Fixed file paths, silenced a title mistmatch issue, and renamed chunk…

…s with duplicate chunk names

vignettes/dataset-single-DataOne.Rmd

@@ -14,6 +14,9 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
+
+# Ignore difference in YAML title versus `\VignetteIndexEntry{}`
+options(rmarkdown.html_vignette.check_title = FALSE)
 ```
 
 ## Summary
@@ -92,7 +95,7 @@ At this point, you should have the data and the metadata downloaded inside your
 
 
 ```{r, out.width="90%", echo=FALSE, fig.align="center", fig.cap="Local file structure of a dataset downloaded by metajam"}
-knitr::include_graphics("../inst/images/metajam_v1_folder.png")
+knitr::include_graphics("../man/figures/metajam_v1_folder.png")
 ```  
 
 
@@ -115,13 +118,13 @@ For the second example, we are using Marine bird survey observation and density
 
 ## Libraries and constants
 
-```{r libraries, warning=FALSE}
+```{r libraries-2, warning=FALSE}
 # devtools::install_github("NCEAS/metajam")
 library(metajam)  
 
 ```
 
-```{r constants}
+```{r constants-2}
 # Directory to save the data set
 path_folder <- "Data_alaska"
 
@@ -133,7 +136,7 @@ data_url <- "https://cn.dataone.org/cn/v2/resolve/4139539e-94e7-49cc-9c7a-5f879e
 
 ## Download the dataset
 
-```{r download, eval=FALSE}
+```{r download-2, eval=FALSE}
 
 # Create the local directory to download the datasets
 dir.create(path_folder, showWarnings = FALSE)
@@ -155,13 +158,13 @@ At this point, you should have the data and the metadata downloaded inside your
 
 
 ```{r, out.width="90%", echo=FALSE, fig.align="center", fig.cap="Local file structure of a dataset downloaded by metajam"}
-knitr::include_graphics("../inst/images/metajam_v1_folder.png")
+knitr::include_graphics("../man/figures/metajam_v1_folder.png")
 ```  
 
 
 ## Read the data and metadata in your R environment
 
-```{r read_data, eval=FALSE}
+```{r read_data-2, eval=FALSE}
 # Read all the datasets and their associated metadata in as a named list
 coweeta_diatom <- metajam::read_d1_files(data_folder)
 
@@ -173,5 +176,5 @@ You have now loaded in your R environment one named list object that contains th
 
 
 ```{r, out.width="90%", echo=FALSE, fig.align="center", fig.cap="Structure of the named list object containing tabular metadata and data as loaded by metajam"}
-knitr::include_graphics("../inst/images/metajam_v1_named_list.png")
+knitr::include_graphics("../man/figures/metajam_v1_named_list.png")
 ```