Plot method demonstration

library(osmose)

Create, run and read an example

Define a folder for copy example files:

exampleFolder <- tempdir()

# Show the temporary folder
cat(exampleFolder)
#> /var/folders/3c/807k30_50mv_53hr_lqb6q0c0000gn/T//Rtmp1DrbUl

# Copy files
demoPaths <- osmose_demo(path = exampleFolder, config = "gog")

Run the example using run_osmose function (it will take less than 1 min):

run_osmose(input = demoPaths$config_file)
#> This is OSMOSE version 3.3.3
#> Your file osmose_3.3.3.jar has been download and/or deziped in this folder : /var/folders/3c/807k30_50mv_53hr_lqb6q0c0000gn/T//Rtmp1DrbUl/osmose_3.3.3.jar
#> Running: 'java'  -jar '/var/folders/3c/807k30_50mv_53hr_lqb6q0c0000gn/T//Rtmp1DrbUl/osmose_3.3.3.jar' /var/folders/3c/807k30_50mv_53hr_lqb6q0c0000gn/T//Rtmp1DrbUl/gog/osm_all-parameters.csv

Read outputs and config using read_osmose function

outputs <- read_osmose(path = demoPaths$output_dir, 
                       input = demoPaths$config_file)

# Print osmose outputs
print(outputs)
#> OSMOSE v.3u2
#> Model 'gogosm' 
#> 
#> 11 species modeled (3 simulations):
#>  [sp0] OctopusVulgaris 
#>  [sp1] MelicertusKerathurus 
#>  [sp2] MetapenaeusMonoceros 
#>  [sp3] TrachurusTrachurus 
#>  [sp4] SardinaPilchardus 
#>  [sp5] SardinellaAurita 
#>  [sp6] EngraulisEncrasicolus 
#>  [sp7] DiplodusAnnularis 
#>  [sp8] MustelusMustelus 
#>  [sp9] MerlucciusMerluccius 
#>  [sp10] PagellusErythrinus 
#> 
#> Available fields:
#>                                             
#>  "model"            "yieldBySize"           
#>  "species"          "yieldNBySize"          
#>  "biomass"          "meanTLBySize"          
#>  "abundance"        "mortalityBySize"       
#>  "yield"            "dietMatrixBySize (*)"  
#>  "yieldN"           "predatorPressureBySize"
#>  "mortality"        "abundanceByAge"        
#>  "meanTL"           "biomassByAge"          
#>  "meanTLCatch"      "yieldByAge"            
#>  "biomassByTL"      "yieldNByAge"           
#>  "predatorPressure" "meanSizeByAge"         
#>  "predPreyIni"      "meanTLByAge"           
#>  "dietMatrix"       "mortalityByAge"        
#>  "meanSize"         "dietMatrixByAge (*)"   
#>  "meanSizeCatch"    "predatorPressureByAge" 
#>  "abundanceBySize"  "config"                
#>  "biomassBySize"    "---------"             
#> 
#> (*) Empty fields.

Plot methods for osmose class

plot(outputs, what = "biomass")

plot(outputs, what = "biomass", type = 2)

plot(outputs, what = "abundance", ts = FALSE, type = 1)

plot(outputs, what = "yield", ts = FALSE, type = 2)


plot(outputs, what = "abundanceByAge")

plot(outputs, what = "biomassBySize", type = 2)

plot(outputs, what = "biomassByTL", type = 1)

plot(outputs, what = "yieldBySize", type = 2)

Plot methods for osmose.config class

It is important to remember that config info has already been read in outputs object and you can access just by indexing outputs$config.

plot(outputs$config, what = "species")

plot(outputs$config, what = "predation")

plot(outputs$config, what = "reproduction", type = 1)

plot(outputs$config, what = "reproduction", type = 2)