JustinCally

@JustinCally·7 public vizzes

Bioregions + Dingo/Dog Records (public)

This visualization overlays recent Dingo and Dingo/Dog (feral) records from the Victorian Biodiversity Atlas onto selected bioregions in eastern Victoria. It shows the spatial distribution of species observations against bioregion boundaries. The map uses the `VicmapR` package to query and collect spatial data from the Victorian government’s open-data platform, filtering records to those since 2010 and combining high and low spatial accuracy datasets. Bioregions are styled by their code via `mapview`, which renders the interactive map, while dingo records are drawn as white points over the colored regions.

Jan 31, 2024

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Example to Access VBA Data through VicmapR

This example displays koala and Manna Gum sightings across Victoria, using high- and low-spatial-accuracy records from the Victorian Biodiversity Atlas (VBA) via the `VicmapR` package. The map shows species distributions colored by common name, integrating data from the `vba_fauna25`, `vba_fauna100`, `vba_flora25`, and `vba_flora100` layers for observations since 1990. The code queries these layers with `vicmap_query()`, filters records by species and year, then binds the results and renders an interactive map using `mapview`.

Nov 14, 2023

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Plots in Tables

This example demonstrates how to embed small, arrow-based line charts directly within the cells of a LaTeX table, creating an integrated display of data and its visual summary. The R code uses `ggplot2` to generate four separate horizontal arrow segments (each representing a different x-range on a common scale), saving each as a PNG file with `ggsave`. The `dplyr` and `kableExtra` libraries then build a table where the second column contains LaTeX `\includegraphics` commands, referencing those saved images. The `kbl` function formats the table with `escape = F` to allow the raw LaTeX code, and `column_spec` sets the plot column's width. Overall, it shows a workflow for combining statistical graphics and tabular text in a single rendered document.

May 28, 2021

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rolling_join

This example demonstrates a self-referencing rolling join that repeatedly chains a dataset to itself through linked ID columns until no further matches remain. The `rolling_join` function takes an initial table and a lookup table, then iteratively joins the current result to the lookup using `dplyr::left_join`, renaming the target columns at each step to create a new hierarchy level. The loop continues while new matches are found, producing a flattened table that traces the full ancestry or downstream relationships from the starting IDs. The code uses base R for column renaming and the `dplyr` package for the join operations.

Jan 16, 2020

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Selectively colouring cells in gt::gt()

This example uses the R package `gt()` to display a data table where individual cells are selectively colored grey, and then a second table where cells are filled with colors from a predefined palette based on a comparison. The code first identifies cells containing "<" characters using `grepl` and applies a uniform grey fill via `tab_style` and `cell_fill`. A more complex workflow melts data frames with `data.table::melt`, merges them with guideline thresholds, and determines which numeric results exceed those thresholds, assigning a color from `RColorBrewer` to each qualifying cell. The `mapply` function iterates over row and column indices to apply the styling individually, producing a table where colored cells highlight values that meet specific criteria. The data is created inline as sample data frames, and the rendering approach relies on the `gt` package's HTML table output.

Jan 7, 2020

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Function for Calculating the Achievable Benchmark of Care aspirational target; which is based on an adjusted performance fraction. The Achievable Benchmark of Care Approach estimates the benchmark based on the top performing records (e.g. clinicians, hospitals) that account for 10% of patients in the data.

This example demonstrates how a dplyr workflow can compute the Achievable Benchmark of Care (ABC), an aspirational quality target derived from the top-performing clinicians or hospitals that together cover at least 10% of patients. The ABCBenchmark function uses an adjusted performance fraction to rank records, then calculates cumulative totals and applies a minimum-contribution filter to select the benchmark group. It supports optional grouping by site or region and returns the benchmark as a new column. The code relies on the dplyr and rlang packages for tidy evaluation and piping.

Aug 26, 2019

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Function for assigning a date to a bi-annual period: Useful when needing to group dates into a period for time-series visualisation

This visualization example demonstrates a utility function for converting individual dates into bi-annual period groupings, a preprocessing step for time-series analysis. The function uses `lubridate`'s `dmy`, `year`, and `floor_date` functions to compare each input date against two fixed cutpoints (June 30th and December 31st), then returns the first day of the month for the appropriate six-month period. Dates falling after the second cutpoint are assigned to the following year’s first period, ensuring all data maps to a two-category annual cycle. The code explicitly handles year boundaries through conditional `ifelse` logic.

Aug 19, 2019