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Merge branch 'main' into 712-tm_a_pca@main
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‎DESCRIPTION

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Type: Package
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Package: teal.modules.general
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Title: General Modules for 'teal' Applications
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Version: 0.3.0.9017
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Version: 0.3.0.9021
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Date: 2024-04-19
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Authors@R: c(
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person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")),

‎NEWS.md

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# teal.modules.general 0.3.0.9017
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# teal.modules.general 0.3.0.9021
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# teal.modules.general 0.3.0
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‎R/tm_g_bivariate.R

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#' CO2 <- data.frame(CO2)
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#' })
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#' datanames(data) <- c("CO2")
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#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
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#'
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#' app <- init(
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#' data = data,
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#' modules = modules(
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#' tm_g_bivariate(
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#' x = data_extract_spec(
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#' dataname = "CO2",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["CO2"]]),
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#' selected = "conc",
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#' fixed = FALSE
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#' )
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#' ),
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#' y = data_extract_spec(
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#' dataname = "CO2",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["CO2"]]),
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#' selected = "uptake",
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#' multiple = FALSE,
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#' fixed = FALSE
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#' )
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#' ),
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#' row_facet = data_extract_spec(
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#' dataname = "CO2",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["CO2"]]),
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#' selected = "Type",
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#' fixed = FALSE
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#' )
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#' ),
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#' col_facet = data_extract_spec(
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#' dataname = "CO2",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["CO2"]]),
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#' selected = "Treatment",
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#' fixed = FALSE
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#' )
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#' ),
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#' ggplot2_args = ggplot2_args(
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#' labs = list(subtitle = "Plot generated by Bivariate Module")
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#' modules = tm_g_bivariate(
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#' x = data_extract_spec(
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#' dataname = "CO2",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["CO2"]]),
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#' selected = "conc",
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#' fixed = FALSE
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#' )
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#' ),
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#' y = data_extract_spec(
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#' dataname = "CO2",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["CO2"]]),
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#' selected = "uptake",
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#' multiple = FALSE,
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#' fixed = FALSE
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#' )
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#' ),
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#' row_facet = data_extract_spec(
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#' dataname = "CO2",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["CO2"]]),
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#' selected = "Type",
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#' fixed = FALSE
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#' )
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#' ),
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#' col_facet = data_extract_spec(
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#' dataname = "CO2",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["CO2"]]),
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#' selected = "Treatment",
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#' fixed = FALSE
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#' )
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#' ),
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#' ggplot2_args = ggplot2_args(
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#' labs = list(subtitle = "Plot generated by Bivariate Module")
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#' )
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#' )
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#' )
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#'
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#' app <- init(
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#' data = data,
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#' modules = modules(
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#' tm_g_bivariate(
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#' x = data_extract_spec(
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#' dataname = "ADSL",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["ADSL"]]),
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#' selected = "AGE",
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#' fixed = FALSE
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#' )
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#' ),
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#' y = data_extract_spec(
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#' dataname = "ADSL",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["ADSL"]]),
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#' selected = "SEX",
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#' multiple = FALSE,
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#' fixed = FALSE
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#' )
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#' ),
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#' row_facet = data_extract_spec(
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#' dataname = "ADSL",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["ADSL"]]),
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#' selected = "ARM",
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#' fixed = FALSE
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#' )
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#' ),
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#' col_facet = data_extract_spec(
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#' dataname = "ADSL",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["ADSL"]]),
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#' selected = "COUNTRY",
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#' fixed = FALSE
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#' )
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#' ),
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#' ggplot2_args = ggplot2_args(
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#' labs = list(subtitle = "Plot generated by Bivariate Module")
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#' modules = tm_g_bivariate(
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#' x = data_extract_spec(
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#' dataname = "ADSL",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["ADSL"]]),
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#' selected = "AGE",
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#' fixed = FALSE
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#' )
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#' ),
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#' y = data_extract_spec(
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#' dataname = "ADSL",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["ADSL"]]),
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#' selected = "SEX",
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#' multiple = FALSE,
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#' fixed = FALSE
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#' )
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#' ),
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#' row_facet = data_extract_spec(
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#' dataname = "ADSL",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["ADSL"]]),
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#' selected = "ARM",
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#' fixed = FALSE
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#' )
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#' ),
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#' col_facet = data_extract_spec(
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#' dataname = "ADSL",
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#' select = select_spec(
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#' label = "Select variable:",
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#' choices = variable_choices(data[["ADSL"]]),
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#' selected = "COUNTRY",
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#' fixed = FALSE
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#' )
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#' ),
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#' ggplot2_args = ggplot2_args(
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#' labs = list(subtitle = "Plot generated by Bivariate Module")
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#' )
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#' )
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#' )
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expr = {
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# Add facetting labels
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# optional: grid.newpage() # nolint: commented_code.
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p <- add_facet_labels(p, xfacet_label = nulled_col_facet_name, yfacet_label = nulled_row_facet_name)
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# Prefixed with teal.modules.general as its usage will appear in "Show R code"
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p <- teal.modules.general::add_facet_labels(
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p,
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xfacet_label = nulled_col_facet_name,
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yfacet_label = nulled_row_facet_name
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)
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grid::grid.newpage()
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grid::grid.draw(p)
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},

‎R/tm_missing_data.R

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@@ -730,7 +730,11 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
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values = c("grey90", c(getOption("ggplot2.discrete.colour")[2], "#ff2951ff")[1]),
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labels = c("Present", "Missing")
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) +
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scale_y_continuous(labels = scales::percent_format(), breaks = seq(0, 1, by = 0.1), expand = c(0, 0)) +
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scale_y_continuous(
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labels = scales::percent_format(),
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breaks = seq(0, 1, by = 0.1),
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expand = c(0, 0)
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) +
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geom_text(
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aes(label = ifelse(isna == TRUE, sprintf("%d [%.02f%%]", n, n_pct), ""), y = 1),
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hjust = 1,
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fill = ~isna
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) +
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geom_bar(alpha = 1, stat = "identity", position = "fill") +
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scale_y_continuous(labels = scales::percent_format(), breaks = seq(0, 1, by = 0.1), expand = c(0, 0)) +
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scale_y_continuous(
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labels = scales::percent_format(),
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breaks = seq(0, 1, by = 0.1),
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expand = c(0, 0)
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) +
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scale_fill_manual(
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name = "",
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values = c("grey90", c(getOption("ggplot2.discrete.colour")[2], "#ff2951ff")[1]),
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dplyr::distinct() %>%
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ggplot(aes(x = id, y = n)) +
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geom_bar(stat = "identity", fill = c(getOption("ggplot2.discrete.colour")[2], "#ff2951ff")[1]) +
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geom_text(aes(label = n), position = position_dodge(width = 0.9), vjust = -0.25) +
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geom_text(
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aes(label = n),
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position = position_dodge(width = 0.9),
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vjust = -0.25
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) +
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ylim(c(0, max(data_combination_plot_cutoff$n) * 1.5)) +
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labs1 +
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ggthemes1 +

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