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| --- | ||
| output: github_document | ||
| --- | ||
| <!-- badges: start --> | ||
| [](https://github.com/shug0131/eudract_pkg/actions) | ||
| [](https://ci.appveyor.com/project/shug0131/eudract_pkg) | ||
| [](https://app.codecov.io/gh/shug0131/eudract_pkg?branch=master) | ||
| <!-- badges: end --> | ||
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| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
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| ```{r setup, include = FALSE} | ||
| knitr::opts_chunk$set( | ||
| collapse = TRUE, | ||
| comment = "#>", | ||
| out.width = "100%" | ||
| ) | ||
| ``` | ||
| # eudract | ||
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| The goal of eudract is to provide tools to easily produce summaries of safety data from clinical trials that can easily be uploaded into eudraCT or ClinTrials.gov . | ||
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| ## Installation | ||
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| You can install from CRAN directly with | ||
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| ```r | ||
| install.packages("eudract") | ||
| ``` | ||
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| You can install the very latest version on github with: | ||
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| ``` r | ||
| install.packages("devtools") | ||
| devtools::install_github("shug0131/eudract_pkg") | ||
| ``` | ||
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| ## Documentation | ||
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| https://eudract-tool.medschl.cam.ac.uk provides full documentation | ||
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| Go and read the help pages within R | ||
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| ```{r example} | ||
| ?eudract::safety_summary | ||
| ``` | ||
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| --- | ||
| output: github_document | ||
| --- | ||
| <!-- badges: start --> | ||
| [](https://github.com/shug0131/eudract_pkg/actions) | ||
| [](https://ci.appveyor.com/project/shug0131/eudract_pkg) | ||
| [](https://app.codecov.io/gh/shug0131/eudract_pkg?branch=master) | ||
| <!-- badges: end --> | ||
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| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
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| ```{r setup, include = FALSE} | ||
| knitr::opts_chunk$set( | ||
| collapse = TRUE, | ||
| comment = "#>", | ||
| out.width = "100%" | ||
| ) | ||
| ``` | ||
| # eudract | ||
|
|
||
| The goal of eudract is to provide tools to easily produce summaries of safety data from clinical trials that can easily be uploaded into eudraCT or ClinTrials.gov . | ||
|
|
||
| An additional feature produces commonly used tables and figures that feature in statistical reports and papers for clinical trials. | ||
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||
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||
| ## Installation | ||
|
|
||
| You can install from CRAN directly with | ||
|
|
||
| ```r | ||
| install.packages("eudract") | ||
| ``` | ||
|
|
||
|
|
||
| You can install the very latest version on github with: | ||
|
|
||
| ``` r | ||
| install.packages("devtools") | ||
| devtools::install_github("shug0131/eudract_pkg") | ||
| ``` | ||
|
|
||
| ## Documentation | ||
|
|
||
| https://eudract-tool.medschl.cam.ac.uk provides full documentation | ||
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| Go and read the help pages within R `?eudract::safety_summary` | ||
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| ```{r example, file="example/canonical.R", eval=FALSE} | ||
| ``` | ||
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| And for produce standard reporting outputs | ||
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| ```{r report_example, file="example/reporting.R"} | ||
| ``` |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,109 @@ | ||
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| <!-- badges: start --> | ||
|
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||
| [](https://github.com/shug0131/eudract_pkg/actions) | ||
| [](https://ci.appveyor.com/project/shug0131/eudract_pkg) | ||
| [](https://app.codecov.io/gh/shug0131/eudract_pkg?branch=master) | ||
| <!-- badges: end --> | ||
|
|
||
| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
|
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||
| # eudract | ||
|
|
||
| The goal of eudract is to provide tools to easily produce summaries of | ||
| safety data from clinical trials that can easily be uploaded into | ||
| eudraCT or ClinTrials.gov . | ||
|
|
||
| ## Installation | ||
|
|
||
| You can install from CRAN directly with | ||
|
|
||
| ``` r | ||
| install.packages("eudract") | ||
| ``` | ||
|
|
||
| You can install the very latest version on github with: | ||
|
|
||
| ``` r | ||
| install.packages("devtools") | ||
| devtools::install_github("shug0131/eudract_pkg") | ||
| ``` | ||
|
|
||
| ## Documentation | ||
|
|
||
| <https://eudract-tool.medschl.cam.ac.uk> provides full documentation | ||
|
|
||
| Go and read the help pages within R | ||
|
|
||
| ``` r | ||
| ?eudract::safety_summary | ||
| #> starting httpd help server ... done | ||
| ``` | ||
|
|
||
| <!-- badges: start --> | ||
|
|
||
| [](https://github.com/shug0131/eudract_pkg/actions) | ||
| [](https://ci.appveyor.com/project/shug0131/eudract_pkg) | ||
| [](https://app.codecov.io/gh/shug0131/eudract_pkg?branch=master) | ||
| <!-- badges: end --> | ||
|
|
||
| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
|
|
||
| # eudract | ||
|
|
||
| The goal of eudract is to provide tools to easily produce summaries of | ||
| safety data from clinical trials that can easily be uploaded into | ||
| eudraCT or ClinTrials.gov . | ||
|
|
||
| An additional feature produces commonly used tables and figures that | ||
| feature in statistical reports and papers for clinical trials. | ||
|
|
||
| ## Installation | ||
|
|
||
| You can install from CRAN directly with | ||
|
|
||
| ``` r | ||
| install.packages("eudract") | ||
| ``` | ||
|
|
||
| You can install the very latest version on github with: | ||
|
|
||
| ``` r | ||
| install.packages("devtools") | ||
| devtools::install_github("shug0131/eudract_pkg") | ||
| ``` | ||
|
|
||
| ## Documentation | ||
|
|
||
| <https://eudract-tool.medschl.cam.ac.uk> provides full documentation | ||
|
|
||
| Go and read the help pages within R `?eudract::safety_summary` | ||
|
|
||
| ``` r | ||
| safety_statistics <- safety_summary(safety, | ||
| exposed=c("Experimental"=60,"Control"=67)) | ||
| simple <- tempfile(fileext = ".xml") | ||
| eudract <- tempfile(fileext = ".xml") | ||
| ct <- tempfile(fileext = ".xml") | ||
| simple_safety_xml(safety_statistics, simple) | ||
| eudract_convert(input=simple, | ||
| output=eudract) | ||
| clintrials_gov_convert(input=simple, | ||
| original=system.file("extdata", "1234.xml", package ="eudract"), | ||
| output=ct) | ||
| \dontrun{ | ||
| # This needs a real user account to work | ||
| clintrials_gov_upload( | ||
| input=simple, | ||
| orgname="CTU", | ||
| username="Student", | ||
| password="Guinness", | ||
| studyid="1234" | ||
| ) | ||
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| } | ||
| ``` | ||
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| And for produce standard reporting outputs | ||
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| ``` r | ||
| library(eudract) | ||
| safety_statistics <- safety_summary(safety, | ||
| exposed=c("Control"=99, "Experimental"=101)) | ||
| safety_statistics$GROUP | ||
| #> title subjectsAffectedBySeriousAdverseEvents | ||
| #> 1 Control 15 | ||
| #> 2 Experimental 33 | ||
| #> subjectsAffectedByNonSeriousAdverseEvents deathsResultingFromAdverseEvents | ||
| #> 1 15 9 | ||
| #> 2 24 22 | ||
| #> subjectsExposed deathsAllCauses | ||
| #> 1 99 9 | ||
| #> 2 101 22 | ||
| head( incidence_table(safety_statistics, type="serious") ) | ||
| #> System Organ Class Preferred Term | ||
| #> 1 Blood and lymphatic system disorders B-cell lymphoma | ||
| #> 2 Cardiac disorders Cardiac arrest | ||
| #> 3 Cardiac failure congestive | ||
| #> 4 Gastrointestinal disorders Abdominal pain | ||
| #> 5 Gastroenteritis viral | ||
| #> 6 Gastrointestinal haemorrhage | ||
| #> Control (N = 99) Experimental (N = 101) | ||
| #> 1 1% (1, 1) 0% (0, 0) | ||
| #> 2 1% (1, 1) 0% (0, 0) | ||
| #> 3 0% (0, 0) 1% (1, 1) | ||
| #> 4 1% (1, 1) 0% (0, 0) | ||
| #> 5 0% (0, 0) 1% (1, 1) | ||
| #> 6 0% (0, 0) 1% (1, 1) | ||
| relative_risk_table(safety_statistics, type="serious") | ||
| #> System Organ Class Preferred Term Relative Risk (C.I.) | ||
| #> 1 Hepatobiliary disorders Cholecystitis acute 0.98 (0.0605, 15.9) | ||
| #> 2 Immune system disorders Vasculitis 1.96 (0.175, 22) | ||
| #> 3 Surgical and medical procedures Hip arthroplasty 1.96 (0.175, 22) | ||
| #> 4 Vascular disorders Deep vein thrombosis 2.94 (0.301, 28.8) | ||
| #> 5 Pulmonary embolism 0.98 (0.0605, 15.9) | ||
| dot_plot(safety_statistics, type="serious", base=4) | ||
| ``` | ||
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| <img src="README_files/figure-gfm/report_example-1.png" width="100%" /> |
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| library(eudract) | ||
| safety_statistics <- safety_summary(safety, | ||
| exposed=c("Control"=99, "Experimental"=101)) | ||
| safety_statistics$GROUP | ||
| head( incidence_table(safety_statistics, type="serious") ) | ||
| relative_risk_table(safety_statistics, type="serious") | ||
| dot_plot(safety_statistics, type="serious", base=4) |
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| --- | ||
| title: "Standard tables and figures" | ||
| output: rmarkdown::html_vignette | ||
| vignette: > | ||
| %\VignetteIndexEntry{standard_reporting} | ||
| %\VignetteEncoding{UTF-8} | ||
| %\VignetteEngine{knitr::rmarkdown} | ||
| editor_options: | ||
| chunk_output_type: console | ||
| --- | ||
|
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| ```{r, include = FALSE} | ||
| knitr::opts_chunk$set( | ||
| collapse = TRUE, | ||
| comment = "#>" | ||
| ) | ||
| ``` | ||
|
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| ```{r setup} | ||
| library(eudract) | ||
| library(knitr) | ||
| ``` | ||
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| We can easily produce some of the standard reports needed for most clinical trials, as well | ||
| as producing the xml files needed to upload to EudraCT or ClinicalTrials.gov. See the [other vignette](eudract.html) | ||
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| We first ensure the data is in the correct format, column names to produce a basic safety object | ||
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| ```{r safety} | ||
| head(safety) | ||
| safety_statistics <- safety_summary(safety,exposed=c("Control"=99, "Experimental"=101)) | ||
| ``` | ||
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| A top level table is the `$GROUP` data frame with slightly improved column names | ||
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| ```{r group} | ||
| df <- safety_statistics$GROUP | ||
| names(df) <- c("Arm", "SAE count", "Non Serious AE count", "Death from AE count", "N", "All cause deaths count") | ||
| kable(df, caption = "Total Adverse Events") | ||
| ``` | ||
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| Next we provide an incidence table | ||
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| ```{r incidence} | ||
| incidence <- incidence_table(safety_statistics, type ="serious") | ||
| kable(incidence, caption="SAE incidence") | ||
| incidence <- incidence_table(safety_statistics, type ="non_serious") | ||
| kable(incidence, caption="Non-serious AE incidence") | ||
| ``` | ||
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| A table of relative risk can be given | ||
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| ```{r relative_risk} | ||
| rr <- relative_risk_table(safety_statistics, type="serious") | ||
| kable(rr, caption="SAE relative risks") | ||
| rr <- relative_risk_table(safety_statistics, type="non_serious") | ||
| kable(rr, caption="Non-serious AE relative risks") | ||
| ``` | ||
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| Finally a set of dot-plots to show graphically and compare, using functions from [patchwork](https://patchwork.data-imaginist.com/) to add titles | ||
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| ```{r dotplot_sae, fig.cap="SAE", fig.height=8, fig.width=8, out.width="90%"} | ||
| dot_plot(safety_statistics, type="serious", base=4) | ||
| ``` | ||
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| ```{r dotplot_ae, fig.cap="Non-Serious AE", fig.height=8, fig.width=8, out.width="90%"} | ||
| dot_plot(safety_statistics, type="non_serious", base=4) | ||
| ``` | ||
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| If you want to modify, then access the two elements `$left.panel` and `$right.panel` to modify as standard `ggplot` objects. The `print` and `plot` methods glue them back together within the framework of the [patchwork](https://patchwork.data-imaginist.com/) package. Or you can dissect, edit, save, and use however you want. | ||
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| ```{r dotplot_edit, fig.height=8, fig.width=8, out.width="90%"} | ||
| fig <- dot_plot(safety_statistics, type="non_serious", base=4) | ||
| fig$left.panel <- fig$left.panel + ggplot2::labs(title="Absolute Risk") | ||
| fig | ||
| ``` | ||
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| Should you wish to save to a file, then using the workflow below will work, using a graphics device such as, `png`, `jpeg`, `pdf`, `svg`. You will need to explicitly call the `print(fig)` function, and just `fig` on its own may not work. | ||
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| ```{r dotplot_save, eval=FALSE} | ||
| temp <- tempfile(fileext=".png") | ||
| png(filename = temp) | ||
| print(fig) | ||
| dev.off() | ||
| ``` | ||
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| Further filtering and refinements to the labels may be provided using the `relative_risk` and `order_filter` functions. See help pages for more details. | ||
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