Follow changes in gamma

crp2a · Sep 19, 2024 · ef286ac · ef286ac
1 parent ed1e375
commit ef286ac
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Showing 8 changed files with 103 additions and 109 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -24,7 +24,7 @@ Imports:
     gamma (>= 1.0.3),
     ggplot2,
     grDevices,
-    kableExtra,
+    gt,
     khroma,
     knitr,
     methods,

diff --git a/NAMESPACE b/NAMESPACE
@@ -17,11 +17,6 @@ importFrom(DT,datatable)
 importFrom(DT,editData)
 importFrom(ggplot2,theme_bw)
 importFrom(grDevices,hcl)
-importFrom(kableExtra,add_header_above)
-importFrom(kableExtra,cell_spec)
-importFrom(kableExtra,kable_styling)
-importFrom(kableExtra,row_spec)
-importFrom(kableExtra,spec_color)
 importFrom(khroma,colour)
 importFrom(khroma,scale_color_bright)
 importFrom(khroma,scale_color_dark)

diff --git a/R/gammaShiny-package.R b/R/gammaShiny-package.R
@@ -41,8 +41,6 @@
 #' @importFrom DT datatable editData
 #' @importFrom ggplot2 theme_bw
 #' @importFrom grDevices hcl
-#' @importFrom kableExtra add_header_above cell_spec kable_styling row_spec
-#' spec_color
 #' @importFrom knitr kable
 #' @importFrom khroma colour scale_color_discreterainbow scale_color_bright
 #' scale_color_highcontrast scale_color_vibrant scale_color_muted

diff --git a/R/module_dose_server.R b/R/module_dose_server.R
@@ -32,34 +32,16 @@ module_dose_server <- function(input, output, session,
     get(input$select_curve, envir = env_calibration)
   })
 
-  user_integrate <- reactive({
-    req(user_curve(), user_spectra())
-
-    ni <- signal_integrate(
-      user_spectra(),
-      background = user_curve()[["Ni"]][["background"]],
-      range = user_curve()[["Ni"]][["range"]],
-      energy = FALSE,
-      simplify = TRUE
-    )
-
-    niei <- signal_integrate(
-      user_spectra(),
-      background = user_curve()[["NiEi"]][["background"]],
-      range = user_curve()[["NiEi"]][["range"]],
-      energy = TRUE,
-      simplify = TRUE
-    )
-
-    as.data.frame(cbind(ni, niei))
-  })
-
   user_dose <- reactive({
     req(input$sigma, input$epsilon, user_spectra(), user_curve())
     withCallingHandlers(
       {
-        dose_predict(user_curve(), user_spectra(),
-                     sigma = input$sigma, epsilon = input$epsilon / 100)
+        dose_predict(
+          object = user_curve(),
+          spectrum = user_spectra(),
+          sigma = input$sigma,
+          epsilon = input$epsilon / 100
+        )
       },
       warning = function(e) {
         warn <- gsub("\n|\\*", "", e$message)
@@ -141,56 +123,78 @@ module_dose_server <- function(input, output, session,
     }
   })
 
-  output$integration <- renderText({
+  output$integration <- gt::render_gt({
     req(user_spectra())
+    req(user_dose())
     energy_calib <- has_calibration(user_spectra())
 
-    tbl <- knitr::kable(
-      user_integrate(),
-      digits = user_settings$digits,
-      row.names = TRUE,
-      col.names = c("Value", "Error", "Value", "Error")
-    )
-    tbl <- kableExtra::kable_styling(
-      kable_input = tbl,
-      bootstrap_options = c("striped", "hover"),
-      full_width = TRUE, fixed_thead = TRUE
-    )
-    tbl <- kableExtra::add_header_above(
-      kable_input = tbl,
-      header = c(" " = 1, "Integration (Ni)" = 2, "Integration (NiEi)" = 2)
-    )
-    tbl <- kableExtra::row_spec(
-      kable_input = tbl,
-      row = which(!energy_calib), bold = FALSE,
-      color = "black", background = "orange"
-    )
+    tbl <- user_dose()
+    col <- which(startsWith(colnames(tbl), "signal"))
+
+    tbl <- tbl[, c(1, col)]
+    tbl |>
+      gt::gt(
+        rowname_col = "name"
+      ) |>
+      gt::tab_spanner(
+        label = "Integration (Ni)",
+        columns = gt::ends_with("Ni")
+      ) |>
+      gt::tab_spanner(
+        label = "Integration (NiEi)",
+        columns = gt::ends_with("NiEi")
+      ) |>
+      gt::cols_label(
+        gt::starts_with("signal_Ni") ~ "Value",
+        gt::starts_with("signal_err") ~ "Error"
+      ) |>
+      gt::fmt_number(
+        decimals = user_settings$digits
+      ) |>
+      gt::data_color(
+        rows = which(!energy_calib),
+        palette = "orange"
+      ) |>
+      gt::tab_options(table.width = "100%")
   })
 
-  output$results <- renderText({
+  output$results <- gt::render_gt({
     req(user_spectra())
+    req(user_dose())
     energy_calib <- has_calibration(user_spectra())
 
-    tbl <- knitr::kable(
-      user_dose(),
-      digits = user_settings$digits,
-      row.names = FALSE,
-      col.names = c("Name", "Value", "Error", "Value", "Error")
-    )
-    tbl <- kableExtra::kable_styling(
-      kable_input = tbl,
-      bootstrap_options = c("striped", "hover"),
-      full_width = TRUE, fixed_thead = TRUE
-    )
-    tbl <- kableExtra::add_header_above(
-      kable_input = tbl,
-      header = c(" " = 1, "Dose rate (Ni)" = 2, "Dose rate (NiEi)" = 2)
-    )
-    tbl <- kableExtra::row_spec(
-      kable_input = tbl,
-      row = which(!energy_calib), bold = FALSE,
-      color = "black", background = "orange"
-    )
+    tbl <- user_dose()
+    col <- which(startsWith(colnames(tbl), "dose"))
+
+    tbl <- tbl[, c(1, col)]
+    tbl |>
+      gt::gt(
+        rowname_col = "name"
+      ) |>
+      gt::tab_spanner(
+        label = "Dose rate (Ni)",
+        columns = gt::ends_with("Ni")
+      ) |>
+      gt::tab_spanner(
+        label = "Dose rate (NiEi)",
+        columns = gt::ends_with("NiEi")
+      ) |>
+      gt::tab_spanner(
+        label = "Mean dose rate",
+        columns = gt::ends_with("final")
+      ) |>
+      gt::cols_label(
+        gt::starts_with(c("dose_Ni", "dose_final")) ~ "Value",
+        gt::starts_with(c("dose_err", "dose_err_final")) ~ "Error"
+      ) |>
+      gt::fmt_number(
+        decimals = user_settings$digits
+      ) |>
+      gt::data_color(
+        rows = which(!energy_calib),
+        palette = "orange"
+      ) |>
+      gt::tab_options(table.width = "100%")
   })
 
   output$export_table <- downloadHandler(

diff --git a/R/module_dose_ui.R b/R/module_dose_ui.R
@@ -72,8 +72,8 @@ module_dose_ui <- function(id) {
               ),
               numericInput(
                 inputId = ns("epsilon"),
-                label = "Energy calibration error (%)",
-                min = 0, max = 100, value = 1.5, step = 0.5
+                label = "Extra relative error term (%; calibration of the energy scale)",
+                min = 0, max = 100, value = 1.5, step = 0.05
               )
             ),
             plotOutput(outputId = ns("curve")),
@@ -99,15 +99,15 @@ module_dose_ui <- function(id) {
               icon = icon("circle-radiation"),
               column(
                 width = 12,
-                htmlOutput(outputId = ns("results"))
+                gt::gt_output(outputId = ns("results"))
               )
             ),
             tabPanel(
               "Signal Integration",
               icon = icon("calculator"),
               column(
                 width = 12,
-                htmlOutput(outputId = ns("integration"))
+                gt::gt_output(outputId = ns("integration"))
               )
             )
           )

diff --git a/R/module_import_server.R b/R/module_import_server.R
@@ -73,34 +73,31 @@ module_import_server <- function(input, output, session,
     plotly::ggplotly(plot_spectra())
   })
 
-  output$summary <- renderText({
+  output$summary <- gt::render_gt({
     tbl <- user_table()
     id <- tbl$name
-    tbl$name <- kableExtra::cell_spec(
-      x = tbl$name,
-      format = "html",
-      bold = TRUE,
-      color = "white",
-      background = factor(id, id, user_settings$fig_colour(length(id)))
-    )
-    tbl <- knitr::kable(
-      x = tbl,
-      format = "html",
-      escape = FALSE,
-      digits = user_settings$digits,
-      row.names = FALSE,
-      col.names = c("Name", "Date", "Live time", "Real time", "Channels",
-                    "Min.", "Max.")
-    )
-    tbl <- kableExtra::kable_styling(
-      kable_input = tbl,
-      bootstrap_options = c("striped", "hover"),
-      full_width = TRUE, fixed_thead = TRUE
-    )
-    kableExtra::add_header_above(
-      kable_input = tbl,
-      header = c(" " = 5, "Energy Range" = 2)
-    )
+    pal <- unclass(user_settings$fig_colour(length(id)))
+
+    tbl |>
+      gt::gt() |>
+      gt::tab_spanner(
+        label = "Energy Range",
+        columns = gt::starts_with("energy")
+      ) |>
+      gt::cols_label(
+        name = "Name", date = "Date", live_time = "Live time",
+        real_time = "Real time", channels = "Channels",
+        energy_min = "Min.", energy_max = "Max."
+      ) |>
+      gt::fmt_number(
+        decimals = user_settings$digits
+      ) |>
+      gt::data_color(
+        columns = 1,
+        method = "factor",
+        palette = pal
+      ) |>
+      gt::tab_options(table.width = "100%")
   })
 
   output$export_plot <- downloadHandler(

diff --git a/R/module_import_ui.R b/R/module_import_ui.R
@@ -69,7 +69,7 @@ module_import_ui <- function(id) {
       fluidRow(
         column(
           width = 12,
-          tableOutput(outputId = ns("summary"))
+          gt::gt_output(outputId = ns("summary"))
         )
       )
     )

diff --git a/codemeta.json b/codemeta.json
@@ -115,15 +115,15 @@
     },
     "5": {
       "@type": "SoftwareApplication",
-      "identifier": "kableExtra",
-      "name": "kableExtra",
+      "identifier": "gt",
+      "name": "gt",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
         "name": "Comprehensive R Archive Network (CRAN)",
         "url": "https://cran.r-project.org"
       },
-      "sameAs": "https://CRAN.R-project.org/package=kableExtra"
+      "sameAs": "https://CRAN.R-project.org/package=gt"
     },
     "6": {
       "@type": "SoftwareApplication",
@@ -202,7 +202,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "328.609KB",
+  "fileSize": "328.081KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",