EcoTroph example dataset: Guinean data

Description

This example dataset is extracted from the 2004 Guinean Ecopath model (Gascuel et al., 2009). It provides a template for the input table formatting, the wanted variables names and the different capabilities of this package (used in function's examples).

Usage

data(ecopath_guinee)

Format

A data.frame with 35 observations on the following 8 variables.

group_name

a character vector corresponding to the names of the trophic groups used in the Ecopath model. Has obligatory to be written 'group_name'.

TL

a numeric vector corresponding to the trophic level of the associated trophic groups. Has obligatory to be written 'TL'.

biomass

a numeric vector corresponding to the biomass of the associated trophic groups. Has obligatory to be written 'biomass'.

prod

a numeric vector corresponding to the production on biomass ratio. For the Detritus groups (no P/B value entered in Ecopath), put 0 as a value. Has obligatory to be written 'prod'.

catch.1

a numeric vector corresponding to the catch of the artisanal fleet. A value must be entered for all groups, with a 0-value if no catch are made. Has obligatory to be written 'catch.something'.

catch.2

a numeric vector corresponding to the catch of the industrial fleet. A value must be entered for all groups, with a 0-value if no catch are made. Has obligatory to be written 'catch.something'

accessibility

a numeric vector corresponding to the fraction of the trophic group that can be catch assuming an infinite fishing effort. Has obligatory to be written 'accessibility'.

OI

a numeric vector corresponding to the omnivory index calculated by Ecopath for each trophic group. Has obligatory to be written 'OI'.

Details

No NA are accepted in the dataset (0 for the P/B of the detritus groups, 0 for the catch...). Follow the instructions stated in the variables descriptions. Different fleets can be entered in the model using the following system: catch.1, catch.2, catch.whatyouwant... If there is only one fleet, you just have to put catch as a variable name.

Source

Gascuel et al. (2009) Impact de la peche sur l'ecosysteme marin de Guinee - Modelisation EwE 1985/2005 -

Examples

data(ecopath_guinee)
ecopath_guinee
names(ecopath_guinee)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(EcoTroph)
Loading required package: XML
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/EcoTroph/ecopath_guinee.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ecopath_guinee
> ### Title: EcoTroph example dataset: Guinean data
> ### Aliases: ecopath_guinee
> ### Keywords: ~EcoTroph ~datasets
> 
> ### ** Examples
> 
> data(ecopath_guinee)
> ecopath_guinee
                  group_name   TL   biomass   prod catch.1 catch.2
1                     Whales 4.01   0.03090  0.020   0.000   0.000
2                   Dolphins 4.48   0.04330  0.070   0.000   0.000
3                    Turtles 2.19   0.02960  0.150   0.000   0.000
4                  Sea birds 3.81   0.00128  0.300   0.000   0.000
5                      Rays+ 3.97   0.38600  0.363   0.012   0.024
6                    Sharks+ 4.31   0.10500  0.410   0.007   0.003
7             Large pelagics 4.21   0.38400  0.850   0.025   0.069
8                Barracudas+ 4.12   0.05830  0.920   0.009   0.022
9                  Carangids 4.16   0.06270  1.000   0.010   0.024
10          Horse mackerels+ 3.13   2.33300  0.700   0.000   0.115
11                 Ethmalosa 2.53   1.52200  1.420   0.946   0.000
12               Sardinella+ 2.85   0.99900  2.110   0.058   0.139
13              Bobo croaker 3.92   0.50900  0.830   0.191   0.069
14            Other croakers 3.92   0.25900  0.848   0.074   0.060
15     Lesser Afr. threadfin 3.88   0.19700  0.784   0.002   0.075
16      Giant Afr. threadfin 4.11   0.05400  0.911   0.023   0.004
17           Royal threadfin 3.96   0.06800  0.560   0.007   0.004
18                 Seabream+ 3.62   0.47900  0.725   0.038   0.070
19               Sea catfish 3.70   0.46200  0.682   0.183   0.035
20                  Mullets+ 2.33   0.41500  0.681   0.054   0.002
21                   Grunts+ 3.60   0.09400  0.650   0.002   0.036
22                    Soles+ 3.30   0.28400  1.002   0.009   0.095
23   L. demersal pred.eaters 3.95   0.40000  0.444   0.007   0.038
24   SM demersal pred.eaters 3.57   0.77200  0.856   0.002   0.016
25  ML demers. invert.eaters 3.30   0.85300  0.775   0.001   0.042
26 S. demersal invert.eaters 3.32   0.84900  1.090   0.003   0.024
27     Bathy-dem pred.eaters 3.79   0.34100  0.755   0.001   0.004
28   Bathy-dem invert.eaters 3.55   0.55000  0.370   0.001   0.003
29                 Crustacea 3.03   3.44200  2.600   0.000   0.037
30               Cephalopods 3.60   0.70100  2.700   0.000   0.155
31                   Benthos 2.21 100.00000  1.800   0.000   0.000
32         Large zooplankton 2.94   4.31400 10.000   0.000   0.000
33         Small zooplankton 2.00  25.78700 40.000   0.000   0.000
34         Primary producers 1.00  69.00000 84.000   0.000   0.000
35                  Detritus 1.00 290.00000  0.000   0.000   0.000
   accessibility    OI
1            0.0 0.059
2            0.0 0.331
3            0.0 0.338
4            0.0 0.353
5            0.9 0.329
6            0.8 0.633
7            0.8 0.263
8            0.9 0.259
9            0.8 0.139
10           0.8 0.366
11           1.0 0.287
12           1.0 0.587
13           1.0 0.153
14           1.0 0.206
15           1.0 0.118
16           1.0 0.139
17           1.0 0.085
18           1.0 0.487
19           1.0 0.285
20           0.9 0.422
21           0.9 0.437
22           1.0 0.282
23           0.5 0.331
24           0.5 0.600
25           0.5 0.223
26           0.2 0.355
27           0.1 0.567
28           0.1 0.200
29           0.5 0.453
30           0.5 0.239
31           0.0 0.175
32           0.0 0.131
33           0.0 0.000
34           0.0 0.000
35           0.0 0.193
> names(ecopath_guinee)
[1] "group_name"    "TL"            "biomass"       "prod"         
[5] "catch.1"       "catch.2"       "accessibility" "OI"           
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>