From 245483e41ca0b9853b672ec05e596ee2c794669f Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Fri, 7 Mar 2025 23:01:25 +0100 Subject: [PATCH] (v2.1.1.9188) fix antibiogram plot --- DESCRIPTION | 2 +- NEWS.md | 2 +- PythonPackage/AMR/AMR.egg-info/PKG-INFO | 2 +- PythonPackage/AMR/dist/amr-2.1.1.9187.tar.gz | Bin 10098 -> 0 bytes ...ny.whl => amr-2.1.1.9188-py3-none-any.whl} | Bin 10282 -> 10281 bytes PythonPackage/AMR/dist/amr-2.1.1.9188.tar.gz | Bin 0 -> 10087 bytes PythonPackage/AMR/setup.py | 2 +- R/antibiogram.R | 46 ++++++++++++------ ....txt => gpt_training_text_v2.1.1.9188.txt} | 2 +- tests/testthat/test-antibiogram.R | 2 + 10 files changed, 39 insertions(+), 19 deletions(-) delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9187.tar.gz rename PythonPackage/AMR/dist/{amr-2.1.1.9187-py3-none-any.whl => amr-2.1.1.9188-py3-none-any.whl} (52%) create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9188.tar.gz rename data-raw/{gpt_training_text_v2.1.1.9187.txt => gpt_training_text_v2.1.1.9188.txt} (99%) diff --git a/DESCRIPTION b/DESCRIPTION index 5c98dfcad..ebd6c8f5e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9187 +Version: 2.1.1.9188 Date: 2025-03-07 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 46a72496a..5382df1de 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9187 +# AMR 2.1.1.9188 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)* diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index 6ffb36834..a6cae88a7 100644 --- a/PythonPackage/AMR/AMR.egg-info/PKG-INFO +++ b/PythonPackage/AMR/AMR.egg-info/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 2.2 Name: AMR -Version: 2.1.1.9187 +Version: 2.1.1.9188 Summary: A Python wrapper for the AMR R package Home-page: https://github.com/msberends/AMR Author: Matthijs Berends diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9187.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9187.tar.gz deleted file mode 100644 index c99d56927ac0272cf24596313ee713f97a10e37e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 10098 zcmch7RZtv2(=G1qzBs{x27-h|LeO9#xVyXC;_gleP9OxA4eoBi-4_k+i|+pUzWN{T z(|xq$mukj` zf4^5vOzP5s1L=}>yVD+=o$D44v0p*FbhNjF(V9uLo_~bIY*J2KapYaMJcn0b;!r9n1@*7^Z z8eW$?59-vG+Bc7H?%<;~nr86l;m%Q$YIssq=M_^mH2D=y4TcMBfx$Hj(nQm|)7fXO zK|g2o&HTw0bhq`GOQr0^awc)MJYPjzbxg7d3DHlniBu@-$D(ntJ^s*VO5Cxx-Wwc* zWB%oGi%)J<(c0D&<{}!oMz&LD@(9GlJUC+L#AOl0tFOR86|khxN<67@pq!YFk|O6! 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prepare for definitive output out <- out_wisca wisca_parameters <- wisca_parameters[, colnames(wisca_parameters)[!colnames(wisca_parameters) %in% c(levels(NA_sir_), "lower_ci", "upper_ci", "group")], drop = FALSE] + if (isTRUE(has_syndromic_group)) { + long_numeric <- out_wisca %pm>% + pm_ungroup() %pm>% + pm_select( + syndromic_group = syndromic_group, + ab = ab, + coverage = coverage, + lower_ci = lower_ci, + upper_ci = upper_ci, + n_total = n_total, + n_tested = n_tested, + n_susceptible = n_susceptible + ) + } else { + long_numeric <- out_wisca %pm>% + pm_ungroup() %pm>% + pm_select( + ab = ab, + coverage = coverage, + lower_ci = lower_ci, + upper_ci = upper_ci, + n_total = n_total, + n_tested = n_tested, + n_susceptible = n_susceptible + ) + } } out$digits <- digits # since pm_sumarise() cannot work with an object outside the current frame @@ -1170,9 +1196,7 @@ tbl_format_footer.antibiogram <- function(x, ...) { plot.antibiogram <- function(x, ...) { df <- attributes(x)$long_numeric if (!"mo" %in% colnames(df)) { - stop_("Plotting antibiograms using `plot()` is only possible if they were not created using dplyr groups. See `?antibiogram` for how to retrieve numeric values in a long format for advanced plotting.", - call = FALSE - ) + df$mo <- "" } if ("syndromic_group" %in% colnames(df)) { # barplot in base R does not support facets - paste columns together @@ -1226,9 +1250,7 @@ barplot.antibiogram <- function(height, ...) { autoplot.antibiogram <- function(object, ...) { df <- attributes(object)$long_numeric if (!"mo" %in% colnames(df)) { - stop_("Plotting antibiograms using `autoplot()` is only possible if they were not created using dplyr groups. See `?antibiogram` for how to retrieve numeric values in a long format for advanced plotting.", - call = FALSE - ) + df$mo <- "" } out <- ggplot2::ggplot(df, mapping = ggplot2::aes( @@ -1243,6 +1265,10 @@ autoplot.antibiogram <- function(object, ...) { ) + ggplot2::geom_col(position = ggplot2::position_dodge2(preserve = "single")) + ggplot2::facet_wrap("mo") + + ggplot2::geom_errorbar( + mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100), + position = ggplot2::position_dodge2(preserve = "single", width = 1) + ) + ggplot2::labs( y = ifelse(isTRUE(attributes(object)$combine_SI), "%SI", "%S"), x = NULL, @@ -1252,14 +1278,6 @@ autoplot.antibiogram <- function(object, ...) { NULL } ) - if (isTRUE(attributes(object)$wisca)) { - out <- out + - ggplot2::geom_errorbar( - mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100), - position = ggplot2::position_dodge2(preserve = "single"), - width = 0.5 - ) - } out } diff --git a/data-raw/gpt_training_text_v2.1.1.9187.txt b/data-raw/gpt_training_text_v2.1.1.9188.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9187.txt rename to data-raw/gpt_training_text_v2.1.1.9188.txt index e7b496041..70300339f 100644 --- a/data-raw/gpt_training_text_v2.1.1.9187.txt +++ b/data-raw/gpt_training_text_v2.1.1.9188.txt @@ -1,6 +1,6 @@ This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse. -First and foremost, you are trained on version 2.1.1.9187. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9188. Remember this whenever someone asks which AMR package version you’re at. Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens. ---------------------------------------------------------------------------------------------------- diff --git a/tests/testthat/test-antibiogram.R b/tests/testthat/test-antibiogram.R index 09adef1f0..16a828992 100644 --- a/tests/testthat/test-antibiogram.R +++ b/tests/testthat/test-antibiogram.R @@ -113,6 +113,8 @@ test_that("antibiogram works", { )) expect_inherits(ab8, "antibiogram") + expect_inherits(retrieve_wisca_parameters(ab8), "data.frame") + expect_inherits(attributes(ab8)$long_numeric, "data.frame") expect_equal(colnames(ab8), c("Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin")) # grouped tibbles