I had been running a shiny app in which I could halt a long-running process. The process would update the shiny app and constantly looked for an updated shiny variable to inform if a cancel button had been pressed. The code had been adapted from a SO post at …

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After our IT colleagues updated R to version 3.5.0 I found that I have many packages duplicated between the system library and my user library. This short piece of code lists all packages with their version for all libraries. It helps identify those that can be removed from the user library or updated. 1## assess user …

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Redmine is a great tool for tracking project progress and bugs. With a little configuration it can integrate git repositories and integrate with R program / package development. The following assumes that Redmine, R and RStudio server are all configured and working. Linking a repository to Redmine Without changing file …

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There are many reasons why data analysis should be performed using a language such as R or python over Excel but I'm constantly fighting with colleagues who refuse to adapt. Here are five reasons to stop using Excel: Reproducibility It's very challenging to use what's been done before with a spreadsheet. You can make …

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The datatable widget is a powerful table-building tool used to display data in shiny apps. It can use many of the datatable plugins and extensions but a small javascript hack is needed for the rowReorder extension which allows rows to be reordered using drag and drop. In the example below, the rowReorder options are …

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Plotly is a great plotting library that I've started to use extensively in part due to the ease in connecting graphs together under R. There is, however, a bug when using error bars in conjunction with a group variable - error bars are not drawn in the correct order. This can be fixed with a hack by adding each group …

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Using RMarkdown with knitr is a great way of automating reports under R and I've used this approach extensively in shiny apps. For one particular project we're storing raw data in a SQL database and processing on the fly under shiny. Results are displayed using heatmaps and graphs. We're now considering pushing data …

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The KEGG (Kyoto Encyclopedia of Genes and Genomes) database is a useful reference of biochemical pathways often employed in metabolomics and proteomics studies. Various tables from the database can be downloaded in flat file format via ftp (ftp://ftp.pathway.jp/kegg). In addition, xml files containing information on …

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Connecting R to a SQL Server can be achieved using the RODBC or RJDBC libraries. Under CentOS this is a little more challenging than Windows and is generally achieved by installing the freeTDS ODBC driver and using the RODBC library. I found compilation a little difficult under CentOS 5.7 and so I moved on to JDBC …

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Introduction I’m a big fan of the R packages in the tidyverse and dplyr in particular for performing routine data analysis. I'm currently working on a project that requires fitting dose-repsonse curves to data. All works well when the amount of data is small but as the dataset grows so does the computational time. …

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