add required stuff around vignettes via usethis

.Rbuildignore

@@ -11,4 +11,4 @@
 .github
 database
 companion_scripts
-cran-comments.md
+cran-comments.md

.devcontainer/Dockerfile

@@ -7,6 +7,7 @@ RUN apt update \
         libgdal-dev \
         libudunits2-dev \
         cmake \
+        pandoc \
     && :
 
 # install dev dependencies

.gitignore

@@ -43,3 +43,4 @@ vignettes/*.pdf
 
 # R Environment Variables
 .Renviron
+inst/doc

DESCRIPTION

@@ -30,5 +30,8 @@ Imports:
     rappdirs,
     doParallel
 Suggests: 
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
+VignetteBuilder: knitr

NEWS.md

@@ -1,3 +1,3 @@
-# InvertR 
+# InvTraitR (0.0.0.1)
 
 * Added a `NEWS.md` file to track changes to the package.

vignettes/.gitignore

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

vignettes/InvTraitR_vignette.Rmd

@@ -1,10 +1,24 @@
 ---
 title: "Dry biomass of freshwater invertebrates using InvTraitR"
-author: "James Hagan"
-date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
+author: "James Hagan"
+vignette: >
+  %\VignetteIndexEntry{Dry biomass of freshwater invertebrates using InvTraitR}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---
 
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup}
+library(InvTraitR)
+```
+
 To see how we can use *InvTraitR* to obtain estimates of the dry biomass of freshwater invertebrates using taxon names and geographical coordinates, we will start by loading some relevant packages and some test data. The test data consist of a set of 89 invertebrate taxa collected in freshwater rockpools on six rocky outcrops (often called inselbergs) in five countries.
 
 In addition, the data consist of latitude-longitude coordinates for the samples as well as measured body lengths for all the taxa (some body lenghts were compiled from the literature)
@@ -53,14 +67,13 @@ length(unique(dol_df$country_code_XXX))
 
 # check the summary statistics
 summary(dol_df)
-
 ```
 
 We want to use the body length data to estimate the dry biomass for each of these samples using length-dry biomass allometric equations. The *InvTraitR* package houses a database of more than 350 length-dry biomass allometric equations that represent most major groups of freshwater invertebrates globally. We can use *InvTraitR* to search this database for appropriate length-dry biomass equations for the samples in our test data (`dol_df`).
 
 To do this, we have two options both of which rely on the `get_trait_from_taxon()` function. This function (see below) takes a data.frame with at least five columns. These columns are the taxon name for which dry biomass data are required, the life stage of the taxon, the latitude and longitude coordinates from which the taxon was sampled and body size of the taxon:
 
-```r
+```{r}
 get_trait_from_taxon(
     data,                   # data.frame with at least five columns: target taxon, life stage, latitude (dd), longitude (dd) and body size (mm) if trait == "equation"
     target_taxon,           # character string with the column name containing the taxon names
@@ -115,5 +128,3 @@ print(dol_df[1,])
 print(dplyr::filter(dol_df_equ$data, row == 1))
 
 ```
-
-