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Merge pull request #13 from mrc-ide/alternative-outbreak
Allow tuning of outbreak detection
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@@ -17,3 +17,4 @@ inst/doc | |
pkgdown | ||
artwork | ||
scratchpads | ||
papers |
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@@ -1,6 +1,6 @@ | ||
Package: cowflu | ||
Title: Cows With Flu | ||
Version: 0.1.0 | ||
Version: 0.2.0 | ||
Authors@R: c(person("Thomas", "Rawson", role = c("aut", "cre"), | ||
email = "[email protected]"), | ||
person("Rich", "FitzJohn", role = "aut"), | ||
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@@ -23,6 +23,8 @@ LinkingTo: | |
Suggests: | ||
knitr, | ||
rmarkdown, | ||
ggplot2, | ||
gridExtra, | ||
testthat (>= 3.0.0) | ||
Remotes: | ||
mrc-ide/dust2 | ||
|
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@@ -0,0 +1,132 @@ | ||
plot_chains_ll <- function(samples) { | ||
if (!requireNamespace("ggplot2", quietly = TRUE)) { | ||
stop( | ||
"Package \"ggplot2\" must be installed to use this function.", | ||
call. = FALSE | ||
) | ||
} | ||
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n_pars <- dim(samples$par)[1] | ||
n_samples <- dim(samples$par)[2] | ||
n_chains <- dim(samples$par)[3] | ||
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plot_data <- data.frame( density = as.vector(samples$density), | ||
index = rep(1:n_samples, n_chains), | ||
chain = rep(1:n_chains, each = n_samples)) | ||
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ggplot2::ggplot(plot_data) + | ||
ggplot2::geom_line(ggplot2::aes(x = index, y = density, color = factor(chain)), size = 1) + | ||
ggplot2::labs(title = "Log-likelihood density by chain", | ||
x = "Sample index", | ||
y = "Log-likelihood", | ||
color = "Chain") + | ||
ggplot2::theme_classic() + | ||
ggplot2::theme(axis.text = ggplot2::element_text(size = 12), | ||
axis.title = ggplot2::element_text(size = 14), | ||
legend.title = ggplot2::element_text(size = 14), | ||
plot.title = ggplot2::element_text(size = 16, face = "bold")) | ||
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} | ||
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plot_param_traj <- function(samples, one_panel = FALSE){ | ||
if (!requireNamespace("ggplot2", quietly = TRUE)) { | ||
stop( | ||
"Package \"ggplot2\" must be installed to use this function.", | ||
call. = FALSE | ||
) | ||
} | ||
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n_pars <- dim(samples$par)[1] | ||
n_samples <- dim(samples$par)[2] | ||
n_chains <- dim(samples$par)[3] | ||
param_names <- row.names(samples$pars) | ||
plot_list <- list() | ||
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for(i in 1:length(param_names)){ | ||
hold_param_name <- param_names[i] | ||
hold_samples <- samples$pars[i,,] | ||
plot_data <- data.frame( value = as.vector(hold_samples), | ||
index = rep(1:n_samples, n_chains), | ||
chain = rep(1:n_chains, each = n_samples)) | ||
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ggplot2::ggplot(plot_data) + | ||
ggplot2::geom_line(ggplot2::aes(x = index, y = value, color = factor(chain)), linewidth = 1) + | ||
ggplot2::labs(title = sprintf("Posterior samples for %s", hold_param_name), | ||
x = "Sample index", | ||
y = "Value", | ||
color = "Chain") + | ||
ggplot2::theme_classic() + | ||
ggplot2::theme(axis.text = ggplot2::element_text(size = 12), | ||
axis.title = ggplot2::element_text(size = 14), | ||
legend.title = ggplot2::element_text(size = 14), | ||
plot.title = ggplot2::element_text(size = 16, face = "bold")) -> plot | ||
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plot_list[[i]] <- plot | ||
} | ||
if(one_panel){ | ||
if (!requireNamespace("gridExtra", quietly = TRUE)) { | ||
stop( | ||
"Package \"gridExtra\" must be installed to return all trajectories on one panel.", | ||
call. = FALSE | ||
) | ||
} | ||
one_plot <- gridExtra::grid.arrange(grobs = plot_list, ncol = 2) | ||
one_plot | ||
}else{ | ||
plot_list | ||
} | ||
} | ||
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plot_param_posterior <- function(samples, one_panel = FALSE){ | ||
if (!requireNamespace("ggplot2", quietly = TRUE)) { | ||
stop( | ||
"Package \"ggplot2\" must be installed to use this function.", | ||
call. = FALSE | ||
) | ||
} | ||
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n_pars <- dim(samples$par)[1] | ||
n_samples <- dim(samples$par)[2] | ||
n_chains <- dim(samples$par)[3] | ||
param_names <- row.names(samples$pars) | ||
plot_list <- list() | ||
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for(i in 1:length(param_names)){ | ||
hold_param_name <- param_names[i] | ||
hold_samples <- samples$pars[i,,] | ||
plot_data <- data.frame( value = as.vector(hold_samples), | ||
index = rep(1:n_samples, n_chains), | ||
chain = rep(1:n_chains, each = n_samples)) | ||
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ggplot2::ggplot(plot_data, ggplot2::aes(x = value, group = factor(chain), color = factor(chain)) ) + | ||
# Faint histogram in the background | ||
ggplot2::geom_histogram(ggplot2::aes(y = ..density.., fill = factor(chain) ), color = NA, position = "identity", alpha = 0.3, bins = 30) + | ||
# Density plot colored by "chain" | ||
ggplot2::geom_density(size = 1) + | ||
ggplot2::labs(title = sprintf("Posterior density for %s", hold_param_name), | ||
x = "Value", | ||
y = "Density", | ||
color = "Chain", | ||
fill = "Chain") + | ||
ggplot2::theme_classic() + | ||
ggplot2::theme(axis.text = ggplot2::element_text(size = 12), | ||
axis.title = ggplot2::element_text(size = 14), | ||
legend.title = ggplot2::element_text(size = 14), | ||
plot.title = ggplot2::element_text(size = 16, face = "bold")) -> plot | ||
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plot_list[[i]] <- plot | ||
} | ||
if(one_panel){ | ||
if (!requireNamespace("gridExtra", quietly = TRUE)) { | ||
stop( | ||
"Package \"gridExtra\" must be installed to return all trajectories on one panel.", | ||
call. = FALSE | ||
) | ||
} | ||
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one_plot <- gridExtra::grid.arrange(grobs = plot_list, ncol = 2) | ||
one_plot | ||
}else{ | ||
plot_list | ||
} | ||
} |
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