Remove pre-generated images from vignette

.Rbuildignore

@@ -1,18 +1,11 @@
-^README\.Rmd$
-^CONDUCT\.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^appveyor\.yml$
 ^\.travis\.yml$
 
-cache$
-assets
 cran-comments.md
-preparePackage.R
-reviewJOSS.md
-reviewROPENSCI.md
 inst/extdata
 inst/paper
-BugFixing.R
 _pkgdown.yml
-^docs$
+vignettes/rdefra_vignette.R
+vignettes/rdefra_vignette.html

.gitignore

@@ -1,18 +1,3 @@
 .Rproj.user
 .Rhistory
-.RData
-
 *.Rproj
-*.tar.gz
-
-*.html
-
-README_cache/*
-vignettes/rdefra_vignette_cache/*
-vignettes/*.R
-vignettes/*.md
-vignettes/figure/*
-BugFixing.R
-
-# Remove docs folder (site builds automatically)
-docs/*

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rdefra
 Title: Interact with the UK AIR Pollution Database from DEFRA
-Version: 0.3.7
+Version: 0.3.8
 Authors@R: c(person(given = "Claudia",
                     family = "Vitolo",
                     role = c("aut", "cre"),

NEWS.md

@@ -1,11 +1,13 @@
-rdefra 0.3.7
+rdefra 0.3.8
 ==============
 
 ## BUG FIXES
 * Updated tests to be compatible with PROJ6 [#9](https://github.com/ropensci/rdefra/issues/9)
 
 ## MINOR CHANGES
 * Removed obsolete packages in 'Suggests'
+* Fixed invalid URIs
+* The following directory looks like a leftover from knitr
 
 rdefra 0.3.6
 ==============

README.md

@@ -82,13 +82,11 @@ fllowing steps:
 
 For an in-depth description of the various functionalities andexample
 applications, please refer to the package
-[vignette](vignettes/rdefra_vignette.md).
+[vignette](vignettes/rdefra_vignette.Rmd).
 
 ## Meta
 
-  - Please note that this project is released with a [Contributor Code
-    of Conduct](CONDUCT.md). By participating in this project you agree
-    to abide by its terms.
+  - This package and functions herein are part of an experimental open-source project. They are provided as is, without any guarantee.
   - Please [report any issues or
     bugs](https://github.com/ropensci/rdefra/issues).
   - License: [GPL-3](https://opensource.org/licenses/GPL-3.0)

cran-comments.md

@@ -9,6 +9,8 @@ This is a resubmission due to bug fixing.
 
 ## MINOR CHANGES
 * Removed obsolete packages in 'Suggests'
+* Fixed invalid URIs
+* The following directory looks like a leftover from knitr
 
 ## Test environment
 * Ubuntu 18.04, R 3.6.3

vignettes/rdefra_vignette.Rmd

@@ -5,8 +5,8 @@ date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{rdefra}
-  %\VignetteEngine{knitr::knitr}
-  %\usepackage[UTF-8]{inputenc}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r setup, echo = FALSE}
@@ -138,7 +138,7 @@ plot(daily_means, main = "", xlab = "",
 
 The above figure \ref{fig:hdata} shows the highest concentrations happen in late spring and at the beginning of summer. In order to check whether this happens every year, we can download multiple years of data and then compare them.
 
-```{r ozone_data, eval = FALSE}
+```{r ozone_data, eval = TRUE}
 # Get 15 years of hourly ozone data from the same monitoring station
 library("ggplot2")
 library("dplyr")
@@ -157,11 +157,8 @@ df %>%
   geom_boxplot(aes(x = as.factor(month), y = ozone, group = month),
                outlier.shape = NA) +
   xlab("Month of the year") +
-  ylab(expression(paste("Ozone concentration (", mu, "g/",m^3,")")))
-```
-
-```{r ozone, echo = FALSE, eval = TRUE, fig.width = 7, out.width = "600px", fig.cap = "\\label{fig:ozone}15 years of hourly ozone data from London Marylebone Road monitoring station."}
-knitr::include_graphics("ozone.png")
+  ylab(expression(paste("Ozone concentration (", mu, "g/",m^3,")"))) +
+  ggtitle("15 years of hourly ozone data from London Marylebone Road monitoring station")
 ```
 
 The above box plots show that the highest concentrations usually occurr during April/May and that these vary year-by-year.
@@ -172,13 +169,14 @@ The above box plots show that the highest concentrations usually occurr during A
 
 After scraping DEFRA's web pages, almost all the stations have valid coordinates. In the figure below, blue circles show all the stations with valid coordinates, while red circles show stations with available hourly data.
 
-```{r map_data, eval = FALSE}
+```{r map_data, eval = TRUE}
 # Keep only station with coordinates
 stations_with_coords <- stations[complete.cases(stations[, c("Longitude",
                                                              "Latitude")]), ]
 # Keep only station with known SiteID
 stations_with_SiteID <- which(!is.na(stations_with_coords$SiteID))
 
+# Blue circles show stations with valid coordinates, while red circles show stations with available hourly data.
 library("leaflet")
 leaflet(data = stations_with_coords) %>% addTiles() %>% 
   addCircleMarkers(lng = ~Longitude, 
@@ -191,10 +189,6 @@ leaflet(data = stations_with_coords) %>% addTiles() %>%
                    popup = ~SiteID[stations_with_SiteID])
 ```
 
-```{r map, echo = FALSE, eval = TRUE, fig.width = 7, out.width = "600px", fig.cap = "\\label{fig:map}Blue circles show stations with valid coordinates, while red circles show stations with available hourly data."}
-knitr::include_graphics("map.png")
-```
-
 ### Analyse the spatial distribution of the monitoring stations
 
 Below are two plots showing the spatial distribution of the monitoring stations. These are concentrated largely in urban areas and mostly estimate the background level of concentration of pollutants.