In osmose-model/osmose: Object Oriented Simulator of Marine Ecosystems

\pagenumbering{gobble}

knitr::opts_chunk$set(echo = TRUE)

Automathic report for osmose output class.

Time series of biomass: for all species with replicates

plot(outputs, what="biomass", ts = TRUE, type=1, col = "gray40")

plot(outputs, what="biomass", ts = TRUE, type=1, col = "gray40")

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Time series of biomass: for four species without replicates

plot(outputs, what="biomass", ts = TRUE, type=1, col = "blue", species = c(0,1,2,3) , replicates = FALSE)

plot(outputs, what="biomass", ts = TRUE, type=1, col = "blue", species = c(0,1,2,3) , replicates = FALSE, initialYear = 1992)

Time series of biomass: type = 2

plot(outputs, what="biomass", type=2, species = c(0,1,2,4,5,6), initialYear = 2000)

plot(outputs, what="biomass", type=2, species = c(0,1,2,4,5,6), initialYear = 2000)

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Time series of biomass: type = 3

plot(outputs, what="biomass", type=3, start = 25, initialYear = 2002)

plot(outputs, what="biomass", type=3, start = 25, initialYear = 2002) 

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Total biomass: type = 1

plot(outputs, what="biomass", ts = FALSE, type=1, factor = 1e-6)

plot(outputs, what="biomass", ts = FALSE, type=1, factor = 1e-6, ci = TRUE)

plot(outputs, what="biomass", ts = FALSE, type=1, horizontal=TRUE, ci = FALSE, , cex.names = 0.6)

plot(outputs, what="biomass", ts = FALSE, type=1, horizontal=TRUE, ci = FALSE, cex.names = 0.6) 

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Total biomass: type = 2 - means over replicates

plot(outputs, what="biomass", ts = FALSE, type=2, col = "green")

plot(outputs, what="biomass", ts = FALSE, type=2, col = "green")

Total biomass: type = 3 - means over the time

plot(outputs, what="biomass", ts = FALSE, type=1, horizontal=TRUE, ci = FALSE, , cex.names = 0.6)

plot(outputs, what="biomass", ts = FALSE, type=3, col = "blue")

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Total biomass by size for all species (with replicates): type = 1 - individual plots by species

plot(outputs, what = "biomassBySize", type = 1, col = "red",cex.axis = 1.4)

plot(outputs, what = "biomassBySize", type = 1, col = "red",cex.axis = 1.4)

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Total biomass by size for all species (with replicates): type = 2 - single plot for all species

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

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

osmose-model/osmose documentation built on Feb. 16, 2023, 5 a.m.