Author: chatellier Date: 2011-03-23 14:28:09 +0000 (Wed, 23 Mar 2011) New Revision: 790 Log: Add verena corrections Modified: trunk/src/site/en/rst/user/configuration.rst trunk/src/site/en/rst/user/controls.rst trunk/src/site/en/rst/user/dataformat.rst trunk/src/site/en/rst/user/faq.rst trunk/src/site/en/rst/user/guide_control.rst trunk/src/site/en/rst/user/guide_listcontrols.rst trunk/src/site/en/rst/user/guide_project.rst trunk/src/site/en/rst/user/guide_results.rst trunk/src/site/en/rst/user/guide_selection.rst Modified: trunk/src/site/en/rst/user/configuration.rst =================================================================== --- trunk/src/site/en/rst/user/configuration.rst 2011-03-21 10:22:19 UTC (rev 789) +++ trunk/src/site/en/rst/user/configuration.rst 2011-03-23 14:28:09 UTC (rev 790) @@ -25,8 +25,7 @@ Configuration ============= -Before using Coser, it need to be configured, especially about files not -provided with it. +Before using Coser, the software needs to be configured, especially for the files that have to be supplied by the user. A wizard is available with the menu *Options/Configuration* @@ -41,7 +40,7 @@ Coser projects directory location. coser.validator.directory - Coser controls directory localtion. Used to store user custom validators. + Coser controls directory location. Used to store user defined control rules. coser.reference.species Taxonomy reference file location. @@ -50,30 +49,30 @@ Species types code file location. coser.web.frontend - SIH indice campagne website address (used by administrator to publish results). + SIH indice campagne website address (used by Ifremer administrator to publish results). coser.web.zones.file - Application zone file location (used to affect zone to rsufi results). + Application zone file location (used to store Rsufi results). Control step configuration -------------------------- .. image:: ../../images/en/91-configurationvalues.png -In this view, you can define configuration values used during control step : +In this view, you can define configuration values used for data controls : coser.control.nobsmin - Minimum individual observation count. + Minimum number of individuals per species per stratum per year for data to be useable. coser.control.diffcatchlength - Percentage of acceptable difference between the total numbers of individual - captured in the capture file and the same amount in length file. + Maximum absolute acceptable difference (percentage) between total numbers in the catch data file and corresponding + total numbers in the length data file. coser.control.typeFish - Fish species type code name. Used by some controls to exclude some species. + Species type code (fish, crustacean,...). Used by some controls to exclude certain types. coser.selection.occurrenceFilter - Default percentage used in minimum occurrence field filter in selection step. + Default percentage value used in minimum occurrence field filter in selection step. coser.selection.densityFilter - Default percentage used in minimum density field filter in selection step. + Default percentage value used in minimum density (No per km2) field filter in selection step. Modified: trunk/src/site/en/rst/user/controls.rst =================================================================== --- trunk/src/site/en/rst/user/controls.rst 2011-03-21 10:22:19 UTC (rev 789) +++ trunk/src/site/en/rst/user/controls.rst 2011-03-23 14:28:09 UTC (rev 790) @@ -26,41 +26,39 @@ Controls ======== -Coser provides a user interface allowing to customize the controls. +Coser has a user interface for customizing the data controls. -But this customization is quite technical and must be performed only by -advanced users. +Warning: this customization is quite technical and must only be performed by +advanced users! -This interface is made of a tree with the list of the 4 files (catch, length, -hauls, strata) and for each one of them, the level of error possible. +This interface consists of a tree with the four main data file branches (catch, length, +hauls, strata). For each main branch the controls to be carried out are specified as well +as their error level (fatal, error, warning). -For each level, a XML file describing the controls can be associated in order -to describe them. +For each branch, a XML file describing the controls can be associated. Documentation ------------- -The XML files are based on a syntax used by the Java framework XWork. +The XML files are based on the syntax used by the Java framework XWork. -The documentation of this syntax can be found at this address : +The documentation of this syntax can be found at the address: http://struts.apache.org/2.x/docs/validation.html Fields ------ -For each file, the fields are reachable by their english name (``survey``, +For each file, the fields are accessible using the english name (``survey``, ``stratum``…) in their relative type (for example,``number`` is a Java double). -For each field, there is also an other field corresponding to its data under a -String form. For example, the field ``survey`` is also reachable using the name -``surveyAsString``. -The field ``number`` (of type double) is also reachable under the name -``numberAsString`` (of string type). +All fields, including numeric fields, are also accesible in String format. For example, the field ``survey`` +is also accessible using the name ``surveyAsString``. +The field ``number`` (of type double) is also accessible under the name ``numberAsString`` (of string type). Example ------- -Example of the strata validation file (error level) :: +Example of a strata control file (error level) :: <validators> <field name="survey"> @@ -78,7 +76,7 @@ <field name="surfaceAsString"> <field-validator type="checkDouble"> <param name="notAvailable">NA</param> - <message>surface attribute is not a valid double</message> + <message>Surface attribute is not a valid double</message> </field-validator> </field> </validators> @@ -86,4 +84,5 @@ In this example: * the field ``survey`` is mandatory (requiredstring) - * the field ``surface`` must be a valid number (the value NA is valid). \ No newline at end of file + * the field ``surface`` must be a valid double number (the value NA is valid). + \ No newline at end of file Modified: trunk/src/site/en/rst/user/dataformat.rst =================================================================== --- trunk/src/site/en/rst/user/dataformat.rst 2011-03-21 10:22:19 UTC (rev 789) +++ trunk/src/site/en/rst/user/dataformat.rst 2011-03-23 14:28:09 UTC (rev 790) @@ -25,22 +25,22 @@ Tables file format ================== -Coser needs 4 tables by project : +Coser needs four data tables for each project : - * catchs - * stratas - * lengths + * catches + * strata + * length * hauls -Each table must be formatted using CSV file format with ';' (semicolon) -separator and begin with predefined CSV headers (english or french) -**respecting header order**. +Each data table must be formatted using the CSV file format with ';' (semicolon) +separator and begin with predefined CSV headers (in English or French) +**respecting the colomn order**. Tables details -------------- -catchs -~~~~~~ +catches +~~~~~~~ French headers:: @@ -50,7 +50,7 @@ Survey;Year;Haul;Species;Number;Weight -Sample (catchs.csv):: +Example (catches.csv):: Survey;Year;Haul;Species;Number;Weight EVHOE_TOT;1997;B1008;ALLO;160.00;0.47 @@ -69,7 +69,7 @@ Survey;Stratum;Surface -Sample (strata.csv):: +Example (strata.csv):: Survey;Stratum;Surface EVHOE_TOT;Gn1;8201.69199214 @@ -88,7 +88,7 @@ Survey;Year;Haul;Species;Sex;Maturity;Length;Number;Weight;Age -Sample (length.csv):: +Example (length.csv):: Survey;Year;Haul;Species;Sex;Maturity;Length;Number;Weight;Age EVHOE_TOT;1997;B1008;ARNOLAT;i;NA;11.00;1.00;;NA @@ -107,7 +107,7 @@ Survey;Year;Haul;Month;Stratum;SweptSurface;Lat;Long;Depth -Sample (hauls.csv):: +Example (hauls.csv):: Survey;Year;Haul;Month;Stratum;SweptSurface;Lat;Long;Depth EVHOE_TOT;1997;B1008;10;Gs2;0.06;43.75;-1.50;45.50 Modified: trunk/src/site/en/rst/user/faq.rst =================================================================== --- trunk/src/site/en/rst/user/faq.rst 2011-03-21 10:22:19 UTC (rev 789) +++ trunk/src/site/en/rst/user/faq.rst 2011-03-23 14:28:09 UTC (rev 790) @@ -22,13 +22,13 @@ .. * <http://www.gnu.org/licenses/lgpl-3.0.html>. .. * #L% .. - -Requently Asked Questions -========================= +Frequently Asked Questions +========================== .. contents:: When I launch the JavaWebStart application, I got the message "Cannot launch the application" --------------------------------------------------------------------------------------------- -If the detail of this error talks about certificates, try to update Java and +If the details of this error message talks about certificates, try to update Java and then start again. Modified: trunk/src/site/en/rst/user/guide_control.rst =================================================================== --- trunk/src/site/en/rst/user/guide_control.rst 2011-03-21 10:22:19 UTC (rev 789) +++ trunk/src/site/en/rst/user/guide_control.rst 2011-03-23 14:28:09 UTC (rev 790) @@ -22,10 +22,10 @@ .. * <http://www.gnu.org/licenses/lgpl-3.0.html>. .. * #L% .. - -Control step -============ +Data control step +================= -The control step goal is to detect errors on the 4 data tables +The aim of the data control step is to detect errors in the four data tables and possibly correct them if possible. .. image:: ../../images/en/10-controlmain.png @@ -34,42 +34,40 @@ ---------- During this step, the first action to do is launching global check, by clicking -on ``Check data`` button. +on the ``Check data`` button. Coser will check: - * line by line errors on 4 tables + * line by line for errors in each of the 4 tables * verification by cross-checking files - * verification by cross-checking with the taxonomic referential + * verification by cross-checking with the taxonomic reference file -After the 10 verifications steps, a tree with all the errors is displayed with -all the errors detected. +After the 10 verifications steps, a tree with all the detected errors is displayed. For more information on the errors : `controls list`_. .. _controls list: guide_listcontrols.html -Fixing data ------------ +Correcting data (fixing errors) +------------------------------- -When selecting an error, Coser displays the line of the error allowing you to -fix it. -The lines in red corresponds to the fields with errors. The right part details +When selecting an error, Coser displays the corresponding line of the data allowing you to +correct it. +The lines in red corresponds to the fields with detected errors. The right part details the error messages. -In the previous example, the year is missing, the user can add it by hand and -then validate the modification. +If for example the year is missing, the user can add it by hand and then validate the modification. -Bulk fixing ------------ +Bulk data correction +-------------------- In the case of the same error on several lines : - * either the error is caused by an export error of the 4 tables and it is - better to do the export again, fixing being impossible in coser. - * either the error can be fixed. + * either the error is caused by an export error of the 4 tables from the original data base and it is + better to do the export again, bulk correction being impossible in coser. + * or the errors can be corrected line by line. -The table that displays the data got a contextual menu allowing to : +The table that displays the data has a contextual menu allowing to : * delete several selected lines. * find a pattern and replace it by another one @@ -77,61 +75,59 @@ .. image:: ../../images/en/11-controlmenu1.png -For example, if all the numbers got a comma (,) instead of a point (.) for -decimal separation, it is possible to replace all the commas by points in one -operation. +For example, if all numbers have a decimal comma (,) instead of a decimal point (.), +it is possible to replace all commas by points in a single operation. Charts ------ -Coser can also generate charts to ease the decision taking (specifically -regarding warning errors). +Coser generates figures to facilitate decision making (specifically for warnings). -The button ``Comparison Catch/Length`` displays an interface where a chart -is generated for each species. The data corresponds to the sum of the -``Number``s in the catch and length per year files. A difference can show an -error in the original data. +The button ``Comparison Catch/Length`` displays an interface where a figure +is generated for each species. The data correspond to total ``Number``s per year in the +catch and length files. A difference between the two values indicates an error in the original data, most +likely caused during the raising procedure from the sub-sample to the haul level. .. image:: ../../images/en/13-controlgraphdiff.png -The button``Length structures`` displays an interface that can generate -charts on a subset of data. +The button``Length structures`` displays an interface for generating +figures for a data subset. It is for example possible to display the length structure but only for a -stratum, or a species, or get the sum… +stratum, or a species, or cumulated… .. image:: ../../images/en/14-controlgraphlength.png Reports ------- -In the control step, it is possible to generate 2 reports. +In the control step, it is possible to generate two reports. Modifications report ~~~~~~~~~~~~~~~~~~~~ -The modifications report, reachable through the ``Modifications report`` -button, is generated in HTML and should open in a web browser. You can visualize +The modifications report, accessible through the ``Modifications report`` +button, is generated in HTML format and should be opened in a web browser. You can visualize and print the report in/from the browser. Controls report ~~~~~~~~~~~~~~~ -This report is reachable by right clic on the errors tree after verifying the +This report is accessible by a right clic on the errors tree after verifying the errors in the data. .. image:: ../../images/en/12-controlmenu2.png -This report contains the same errors that the one displayed in the tree and the -Catch/length comparison charts. +This report contains the same errors that are displayed in the tree and the +Catch/length comparison figures. Save and validation ------------------- -You can save whenever you want the state of the data while fixing data. +You can save the current state of the corrected data at any time. -After the data verification, and if this one ended with **no errors** the -``Valid control`` button become active and allows you to validate. +After the data verification ended with **no errors** the +``Valid control`` button becomes active to validate the (corrected) data. -The validation of the control step is necessary to go the `selection step`_. +Validation of the control step is necessary to be able to move on to the `selection step`_. .. _selection step: guide_selection.html Modified: trunk/src/site/en/rst/user/guide_listcontrols.rst =================================================================== --- trunk/src/site/en/rst/user/guide_listcontrols.rst 2011-03-21 10:22:19 UTC (rev 789) +++ trunk/src/site/en/rst/user/guide_listcontrols.rst 2011-03-23 14:28:09 UTC (rev 790) @@ -25,8 +25,7 @@ Controls list ============= -This page details the list of the controls made by Coser when verifying the -data. +This page lists the controls made by Coser when verifying the data. Catches ------- @@ -51,14 +50,14 @@ +-----------------------------------------------------------------------------+----------+ | Other checks | Level | +=============================================================================+==========+ -| If the weight is a number different of 0, then the number also needs to be | | +| If Weight has a value different from 0, then Number also needs to be | | | different from 0 | Error | +-----------------------------------------------------------------------------+----------+ -| Check of duplicate entries with the keys "Survey", "Year", "Haul", | | +| Check for duplicate entries with the keys "Survey", "Year", "Haul", | | | "Species" | Error | +-----------------------------------------------------------------------------+----------+ -| Check of the minimal number of observations in the table CATCH$Number | | -| by species by stratum by year | Warning | +| Check of the minimum number of observations (minobs) in the table | | +| CATCH$Number by species by stratum by year | Warning | +-----------------------------------------------------------------------------+----------+ Stratas @@ -77,7 +76,7 @@ +-----------------------------------------------------------------------------+----------+ | Other Checks | Level | +=============================================================================+==========+ -| Check the duplicate lines on the keys "Survey", "Stratum" | Error | +| Check for duplicated lines using the key "Survey", "Stratum" | Error | +-----------------------------------------------------------------------------+----------+ Lengths @@ -111,16 +110,16 @@ +-----------------------------------------------------------------------------+----------+ | Other Checks | Level | +=============================================================================+==========+ -| If the Weight is a number different from 0, the Number must be also | Error | -| different from 0 | | +| If Weight has a value different from 0, the corresponding Number must aslo | Error | +| be different from 0 | | +-----------------------------------------------------------------------------+----------+ -| Check duplicate lines on keys "Survey", "Year", "Haul", | Error | +| Check for duplicated lines using the key "Survey", "Year", "Haul", | Error | | "Species", "Sex", "Maturity", "Length" | | +-----------------------------------------------------------------------------+----------+ -| Check the minimal number of observations in the table LENGTH$Number by | Error | -| species by stratum by year | | +| Check the minumum number of observations is >=minobs in the table | Error | +| LENGTH$Number by species by stratum by year | | +-----------------------------------------------------------------------------+----------+ -| For the fishes, the Length field must have a full or half step | Warning | +| For the fishes, the Length field must be integer cm or half cm | Warning | | (for example: 4.0 or 4.5 but not 4.25) | | +-----------------------------------------------------------------------------+----------+ @@ -149,17 +148,17 @@ +-----------------+----------------------------------------------------------------+----------+ | Depth | Number, empty or NA | Error | +-----------------+----------------------------------------------------------------+----------+ -| SweptSurface | With at least 3 decimals | Fatal | +| SweptSurface | In km2 with at least 3 decimal values | Fatal | +-----------------+----------------------------------------------------------------+----------+ -| Lat | With at least 4 decimals | Warning | +| Lat | Decimal degrees with at least 4 decimal values (ex. 50.4443) | Warning | +-----------------+----------------------------------------------------------------+----------+ -| Long | With at least 4 decimals | Warning | +| Long | Decimal degress with at least 4 decimal values (ex. -7.5554) | Warning | +-----------------+----------------------------------------------------------------+----------+ +-----------------------------------------------------------------------------+----------+ | Other Checks | Level | +=============================================================================+==========+ -| Check duplicate lines on keys "Survey", "Year", "Haul", "Month" | Error | +| Check for duplicated lines using key "Survey", "Year", "Haul", "Month" | Error | +-----------------------------------------------------------------------------+----------+ Files cross-checking @@ -168,50 +167,51 @@ +-----------------------------------------------------------------------------+----------+ | Checks | Level | +=============================================================================+==========+ -| Check the campaign name is the same in the 4 files | Fatal | +| Check the survey name is the same in the 4 files | Fatal | +-----------------------------------------------------------------------------+----------+ | The list of years must be the same in the Catchs, Length and Hauls files | Fatal | +-----------------------------------------------------------------------------+----------+ | Check that for each species present in a haul of a year in the length file | Fatal | -| (noted Year/Haul/Species) there is a data in the catch files (the opposite |  | +| (noted Year/Haul/Species) there is an entry in the catch file (the opposite |  | | is not true) |  | +-----------------------------------------------------------------------------+----------+ | Check that for each haul present in a year (noted Year/Haul) in the | Fatal | -| length files and catches, there is a data in the haul file | | +| length and catch files, there is an entry in the haul file | | +-----------------------------------------------------------------------------+----------+ -| Check if, for a year, there is catch in catch file, there is catch in | Warning | -| length file too. | | +| Check if, for a given year, there is an entry in catch file, there is a | Warning | +| corresponding one in the length file too. | | +-----------------------------------------------------------------------------+----------+ -| Check that the difference between catch in catch file and catch in length | Warning | -| file in belong percentage defined in configuration for a year. | | +| Check that the difference between total numbers in the catch file and | Warning | +| the corresonding numbers in the length file is below the percentage | | +| defined in configuration file. | | +-----------------------------------------------------------------------------+----------+ -| Check that each strata present in haul file is also present in strata file | Fatal | +| Check that all strata in the haul file are also present in strata file. | Fatal | +-----------------------------------------------------------------------------+----------+ -| Check that each strata present in strata file is also present in haul file | Warning | +| Check that all strata present in strata file are also in the haul file. | Warning | +-----------------------------------------------------------------------------+----------+ -| Check that each haul present in catch file is also present in haul file | Fatal | +| Check that each haul present in the catch file is also in the haul file. | Fatal | +-----------------------------------------------------------------------------+----------+ -| Check that each haul present in haul file is also present in catch file | Warning | +| Check that each haul present in the haul file is also in the catch file. | Warning | +-----------------------------------------------------------------------------+----------+ -| Check that each haul present in length file is also present in catch file | Fatal | +| Check that each haul present in the length file is also in the catch file. | Fatal | +-----------------------------------------------------------------------------+----------+ -| Check that each haul present in catch file is also present in length file | Warning | +| Check that each haul present in the catch file is also in the length file. | Warning | +-----------------------------------------------------------------------------+----------+ -| Check that each species present in length file is also present in catch file| Fatal | +| Check that each species present in the length file is also in the catch file| Fatal | +-----------------------------------------------------------------------------+----------+ -| Check that each species present in catch file is also present in length file| Warning | +| Check that each species present in the catch file is also in the length file| Warning | +-----------------------------------------------------------------------------+----------+ -Cross checking with the taxonomic referential +Cross checking with the taxonomic reference file --------------------------------------------- +-----------------------------------------------------------------------------+----------+ | Checks | Level | +=============================================================================+==========+ -| The Field Species of the catchs file must correspond to a species | Error | -| present in the taxonomic referential | | +| The Species field in the catch file must correspond to a species | Error | +| present in the taxonomic reference file | | +-----------------------------------------------------------------------------+----------+ -| The Field Species of the length file must correspond to a species | Error | -| present in the taxonomic referential | | +| The Species filed in the length file must correspond to a species | Error | +| present in the taxonomic reference file | | +-----------------------------------------------------------------------------+----------+ Modified: trunk/src/site/en/rst/user/guide_project.rst =================================================================== --- trunk/src/site/en/rst/user/guide_project.rst 2011-03-21 10:22:19 UTC (rev 789) +++ trunk/src/site/en/rst/user/guide_project.rst 2011-03-23 14:28:09 UTC (rev 790) @@ -25,8 +25,7 @@ Project ======= -The first thing to do to treat the 4 data tables is to create a project by -filling its parameters (and the 4 tables). +The first step is to create a project by providing file paths and parameters. Configuration ------------- @@ -39,23 +38,22 @@ This interface must contains: * the project name (only alphanumerical characters are allowed). - * the name of the author (mandatory) - * The csv files correspond to the 4 tables (mandatory) + * the name of the author (mandatory!) + * The csv files correspond to the 4 data tables (mandatory!) * the maps in shapes format (*.shp) used in the selection step to display the - application zone on the world map. - * a comment + application zone on the world map (optional). + * a comment (optional) -It is also possible to use, only for this project, an other taxonomic -referential file than the one present in the default configuration of the -software. It will be used only for this project. +It is also possible to use, only for this project, a specific taxonomic +reference file instead of the default file which is part of Coser. Validation ---------- -After having clicked on the ``Create project``, the 4 tables and the -taxonomic referential are loaded into memory. -The software checks then than the files are in the correct format (CSV, -separator, headers names) then create the project and displays the project +After having clicked on ``Create project``, the 4 data tables and the +taxonomic reference file are loaded into memory. +The software then checks that the files are in the correct format (CSV, +separator, headers names) then creates the project and displays the project summary interface : .. image:: ../../images/en/04-projectsummary.png Modified: trunk/src/site/en/rst/user/guide_results.rst =================================================================== --- trunk/src/site/en/rst/user/guide_results.rst 2011-03-21 10:22:19 UTC (rev 789) +++ trunk/src/site/en/rst/user/guide_results.rst 2011-03-23 14:28:09 UTC (rev 790) @@ -25,41 +25,41 @@ RSufi Results ============= -Once your selection data have been used in RSufi, it gives you the result that -is possible to add in the result list of a selection. +Once your selected data have been used in RSufi, the results can be +added to the results list of the project selection. -To do so, reopen the concerned selection using the -*Data/Selection/<selectionname>* menu and Select the thirs tab ``RSufi``. +To do so, reopen the corresponding selection using the +*Data/Selection/<selectionname>* menu and Select the third tab ``RSufi``. .. image:: ../../images/en/25-selectionresults.png -This time, this is the second part on the interface that interest us. It -summarize the list of results stored in Coser. +Now, the second part of the interface is of interest. It +lists the results stored in Coser. To add a new result, click on the button ``Add a result``. .. image:: ../../images/en/26-selectionaddresult.png -A result is compounded of : +A Rsufi result is composed of : - * a name unique amongst the selection results (mandatory and compounded only + * a unique name amongst the selection results (mandatory and composed only of alphanumerical characters) * the RSufi version with which the result have been obtained (mandatory) - * the result addition date (mandatory) - * the ``estcomind`` data file (mandatory) - * the ``estpopind`` data file (mandatory) + * the date of the results addition (mandatory) + * the ``estcomind`` (commnity indicators) Rsufi results file (mandatory) + * the ``estpopind`` (population indicators) Rsufi results file (mandatory) -You got also optional informations : +You can add optionally information on: - * the application zone (used when publishing result in the internet website - to place the results in a defined zone) - * the maps directory (used by the website to display the distribution maps) - * publishable (used by admins to differenciate publishable results from + * the study area (used when publishing results on the internet website + to place the results in the appropriate geographic zone) + * the maps directory (used by the website to display the species distribution maps) + * publishable flag (used by administrator to differenciate publishable results from others) - * other file (other file that needs to be stored by Coser) + * other files (other files that need to be stored by Coser) -Once the result is parmaterized with no error, click on ``Add the result`` to -validate the action. This result will be then available to the Coser admins so -that they can publish it on the internet website : +Once the results are parmaterized with no error, click on ``Add the result`` to +validate the action. This result will be then available to the Coser administrator so +that they can publish it on the Ifremer internet website : http://www.ifremer.fr/SIH-indices-campagnes/ Modified: trunk/src/site/en/rst/user/guide_selection.rst =================================================================== --- trunk/src/site/en/rst/user/guide_selection.rst 2011-03-21 10:22:19 UTC (rev 789) +++ trunk/src/site/en/rst/user/guide_selection.rst 2011-03-23 14:28:09 UTC (rev 790) @@ -24,58 +24,58 @@ .. - Selection ========= +The objective of the selection phase is to create coherent and consistent data tables +for use in the Rsufi package. -The selection step consist in selecting the following lists as RSufi -parameters : +During the selection the following lists are created: * L1 : List of the selected species - * L2 : List of species from L1 respecting an occurence/density filter - * L3 : List of species form L2 with lengthes for all the years - * L4 : List of species from L3 with maturity + * L2 : List of species as subset from L1 respecting an occurence & density filter + * L3 : List of species as subset from L2 with length measurements for all years + * L4 : List of species as subset from L3 with maturity information Selection creation ------------------ -The first step consist in defining the selection parameters for Coser. +The first step consists in defining the selection parameters for Coser. To do so, use the menu ``Selection/New selection`` .. image:: ../../images/en/27-selectionmenu0.png -**Note**: This menu is available only if the control step have been validated. +**Note**: This menu is available only if the control step has been validated. .. image:: ../../images/en/20-selectiondetail.png -This name is mandatory and can contain only alphanumerical characters. +Providing a name is mandatory; the name can only contain alphanumerical characters. -You have then to select the years of the selection data. The 4 tables data will +In the second step, the years are selected (gaps are possible). The 4 tables data will be restricted to those years. .. image:: ../../images/en/21-selectionyears.png -You then need to select the stratas for which you want to select species. +In the third step the strata are selected. .. image:: ../../images/en/22-selectionstrata.png -In this step, it is also possible to display sampling effort data by clicking on -the table-shape icon. +To aid the selection of strata it is also possible to display the sampling effort table by clicking on +the table-shaped icon. -Then comes the species selection step to include in the L1 list. This step -summarize the list of all the species available after the choice of years and -stratas. +In the fourth step the species to be included in species list L1 are selected. At this point only +species present in the previously selected years and strata can be selected. .. image:: ../../images/en/23-selectionspecies.png -The list ``Filtered species`` correspond to the list of all the species. This +The list L1 ``Filtered species`` correspond to the list of all the species. This list is filterable by the ``Filter by type`` list types. -To adjust a species in the L1 list, you have to select it and click on the +To add a species in the L1 list, you have to select it and click on the ``right arrow`` button. -The two lists of this step got contextual menus allowing to : +The two lists of this step have a contextual menu allowing to : - * merge species - * generate catch/length comparison charts + * merge species, e.g. merge two species at the genus level + * generate catch/length comparison figures * etc… .. image:: ../../images/en/28-selectionmenu1.png @@ -84,59 +84,59 @@ Report ------ -It is possible to generate a report that got all the selection information by +It is possible to generate a report that contains all selection information by clicking on the ``Selection report`` button. This report is in html format and -should open in your browser to be visualised and printed. +should be opened in your browser to be visualised and printed. Species list ------------ -Once the L1 list have been defined, you need to save the selection so that -the ``Species list`` tab become active. +Once the L1 list has been defined, it needs to be saved so that the ``Species list`` +tab becomes active. .. image:: ../../images/en/24-selectionlists.png -In this screen : +On this screen : - * The L1 list correspond to the list defined in the previous step - * The L2 list correspond to the list of filtered species using the minimum - occurence percentage and the minimum number of individuals per square - kilometers - * The L3 list summarize the species selected in L2 list that got lengthes for - every year - * The L4 list summarize, amongst the L3 species, the ones that got maturities. + * The L1 list corresponds to the species list defined in the previous step + * The L2 list correspond to the species list of filtered species using the average + occurence percentage and the average number of individuals per square + kilometers as selection criteria + * The L3 list summarize the species selected in L2 list that have length + measurements for every year + * The L4 list summarize, amongst the L3 species, those with maturity information. To be noted : * Only the **selected** species (highlighted) are taken into account - * If you modify the default selection, you will have to justify your choice by - filling in a comment bellow the concerned list + * If the default selection is modified, the choice needs to be justified by + filling in a comment box below the corresponding list -Once the 4 species list defined, you can finalize the selection by validating +Once the 4 species lists have been defined, final selection is validated it clicking on the `` Validate selection`` button. -Export the data for RSufi -------------------------- +Export data for RSufi +--------------------- -Once the 4 lists are defined and the selection validated, the third tab "RSufi" -become active. +Once the 4 lists have been defined and the selection validated, the third menu tab "RSufi" +becomes active. .. image: ../../images/en/25-selectionresults.png -In this screen, you can export the necessary files for RSufi's execution. Take -care, Coser does not pilot RSufi, it only generates the files needed for its -execution. +On this screen, the necessary data files for RSufi can be exported. The consist of +the controlled and selected data from previous steps. Attention, Coser does not +run RSufi, it only generates the files needed for its execution. -The generated file contains : +The generated files contain: - * the 4 data tables (with only the years selected) + * the 4 data tables (with only the selected years, strata and species) * a file detailing the 4 species lists (L1, L2, L3 and L4) * a project information file -Result ------- +Results +------- -Once RSufi have been executed with your selection, you can go to the +Once RSufi has been executed with the selected data, move to `results storing`_ step. .. _results storing: guide_results.html