Technical Description of PIR
PIR is a system for storing and extracting fishing data for presentation and statistical analysis.
Experimental fishing is performed for a varity of reasons mostly for scientific inventorying and sampling of aquatic fauna.
Personnel and material are deployed at pre-selected aquatic sites in order to record data concerning the specimens capture. The data obtained usually concerns the species, it’s size (length, weight), sex, body conditions, also relative abundance and if necessary the concentration of inorganic elements in body tissue.
Data from these field captures is recorded for later study, which is the purpose of PIR.
This project had several members, the lead organization was RDI (ex. ORSTOM). The application was developed using FOXPRO2 while the user interface is French.
The 11 main files of PIR are organized as follows :
 |
|
Another way of seeing the file structure is :
 |
|
Menu
The menu has 4 major choices : dynamic files (Gestion), list files (Listes), processing (Exploitation) and utilities (Utilitaires). Sub-choices are shown under the principle menus.
Dynamic files are : The source (river or data collection, i.e. Amazon, Guinée, etc.), Fishing effort (Pêche), Habitat (Habitat), Operation (Opération) and Fish (Poison).
List files are :
Station, Sector (Secteur), Basin (Bassin), Species (Especes), Species Details (Détail d’Espece), Equipment (Engins), Stomach Content (Contenu Stomacal).
Processing manipulates files and data and performs user commands.
View Files/data (Vue), Reset Selections (R à Z Sélection), Selection level (Niveaux de Sélection), Extract Data (Extraction) and Calculations (Calculs).
Utilities provide a DOS interface, file indexing and file compression, sorting and re-indexing
File Control
All data entry mask are accompanied by a control window, shown below. This menu permits the users to perform operation upon the data file.
Operations include : Add – add a record, Beg – go to beginning of file, Copy – copy the current record, Del – delete current record, End – go to the end of the file, Find – locate and list specific records, Next – skip to next record, Prev – skip back one record, Quit – quit and return to main menu.
Fish
The biggest and most dynamic data files are the fish files. One file for each different data collection or a file for a concatenated data sets.
This file stores the : length, weight, evaluation type for weight (1=individual, 2=average for a group, 3=part of an individual), sex code, (1=not observed, 2=undetermined, 3=Male, 4=female), maturity (1=not observed, 2=immature, 3=not mature, 4=pre-mature, 5=advanced maturity, 6=spawning, 7=post-spawn), gonad weight, jar number (if individual is stored), stomach fill (1=not observed, 2=empty, 3=a quarter full, 4=half full, 5=full), content of stomach (maximum of 6 different items selected from a list), comments and notes.
Plus the key values for each individual. The Species Code and Operation Code.
Stomach Content
Contains a code for the food and a type or name : 99=Not Observed, 1=Plankton, 2=Detritus, 3=Algues, etc..
Operation
This file groups all the other files via the operation code, fishing code and equipment code.
It also stores the starting and ending time, section of the net where individual were captured and the type of net (1=surface, 2=bottom, 3=drift).
Habitat Profile
Environmental features are recorded in this file. The operation code links this record to the Operations file.
A record stores the mean depth of the operation, the nature of the river bank (1=dirt, 2=sand, 3=rocky), distance from the bank, vegetation coverage (1=none, 2=emerged, 3=low cover, 4=high cover), type of river bed (1=flowing, 2=congested, 3=rocky, 4=undercuts bank) and comments or memos.
Equipment
The Equipment Code links this file to the Operations file. A short text for the equipment type describes the material (i.e. Strainer net, Rotenone, etc) while an equipment name is the material name. mesh size (in mm), net length and height (in meters), type of filament (1=mono, 2=multi) and its diameter. Comment and extra fields where added.
Fishing Effort
The Fishing and Station Codes link this file to the Operations and Station files.
Each record contains the date, equipment type, duration (in hours), mean water height (in m), water temperature (in C), transparence (in m), pH, conductivity, oxygen content (in mg/l), vegetation type and comments.
Station
The principle key is the Station Code while the Sector Code relates each record to the Sector file.
This file stores the station name, station type (river, flood plain, dead end, etc.), river name, river sequence, Latitude (in degrees, minutes and seconds), Longitude, (ddd:mm:ss), altitude (in m), distance from source (in km), distance from mouth (in km) and comments.
Sector
The principle key is the sector code, the secondary key the basin code which relates the sector file to the Basin file.
This file stores the sector name and comments
.
Basin
This file describes the river basin. Its only key is the Basin code. The files stores the basin name, basin sequence number
length (in km), surface (of drainage basin), mean flow volume (in M3), maximum volume, minimum volume, continent, minimum latitude, maximum latitude, minimum longitude, maximum longitude, climatic zone (humid, tropical, arid, etc.),
vegetation zone and comments.
Species
The principle key is the species code which relates this file to the Fish file. A record stores the genius, species, family, 3 synonyms for the genius and species, 2 common names and bibliographic reference.
Details of Species
This data file stores information related to the species and how certain calculations are to be performed during processing and analysis. The principle key is the species code which relates to the Species and Fish files. It stores the minimum length, maximum length, length step (length in cm of a size group. This determines how many size groups a species is classified into.).
This screen allows the user to display all the files (Vue Oui/Non) and set their relationship to one of three configurations.
1) Standard, just list the files and permits access without sequences or relations to other files. 2) Relational which organizes the files using the Operation as the master file. 3) Filter, set the Basin file as master file
| 2) Relational – structures the data around an Operation | 3) Filtered – generates a Basin -> Operation relationship |
|
|
Reset Selection, Selection and Extraction.
Creating a SQL Results file requires 3 steps :
1) Resetting the selection to initializes all data to unselected. Without resetting, the SQL program will include selections from previous analysis.
2) Select the level of selection. The selection levels are Basin, Sector, Station, Fishing Effort, Operation or Species. In this example the user selects the species by placing a “T” in the active column.
3) Extract which will create an SQL program based upon the selections and generate the Results data file.
SQL code generation
Extraction of the data is simple as it requires the user to select the level of intervention (Basin, Sector, Station, Fishing Effort, Operation or Species) and the data required (a species or group of species, a date, or section, etc.) . Selected records require the user to activate it by placing a .T. in the active field.
Once the selections have been made an SQL program is generated, based upon a template and the activated records. The SQL program is executed and corresponding records extracted to a new data file (Result_sql.dbf).
The user then executes the required calculation and report type. There are 10 different data files required to generate the 10 different reports. The reports are : 1) Size, 2) Minimum Reproduction Size, 3) Number of Reproduction Cycles per Year, 4) Migration, 5) Diet, 6) Size Structure, 7) Fish Size vs. Net Size, 8) Seasonal Body Condition, 9) Species Table, and 10) Environment.
Calculations
1) Size
Sizes (by species), displaying the number of individuals, maximum, mean and minimum and standard deviation for weight and length. If a species has a minimum number of individuals the relation for the body size and weight (r,a,& b) can be calculated.
Species Number Max Min Mean STD Max Min Mean STD R A B
Longer Weight
ABREV 1 140.0 140.0 140.0 0.00 45.0 45.0 45.00 0.00 0.0000 0.0000 0.0000
ADEN2 4 240.0 230.0 235.0 5.00 145.0 137.0 141.0 4.00 0.0000 0.0000 0.0000
AFALC 95 365.0 179.0 253.9 37.11 480.0 48.0 161.1 75.63 0.9649 2.9419 -11.27
AGEN2 1 133.0 133.0 133.0 0.00 44.0 44.0 44.00 0.00 0.0000 0.0000 0.0000
2 Minimum Reproduction Size.
This is a table generated for each species, by sex. The species is divided and grouped according to lengths described in the Details of Species. The number of individuals per group and their maturity is totaled and displayed.
Species AFALC sex 3 Maturity‚
min max group non obs/immature/nonmat/debutmat/matadvn/ponte/postpont/Total
10.0 - 20.0 1 0 0 0 0 0 0 0 0
20.0 - 30.0 2 0 0 0 0 0 0 0 0
30.0 - 40.0 3 0 0 0 0 0 0 0 0
40.0 - 50.0 4 0 0 0 0 0 0 0 0
..........................................................................................
130 - 140 13 0 0 0 0 0 0 0 0
140 - 150 14 0 0 0 0 0 0 0 0
150 - 160 15 0 0 0 0 0 0 0 0
160 - 170 16 0 0 0 0 0 0 0 0
170 - 180 17 0 0 0 0 0 0 0 0
180 - 190 18 0 1 0 0 0 0 0 1
190 - 200 19 0 0 0 0 0 0 0 0
200 - 210 20 1 1 0 0 0 0 0 2
210 - 220 21 1 3 1 0 0 0 0 5
220 - 230 22 0 5 0 0 0 0 0 5
230 - 240 23 1 4 6 0 0 0 0 11
240 - 250 24 2 5 7 0 0 0 0 14
250 - 260 25 1 5 4 0 0 0 0 10
260 - 270 26 0 3 0 0 0 0 0 3
270 - 280 27 0 0 0 0 0 0 0 0
280 - 290 28 0 0 0 0 0 0 0 0
..........................................................................................
350 - 360 35 0 0 0 0 0 0 0 0
360 - 370 36 0 0 0 0 0 0 0 0
370 - 380 37 0 0 0 0 0 0 0 0
6 27 18 0 0 0 0 51
Species AFALC sex 4 Maturity
min max group non obs/immature/nonmat/debutmat/matadvn/ponte/postpont/Total
10.0 - 20.0 1 0 0 0 0 0 0 0 0
20.0 - 30.0 2 0 0 0 0 0 0 0 0
30.0 - 40.0 3 0 0 0 0 0 0 0 0
40.0 - 50.0 4 0 0 0 0 0 0 0 0
..........................................................................................
170 - 180 17 0 0 0 0 0 0 0 0
180 - 190 18 0 0 0 0 0 0 0 0
190 - 200 19 0 0 0 0 0 0 0 0
200 - 210 20 0 0 0 0 0 0 0 0
210 - 220 21 1 0 0 0 0 0 0 1
220 - 230 22 0 1 0 0 0 0 0 1
230 - 240 23 1 2 1 0 0 0 0 4
240 - 250 24 3 8 1 0 0 0 0 12
250 - 260 25 4 8 2 0 0 0 0 14
260 - 270 26 2 7 1 0 0 0 0 10
270 - 280 27 1 3 3 0 0 0 0 7
280 - 290 28 1 1 1 0 0 0 0 3
..........................................................................................
350 - 360 35 0 1 0 0 0 0 0 1
360 - 370 36 0 1 0 0 0 0 0 1
370 - 380 37 0 0 0 0 0 0 0 0
13 37 16 0 1 0 0 67
3 Number of Reproduction Cycles per Year
This table also groups species by sex and presents the dates they where captured and the total number of individuals per maturity type.
Species PMONT sex 3 Maturity
date 1 2 3 4 5 6 7
non obs/immat / non mat/déb mat/mat adv/ ponte/post ponte
09/10/86 0 1 0 0 0 0 0
06/12/86 0 5 0 0 0 0 0
29/06/87 1 7 16 1 0 0 0
04/09/87 1 2 4 0 0 0 0
02/11/87 1 2 3 0 0 0 0
Species PMONT sex 4 Maturity
date 1 2 3 4 5 6 7
non obs/immat / non mat/déb mat/mat adv/ ponte/post ponte
09/10/86 0 0 0 0 0 0 0
06/12/86 3 14 5 0 0 0 0
29/06/87 8 5 8 0 0 0 0
04/09/87 2 14 38 0 0 0 0
02/11/87 1 2 14 0 0 0 0
4 Migration
This program creates a table of the species captured at a station for a given date. The number of individuals is presented next to the total weight.
Station = LGPD
Number/Weight Number/Weight Number/Weight Number/Weight
18/08/86 09/10/86 06/12/86 29/06/87
1 0,00 0 0 0
PCAST 37 19139 26 4701,0 7 3137,0 26 8892,0
PMONT 0 4 508,00 59 12691 154 22201
SNATT 47 8049,0 315 57155 55 8226,0 71 16213
TANGU 10 1220,0 111 8798,0 45 3577,0 23 2384,0
TELON 27 1583,0 137 7926,0 58 3954,0 61 7508,0
Station = LGPD
Number/Weight Number/Weight
04/09/87 02/11/87
0 0
PCAST 1 976,00 24 6398,0
PMONT 67 9740,0 33 4377,0
SNATT 12 1505,0 6 1321,0
TANGU 113 9223,0 110 3143,0
TELON 15 1081,0 0
5 Diet
This report creates a table of species (1 species per line) with the total occurrence of an aliment found in the stomach.
1 2 3 4 5 ………….. 14 15 16 99
Planc/Detri/Algue/Fruit/Fleur/…………../Autre/Ecail/Oeufs/Frenc/Non o/
ABREV 1 1 1 1 1 …………. 0 0 0 0 0
AELON 0 0 0 0 0 …………. 0 0 0 0 25
AEQUI 0 0 0 0 0 …………. 0 0 0 0 11
AFALC 0 0 0 0 0 …………. 2 7 0 0 167
6 Size Structure
For every species, the amount of food in the stomach (1=not observed, 2=empty, 3=a quarter full, 4=half full, 5=full), in relation to the time of capture.
Species ABREV Debut Fin Matin Apres
Remp Sto 1 2 3 4
Vide 1/3 2/3 Plein
19,00 1,00 7,00 13,00
1 0 0 0 0
2 0 0 0 0
3 0 0 0 0
4 0 0 0 0
5 0 0 0 0
Species ADEN2 Debut Fin Matin Apres
Remp Sto 1 2 3 4
Vide 1/3 2/3 Plein
19,00 1,00 7,00 13,00
1 0 0 0 0
2 0 0 0 0
3 0 0 0 0
4 0 0 0 0
5 0 0 0 0
This report groups the species by size and calculates the number of individual per group in relation the size of net used to capture the individuals.
Species group min max nom ind
AEQUI 1 60,0 – 70,0 0,0000
AEQUI 2 70,0 – 80,0 0,0000
AEQUI 3 80,0 – 90,0 0,0000
AEQUI 4 90,0 – 100 0,0000
AEQUI 5 100 – 110 2,8302
AEQUI 6 110 – 120 8,4906
AEQUI 7 120 – 130 0,0000
AEQUI 8 130 – 140 0,0000
8 Seasonal Body Condition
This report performs an analysis of variance of individuals in relation to their weight, length, sex, body condition, date captured and the station.
Species Weight Length Sex K Date Station
PCAST 142,0 209,0 3 4,65 29/06/87 LGPD
PCAST 411,0 211,0 4 13,11 18/08/86 LGPD
PCAST 410,0 214,0 4 12,58 18/08/86 LGPD
PCAST 174,0 226,0 1 4,58 29/06/87 LGPD
PCAST 188,0 228,0 3 4,83 29/06/87 LGPD
PCAST 200,0 228,0 3 5,14 29/06/87 LGPD
PCAST 190,0 230,0 3 4,76 29/06/87 LGPD
……………………………………………………………………………….
PCAST 274,0 250,0 3 5,44 29/06/87 LGPD
PCAST 260,0 252,0 3 5,05 29/06/87 LGPD
PCAST 220,0 252,0 4 4,27 02/11/87 LGPD
PCAST 228,0 252,0 3 4,43 02/11/87 LGPD
PCAST 240,0 253,0 1 4,61 18/08/86 LGPD
PCAST 245,0 253,0 1 4,71 09/10/86 LGPD
PCAST 228,0 253,0 3 4,38 02/11/87 LGPD
PCAST 212,0 254,0 4 4,03 02/11/87 LGPD
PCAST 285,0 260,0 4 5,07 29/06/87 LGPD
……………………………………………………………………………….
PCAST 322,0 274,0 1 4,95 09/10/86 LGPD
PCAST 332,0 276,0 3 5,00 29/06/87 LGPD
PCAST 372,0 278,0 3 5,49 29/06/87 LGPD
PCAST 181,0 278,0 3 2,67 06/12/86 LGPD
PCAST 315,0 280,0 3 4,56 02/11/87 LGPD
PCAST 325,0 283,0 4 4,56 02/11/87 LGPD
PCAST 350,0 288,0 3 4,68 06/12/86 LGPD
PCAST 375,0 299,0 3 4,52 02/11/87 LGPD
9 Species Table
This report requires the user to select the level (Station, Fishing Effort, Operation or Date) of analysis for a species. The screen presents the number of elements per level. In the example below the report is by Fishing Effort (PECHE).
Number PECHE rpt no = 2
37 38 40 44 45
AEQUI 0 0 0 0 9,434
AFALC 0,943 0 0 0 0
Weight PECHE rpt no = 2
37 38 40 44 45
130,84 0 0 0 0
AEQUI 0 0 0 0 583,96
AFALC 41330,11 0 0 0 0
10 Environment
As in the Species Table, the use selects the level (Station, Fishing Effort or Operation) of analysis. In the example below the report is by Fishing Effort. The report summarizes the environmental conditions for each effort.
Parameters Peche
37 38 40 44 45
CODE_STA LGPD LGPD LGPD LGPD LGPD
TYPE_STA
LAT
LON
ALT 0 0 0 0 0
DIST_SRC 0 0 0 0 0
DIST_EMB 0 0 0 0 0
COUR_EAU
ORDRE 0 0 0 0 0
CODE_PEC 37 38 40 44 45
DATE_PEC 18/08/86 04/09/87 09/10/86 02/11/87 06/12/86
TYPE_ENG FM FM FM FM FM
TEMP
HAUT_EAU 0 0 0 0 0
TEMP 0.00 0.00 0.00 0.00 0.00
TRAN 0.00 0.00 0.00 0.00 0.00
PH 0.00 0.00 0.00 0.00 0.00
COND 0.0 0.0 0.0 0.0 0.0
COUV 0 0 0 0 0
OXY 0.0 0.0 0.0 0.0 0.0
]]>