIMUM_BOTTOM_SALINITY = 40.9 |
Definition at line 109 of file aquamaps.hh.
| const Scalar MAXIMUM_BOTTOM_TEMPERATURE = 30.0 |
Definition at line 117 of file aquamaps.hh.
| const Scalar MAXIMUM_DISTANCE_TO_LAND = 4200.0 |
Definition at line 98 of file aquamaps.hh.
| const Scalar MAXIMUM_ICE_CONCENTRATION = 1.5 |
Definition at line 94 of file aquamaps.hh.
| const Scalar MAXIMUM_MAXDEPTH = 9999.0 |
Definition at line 86 of file aquamaps.hh.
| const Scalar MAXIMUM_MINDEPTH = 9999.0 |
Definition at line 90 of file aquamaps.hh.
| const Scalar MAXIMUM_PRIMARY_PRODUCTION = 6000.0 |
Definition at line 102 of file aquamaps.hh.
| const Scalar MAXIMUM_SURFACE_SALINITY = 40.2 |
Definition at line 106 of file aquamaps.hh.
| const Scalar MAXIMUM_SURFACE_TEMPERATURE = 30.0 |
Definition at line 114 of file aquamaps.hh.
| const int MINDEPTH = 1 |
Definition at line 172 of file aquamaps.hh.
Referenced by AquaMaps::_calculateEnvelopes(), AquaMaps::_readSpeciesData(), AquaMaps::getValue(), and AquaMaps::initialize().
| const Scalar MINIMUM_BOTTOM_SALINITY = 3.5 |
Definition at line 108 of file aquamaps.hh.
| const Scalar MINIMUM_BOTTOM_TEMPERATURE = -2.0 |
Definition at line 116 of file aquamaps.hh.
| const Scalar MINIMUM_DISTANCE_TO_LAND = 0.0 |
Definition at line 97 of file aquamaps.hh.
| const Scalar MINIMUM_ENVELOPE_SIZE_FOR_DISTANCE_TO_LAND = 2.0 |
Definition at line 99 of file aquamaps.hh.
| const Scalar MINIMUM_ENVELOPE_SIZE_FOR_ICE_CONCENTRATION = 0.0 |
Definition at line 95 of file aquamaps.hh.
| const Scalar MINIMUM_ENVELOPE_SIZE_FOR_MAXDEPTH = 0.0 |
Definition at line 87 of file aquamaps.hh.
| const Scalar MINIMUM_ENVELOPE_SIZE_FOR_MINDEPTH = 0.0 |
Definition at line 91 of file aquamaps.hh.
| const Scalar MINIMUM_ENVELOPE_SIZE_FOR_PRIMARY_PRODUCTION = 2.0 |
Definition at line 103 of file aquamaps.hh.
| const Scalar MINIMUM_ENVELOPE_SIZE_FOR_SALINITY = 1.0 |
Definition at line 111 of file aquamaps.hh.
| const Scalar MINIMUM_ENVELOPE_SIZE_FOR_TEMPERATURE = 1.0 |
Definition at line 119 of file aquamaps.hh.
| const Scalar MINIMUM_ICE_CONCENTRATION = 0.0 |
Definition at line 93 of file aquamaps.hh.
| const Scalar MINIMUM_MAXDEPTH = 0.0 |
Definition at line 85 of file aquamaps.hh.
| const Scalar MINIMUM_MINDEPTH = 0.0 |
Definition at line 89 of file aquamaps.hh.
| const Scalar MINIMUM_PRIMARY_PRODUCTION = 0.0 |
Definition at line 101 of file aquamaps.hh.
| const Scalar MINIMUM_SURFACE_SALINITY = 3.56 |
Definition at line 105 of file aquamaps.hh.
| const Scalar MINIMUM_SURFACE_TEMPERATURE = -2.0 |
Definition at line 113 of file aquamaps.hh.
| const std::string NAME[7] |
Definition at line 161 of file aquamaps.hh.
Referenced by AquaMaps::_readSpeciesData().
| const int PRIMARY_PRODUCTION = 4 |
Definition at line 175 of file aquamaps.hh.
Referenced by AquaMaps::_hasExpertRange(), and AquaMaps::initialize().
| const int SALINITY = 5 |
Definition at line 176 of file aquamaps.hh.
Referenced by AquaMaps::_calculateEnvelopes(), AquaMaps::_hasExpertRange(), AquaMaps::getValue(), and AquaMaps::initialize().
| const Scalar SURFACE_LOWER_LIMIT[7] |
Definition at line 121 of file aquamaps.hh.
| const Scalar SURFACE_UPPER_LIMIT[7] |
Definition at line 137 of file aquamaps.hh.
| const int TEMPERATURE = 6 |
Definition at line 177 of file aquamaps.hh.
Referenced by AquaMaps::_calculateEnvelopes(), AquaMaps::_hasExpertRange(), AquaMaps::_readSpeciesData(), AquaMaps::getValue(), and AquaMaps::initialize().
