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Merge pull request #11 from oxford-pharmacoepi/dev_cc
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OmopSketch 0.2.1
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@cecicampanile
cecicampanile authored Jan 17, 2025
2 parents 1d54ba5 + abfeb29 commit 1ba18d5
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Showing 4 changed files with 79 additions and 68 deletions.
17 changes: 8 additions & 9 deletions CharacterisationCode/renv.lock
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Expand Up @@ -102,7 +102,7 @@
},
"OmopSketch": {
"Package": "OmopSketch",
"Version": "0.2.0",
"Version": "0.2.1",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
Expand All @@ -122,7 +122,7 @@
"tibble",
"tidyr"
],
"Hash": "0c37ddc951ee1dafd9ef3ef7998db507"
"Hash": "1267f40708ddba6cd56b623d5c386ad3"
},
"PatientProfiles": {
"Package": "PatientProfiles",
Expand Down Expand Up @@ -441,9 +441,9 @@
},
"pillar": {
"Package": "pillar",
"Version": "1.10.0",
"Version": "1.10.1",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Requirements": [
"cli",
"glue",
Expand All @@ -453,7 +453,7 @@
"utils",
"vctrs"
],
"Hash": "101ca350beea21261a15ba169d7a8513"
"Hash": "8b16b6097daef84cd3c40a6a7c5c9d86"
},
"pkgconfig": {
"Package": "pkgconfig",
Expand Down Expand Up @@ -695,22 +695,21 @@
},
"visOmopResults": {
"Package": "visOmopResults",
"Version": "0.5.1",
"Version": "1.0.0",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Requirements": [
"cli",
"dplyr",
"generics",
"glue",
"lifecycle",
"omopgenerics",
"purrr",
"rlang",
"stringr",
"tidyr"
],
"Hash": "62111b2c7b941ffe31fc68fbe1cae436"
"Hash": "4a6d832d0cf4775f7a3f865982b92231"
},
"vroom": {
"Package": "vroom",
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16 changes: 14 additions & 2 deletions shiny/data/preprocess.R
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Expand Up @@ -3,7 +3,7 @@ resultList <- list(
"summarise_omop_snapshot" = c(1L),
"summarise_characteristics" = c(2L),
"summarise_missing_data" = c(3L),
"summarise_all_concept_counts" = c(4L),
"summarise_concept_id_counts" = c(4L),
"summarise_clinical_records" = c(5L),
"summarise_record_count" = c(6L),
"summarise_in_observation" = c(7L),
Expand All @@ -12,7 +12,19 @@ resultList <- list(

source(file.path(getwd(), "functions.R"))

result <- omopgenerics::importSummarisedResult(file.path(getwd(), "data"))
data_path <- file.path(getwd(), "data")
csv_files <- list.files(data_path, pattern = "\\.csv$", full.names = TRUE)

result <- purrr::map(csv_files, \(x){
d <- omopgenerics::importSummarisedResult(x)
attr(d, "settings") <- attr(d, "settings")|>dplyr::mutate(result_type = dplyr::if_else(.data$result_type == "summarise_all_concept_counts", "summarise_concept_id_counts", .data$result_type))
d
}) |>
dplyr::bind_rows() |>
omopgenerics::newSummarisedResult()

# result <- omopgenerics::importSummarisedResult(file.path(getwd(), "data"))

data <- prepareResult(result, resultList)
filterValues <- defaultFilterValues(result, resultList)

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34 changes: 17 additions & 17 deletions shiny/server.R
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Expand Up @@ -259,24 +259,24 @@ server <- function(input, output, session) {
)


# summarise_all_concept_counts -----
## tidy summarise_all_concept_counts -----
# summarise_concept_id_counts -----
## tidy summarise_concept_id_counts -----
getTidyDataSummariseAllConceptCounts <- shiny::reactive({
res <- data |>
filterData("summarise_all_concept_counts", input) |>
filterData("summarise_concept_id_counts", input) |>
omopgenerics::addSettings() |>
omopgenerics::splitAll() |>
dplyr::select(!"result_id")

# columns to eliminate
colsEliminate <- colnames(res)
colsEliminate <- colsEliminate[!colsEliminate %in% c(
input$summarise_all_concept_counts_tidy_columns, "variable_name", "variable_level",
input$summarise_concept_id_counts_tidy_columns, "variable_name", "variable_level",
"estimate_name", "estimate_type", "estimate_value"
)]

# pivot
pivot <- input$summarise_all_concept_counts_tidy_pivot
pivot <- input$summarise_concept_id_counts_tidy_pivot
if (pivot != "none") {
vars <- switch(pivot,
"estimates" = "estimate_name",
Expand All @@ -289,28 +289,28 @@ server <- function(input, output, session) {
res |>
dplyr::select(!dplyr::all_of(colsEliminate))
})
output$summarise_all_concept_counts_tidy <- DT::renderDT({
output$summarise_concept_id_counts_tidy <- DT::renderDT({
DT::datatable(
getTidyDataSummariseAllConceptCounts(),
options = list(scrollX = TRUE),
rownames = FALSE
)
})
output$summarise_all_concept_counts_tidy_download <- shiny::downloadHandler(
filename = "tidy_summarise_all_concept_counts.csv",
output$summarise_concept_id_counts_tidy_download <- shiny::downloadHandler(
filename = "tidy_summarise_concept_id_counts.csv",
content = function(file) {
getTidyDataSummariseAllConceptCounts() |>
readr::write_csv(file = file)
}
)
## output summarise_all_concept_counts -----
## output summarise_concept_id_counts -----
## output 0 -----
createOutput27 <- shiny::reactive({
result <- data |>
filterData("summarise_all_concept_counts", input)
header <- input$summarise_all_concept_counts_gt_0_header
group <- input$summarise_all_concept_counts_gt_0_group
hide <- input$summarise_all_concept_counts_gt_0_hide
filterData("summarise_concept_id_counts", input)
header <- input$summarise_concept_id_counts_gt_0_header
group <- input$summarise_concept_id_counts_gt_0_group
hide <- input$summarise_concept_id_counts_gt_0_hide

if (is.null(header) || length(header) == 0) header <- c("cdm_name")
if (is.null(group) || length(group) == 0) group <- c("omop_table","year")
Expand All @@ -322,11 +322,11 @@ server <- function(input, output, session) {
hide = hide
)
})
output$summarise_all_concept_counts_gt_0 <- gt::render_gt({
output$summarise_concept_id_counts_gt_0 <- gt::render_gt({
createOutput27()
})
output$summarise_all_concept_counts_gt_0_download <- shiny::downloadHandler(
filename = paste0("output_gt_summarise_all_concept_counts.", input$summarise_all_concept_counts_gt_0_download_type),
output$summarise_concept_id_counts_gt_0_download <- shiny::downloadHandler(
filename = paste0("output_gt_summarise_concept_id_counts.", input$summarise_concept_id_counts_gt_0_download_type),
content = function(file) {
obj <- createOutput27()
gt::gtsave(data = obj, filename = file)
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80 changes: 40 additions & 40 deletions shiny/ui.R
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Expand Up @@ -554,83 +554,83 @@ ui <- bslib::page_navbar(
bslib::accordion_panel(
title = "Settings",
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_settings_study_period_end",
inputId = "summarise_concept_id_counts_settings_study_period_end",
label = "Study period end",
choices = filterValues$summarise_all_concept_counts_settings_study_period_end,
selected = filterValues$summarise_all_concept_counts_settings_study_period_end,
choices = filterValues$summarise_concept_id_counts_settings_study_period_end,
selected = filterValues$summarise_concept_id_counts_settings_study_period_end,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_settings_study_period_start",
inputId = "summarise_concept_id_counts_settings_study_period_start",
label = "Study period start",
choices = filterValues$summarise_all_concept_counts_settings_study_period_start,
selected = filterValues$summarise_all_concept_counts_settings_study_period_start,
choices = filterValues$summarise_concept_id_counts_settings_study_period_start,
selected = filterValues$summarise_concept_id_counts_settings_study_period_start,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
bslib::accordion_panel(
title = "Grouping",
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_grouping_cdm_name",
inputId = "summarise_concept_id_counts_grouping_cdm_name",
label = "Cdm name",
choices = filterValues$summarise_all_concept_counts_grouping_cdm_name,
selected = filterValues$summarise_all_concept_counts_grouping_cdm_name,
choices = filterValues$summarise_concept_id_counts_grouping_cdm_name,
selected = filterValues$summarise_concept_id_counts_grouping_cdm_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_grouping_omop_table",
inputId = "summarise_concept_id_counts_grouping_omop_table",
label = "Omop table",
choices = filterValues$summarise_all_concept_counts_grouping_omop_table,
selected = filterValues$summarise_all_concept_counts_grouping_omop_table,
choices = filterValues$summarise_concept_id_counts_grouping_omop_table,
selected = filterValues$summarise_concept_id_counts_grouping_omop_table,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_grouping_age_group",
inputId = "summarise_concept_id_counts_grouping_age_group",
label = "Age group",
choices = filterValues$summarise_all_concept_counts_grouping_age_group,
selected = filterValues$summarise_all_concept_counts_grouping_age_group,
choices = filterValues$summarise_concept_id_counts_grouping_age_group,
selected = filterValues$summarise_concept_id_counts_grouping_age_group,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_grouping_sex",
inputId = "summarise_concept_id_counts_grouping_sex",
label = "Sex",
choices = filterValues$summarise_all_concept_counts_grouping_sex,
selected = filterValues$summarise_all_concept_counts_grouping_sex,
choices = filterValues$summarise_concept_id_counts_grouping_sex,
selected = filterValues$summarise_concept_id_counts_grouping_sex,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_grouping_year",
inputId = "summarise_concept_id_counts_grouping_year",
label = "Year",
choices = filterValues$summarise_all_concept_counts_grouping_year,
selected = filterValues$summarise_all_concept_counts_grouping_year,
choices = filterValues$summarise_concept_id_counts_grouping_year,
selected = filterValues$summarise_concept_id_counts_grouping_year,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
bslib::accordion_panel(
title = "Variables",
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_variable_name",
inputId = "summarise_concept_id_counts_variable_name",
label = "Variable name",
choices = filterValues$summarise_all_concept_counts_variable_name,
selected = filterValues$summarise_all_concept_counts_variable_name,
choices = filterValues$summarise_concept_id_counts_variable_name,
selected = filterValues$summarise_concept_id_counts_variable_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
),
bslib::accordion_panel(
title = "Estimates",
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_estimate_name",
inputId = "summarise_concept_id_counts_estimate_name",
label = "Estimate name",
choices = filterValues$summarise_all_concept_counts_estimate_name,
selected = filterValues$summarise_all_concept_counts_estimate_name,
choices = filterValues$summarise_concept_id_counts_estimate_name,
selected = filterValues$summarise_concept_id_counts_estimate_name,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
)
Expand All @@ -645,29 +645,29 @@ ui <- bslib::page_navbar(
bslib::card_header(
bslib::popover(
shiny::icon("download"),
shiny::downloadButton(outputId = "summarise_all_concept_counts_tidy_download", label = "Download csv")
shiny::downloadButton(outputId = "summarise_concept_id_counts_tidy_download", label = "Download csv")
),
class = "text-end"
),
bslib::layout_sidebar(
sidebar = bslib::sidebar(
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_tidy_columns",
inputId = "summarise_concept_id_counts_tidy_columns",
label = "Columns",
choices = filterValues$summarise_all_concept_counts_tidy_columns,
selected = filterValues$summarise_all_concept_counts_tidy_columns,
choices = filterValues$summarise_concept_id_counts_tidy_columns,
selected = filterValues$summarise_concept_id_counts_tidy_columns,
multiple = TRUE,
options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
),
shiny::radioButtons(
inputId = "summarise_all_concept_counts_tidy_pivot",
inputId = "summarise_concept_id_counts_tidy_pivot",
label = "Pivot estimates/variables",
choices = c("none", "estimates", "estimates and variables"),
selected = "none"
),
position = "right"
),
DT::dataTableOutput("summarise_all_concept_counts_tidy")
DT::dataTableOutput("summarise_concept_id_counts_tidy")
)
)
),
Expand All @@ -679,13 +679,13 @@ ui <- bslib::page_navbar(
bslib::popover(
shiny::icon("download"),
shinyWidgets::pickerInput(
inputId = "summarise_all_concept_counts_gt_0_download_type",
inputId = "summarise_concept_id_counts_gt_0_download_type",
label = "File type",
selected = "docx",
choices = c("docx", "png", "pdf", "html"),
multiple = FALSE
),
shiny::downloadButton(outputId = "summarise_all_concept_counts_gt_0_download", label = "Download")
shiny::downloadButton(outputId = "summarise_concept_id_counts_gt_0_download", label = "Download")
),
class = "text-end"
),
Expand All @@ -696,27 +696,27 @@ ui <- bslib::page_navbar(
sortable::add_rank_list(
text = "none",
labels = c("variable_name", "estimate_name", "estimate_level", "sex", "age-group"),
input_id = "summarise_all_concept_counts_gt_0_none"
input_id = "summarise_concept_id_counts_gt_0_none"
),
sortable::add_rank_list(
text = "header",
labels = "cdm_name",
input_id = "summarise_all_concept_counts_gt_0_header"
input_id = "summarise_concept_id_counts_gt_0_header"
),
sortable::add_rank_list(
text = "group",
labels = c("omop_table","year"),
input_id = "summarise_all_concept_counts_gt_0_group"
input_id = "summarise_concept_id_counts_gt_0_group"
),
sortable::add_rank_list(
text = "hide",
labels = c("study_period_end", "study_period_start"),
input_id = "summarise_all_concept_counts_gt_0_hide"
input_id = "summarise_concept_id_counts_gt_0_hide"
)
),
position = "right"
),
gt::gt_output("summarise_all_concept_counts_gt_0")
gt::gt_output("summarise_concept_id_counts_gt_0")
)
)
)
Expand Down

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