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Remove unnecessary arguments and add plots by group (thesis) #5

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Remove unnecessary arguments and add plots by group (thesis) #5

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8671887
tidy code, remove legend title
R-Walmsley Jun 14, 2022
80a407a
add acc plots by group
R-Walmsley Jun 14, 2022
eef5910
remove unused arguments from helper functions
R-Walmsley Nov 2, 2022
fdd3254
add amendments to plots by group
R-Walmsley Nov 2, 2022
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24 changes: 6 additions & 18 deletions epiAnalysis/scripts/analysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ df_sensitivity <-
"_sensitivity.RDS"
))


name_of_current_run <- paste0("remove_unnecessary_args_", Sys.Date())
## Set up values used throughout for comp_labels and covariates--------------------------------------------------------------------
# Comp labels
comp_labels <-
Expand Down Expand Up @@ -810,11 +810,8 @@ plot_maxi_matrix_transfers(
yllimit = 0.8,
yulimit = 1.3,
plot_log = TRUE,
units = "hr/day",
granularity = 2000,
theme = NULL,
point_specification = ggplot2::geom_point(size = 1)
)
granularity = 2000,
)
dev.off()

## Matrix plots: model comparison-----------------------------------------
Expand Down Expand Up @@ -901,10 +898,7 @@ for (pair in model_pair_list) {
yllimit = 0.8,
yulimit = 1.3,
plot_log = TRUE,
units = "hr/day",
granularity = 1000,
point_specification = ggplot2::geom_point(size = 2)
)
granularity = 1000)

dev.off()

Expand All @@ -928,10 +922,8 @@ compare_all_transfers_side_by_side_three(
yllimit = 0.8,
yulimit = 1.3,
plot_log = TRUE,
units = "hr/day",
granularity = 1000,
point_specification = ggplot2::geom_point(size = 2)
)
)
dev.off()

### Write these models into df of numbers
Expand Down Expand Up @@ -981,12 +973,8 @@ compare_all_transfers_ism_side_by_side(
yllimit = 0.8,
yulimit = 1.3,
plot_log = TRUE,
lower_quantile = 0.05,
upper_quantile = 0.95,
units = "hr/day",
granularity = 1000,
point_specification = ggplot2::geom_point(size = 2)
)
)
dev.off()

### Write numbers_df --------------------------------------------------
Expand Down
16 changes: 1 addition & 15 deletions epiAnalysis/useful_functions/arrange_plots_matrix.R
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Original file line number Diff line number Diff line change
@@ -1,18 +1,10 @@
plot_maxi_matrix_transfers <-
function(comp_model,
fixed_values = NULL,
part_1 = NULL,
comp_labels,
yllimit = NULL,
yulimit = NULL,
plot_log = FALSE,
lower_quantile = 0.05,
upper_quantile = 0.95,
units = "unitless",
specified_units = NULL,
terms = TRUE,
granularity = 10000,
point_specification = ggplot2::geom_point(size = 2),
theme = NULL,
plotstitle = NULL) {
#------------------------------------------------------------------
Expand All @@ -22,13 +14,9 @@ plot_maxi_matrix_transfers <-
type <- epicoda:::process_model_type(comp_model)

# Labels
if (!is.null(part_1)) {
comp_labels <- alter_order_comp_labels(comp_labels, part_1)
}
transf_labels <-
transf_labels(comp_labels,
transformation_type = "ilr",
part_1 = part_1)
transformation_type = "ilr")
# Datasets
dataset1 <- get_dataset_from_model(model = comp_model, comp_labels = comp_labels, transf_labels = transf_labels, type = type)

Expand Down Expand Up @@ -59,14 +47,12 @@ plot_maxi_matrix_transfers <-
granularity = granularity,
units = "hr/day",
comp_labels = comp_labels,
terms = terms,
plot_log = plot_log,
yllimit = yllimit,
yulimit = yulimit,
xllimit = xllimit,
xulimit = xulimit,
y_label = y_label,
fixed_values = fixed_values,
point_specification = ggplot2::geom_point(size = 1.5)
)
assign(paste0("p_", comp_labels[i], "_", comp_labels[j], "_model1"), pfirst )
Expand Down
18 changes: 1 addition & 17 deletions epiAnalysis/useful_functions/compare_plot2.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,19 +10,11 @@ compare_all_transfers_side_by_side <-
ebc2 = "peachpuff",
pc1 = "blue",
pc2 = "darkred",
fixed_values = NULL,
part_1 = NULL,
comp_labels,
yllimit = NULL,
yulimit = NULL,
plot_log = FALSE,
lower_quantile = 0.05,
upper_quantile = 0.95,
units = "unitless",
specified_units = NULL,
terms = TRUE,
granularity = 10000,
point_specification = ggplot2::geom_point(size = 2),
theme = NULL,
plotstitle = NULL) {
#------------------------------------------------------------------
Expand All @@ -36,13 +28,9 @@ compare_all_transfers_side_by_side <-
}

# Labels
if (!is.null(part_1)) {
comp_labels <- alter_order_comp_labels(comp_labels, part_1)
}
transf_labels <-
transf_labels(comp_labels,
transformation_type = "ilr",
part_1 = part_1)
transformation_type = "ilr")
# Datasets
dataset1 <- get_dataset_from_model(model = comp_model, comp_labels = comp_labels, transf_labels = transf_labels, type = type)
dataset2 <- get_dataset_from_model(model = comp_model2, comp_labels = comp_labels, transf_labels = transf_labels, type = type)
Expand Down Expand Up @@ -74,14 +62,12 @@ compare_all_transfers_side_by_side <-
granularity = granularity,
units = "hr/day",
comp_labels = comp_labels,
terms = terms,
plot_log = plot_log,
yllimit = yllimit,
yulimit = yulimit,
xllimit = xllimit,
xulimit = xulimit,
y_label = y_label,
fixed_values = fixed_values,
point_specification = ggplot2::geom_point(size = 1.5, colour = pc1),
error_bar_colour = ebc1
)
Expand All @@ -94,13 +80,11 @@ compare_all_transfers_side_by_side <-
granularity = granularity,
units = "hr/day",
comp_labels = comp_labels,
terms = terms,
plot_log = plot_log,
yllimit = yllimit,
yulimit = yulimit,
xllimit = xllimit,
xulimit = xulimit,
fixed_values = fixed_values,
y_label = " ",
point_specification = ggplot2::geom_point(size = 1.5, colour = pc2),
error_bar_colour = ebc2
Expand Down
25 changes: 3 additions & 22 deletions epiAnalysis/useful_functions/compare_plot3.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,20 +8,11 @@ compare_all_transfers_side_by_side_three <-
pc1 = "blue",
pc2 = "darkred",
pc3 = "darkgreen",
fixed_values = NULL,
part_1 = NULL,
comp_labels,
yllimit = NULL,
yulimit = NULL,
plot_log = FALSE,
lower_quantile = 0.05,
upper_quantile = 0.95,
units = "unitless",
specified_units = NULL,
terms = TRUE,
granularity = 10000,
point_specification = ggplot2::geom_point(size = 2),
theme = NULL,
plotstitle = NULL) {
#------------------------------------------------------------------
# First we calculate the shared limits for all the plots
Expand All @@ -35,13 +26,9 @@ compare_all_transfers_side_by_side_three <-
}

# Labels
if (!is.null(part_1)) {
comp_labels <- alter_order_comp_labels(comp_labels, part_1)
}
transf_labels <-
transf_labels <-
transf_labels(comp_labels,
transformation_type = "ilr",
part_1 = part_1)
transformation_type = "ilr")
# Datasets
dataset1 <- get_dataset_from_model(model = comp_model, comp_labels = comp_labels, transf_labels = transf_labels, type = type)

Expand Down Expand Up @@ -71,14 +58,12 @@ compare_all_transfers_side_by_side_three <-
granularity = granularity,
units = "hr/day",
comp_labels = comp_labels,
terms = terms,
plot_log = plot_log,
yllimit = yllimit,
yulimit = yulimit,
xllimit = xllimit,
xulimit = xulimit,
y_label = y_label,
fixed_values = fixed_values,
point_specification = ggplot2::geom_point(size = 1.5, colour = pc1),
error_bar_colour = ebc1
)
Expand All @@ -91,13 +76,11 @@ compare_all_transfers_side_by_side_three <-
granularity = granularity,
units = "hr/day",
comp_labels = comp_labels,
terms = terms,
plot_log = plot_log,
yllimit = yllimit,
yulimit = yulimit,
xllimit = xllimit,
xulimit = xulimit,
fixed_values = fixed_values,
y_label = " ",
point_specification = ggplot2::geom_point(size = 1.5, colour = pc2),
error_bar_colour = ebc2
Expand All @@ -111,14 +94,12 @@ compare_all_transfers_side_by_side_three <-
granularity = granularity,
units = "hr/day",
comp_labels = comp_labels,
terms = terms,
plot_log = plot_log,
yllimit = yllimit,
yulimit = yulimit,
xllimit = xllimit,
xulimit = xulimit,
fixed_values = fixed_values,
y_label = " ",
y_label = " ",
point_specification = ggplot2::geom_point(size = 1.5, colour = pc3),
error_bar_colour = ebc3
)
Expand Down
22 changes: 1 addition & 21 deletions epiAnalysis/useful_functions/compare_plot_linear.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,23 +6,11 @@ compare_all_transfers_ism_side_by_side <-
ebc2 = "peachpuff",
pc1 = "blue",
pc2 = "darkred",
fixed_values = NULL,
transformation_type = "ilr",
comparison_part = NULL,
part_1 = NULL,
comp_labels,
yllimit = NULL,
yulimit = NULL,
plot_log = FALSE,
lower_quantile = 0.05,
upper_quantile = 0.95,
units = "unitless",
specified_units = NULL,
rounded_zeroes = TRUE,
det_limit = NULL,
terms = TRUE,
granularity = 10000,
point_specification = ggplot2::geom_point(size = 2),
theme = NULL,
plotstitle = NULL) {

Expand All @@ -34,13 +22,9 @@ compare_all_transfers_ism_side_by_side <-
type <- epicoda:::process_model_type(comp_model)

# Labels
if (!is.null(part_1)) {
comp_labels <- alter_order_comp_labels(comp_labels, part_1)
}
transf_labels <-
transf_labels(comp_labels,
transformation_type = "ilr",
part_1 = part_1)
transformation_type = "ilr")
# Datasets
dataset1 <- get_dataset_from_model(model = comp_model, comp_labels = comp_labels, transf_labels = transf_labels, type = type)

Expand Down Expand Up @@ -71,14 +55,12 @@ compare_all_transfers_ism_side_by_side <-
granularity = granularity,
units = "hr/day",
comp_labels = comp_labels,
terms = terms,
plot_log = plot_log,
yllimit = yllimit,
yulimit = yulimit,
xllimit = xllimit,
xulimit = xulimit,
y_label = y_label,
fixed_values = fixed_values,
point_specification = ggplot2::geom_point(size = 1.5, colour = pc1),
error_bar_colour = ebc1
)
Expand All @@ -93,13 +75,11 @@ compare_all_transfers_ism_side_by_side <-
granularity = granularity,
units = "hr/day",
comp_labels = comp_labels,
terms = terms,
plot_log = plot_log,
yllimit = yllimit,
yulimit = yulimit,
xllimit = xllimit,
xulimit = xulimit,
fixed_values = fixed_values,
y_label = " ",
point_specification = ggplot2::geom_point(size = 1.5, colour = pc2),
error_bar_colour = ebc2
Expand Down
4 changes: 2 additions & 2 deletions epiAnalysis/useful_functions/plot_transfers_ism.R
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Original file line number Diff line number Diff line change
Expand Up @@ -99,8 +99,8 @@ plot_transfers_ism <- function(from_part,
dataset = dataset_ready,
units = "hr/day",
comp_labels = comp_labels,
lower_quantile = 0.05,
upper_quantile = 0.95,
lower_quantile = lower_quantile,
upper_quantile = upper_quantile,
granularity = granularity
)
new_data <- epicoda:::normalise_comp(new_data, comp_labels)
Expand Down
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