version 1.0.0

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.5.1
-Date: 2024-12-11 00:41:23 UTC
-SHA: 2790b9fbe5de3031f53f3c42f1892b01f7fb8c91
+Version: 1.0.0
+Date: 2025-01-15 16:23:20 UTC
+SHA: 5fa6a61c0c617060ba437ef02778d0620b8a8489

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: visOmopResults
 Title: Graphs and Tables for OMOP Results
-Version: 0.5.1
+Version: 1.0.99
 Authors@R: c(
     person(
         "Martí", "Català", , "[email protected]", 
@@ -25,7 +25,7 @@ Authors@R: c(
   )
 Maintainer: Núria Mercadé-Besora <[email protected]>
 Description: Provides methods to transform omop_result objects into
-    formatted tables and figures, facilitating the visualization of study
+    formatted tables and figures, facilitating the visualisation of study
     results working with the Observational Medical Outcomes Partnership
     (OMOP) Common Data Model.
 License: Apache License (>= 2)
@@ -36,7 +36,6 @@ Imports:
     dplyr,
     generics,
     glue,
-    lifecycle,
     omopgenerics (>= 0.3.1),
     purrr,
     rlang,
@@ -50,6 +49,7 @@ Suggests:
     gt,
     htmltools,
     knitr,
+    lifecycle,
     officer,
     palmerpenguins,
     PatientProfiles,

NAMESPACE

@@ -6,6 +6,7 @@ export(barPlot)
 export(bind)
 export(boxPlot)
 export(customiseText)
+export(emptyPlot)
 export(emptyTable)
 export(exportSummarisedResult)
 export(filterAdditional)

NEWS.md

@@ -0,0 +1,3 @@
+# visOmopResults 1.0.0
+
+* Added a `NEWS.md` file to track changes to the package.

R/customiseText.R

@@ -11,7 +11,7 @@
 #'
 #' @description
 #' This function styles character vectors or column names in a data frame.
-#' The styling function can be customized, or you can provide specific
+#' The styling function can be customised, or you can provide specific
 #' replacements for certain values.
 #'
 #' @return A character vector of styled text or a data frame with styled column

R/datatableInternal.R

@@ -1,3 +1,19 @@
+# Copyright 2025 DARWIN EU®
+#
+# This file is part of visOmopResults
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 datatableInternal <- function(x,
                               delim = "\n",
                               style = "default",

R/formatEstimateName.R

@@ -1,3 +1,19 @@
+# Copyright 2025 DARWIN EU®
+#
+# This file is part of visOmopResults
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Formats estimate_name and estimate_value column
 #'
 #' @param result A `<summarised_result>`.
@@ -68,7 +84,7 @@ formatEstimateNameInternal <- function(result, format, keepNotFormatted, useForm
   ]
 
   if (nrow(result) == 0) {
-    cli::cli_warn(c("!" = "Empty summarized results provided."))
+    cli::cli_warn(c("!" = "Empty summarised results provided."))
     return(result)
   } else {
     result <- result |>

R/formatEstimateValue.R

@@ -1,3 +1,19 @@
+# Copyright 2025 DARWIN EU®
+#
+# This file is part of visOmopResults
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Formats the estimate_value column
 #'
 #' @param result A `<summarised_result>`.

R/formatHeader.R

@@ -1,3 +1,19 @@
+# Copyright 2025 DARWIN EU®
+#
+# This file is part of visOmopResults
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Create a header for gt and flextable objects
 #'
 #' @param result A `<summarised_result>`.

R/formatTable.R

@@ -1,3 +1,19 @@
+# Copyright 2025 DARWIN EU®
+#
+# This file is part of visOmopResults
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Creates a flextable or gt object from a dataframe
 #'
 #' @param x A dataframe.

R/fxTable.R

@@ -1,3 +1,19 @@
+# Copyright 2025 DARWIN EU®
+#
+# This file is part of visOmopResults
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Creates a flextable object from a dataframe
 #'
 #' @param x A dataframe.

R/gtTable.R

@@ -1,3 +1,19 @@
+# Copyright 2025 DARWIN EU®
+#
+# This file is part of visOmopResults
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Creates a gt object from a dataframe
 #'
 #' @param x A dataframe.

R/helperFunctions.R

@@ -1,10 +1,26 @@
+# Copyright 2025 DARWIN EU®
+#
+# This file is part of visOmopResults
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Additional table formatting options for `visOmopTable()` and `visTable()`
 #'
 #' @description
 #' This function provides a list of allowed inputs for the `.option` argument in
 #' `visOmopTable()` and `visTable()`, and their corresponding default values.
 #'
-#' @return A named list of default options for table customization.
+#' @return A named list of default options for table customisation.
 #'
 #' @export
 #'
@@ -19,8 +35,6 @@ tableOptions <- function() {
 #'
 #' @param type Character string specifying the formatted table class.
 #' See `tableType()` for supported classes. Default is "gt".
-#' @param styleName A character string specifying the style name. Currently, the
-#' package supports only one predefined style: "default".
 #'
 #' @return A code expression for the selected style and table type.
 #'
@@ -30,7 +44,7 @@ tableOptions <- function() {
 #' tableStyle("gt")
 #' tableStyle("flextable")
 #'
-tableStyle <- function(type = "gt", styleName = "default") {
+tableStyle <- function(type = "gt") {
   if (type == "gt") {
     list(
       "header" = list(gt::cell_fill(color = "#c8c8c8"),

R/mockResults.R

@@ -1,3 +1,19 @@
+# Copyright 2025 DARWIN EU®
+#
+# This file is part of visOmopResults
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' A `<summarised_result>` object filled with mock data
 #' @return An object of the class `<summarised_result>` with mock data.
 #' @description Creates an object of the class `<summarised_result>` with mock data

R/plot.R

@@ -1,8 +1,21 @@
+# Copyright 2025 DARWIN EU®
+#
+# This file is part of visOmopResults
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 #' Create a scatter plot visualisation from a `<summarised_result>` object
 #'
-#' `r lifecycle::badge("experimental")`
-#'
 #' @param result A `<summarised_result>` object.
 #' @param x Column or estimate name that is used as x variable.
 #' @param y Column or estimate name that is used as y variable
@@ -69,7 +82,7 @@ scatterPlot <- function(result,
   # empty
   if (nrow(result) == 0) {
     cli::cli_warn(c("!" = "result object is empty, returning empty plot."))
-    return(ggplot2::ggplot())
+    return(emptyPlot())
   }
 
   est <- c(x, y, ymin, ymax, asCharacterFacet(facet), colour, group, label)
@@ -127,8 +140,6 @@ scatterPlot <- function(result,
 
 #' Create a box plot visualisation from a `<summarised_result>` object
 #'
-#' `r lifecycle::badge("experimental")`
-#'
 #' @param result A `<summarised_result>` object.
 #' @param x Columns to use as x axes.
 #' @param lower Estimate name for the lower quantile of the box.
@@ -177,7 +188,7 @@ boxPlot <- function(result,
   # empty
   if (nrow(result) == 0) {
     cli::cli_warn(c("!" = "result object is empty, returning empty plot."))
-    return(ggplot2::ggplot())
+    return(emptyPlot())
   }
 
   est <- c(x, lower, middle, upper, ymin, ymax, asCharacterFacet(facet), colour, label)
@@ -213,7 +224,7 @@ boxPlot <- function(result,
   yminymax <- length(ymin) > 0 & length(ymax) > 0
 
   p <- ggplot2::ggplot(data = result, mapping = aes) +
-    ggplot2::geom_boxplot(stat = "identity")
+    ggplot2::geom_boxplot(stat = "identity", position = "dodge2")
   if(length(facet) > 0){
     p <- plotFacet(p, facet)
   }
@@ -231,8 +242,6 @@ boxPlot <- function(result,
 
 #' Create a bar plot visualisation from a `<summarised_result>` object
 #'
-#' `r lifecycle::badge("experimental")`
-#'
 #' @param result A `<summarised_result>` object.
 #' @param x Column or estimate name that is used as x variable.
 #' @param y Column or estimate name that is used as y variable.
@@ -280,7 +289,7 @@ barPlot <- function(result,
   # empty
   if (nrow(result) == 0) {
     cli::cli_warn(c("!" = "result object is empty, returning empty plot."))
-    return(ggplot2::ggplot())
+    return(emptyPlot())
   }
 
   est <- c(x, y, asCharacterFacet(facet), colour, label)
@@ -326,6 +335,21 @@ barPlot <- function(result,
   return(p)
 }
 
+#' Returns an empty plot
+#'
+#' @return An empty ggplot object
+#'
+#' @export
+#'
+#' @examples
+#' emptyPlot()
+#'
+emptyPlot <- function() {
+  ggplot2::ggplot() +
+    ggplot2::theme_bw() +
+    ggplot2::labs(title = "No data to plot")
+}
+
 tidyResult <- function(result) {
   if (inherits(result, "summarised_result")) {
     result <- tidy(result) |>