Conversation
|
I have read the CLA Document and I hereby sign the CLA You can retrigger this bot by commenting recheck in this Pull Request. Posted by the CLA Assistant Lite bot. |
| # Copyright (c) 2024 Roche | ||
| # SPDX-License-Identifier: MIT | ||
|
|
||
| #' @title Simple tests for gg_lineplot functions | ||
| #' @description Basic tests that can run without full package installation | ||
|
|
||
| # Load required libraries | ||
| if (!require("ggplot2")) install.packages("ggplot2") | ||
| if (!require("dplyr")) install.packages("dplyr") | ||
| if (!require("tidyr")) install.packages("tidyr") | ||
|
|
||
| # Load the functions | ||
| source("R/gg_lineplot.R") |
| # Helper function to create test data | ||
| create_test_data <- function() { | ||
| set.seed(123) |
There was a problem hiding this comment.
I think we can avoid functions for test data and random seed generator by setting some values directly (I use gemini)
| # Test calc_stats function | ||
| #' @description Test calc_stats function | ||
| #' @param x Numeric vector | ||
| #' @param conf_level Confidence level | ||
| #' @param decimal_places Number of decimal places |
There was a problem hiding this comment.
This is very confusing here ahah
| set.seed(456) | ||
| x <- rnorm(100, mean = 10, sd = 2) |
There was a problem hiding this comment.
As above we do not need so many data points, we can directly write them w/o the seed
| # Test default parameters | ||
| result <- calc_stats(x) | ||
| expect_is(result, "list") | ||
| expect_names(result, c("n", "mean", "mean_ci", "mean_ci_lwr", "mean_ci_upr", "median", "sd")) |
There was a problem hiding this comment.
This reminds me tern... We should follow some other naming like gtsummary style
| #' @param x A numeric vector. | ||
| #' @param conf_level The confidence level for the interval (default is 0.95). | ||
| #' @param decimal_places Number of decimal places for numeric values in the table. | ||
| #' @return A list with statistics: `n`, `mean`, `mean_ci_lwr`, `mean_ci_upr`, `median`, `sd`. |
There was a problem hiding this comment.
missing descriptions with our style (list)\cr etc..
| #' @return A list with statistics: `n`, `mean`, `mean_ci_lwr`, `mean_ci_upr`, `median`, `sd`. | ||
| #' @export | ||
| #' @examples | ||
| #' set.seed(123) |
There was a problem hiding this comment.
we do not need seed as we do not test against
| #' set.seed(123) | ||
| #' x <- rnorm(100, mean = 10, sd = 2) | ||
| #' calc_stats(x, conf_level = 0.95, decimal_places = 2) | ||
| calc_stats <- function(x, conf_level = 0.95, decimal_places = 2) { |
There was a problem hiding this comment.
maybe there is out there a simple stats function that does this. We should not rely on our own (as cardx does)
| g_lineplot_with_table <- function(df_stats, | ||
| x = "AVISIT", | ||
| group_var = "ARM", | ||
| strata_N = NULL, | ||
| mid = "mean", | ||
| whiskers = c("mean_ci_lwr", "mean_ci_upr"), | ||
| table = NULL, | ||
| mid_type = "pl", | ||
| mid_point_size = 2, | ||
| position = position_dodge(width = 0.4), | ||
| legend_title = NULL, | ||
| legend_position = "bottom", | ||
| ggtheme = nestcolor::theme_nest(), | ||
| x_lab = NULL, | ||
| y_lab = NULL, | ||
| title = "Plot of Mean and 95% Confidence Limits by Visit", | ||
| subtitle = "", | ||
| caption = NULL, | ||
| table_font_size = 3, | ||
| decimal_places = 2, | ||
| errorbar_width = 0.45, | ||
| col = NULL, | ||
| linetype = NULL, | ||
| rel_height_plot = 0.5) { |
There was a problem hiding this comment.
These are way too many variables. The majority of these details are never modified, and we should keep them set before-hand. We can add options to change them quite easily afterwards if really requested
2 participants
This pull request introduces a new set of utilities for generating line plots with summary statistics and tables, along with comprehensive documentation and extensive tests. The changes add functions for preprocessing data, calculating statistics, and creating publication-ready plots and tables using ggplot2, all supported by both example-based and automated tests.
The most important changes are:
New line plot and statistics utilities:
g_lineplot_table,g_lineplot_with_table, andg_lineplot_without_tableto the package namespace, making these functions available for use.calc_stats: Calculates summary statistics (N, mean, SD, CIs, median) for a numeric vector.g_lineplot_table: Generates a ggplot-formatted table from pre-calculated statistics.g_lineplot_with_table: Combines a line plot and an optional summary table from statistics data.g_lineplot_without_table: Creates a line plot with mean and confidence intervals.preprocess_lineplot_data: Prepares data for line plots by cleaning and calculating statistics.Testing improvements:
test-gg_lineplot-simple.R) that runs basic functionality checks for all new plot and statistics functions, including data creation, function outputs, and expected columns.test-gg_lineplot.R) usingtestthatto validate all new functions, including edge cases (e.g., NA handling, custom statistics functions, confidence intervals, decimal places, and grouped/ungrouped data).These additions significantly enhance the package's capabilities for statistical line plotting and ensure reliability through robust testing.