Chat with Large Language Models
Chat with large language models from a range of providers including Claude, OpenAI, Azure, Bedrock, and Google Gemini. Supports streaming,a asyncronous calls, tool calling, and structured data extraction.
AI
Making Tables Shiny: DT, formattable, and reactable
Demo of popular packages for generating interactive tables suitable for Shiny apps
formattable
Another nice table-making package is formattable.
The cute heatmap-style colour formatting and the easy-to-use formatter functions make formattable very appealing.
color_tile() fills the cells with a colour gradient corresponding to the values
color_bar() adds a colour bar to each cell, where the length is proportional to the value
The true_false_formatter() defined below demonstrates how to define your own formatting function, in this case formatting TRUE, FALSE and NA as green, red and black.
If you want the features of both DT and formattable, you can combine them by converting the formattable() output to as.datatable(), and much of the formattable features will be preserved.
However, one problem I had was that when using DT::datatable, missing values (NA) are left blank in the display (which I prefer), but in the converted from formattable() version, NA’s are printed. Also, color_bar columns seem to be converted to character, which can no longer be sorted numerically.
reactable
Next I tried reactable, a package based on the React Table library.
Columns are customised via the columns argument, which takes a named list of column definitions defined using colDef(). These include format definitions created using colFormat.
In the end, I used DT::datatable() in my Shiny app, because I found it the easiest, fastest, and most comprehensive. I’ve been able to achieve most of the features I wanted using just DT.
Heatmap-like fill effect:
apply the formatStyle() function to the output of datatable() to set the backgroundColor for selected columns:
Abbreviate long cells
Sometimes some cells have a large amount of text that would mess up the table layout if I showed it all. In these cases, I like to abbreviate long values and show the full text in a tooltip.
To do this, you can use JavaScript to format the column to show a substring with “…” and the full string in a tooltip (<span title="Long string">Substring...</span) when values are longer than N characters (in this case 10 characters). You can do this using columnDefs and pass JavaScript with the JS() function:
Really plain table
Sometimes I don’t need any of the faff. Here’s how to get rid of it all:
headerCallbackRemoveHeaderFooter <- c( "function(thead, data, start, end, display){", " $('th', thead).css('display', 'none');", "}" )
datatable( my_pic_villagers, options = list( dom = "t", ordering = FALSE, paging = FALSE, searching = FALSE, headerCallback = JS(headerCallbackRemoveHeaderFooter) ), selection = 'none', callback = JS( "$('table.dataTable.no-footer').css('border-bottom', 'none');" ), class = 'row-border', escape = FALSE, rownames = FALSE, filter = "none", width = 500 )
R - Shiny
Some of the more useful Tidyverse functions
R functions for every data engineer using Tidyverse Tidyverse has long been an amazing collection of R packages, primarily for data engineering and data science. Common among these packages is the …
R#r#tidyverse#data-science#data-engineering#r-programming#data-analysis#data-manipulation#r-language#r-tips#r-package
UNCHARTED DATA: Interactive Tooltip Tables
How to include tables in your {ggiraph} tooltips.
UNCHARTED DATA: Introducing the {reactablefmtr} Package
An R package created to make the styling and customization of {reactable} tables easier.
UNCHARTED DATA: Using Crosstalk to Add User-Interactivity
Linking an interactive plot and table together with the crosstalk package.
Using Crosstalk to Add User-Interactivity
The goal is to link the reactable table I created to a plotly chart and provide additional filter options that control both the table and the chart.
An important note: in order to use crosstalk, you must create a shared dataset and call that dataset within both plotly and reactable. Otherwise, your dataset will not communicate and filter with eachother. The code to do this is SharedData$new(dataset).
If you expand the code below, you’ll see that the code to build a table in reactable is quite extensive. I will not go into the details in this post, but do recommend a couple great tutorials that I used to create the interactive table such as this tutorial from Greg Lin, and this from Tom Mock which really helped me understand how to use CSS and Google fonts to enhance the visual appeal of the table (see the “Additional CSS Used for Table” section below for more info).
If you have ever built something in Shiny before, you’ll notice that the crosstalk filters are very similar. You can add a filter to any existing column in the dataset. As you can see in the code below, I used a mixture of filter_checkbox and filter_select depending on how many unique options were available in the column you’re filtering. My rule of thumb is if there are more than five options to choose from it’s probably better to put them into a list in filter_select like I did with the Division filtering as to not take up too much space on the page.
For the layout of the data visualization, I used bscols to place the crosstalk filters side-by-side with the interactive plotly chart.
I then placed the reactable table underneath and added a legend to the table using tags from the htmltools package.
The final result is shown below. Feel free to click around and the filters and you will notice that both the plot and the table will filter accordingly. Another option is to drag and click on the plot and you will see the table underneath mimic the teams shown.
Design Patterns in R
Build robust and maintainable software with object-oriented design patterns in R. Design patterns abstract and present in neat, well-defined components and interfaces the experience of many software designers and architects over many years of solving similar problems. These are solutions that have withstood the test of time with respect to re-usability, flexibility, and maintainability. R6P provides abstract base classes with examples for a few known design patterns. The patterns were selected by their applicability to analytic projects in R. Using these patterns in R projects have proven effective in dealing with the complexity that data-driven applications possess.
R#r-development#design-patterns#r#software-architecture#object-oriented-programming#r-package#r-package-devt#api#r-api-devtreactable: Column group definitions — colGroup
Use colGroup() to create column groups in a table.
Welcome and Getting Started – Next Generation Shiny Apps with {bslib}
Welcome to the workshop and hello, bslib!
Fast JSON, NDJSON and GeoJSON Parser and Generator
A fast JSON parser, generator and validator which converts JSON, NDJSON (Newline Delimited JSON) and GeoJSON (Geographic JSON) data to/from R objects. The standard R data types are supported (e.g. logical, numeric, integer) with configurable handling of NULL and NA values. Data frames, atomic vectors and lists are all supported as data containers translated to/from JSON. GeoJSON data is read in as simple features objects. This implementation wraps the yyjson C library which is available from .
Getting started with shinytest2
Prompt and empower your LLM, the tidy way
The tidyprompt package allows users to prompt and empower their large language models (LLMs) in a tidy way. It provides a framework to construct LLM prompts using tidyverse-inspired piping syntax, with a library of pre-built prompt wrappers and the option to build custom ones. Additionally, it supports structured LLM output extraction and validation, with automatic feedback and retries if necessary. Moreover, it enables specific LLM reasoning modes, autonomous R function calling for LLMs, and compatibility with any LLM provider.
REST API in R with plumber
API and R Nowadays, it’s pretty much expected that software comes with an HTTP API interface. Every programming language out there offers a way to expose APIs or make GET/POST/PUT requests, including R. In this post, I’ll show you how to create an API using the plumber package. Plus, I’ll give you tips on how to make it more production ready - I’ll tackle scalability, statelessness, caching, and load balancing. You’ll even see how to consume your API with other tools like python, curl, and the R own httr package.
Nowadays, it’s pretty much expected that software comes with an HTTP API interface. Every programming language out there offers a way to expose APIs or make GET/POST/PUT requests, including R. In this post, I’ll show you how to create an API using the plumber package. Plus, I’ll give you tips on how to make it more production ready - I’ll tackle scalability, statelessness, caching, and load balancing. You’ll even see how to consume your API with other tools like python, curl, and the R own httr package
# When an API is started it might take some time to initialize # this function stops the main execution and wait until # plumber API is ready to take queries. wait_for_api <- function(log_path, timeout = 60, check_every = 1) { times <- timeout / check_every for(i in seq_len(times)) { Sys.sleep(check_every) if(any(grepl(readLines(log_path), pattern = "Running plumber API"))) { return(invisible()) } } stop("Waiting timed!") }
Oh, in some examples I am using redis. So, before you dive in, make sure to fire up a simple redis server. At the end of the script, I’ll be turning redis off, so you don’t want to be using it for anything else at the same time. I just want to remind you that this code isn’t meant to be run on a production server.
redis is launched in a background, , so you might want to wait a little bit to make sure it’s fully up and running before moving on.
wait_for_redis <- function(timeout = 60, check_every = 1) { times <- timeout / check_every for(i in seq_len(times)) { Sys.sleep(check_every) status <- suppressWarnings(system2("redis-cli", "PING", stdout = TRUE, stderr = TRUE) == "PONG") if(status) { return(invisible()) } } stop("Redis waiting timed!") }
First off, let’s talk about logging. I try to log as much as possible, especially in critical areas like database accesses, and interactions with other systems. This way, if there’s an issue in the future (and trust me, there will be), I should be able to diagnose the problem just by looking at the logs alone. Logging is like “print debugging” (putting print(“I am here”), print(“I am here 2”) everywhere), but done ahead of time. I always try to think about what information might be needed to make a correct diagnosis, so logging variable values is a must. The logger and glue packages are your best friends in that area.
Next, it might also be useful to add a unique request identifier ((I am doing that in setuuid filter)) to be able to track it across the whole pipeline (since a single request might be passed across many functions). You might also want to add some other identifiers, such as MACHINE_ID - your API might be deployed on many machines, so it could be helpful for diagnosing if the problem is associated with a specific instance or if it’s a global issue.
In general you shouldn’t worry too much about the size of the logs. Even if you generate ~10KB per request, it will take 100000 requests to generate 1GB. And for the plumber API, 100000 requests generated in a short time is A LOT. In such scenario you should look into other languages. And if you have that many requests, you probably have a budget for storing those logs:)
It might also be a good idea to setup some automatic system to monitor those logs (e.g. Amazon CloudWatch if you are on AWS). In my example I would definitely monitor Error when reading key from cache string. That would give me an indication of any ongoing problems with API cache.
Speaking of cache, you might use it to save a lot of resources. Caching is a very broad topic with many pitfalls (what to cache, stale cache, etc) so I won’t spend too much time on it, but you might want to read at least a little bit about it. In my example, I am using redis key-value store, which allows me to save the result for a given request, and if there is another requests that asks for the same data, I can read it from redis much faster.
Note that you could use memoise package to achieve similar thing using R only. However, redis might be useful when you are using multiple workers. Then, one cached request becomes available for all other R processes. But if you need to deploy just one process, memoise is fine, and it does not introduce another dependency - which is always a plus.
info <- function(req, ...) { do.call( log_info, c( list("MachineId: {MACHINE_ID}, ReqId: {req$request_id}"), list(...), .sep = ", " ), envir = parent.frame(1) ) }
#* Log some information about the incoming request #* https://www.rplumber.io/articles/routing-and-input.html - this is a must read! #* @filter setuuid function(req) { req$request_id <- UUIDgenerate(n = 1) plumber::forward() }
#* Log some information about the incoming request #* @filter logger function(req) { if(!grepl(req$PATH_INFO, pattern = "PATH_INFO")) { info( req, "REQUEST_METHOD: {req$REQUEST_METHOD}", "PATH_INFO: {req$PATH_INFO}", "HTTP_USER_AGENT: {req$HTTP_USER_AGENT}", "REMOTE_ADDR: {req$REMOTE_ADDR}" ) } plumber::forward() }
To run the API in background, one additional file is needed. Here I am creating it using a simple bash script.
library(plumber) library(optparse) library(uuid) library(logger) MACHINE_ID <- "MAIN_1" PORT_NUMBER <- 8761 log_level(logger::TRACE) pr("tmp/api_v1.R") %>% pr_run(port = PORT_NUMBER)
React
Draft for adding OAuth support to shiny by thohan88 · Pull Request #518 · r-lib/httr2
Info: This is a draft for discussion purposes. It's not a polished PR and currently includes minimal error handling and documentation. It may be big enough to warrant a separate package, bu...
Roxygen R6 Guide
mlr3: Machine Learning in R - next generation. Contribute to mlr-org/mlr3 development by creating an account on GitHub.
RMarkdowncolearendt/tidyjson: Tidy your JSON data in R with tidyjson
Tidy your JSON data in R with tidyjson.
mgirlich/jsontools: Helpers to work with JSON in R
Helpers to work with JSON in R.
AddinsR: Enter into a specific object and discard all other JSON data
Create a table of shiny inputs
Create an interactive table of Shiny inputs by providing data and a table definition.
R - APIsgexijin/RTutor: Chat with your data via AI. https://RTutor.ai
Chat with your data via AI. https://RTutor.ai.
Shiny
Shiny is a package that makes it easy to create interactive web apps using R and Python.
Shiny was designed with an emphasis on distinct input and output components in the UI. Inputs send values from the client to the server, and when the server has values for the client to display, they are received and rendered by outputs.
You want the server to trigger logic on the client that doesn’t naturally relate to any single output.
You want the server to update a specific (custom) output on the client, but not by totally invalidating the output and replacing the value, just making a targeted modification.
You have some client JavaScript that isn’t related to any particular input, yet wants to trigger some behavior in R. For example, binding keyboard shortcuts on the web page to R functions on the server, or alerting R when the size of the browser window has changed.
agnostic, idiomatic data filter module for shiny
a small data filter module for shiny.
R - JSON Files
R - JSON Files - JSON file stores data as text in human-readable format. Json stands for JavaScript Object Notation. R can read JSON files using the rjson package.
R Development Guide
A guide to R development.
R#r-development#r#r-package#github#r-package-devt#development#r-project#r-devguide#contributor-guideAutomatic Codebooks from Metadata Encoded in Dataset Attributes
Easily automate the following tasks to describe data frames: Summarise the distributions, and labelled missings of variables graphically and using descriptive statistics. For surveys, compute and summarise reliabilities (internal consistencies, retest, multilevel) for psychological scales. Combine this information with metadata (such as item labels and labelled values) that is derived from R attributes. To do so, the package relies on rmarkdown partials, so you can generate HTML, PDF, and Word documents. Codebooks are also available as tables (CSV, Excel, etc.) and in JSON-LD, so that search engines can find your data and index the metadata. The metadata are also available at your fingertips via RStudio Addins.
dreamRs/shinypop: Collection of notifications, confirm dialogs and alerts for 'Shiny' applications
Collection of notifications, confirm dialogs and alerts for 'Shiny' applications - dreamRs/shinypop