README.Rmd

---
output: github_document
---

<!-- badges: start -->
[![tic](https://github.com/fridleylab/spatialTIME/workflows/tic/badge.svg?branch=master)](https://github.com/fridleylab/spatialTIME/actions)
<!-- badges: end -->

```{r setup, include=FALSE}
knitr::opts_chunk$set(
  echo = FALSE,
  collapse = TRUE,
  # fig.path = "man/figures/README-",
  out.width = "100%"
  )

library(spatialTIME)
```

# spatialTIME <img src="man/hex_sticker/hex.png" align="right" height="139" />

<!-- badges: start -->
<!-- badges: end -->

The goal of `spatialTIME` is to perform basic analysis and plotting of IF data from Vectra.

## Installation

You can install `spatialTIME` from GitHub with: 

```r
# install.packages("devtools")
devtools::install_github("fridleylab/spatialTIME")
```

<!--- add CRAN once up and running --->

## Usage 

`spatialTIME` currently implements both univariate and bi-variate Ripley's K
analyses. The basis of the `spatialTIME` functions is the creation of the 
`mif` object. 

```{r, create_example_mif, echo = TRUE}

x <- create_mif(clinical_data = example_clinical,
                sample_data = example_summary,
                spatial_list = example_spatial,
                patient_id = "deidentified_id", sample_id = "deidentified_sample",
                clean_columns = TRUE)
x

```

## Additional resources 

For a more in-depth description of the methods used, please see the included vignette.  

For a point-and-click resource that performs related analyses please check out
[iTIME](https://fridleylab.shinyapps.io/iTIME/).