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2_oneParameterExploration.Rmd
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2_oneParameterExploration.Rmd
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---
site: bookdown::bookdown_site
output:
bookdown::gitbook: default
---
# One parameter exploration
```{r 2_setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, message = FALSE, # hide code and messages
cache=TRUE, autodep=TRUE)
source("library/hpcModel.run.R")
source("library/hpcModel.exploration.R")
source("library/hpcModel.plot.R")
require(reshape2)
require(ggplot2)
require(scales)
require(kableExtra)
```
```{r 2_table-functions}
source("library/plotting/printTableRun.R")
source("library/plotting/printTableExperiment.R")
```
```{r 2_default-values, cache=TRUE}
# this is the 'default' parameter setting (end state is 'fast coevolution'):
# initial populations
initial_population_humans_default = 10
initial_population_plants_default = 10
# number of discrete types
number_types_humans_default = 30
number_types_plants_default = 30
# undirected variation
undirected_variation_humans_default = 0.15
undirected_variation_plants_default = 0.15
# intrinsic growth rate
intrinsic_growth_rate_humans_default = 0.04
intrinsic_growth_rate_plants_default = 0.1
# Utility per capita of individuals of type N
utility_per_capita_type_n_plants_to_humans_default = 1.5
utility_per_capita_type_n_humans_to_plants_default = 1
# Utility per capita of individuals of type 1
utility_per_capita_type_1_plants_to_humans_default = 0.15
utility_per_capita_type_1_humans_to_plants_default = 0
# basic resources:
# population of type N that can be sustained by resources independent of HP relationship
utility_other_to_type_n_humans_default = 10
utility_other_to_type_n_plants_default = 20
# population of type 1 that can be sustained by resources independent of HP relationship
utility_other_to_type_1_humans_default = 80
utility_other_to_type_1_plants_default = 100
# maximum local area to be used by populations (multiplier or scaling effect)
max_area_default = 200
# settings
# simulation flow & data
max_iterations_default = 5000
reltol_exponential_default = 6
coevolution_threshold_default = 0.5
messages_default = TRUE
```
```{r 2_plot-functions, include=FALSE}
# this chunk is specific for this exploration
plotDirectory <- "plots/2_exp_"
source("library/plotting/bifurcationPlot.R")
```
\newpage
## Full example (table+plot alternatives)
### utility per capita **of** type n plants **to** humans ($\bar{U}_{P_{n}H}$):
```{r 2_utility_per_capita_type_n_plants_to_humans-values, cache=TRUE}
exp_utility_per_capita_type_n_plants_to_humans_name <- "utility_per_capita_type_n_plants_to_humans"
exp_utility_per_capita_type_n_plants_to_humans_values <- seq(0.5, 2.5, length.out = 100)
```
```{r 2_utility_per_capita_type_n_plants_to_humans, cache=TRUE, dependson=c('2_default-values', '2_utility_per_capita_type_n_plants_to_humans-values'), include=FALSE}
exp_utility_per_capita_type_n_plants_to_humans <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = exp_utility_per_capita_type_n_plants_to_humans_values, ###
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2mUPnHtablehtml, eval=!params$ispdf, cache=TRUE, dependson='2_utility_per_capita_type_n_plants_to_humans'}
printTableExperiment(exp_utility_per_capita_type_n_plants_to_humans, caption = 'Parameter setting')
```
```{r 2mUPnHtablepdf, eval=params$ispdf, cache=TRUE, dependson='2_utility_per_capita_type_n_plants_to_humans'}
printTableExperiment(exp_utility_per_capita_type_n_plants_to_humans, caption = 'Parameter setting', output = "latex")
```
```{r 2_utility_per_capita_type_n_plants_to_humans-bifplot1, cache=TRUE, dependson='2_utility_per_capita_type_n_plants_to_humans', include=FALSE}
plotScale = 10
#svg('paste0(plotDirectory, exp1_name, "_ggbifplot.png"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_utility_per_capita_type_n_plants_to_humans_name, "_bifurcationPlotSimple.png"),
width = 200 * plotScale, height = 100 * plotScale)
bifurcationPlotSimple(exp_utility_per_capita_type_n_plants_to_humans_values,
cbind(exp_utility_per_capita_type_n_plants_to_humans$coevolution_coefficient_humans,
exp_utility_per_capita_type_n_plants_to_humans$coevolution_coefficient_plants),
legend_position = c(2.2, 0),
parameter_x_label = expression(paste('utility per capita of type n plants to humans (', bar('U')['PnH'], ')')),
variable_y_label = "coevolution coefficient",
variable_names = c("Humans", "Plants"),
cex = plotScale)
dev.off()
```
```{r 2mUPnHbifplot1print, echo=FALSE, dependson='2_utility_per_capita_type_n_plants_to_humans-bifplot1', out.width = '100%', fig.cap='Bifurcation plot (ggplot2)'}
knitr::include_graphics(paste0(plotDirectory, exp_utility_per_capita_type_n_plants_to_humans_name, "_bifurcationPlotSimple.png"))
```
```{r 2_utility_per_capita_type_n_plants_to_humans-bifplot2, cache=TRUE, dependson='2_utility_per_capita_type_n_plants_to_humans', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_utility_per_capita_type_n_plants_to_humans_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_utility_per_capita_type_n_plants_to_humans_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_utility_per_capita_type_n_plants_to_humans_values, exp_utility_per_capita_type_n_plants_to_humans$coevolution_coefficient_humans),
cbind(exp_utility_per_capita_type_n_plants_to_humans_values, exp_utility_per_capita_type_n_plants_to_humans$coevolution_coefficient_plants),
parameter_x_label = expression(paste('utility per capita of type n plants to humans (', bar('U')['PnH'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_utility_per_capita_type_n_plants_to_humans-bifplot2-print, echo=FALSE, dependson='2_utility_per_capita_type_n_plants_to_humans-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_utility_per_capita_type_n_plants_to_humans_name, "_bifurcationPlotPair.png"))
```
\newpage
## Exploration on 'default' setting for each parameter:
### Initial populations of humans and plants ($init_{H},\,init_{P}$)
```{r 2_init-values, cache=TRUE}
exp_initial_population_humans_name <- "initial_population_humans"
exp_initial_population_plants_name <- "initial_population_plants"
exp_initial_population_humans_values <- 5:100
exp_initial_population_plants_values <- 5:100
```
```{r 2_initial_population_humans, cache=TRUE, dependson=c('2_default-values', '2_init-values'), include=FALSE}
exp_initial_population_humans <- hpcModel.exploration(
initial_population_humans = exp_initial_population_humans_values, ###
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_initial_population_plants, cache=TRUE, dependson=c('2_default-values', '2_init-values'), include=FALSE}
exp_initial_population_plants <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = exp_initial_population_plants_values, ###
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_initial_population_humans-bifplot2, cache=TRUE, dependson='2_initial_population_humans', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_initial_population_humans_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_initial_population_humans_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_initial_population_humans_values, exp_initial_population_humans$coevolution_coefficient_humans),
cbind(exp_initial_population_humans_values, exp_initial_population_humans$coevolution_coefficient_plants),
parameter_x_label = expression(paste('Initial human population (',
'ini'['H'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_initial_population_plants-bifplot2, cache=TRUE, dependson='2_initial_population_plants', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_initial_population_plants_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_initial_population_plants_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_initial_population_plants_values, exp_initial_population_plants$coevolution_coefficient_humans),
cbind(exp_initial_population_plants_values, exp_initial_population_plants$coevolution_coefficient_plants),
parameter_x_label = expression(paste('Initial plant population (',
'ini'['P'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_initial_population_humans-bifplot2-print, echo=FALSE, dependson='2_initial_population_humans-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_initial_population_humans_name, "_bifurcationPlotPair.png"))
```
```{r 2_initial_population_plants-bifplot2-print, echo=FALSE, dependson='2_initial_population_plants-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_initial_population_plants_name, "_bifurcationPlotPair.png"))
```
### Number of types of humans and plants ($n_{H},\,n_{P}$):
```{r 2_number_types-values, cache=TRUE}
exp_number_types_humans_name <- "number_types_humans"
exp_number_types_plants_name <- "number_types_plants"
exp_number_types_humans_values <- 5:40
exp_number_types_plants_values <- 5:40
```
```{r 2_number_types_humans, cache=TRUE, dependson=c('2_default-values','2_number_types-values'), include=FALSE}
exp_number_types_humans <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = exp_number_types_humans_values, ###
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_number_types_plants, cache=TRUE, dependson=c('2_default-values', '2_number_types-values'), include=FALSE}
exp_number_types_plants <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = exp_number_types_plants_values, ###
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_number_types_humans-bifplot2, cache=TRUE, dependson='2_number_types_humans', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp1_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_number_types_humans_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_number_types_humans_values, exp_number_types_humans$coevolution_coefficient_humans),
cbind(exp_number_types_humans_values, exp_number_types_humans$coevolution_coefficient_plants),
parameter_x_label = expression(paste('number of human types (',
'n'['H'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_number_types_plants-bifplot2, cache=TRUE, dependson='2_number_types_plants', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_number_types_plants_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_number_types_plants_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_number_types_plants_values, exp_number_types_plants$coevolution_coefficient_humans),
cbind(exp_number_types_plants_values, exp_number_types_plants$coevolution_coefficient_plants),
parameter_x_label = expression(paste('number of plant types (',
'n'['P'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_number_types_humans-bifplot2-print, echo=FALSE, dependson='2_number_types_humans-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_number_types_humans_name, "_bifurcationPlotPair.png"))
```
```{r 2_number_types_plants-bifplot2-print, echo=FALSE, dependson='2_number_types_plants-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_number_types_plants_name, "_bifurcationPlotPair.png"))
```
### level of undirected variation in humans and plants ($v_{H},\,v_{P}$):
```{r 2_undirected_variation-values, cache=TRUE}
exp_undirected_variation_humans_name <- "undirected_variation_humans"
exp_undirected_variation_plants_name <- "undirected_variation_plants"
exp_undirected_variation_humans_values <- seq(0.05, 0.25, length.out = 100)
exp_undirected_variation_plants_values <- seq(0.05, 0.25, length.out = 100)
```
```{r 2_undirected_variation_humans, cache=TRUE, dependson=c('2_default-values', '2_undirected_variation-values'), include=FALSE}
exp_undirected_variation_humans <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = exp_undirected_variation_humans_values, ###
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_undirected_variation_plants, cache=TRUE, dependson=c('2_default-values', '2_undirected_variation-values'), include=FALSE}
exp_undirected_variation_plants <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = exp_undirected_variation_plants_values, ###
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_undirected_variation_humans-bifplot2, cache=TRUE, dependson='2_undirected_variation_humans', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_undirected_variation_humans_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_undirected_variation_humans_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_undirected_variation_humans_values, exp_undirected_variation_humans$coevolution_coefficient_humans),
cbind(exp_undirected_variation_humans_values, exp_undirected_variation_humans$coevolution_coefficient_plants),
parameter_x_label = expression(paste('undirected variation in humans (',
'v'['H'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_undirected_variation_plants-bifplot2, cache=TRUE, dependson='2_undirected_variation_plants', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_undirected_variation_plants_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_undirected_variation_plants_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_undirected_variation_plants_values, exp_undirected_variation_plants$coevolution_coefficient_humans),
cbind(exp_undirected_variation_plants_values, exp_undirected_variation_plants$coevolution_coefficient_plants),
parameter_x_label = expression(paste('undirected variation in plants (',
'v'['P'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_undirected_variation_humans-bifplot2-print, echo=FALSE, dependson='2_undirected_variation_humans-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_undirected_variation_humans_name, "_bifurcationPlotPair.png"))
```
```{r 2_undirected_variation_plants-bifplot2-print, echo=FALSE, dependson='2_undirected_variation_plants-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_undirected_variation_plants_name, "_bifurcationPlotPair.png"))
```
### intrinsic growth rates for human and plant populations ($r_{H},\,r_{P}$):
```{r 2_intrinsic_growth_rate-values, cache=TRUE}
exp_intrinsic_growth_rate_humans_name <- "intrinsic_growth_rate_humans"
exp_intrinsic_growth_rate_plants_name <- "intrinsic_growth_rate_plants"
exp_intrinsic_growth_rate_humans_values <- seq(0.01, 0.25, length.out = 100)
exp_intrinsic_growth_rate_plants_values <- seq(0.01, 0.25, length.out = 100)
```
```{r 2_intrinsic_growth_rate_humans, cache=TRUE, dependson=c('2_default-values', '2_intrinsic_growth_rate-values'), include=FALSE}
exp_intrinsic_growth_rate_humans <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = exp_intrinsic_growth_rate_humans_values, ###
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_intrinsic_growth_rate_plants, cache=TRUE, dependson=c('2_default-values', '2_intrinsic_growth_rate-values'), include=FALSE}
exp_intrinsic_growth_rate_plants <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = exp_intrinsic_growth_rate_plants_values, ###
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_intrinsic_growth_rate_humans-bifplot2, cache=TRUE, dependson='2_intrinsic_growth_rate_humans', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_intrinsic_growth_rate_humans_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_intrinsic_growth_rate_humans_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_intrinsic_growth_rate_humans_values, exp_intrinsic_growth_rate_humans$coevolution_coefficient_humans),
cbind(exp_intrinsic_growth_rate_humans_values, exp_intrinsic_growth_rate_humans$coevolution_coefficient_plants),
parameter_x_label = expression(paste('human instrinsic growth rate (',
'r'['H'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_intrinsic_growth_rate_plants-bifplot2, cache=TRUE, dependson='2_intrinsic_growth_rate_plants', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_intrinsic_growth_rate_plants_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_intrinsic_growth_rate_plants_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_intrinsic_growth_rate_plants_values, exp_intrinsic_growth_rate_plants$coevolution_coefficient_humans),
cbind(exp_intrinsic_growth_rate_plants_values, exp_intrinsic_growth_rate_plants$coevolution_coefficient_plants),
parameter_x_label = expression(paste('plant instrinsic growth rate (',
'r'['P'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_intrinsic_growth_rate_humans-bifplot2-print, echo=FALSE, dependson='2_intrinsic_growth_rate_humans-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_intrinsic_growth_rate_humans_name, "_bifurcationPlotPair.png"))
```
```{r 2_intrinsic_growth_rate_plants-bifplot2-print, echo=FALSE, dependson='2_intrinsic_growth_rate_plants-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_intrinsic_growth_rate_plants_name, "_bifurcationPlotPair.png"))
```
### utility per capita **of** type n plants **to** humans ($\bar{U}_{P_{n}H}$):
```{r 2_utility_per_capita_type_n_plants_to_humans-bifplot2-print2, echo=FALSE, dependson='2_utility_per_capita_type_n_plants_to_humans-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_utility_per_capita_type_n_plants_to_humans_name, "_bifurcationPlotPair.png"))
```
### utility per capita **of** type n human **to** plants ($\bar{U}_{H_{n}P}$):
```{r 2_utility_per_capita_type_n_humans_to_plants-values, cache=TRUE}
exp_utility_per_capita_type_n_humans_to_plants_name <- "utility_per_capita_type_n_humans_to_plants"
exp_utility_per_capita_type_n_humans_to_plants_values <- seq(0, 1.5, length.out = 100)
```
```{r 2_utility_per_capita_type_n_humans_to_plants, cache=TRUE, dependson=c('2_default-values', '2_utility_per_capita_type_n_humans_to_plants-values'), include=FALSE}
exp_utility_per_capita_type_n_humans_to_plants <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = exp_utility_per_capita_type_n_humans_to_plants_values, ###
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_utility_per_capita_type_n_humans_to_plants-bifplot2, cache=TRUE, dependson='2_utility_per_capita_type_n_humans_to_plants', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_utility_per_capita_type_n_humans_to_plants_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_utility_per_capita_type_n_humans_to_plants_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_utility_per_capita_type_n_humans_to_plants_values,
exp_utility_per_capita_type_n_humans_to_plants$coevolution_coefficient_humans),
cbind(exp_utility_per_capita_type_n_humans_to_plants_values,
exp_utility_per_capita_type_n_humans_to_plants$coevolution_coefficient_plants),
parameter_x_label = expression(paste('utility per capita of type n human to plants (', bar('U')['HnP'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_utility_per_capita_type_n_humans_to_plants-bifplot2-print, echo=FALSE, dependson='2_utility_per_capita_type_n_humans_to_plants-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_utility_per_capita_type_n_humans_to_plants_name, "_bifurcationPlotPair.png"))
```
### utility per capita **of** type 1 plants **to** humans ($\bar{U}_{P_{1}H}$):
```{r 2_utility_per_capita_type_1_plants_to_humans-values, cache=TRUE}
exp_utility_per_capita_type_1_plants_to_humans_name <- "utility_per_capita_type_1_plants_to_humans"
exp_utility_per_capita_type_1_plants_to_humans_values <- seq(0, 0.5, length.out = 100)
```
```{r 2_utility_per_capita_type_1_plants_to_humans, cache=TRUE, dependson=c('2_default-values', '2_utility_per_capita_type_1_plants_to_humans-values'), include=FALSE}
exp_utility_per_capita_type_1_plants_to_humans <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = exp_utility_per_capita_type_1_plants_to_humans_values, ###
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_utility_per_capita_type_1_plants_to_humans-bifplot2, cache=TRUE, dependson='2_utility_per_capita_type_1_plants_to_humans', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_utility_per_capita_type_1_plants_to_humans_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_utility_per_capita_type_1_plants_to_humans_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_utility_per_capita_type_1_plants_to_humans_values,
exp_utility_per_capita_type_1_plants_to_humans$coevolution_coefficient_humans),
cbind(exp_utility_per_capita_type_1_plants_to_humans_values,
exp_utility_per_capita_type_1_plants_to_humans$coevolution_coefficient_plants),
parameter_x_label = expression(paste('utility per capita of type 1 plants to humans (', bar('U')['P1H'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_utility_per_capita_type_1_plants_to_humans-bifplot2-print, echo=FALSE, dependson='2_utility_per_capita_type_1_plants_to_humans-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_utility_per_capita_type_1_plants_to_humans_name, "_bifurcationPlotPair.png"))
```
### utility per capita **of** type 1 humans **to** plants ($\bar{U}_{H_{1}P}$):
```{r 2_utility_per_capita_type_1_humans_to_plants-values, cache=TRUE}
exp_utility_per_capita_type_1_humans_to_plants_name <- "utility_per_capita_type_1_humans_to_plants"
exp_utility_per_capita_type_1_humans_to_plants_values <- seq(0, 2, length.out = 100)
```
```{r 2_utility_per_capita_type_1_humans_to_plants, cache=TRUE, dependson=c('2_default-values', '2_utility_per_capita_type_1_humans_to_plants-values'), include=FALSE}
exp_utility_per_capita_type_1_humans_to_plants <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = exp_utility_per_capita_type_1_humans_to_plants_values, ###
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_utility_per_capita_type_1_humans_to_plants-bifplot2, cache=TRUE, dependson='2_utility_per_capita_type_1_humans_to_plants', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_utility_per_capita_type_1_humans_to_plants_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_utility_per_capita_type_1_humans_to_plants_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_utility_per_capita_type_1_humans_to_plants_values,
exp_utility_per_capita_type_1_humans_to_plants$coevolution_coefficient_humans),
cbind(exp_utility_per_capita_type_1_humans_to_plants_values,
exp_utility_per_capita_type_1_humans_to_plants$coevolution_coefficient_plants),
parameter_x_label = expression(paste('utility per capita of type 1 humans to plants (', bar('U')['H1P'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_utility_per_capita_type_1_humans_to_plants-bifplot2-print, echo=FALSE, dependson='2_utility_per_capita_type_1_humans_to_plants-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_utility_per_capita_type_1_humans_to_plants_name, "_bifurcationPlotPair.png"))
```
### utility **of** other resources **to** humans of type 1 ($U_{bH_{1}}$):
```{r 2_utility_other_to_type_1_humans-values, cache=TRUE}
exp_utility_other_to_type_1_humans_name <- "utility_other_to_type_1_humans"
exp_utility_other_to_type_1_humans_values <- seq(5, 400, length.out = 100)
```
```{r 2_utility_other_to_type_1_humans, cache=TRUE, dependson=c('2_default-values', '2_utility_other_to_type_1_humans-values'), include=FALSE}
exp_utility_other_to_type_1_humans <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = exp_utility_other_to_type_1_humans_values, ###
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_utility_other_to_type_1_humans-bifplot2, cache=TRUE, dependson='2_utility_other_to_type_1_humans-exp1', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp1_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_utility_other_to_type_1_humans_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_utility_other_to_type_1_humans_values, exp_utility_other_to_type_1_humans$coevolution_coefficient_humans),
cbind(exp_utility_other_to_type_1_humans_values, exp_utility_other_to_type_1_humans$coevolution_coefficient_plants),
parameter_x_label = expression(paste('Baseline carrying capacity for type 1 humans (', bar(U)['bH'[1]], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_utility_other_to_type_1_humans-bifplot2-print, echo=FALSE, dependson='2_utility_other_to_type_1_humans-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_utility_other_to_type_1_humans_name, "_bifurcationPlotPair.png"))
```
### utility **of** non-anthropic space **to** type 1 plants ($U_{bP_{1}}$):
```{r 2_utility_other_to_type_1_plants-values, cache=TRUE}
exp_utility_other_to_type_1_plants_name <- "utility_other_to_type_1_plants"
exp_utility_other_to_type_1_plants_values <- seq(5, 400, length.out = 100)
```
```{r 2_utility_other_to_type_1_plants, cache=TRUE, dependson=c('2_default-values', '2_utility_other_to_type_1_plants-values'), include=FALSE}
exp_utility_other_to_type_1_plants <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = exp_utility_other_to_type_1_plants_values, ###
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_utility_other_to_type_1_plants-bifplot2, cache=TRUE, dependson='2_utility_other_to_type_1_plants', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_utility_other_to_type_1_plants_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_utility_other_to_type_1_plants_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_utility_other_to_type_1_plants_values, exp_utility_other_to_type_1_plants$coevolution_coefficient_humans),
cbind(exp_utility_other_to_type_1_plants_values, exp_utility_other_to_type_1_plants$coevolution_coefficient_plants),
parameter_x_label = expression(paste('utility of non-anthropic space to type 1 plants (', bar('U')['bP1'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_utility_other_to_type_1_plants-bifplot2-print, echo=FALSE, dependson='2_utility_other_to_type_1_plants-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_utility_other_to_type_1_plants_name, "_bifurcationPlotPair.png"))
```
### utility **of** other resources **to** type n humans ($U_{bH_{n}}$):
```{r 2_utility_other_to_type_n_humans-values, cache=TRUE}
exp_utility_other_to_type_n_humans_name <- "utility_other_to_type_n_humans"
exp_utility_other_to_type_n_humans_values <- seq(5, 400, length.out = 100)
```
```{r 2_utility_other_to_type_n_humans, cache=TRUE, dependson=c('2_default-values', '2_utility_other_to_type_n_humans-values'), include=FALSE}
exp_utility_other_to_type_n_humans <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = exp_utility_other_to_type_n_humans_values, ###
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_utility_other_to_type_n_humans-bifplot2, cache=TRUE, dependson='2_utility_other_to_type_n_humans', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_utility_other_to_type_n_humans_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_utility_other_to_type_n_humans_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_utility_other_to_type_n_humans_values, exp_utility_other_to_type_n_humans$coevolution_coefficient_humans),
cbind(exp_utility_other_to_type_n_humans_values, exp_utility_other_to_type_n_humans$coevolution_coefficient_plants),
parameter_x_label = expression(paste('utility of other resources to type n humans (', bar('U')['bHn'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_utility_other_to_type_n_humans-bifplot2-print, echo=FALSE, dependson='2_utility_other_to_type_n_humans-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_utility_other_to_type_n_humans_name, "_bifurcationPlotPair.png"))
```
### utility **of** non-anthropic space **to** type n plants ($U_{bP_{n}}$):
```{r 2_utility_other_to_type_n_plants-values, cache=TRUE}
exp_utility_other_to_type_n_plants_name <- "utility_other_to_type_n_plants"
exp_utility_other_to_type_n_plants_values <- seq(5, 400, length.out = 100)
```
```{r 2_utility_other_to_type_n_plants, cache=TRUE, dependson=c('2_default-values', '2_utility_other_to_type_n_plants-values'), include=FALSE}
exp_utility_other_to_type_n_plants <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = exp_utility_other_to_type_n_plants_values, ###
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = max_area_default,
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_utility_other_to_type_n_plants-bifplot2, cache=TRUE, dependson='2_utility_other_to_type_n_plants', results='hide'}
plotScale = 10
#svg(paste0(plotDirectory, exp_utility_other_to_type_n_plants_name, "_bifurcationPlotPair.svg"), width=plotScale, height=plot_scale)
png(paste0(plotDirectory, exp_utility_other_to_type_n_plants_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_utility_other_to_type_n_plants_values, exp_utility_other_to_type_n_plants$coevolution_coefficient_humans),
cbind(exp_utility_other_to_type_n_plants_values, exp_utility_other_to_type_n_plants$coevolution_coefficient_plants),
parameter_x_label = expression(paste('utility of non-anthropic space to type n plants (', bar('U')['bPn'], ')')),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_utility_other_to_type_n_plants-bifplot2-print, echo=FALSE, dependson='2_utility_other_to_type_n_plants-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_utility_other_to_type_n_plants_name, "_bifurcationPlotPair.png"))
```
### maximum contiguous area to be used by plants ($max_area$):
```{r 2_max_area-values, cache=TRUE}
exp_max_area_name <- "max_area"
exp_max_area_values <- seq(5, 400, length.out = 100)
```
```{r 2_max_area, cache=TRUE, dependson=c('2_default-values', '2_max_area-values'), include=FALSE}
exp_max_area <- hpcModel.exploration(
initial_population_humans = initial_population_humans_default,
initial_population_plants = initial_population_plants_default,
number_types_humans = number_types_humans_default,
number_types_plants = number_types_plants_default,
undirected_variation_humans = undirected_variation_humans_default,
undirected_variation_plants = undirected_variation_plants_default,
intrinsic_growth_rate_humans = intrinsic_growth_rate_humans_default,
intrinsic_growth_rate_plants = intrinsic_growth_rate_plants_default,
utility_per_capita_type_n_plants_to_humans = utility_per_capita_type_n_plants_to_humans_default,
utility_per_capita_type_n_humans_to_plants = utility_per_capita_type_n_humans_to_plants_default,
utility_per_capita_type_1_plants_to_humans = utility_per_capita_type_1_plants_to_humans_default,
utility_per_capita_type_1_humans_to_plants = utility_per_capita_type_1_humans_to_plants_default,
utility_other_to_type_n_humans = utility_other_to_type_n_humans_default,
utility_other_to_type_n_plants = utility_other_to_type_n_plants_default,
utility_other_to_type_1_humans = utility_other_to_type_1_humans_default,
utility_other_to_type_1_plants = utility_other_to_type_1_plants_default,
max_area = exp_max_area_values, ###
max_iterations = max_iterations_default,
reltol_exponential = reltol_exponential_default,
coevolution_threshold = coevolution_threshold_default,
messages = messages_default
)
```
```{r 2_max_area-bifplot2, cache=TRUE, dependson='2_max_area', results='hide'}
plotScale = 10
png(paste0(plotDirectory, exp_max_area_name, "_bifurcationPlotPair.png"),
width = 400 * plotScale, height = 150 * plotScale)
bifurcationPlotPair(cbind(exp_max_area_values, exp_max_area$coevolution_coefficient_humans),
cbind(exp_max_area_values, exp_max_area$coevolution_coefficient_plants),
parameter_x_label = expression('max_area'),
variable_y_label_A = expression(paste('coevolution coefficient of humans (', 'coevo'['H'], ')')),
variable_y_label_B = expression(paste('coevolution coefficient of plants (', 'coevo'['P'], ')')),
plot_scale = plotScale)
dev.off()
```
```{r 2_max_area-bifplot2-print, echo=FALSE, dependson='2_max_area-bifplot2', out.width = '100%'}
knitr::include_graphics(paste0(plotDirectory, exp_max_area_name, "_bifurcationPlotPair.png"))
```
---
## Oscilations
```{r 2_oscillation-values, cache=TRUE, dependson='2_default-values'}
exp_utility_per_capita_type_n_humans_to_plants_oscillation_name <- "utility_per_capita_type_n_humans_to_plants_oscillation"
exp_utility_per_capita_type_n_plants_to_humans_oscillation_name <- "utility_per_capita_type_n_plants_to_humans_oscillation"
exp_utility_per_capita_type_n_humans_to_plants_oscillation_values <- seq(0.1, 1.5, length.out = 100)
exp_utility_per_capita_type_n_plants_to_humans_oscillation_values <- seq(0.1, 1, length.out = 100)
initial_population_humans_oscillation = initial_population_humans_default