Start 1st vignette, cleanups

.Rbuildignore

@@ -7,3 +7,5 @@
 ^data-raw$
 ^\.github$
 ^LICENSE\.md$
+^doc$
+^Meta$

.gitignore

@@ -5,3 +5,6 @@
 .DS_Store
 .quarto
 docs
+inst/doc
+/doc/
+/Meta/

DESCRIPTION

@@ -4,8 +4,10 @@ Version: 0.0.0.9002
 Authors@R: c(
     person("Maurycy", "Żarczyński", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2989-8152")),
-    person("Nicholas", "McKay", , "[email protected]", role = "aut"),
-    person("David", "Edge", , "[email protected]", role = "aut")
+    person("Nicholas", "McKay", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0003-3598-5113")),
+    person("David", "Edge", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0001-6938-2850"))
   )
 Description: A toolbox to process raw hyperspectral core scanning imaging (HSI) data. Allows normalization, filtering and visualization.
 License: MIT + file LICENSE
@@ -16,7 +18,9 @@ Suggests:
     testthat (>= 3.0.0),
     arrow,
     patchwork,
-    sf
+    sf,
+    knitr,
+    rmarkdown
 Config/testthat/edition: 3
 URL: https://github.com/mzarowka/HSItools
 BugReports: https://github.com/mzarowka/HSItools/issues
@@ -42,3 +46,4 @@ Imports:
 Depends: 
     R (>= 4.1.0)
 LazyData: true
+VignetteBuilder: knitr

R/filters.R

@@ -1,8 +1,9 @@
 #' Smooth raster with focal median
 #'
-#' @param capture a terra SpatRaster of captured data.
+#' @param raster a terra SpatRaster to smooth.
 #' @param window focal window size, default is 3.
 #' @param product logical, whether in the shiny pipeline, what type of filename should be used.
+#' @param ... further parameters such as file path.
 #'
 #' @return smoothed SpatRaster
 #' @export
@@ -28,7 +29,7 @@ filter_median <- function(raster = raster, window = 3, product = TRUE, ...){
   # Apply terra focal statistic with 3 x 3 window
   reflectance <- terra::focal(raster,
                               w = window,
-                              fun = \(x) median(x),
+                              fun = \(x) stats::median(x),
                               filename = filename,
                               overwrite = TRUE,
                               wopt = wopts)
@@ -49,6 +50,7 @@ filter_median <- function(raster = raster, window = 3, product = TRUE, ...){
 #' @param n filter length (must be odd).
 #' @param m return the m-th derivative of the filter coefficients.
 #' @param ts time scaling factor.
+#' @param ... further parameters such as file path.
 #'
 #' @return A filtered terra SpatRaster.
 #' @export

README.Rmd

@@ -18,6 +18,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/mzarowka/HSItools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mzarowka/HSItools/actions/workflows/R-CMD-check.yaml)
+
 <!-- badges: end -->
 
 HSItools is an R package to process and visualize hyperspectral core scanning data.
@@ -44,5 +45,3 @@ core <- run_core()
 ```
 
 Maurycy Żarczyński is founded by the Polish National Agency for Academic Exchange (BPN/BEK/2021/1/00133/U/0001).
-
-[![National Agency for Academic Exchange logo](images/logo-nawa-white.png)](https://nawa.gov.pl)

README.md

@@ -6,6 +6,7 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/mzarowka/HSItools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mzarowka/HSItools/actions/workflows/R-CMD-check.yaml)
+
 <!-- badges: end -->
 
 HSItools is an R package to process and visualize hyperspectral core
@@ -34,6 +35,3 @@ core <- run_core()
 
 Maurycy Żarczyński is founded by the Polish National Agency for Academic
 Exchange (BPN/BEK/2021/1/00133/U/0001).
-
-[![National Agency for Academic Exchange
-logo](images/logo-nawa-white.png)](https://nawa.gov.pl)

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R

vignettes/shiny_gui.Rmd

@@ -0,0 +1,25 @@
+---
+title: "Graphical user interface with Shiny"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Graphical user interface with Shiny}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup}
+library(HSItools)
+```
+
+## Run graphical interface
+
+```{r eval=FALSE}
+settings <- run_core()
+```