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Avoid ! by reordering if/else
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@Bisaloo @ntorresd
Bisaloo authored and ntorresd committed Dec 15, 2023
1 parent 33059c6 commit fe0e2e2
Showing 1 changed file with 96 additions and 96 deletions.
192 changes: 96 additions & 96 deletions R/visualisation.R
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,28 @@ plot_seroprev <- function(serodata,
plot_seroprev_fitted <- function(seromodel_object,
serodata,
size_text = 6) {
if (!is.character(seromodel_object)) {
if (is.character(seromodel_object)) {
message("model did not run")
print_warning <- "errors"

prev_plot <- ggplot2::ggplot(data.frame()) +
ggplot2::geom_point() +
ggplot2::xlim(0, 10) +
ggplot2::ylim(0, 10) +
ggplot2::annotate("text",
x = 4,
y = 5,
label = print_warning
) +
ggplot2::theme_bw(25) +
ggplot2::theme(
axis.text.x = ggplot2::element_blank(),
axis.text.y = ggplot2::element_blank()
) +
ggplot2::ylab(" ") +
ggplot2::xlab(" ")
ggplot2::theme(plot.title = ggplot2::element_text(size = 10))
} else {
if (!is.null(seromodel_object@sim$samples)) {
foi <- rstan::extract(seromodel_object, "foi", inc_warmup = FALSE)[[1]]
prev_expanded <- get_prev_expanded(
Expand Down Expand Up @@ -99,27 +120,6 @@ plot_seroprev_fitted <- function(seromodel_object,
ggplot2::ylab("Sero-positivity") +
ggplot2::xlab("Age")
}
} else {
message("model did not run")
print_warning <- "errors"

prev_plot <- ggplot2::ggplot(data.frame()) +
ggplot2::geom_point() +
ggplot2::xlim(0, 10) +
ggplot2::ylim(0, 10) +
ggplot2::annotate("text",
x = 4,
y = 5,
label = print_warning
) +
ggplot2::theme_bw(25) +
ggplot2::theme(
axis.text.x = ggplot2::element_blank(),
axis.text.y = ggplot2::element_blank()
) +
ggplot2::ylab(" ") +
ggplot2::xlab(" ")
ggplot2::theme(plot.title = ggplot2::element_text(size = 10))
}

return(prev_plot)
Expand Down Expand Up @@ -161,11 +161,32 @@ plot_foi <- function(seromodel_object,
max_lambda = NA,
size_text = 25,
foi_sim = NULL) {
if (!is.character(seromodel_object)) {
if (is.character(seromodel_object)) {
message("model did not run")
print_warning <- "errors"

foi_plot <- ggplot2::ggplot(data.frame()) +
ggplot2::geom_point() +
ggplot2::xlim(0, 10) +
ggplot2::ylim(0, 10) +
ggplot2::annotate("text",
x = 4,
y = 5,
label = print_warning
) +
ggplot2::theme_bw(25) +
ggplot2::theme(
axis.text.x = ggplot2::element_blank(),
axis.text.y = ggplot2::element_blank()
) +
ggplot2::ylab(" ") +
ggplot2::xlab(" ")
ggplot2::theme(plot.title = ggplot2::element_text(size = 10))
} else {
if (!is.null(seromodel_object@sim$samples)) {
foi <- rstan::extract(seromodel_object,
"foi",
inc_warmup = FALSE
"foi",
inc_warmup = FALSE
)[[1]]
#-------- This bit is to get the actual length of the foi data
foi_data <- get_foi_central_estimates(
Expand Down Expand Up @@ -225,27 +246,6 @@ plot_foi <- function(seromodel_object,
}
}
}
} else {
message("model did not run")
print_warning <- "errors"

foi_plot <- ggplot2::ggplot(data.frame()) +
ggplot2::geom_point() +
ggplot2::xlim(0, 10) +
ggplot2::ylim(0, 10) +
ggplot2::annotate("text",
x = 4,
y = 5,
label = print_warning
) +
ggplot2::theme_bw(25) +
ggplot2::theme(
axis.text.x = ggplot2::element_blank(),
axis.text.y = ggplot2::element_blank()
) +
ggplot2::ylab(" ") +
ggplot2::xlab(" ")
ggplot2::theme(plot.title = ggplot2::element_text(size = 10))
}

return(foi_plot)
Expand Down Expand Up @@ -280,7 +280,28 @@ plot_foi <- function(seromodel_object,
plot_rhats <- function(seromodel_object,
cohort_ages,
size_text = 25) {
if (!is.character(seromodel_object)) {
if (is.character(seromodel_object)) {
message("model did not run")
print_warning <- "errors"

rhats_plot <- ggplot2::ggplot(data.frame()) +
ggplot2::geom_point() +
ggplot2::xlim(0, 10) +
ggplot2::ylim(0, 10) +
ggplot2::annotate("text",
x = 4,
y = 5,
label = print_warning
) +
ggplot2::theme_bw(25) +
ggplot2::theme(
axis.text.x = ggplot2::element_blank(),
axis.text.y = ggplot2::element_blank()
) +
ggplot2::ylab(" ") +
ggplot2::xlab(" ")
ggplot2::theme(plot.title = ggplot2::element_text(size = 10))
} else {
if (!is.null(seromodel_object@sim$samples)) {
rhats <- get_table_rhats(
seromodel_object = seromodel_object,
Expand All @@ -300,27 +321,6 @@ plot_rhats <- function(seromodel_object,
ggplot2::theme_bw(size_text) +
ggplot2::ylab("Convergence (R^)")
}
} else {
message("model did not run")
print_warning <- "errors"

rhats_plot <- ggplot2::ggplot(data.frame()) +
ggplot2::geom_point() +
ggplot2::xlim(0, 10) +
ggplot2::ylim(0, 10) +
ggplot2::annotate("text",
x = 4,
y = 5,
label = print_warning
) +
ggplot2::theme_bw(25) +
ggplot2::theme(
axis.text.x = ggplot2::element_blank(),
axis.text.y = ggplot2::element_blank()
) +
ggplot2::ylab(" ") +
ggplot2::xlab(" ")
ggplot2::theme(plot.title = ggplot2::element_text(size = 10))
}

return(rhats_plot)
Expand Down Expand Up @@ -358,7 +358,34 @@ plot_seromodel <- function(seromodel_object,
max_lambda = NA,
size_text = 25,
foi_sim = NULL) {
if (!is.character(seromodel_object)) {
if (is.character(seromodel_object)) {
message("model did not run")
print_warning <- "errors"

g0 <- ggplot2::ggplot(data.frame()) +
ggplot2::geom_point() +
ggplot2::xlim(0, 10) +
ggplot2::ylim(0, 10) +
ggplot2::annotate("text",
x = 4,
y = 5,
label = print_warning
) +
ggplot2::theme_bw(25) +
ggplot2::theme(
axis.text.x = ggplot2::element_blank(),
axis.text.y = ggplot2::element_blank()
) +
ggplot2::ylab(" ") +
ggplot2::xlab(" ")
g1 <- g0
# TODO: This
g0 <- g0 + ggplot2::labs(subtitle = seromodel_object$model_name) +
ggplot2::theme(plot.title = ggplot2::element_text(size = 10))

plot_arrange <-
cowplot::plot_grid(g0, g1, g1, g1, g1, ncol = 1, nrow = 5)
} else {
if (!is.null(seromodel_object@sim$samples)) {
cohort_ages <- get_cohort_ages(serodata = serodata)

Expand Down Expand Up @@ -404,33 +431,6 @@ plot_seromodel <- function(seromodel_object,
rel_heights = c(0.5, 1, 1, 1)
)
}
} else {
message("model did not run")
print_warning <- "errors"

g0 <- ggplot2::ggplot(data.frame()) +
ggplot2::geom_point() +
ggplot2::xlim(0, 10) +
ggplot2::ylim(0, 10) +
ggplot2::annotate("text",
x = 4,
y = 5,
label = print_warning
) +
ggplot2::theme_bw(25) +
ggplot2::theme(
axis.text.x = ggplot2::element_blank(),
axis.text.y = ggplot2::element_blank()
) +
ggplot2::ylab(" ") +
ggplot2::xlab(" ")
g1 <- g0
# TODO: This
g0 <- g0 + ggplot2::labs(subtitle = seromodel_object$model_name) +
ggplot2::theme(plot.title = ggplot2::element_text(size = 10))

plot_arrange <-
cowplot::plot_grid(g0, g1, g1, g1, g1, ncol = 1, nrow = 5)
}

return(plot_arrange)
Expand Down

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