diff --git a/mapping_draft.Rmd b/mapping_draft.Rmd index 36363a2..1335b5f 100644 --- a/mapping_draft.Rmd +++ b/mapping_draft.Rmd @@ -53,21 +53,21 @@ local({r <- getOption("repos") }) # TODO: need to alter this to use new sf data class as sp is deprecated require(sf) # new simplefeature data class, supercedes sp in many ways -require(rgdal) +require(rgdal) # deprecated by sf() require(GISTools) # deprecated by sf() require(sp) # needed for proj4string, deprecated by sf() require(ggplot2) require(broom) # required for tidying SPDF to data.frame for ggplot2 -require(rgeos) +require(rgeos) # deprecated by sf() require(ggmap) require(maptools) -require(RCurl) +require(RCurl) # used for fetching reproducible datasets # require(tibble) # using for grouped bar plot require(tidyr) # using for grouped bar plot require(plyr) require(dplyr) require(reshape2) # using for grouped bar plot -require(pander) +require(pander) # produces tidy formatted tables require(scales) # require(sqldf) # using sqldf to filter while loading very large data sets require(plotly) # allows for export of plots to dynamic web pages @@ -861,6 +861,7 @@ unzip("data/SSSI_SCOTLAND_ESRI.zip", exdir = "data") } sssi <- st_read("data/SSSI_SCOTLAND.shp") +sssi_sp <- readOGR("./data", "SSSI_SCOTLAND.shp") # Download wild land areas: @@ -872,6 +873,7 @@ unzip("data/WILDLAND_SCOTLAND_ESRI.zip", exdir = "data") } wildland <- st_read("data/WILDLAND_SCOTLAND.shp") +wildland_sp <- readOGR("./data", "WILDLAND_SCOTLAND.shp") # Download data for National Forest Inventory: # Note: UK-wide data is here: https://opendata.arcgis.com/datasets/bcd6742a2add4b68962aec073ab44138_0.zip?outSR=%7B%22wkid%22%3A27700%2C%22latestWkid%22%3A27700%7D @@ -883,6 +885,7 @@ unzip("data/National_Forest_Inventory_Woodland_Scotland_2017.zip", exdir = "data } forest_inventory <- st_read("data/National_Forest_Inventory_Woodland_Scotland_2017.shp") +forest_inventory_sp <- readOGR("./data", "National_Forest_Inventory_Woodland_Scotland_2017.shp") # Set symmetrical CRS for analysis below st_crs(sssi) <- 27700 @@ -922,6 +925,29 @@ pow_wilderness_row ```{r wilderness_plots} +# Plot using sp + +ggplot() + + geom_polygon(aes(x = long, y = lat, group = group), + data = sssi_sp, + colour = 'black', + alpha = .7, + size = .005) + + geom_point(aes(X, Y, fill = NULL, group = NULL), size = 1, data=ecs_df, + colour = "black", + fill = "white", + size = .15, + stroke = .002, + alpha = .6, + show.legend = TRUE) + + labs(x = NULL, y = NULL, fill = "Groups", + title = "Figure 11", + subtitle="Sites of Special Scientific Interest with points marked", + caption = paste("Jeremy H. Kidwell :: jeremykidwell.info", + "Data: UK Data Service (OGL) & Jeremy H. Kidwell", + "You may redistribute this graphic under the terms of the CC-by-SA 4.0 license.", + sep = "\n")) + # Plot SSSI polygons with ECS points if (utils::packageVersion("ggplot2") > "2.2.1") @@ -941,7 +967,28 @@ if (utils::packageVersion("ggplot2") > "2.2.1") sep = "\n")) # Plot Forest Inventory - + +ggplot() + + geom_polygon(aes(x = long, y = lat, group = group), + data = forest_inventory_sp, + colour = 'black', + alpha = .7, + size = .005) + + geom_point(aes(X, Y, fill = NULL, group = NULL), size = 1, data=ecs_df, + colour = "black", + fill = "white", + size = .15, + stroke = .002, + alpha = .6, + show.legend = TRUE) + + labs(x = NULL, y = NULL, fill = "Groups", + title = "Figure 11", + subtitle="Sites of Special Scientific Interest with points marked", + caption = paste("Jeremy H. Kidwell :: jeremykidwell.info", + "Data: UK Data Service (OGL) & Jeremy H. Kidwell", + "You may redistribute this graphic under the terms of the CC-by-SA 4.0 license.", + sep = "\n")) + ggplot() + geom_sf(data = forest_inventory) @@ -951,8 +998,6 @@ ggplot() + # Appendix A ```{r pander_admin_table} -# TODO: uncomment admin.shortened lines below -# admin.shortened <- admin_lev1[,c(7,12:22)] # Output CSV files for various levels of admin write.csv(admin_lev1, "derivedData/admin_lev1.csv", row.names=FALSE) write.csv(admin_lev2, "derivedData/admin_lev2.csv", row.names=FALSE) @@ -963,9 +1008,9 @@ write.csv(permaculture, "derivedData/permaculture.csv", row.names=FALSE) write.csv(dtas, "derivedData/dtas.csv", row.names=FALSE) write.csv(simd, "derivedData/simd.csv", row.names=FALSE) -## Output mmd tables using pander -# panderOptions("digits", 2) -# pander(as_data_frame(admin_lev1[,c(3,5,7,11,13)])) +# Output mmd tables using pander +panderOptions("digits", 2) +pander(as_data_frame(admin_lev1[,c(3,5,7,11,13)])) ``` # Appendix B