updated with rayshader plotting

DESCRIPTION

@@ -17,22 +17,27 @@ Depends:
 Imports:
     CoordinateCleaner,
     datelife,
+	elevatr,
     geiger,
     jsonlite,
 	magrittr,
     paleotree,
     phangorn,
     plyr,
+	raster,
+	rayshader,
     rentrez,
     rfishbase,
     rgbif,
     rmarkdown,
     rotl,
 	rvest,
+	sf,
     sp,
     speciesgeocodeR,
     spocc,
     taxize,
+	tidyverse,
     utils
 Suggests:
     testthat (>= 2.1.0)
@@ -41,4 +46,4 @@ Remotes:
     phylotastic/datelife
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1

NAMESPACE

@@ -9,6 +9,8 @@ export(contrasts_correlations)
 export(convert_continuous_to_discrete)
 export(descendant_species)
 export(eol_data)
+export(eol_traits)
+export(eol_traits2)
 export(fishbase_genus_query)
 export(fishbase_species_query)
 export(gbif_species_query)
@@ -24,6 +26,7 @@ export(locality_add_habitat_biome)
 export(locality_clean)
 export(match_data)
 export(pbdb_taxon_query)
+export(plot_gis)
 export(render_chapter2)
 export(run_biogeobears)
 export(run_chapter2)

R/dataFunctions.R

@@ -88,6 +88,53 @@ locality_clean <- function(locations) {
   return(CoordinateCleaner::clean_coordinates(locations, lon="longitude", lat="latitude", species=NULL, tests=c( "centroids", "equal", "gbif", "institutions","zeros"), value="clean"))
 }
 
+#' Plot a map of points
+#' @param gbif_points Data.frame containing points (latitude and longitude, perhaps other data as columns)
+#' @return A ggplot2 map
+#' 
+#' Note that we will need to set zoom automatically, also add points, also make the ocean full of water.
+#' @examples
+#' gis_points <- spocc_taxon_query("Tyto", limit=100, sources="gbif")
+#' plot_gis(gbif_points)
+#' @export
+plot_gis <- function(gbif_points) {
+	min_lat <- min(gbif_points$latitude)
+	max_lat <- max(gbif_points$latitude)
+	min_lon <- min(gbif_points$longitude)
+	max_lon <- max(gbif_points$longitude)
+
+	med_bbox <- sf::st_bbox(c(xmin = min_lon, xmax = max_lon, ymin = min_lat, ymax = max_lat),
+						crs = 4326)
+
+	med_bbox_df <- data.frame(x = c(min_lon, max_lon),
+							y = c(min_lat, max_lat))
+
+
+	extent_zoomed <- raster::extent(med_bbox)
+	prj_dd <- "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"
+
+	elev_med <- elevatr::get_elev_raster(med_bbox_df, prj =  prj_dd, z = 3, clip = "bbox")
+	elev_med_mat <- rayshader::raster_to_matrix(elev_med)
+
+	base_map <- elev_med_mat %>% 
+	height_shade() %>% 
+	add_overlay(
+		sphere_shade(elev_med_mat,
+					texture = rayshader::create_texture(
+					lightcolor = "#b8ff78",
+					shadowcolor = "#193600",
+					leftcolor = "#80d453",
+					rightcolor = "#80d453",
+					centercolor = "#568a27"),
+					sunangle = 0,
+					colorintensity = 5)
+	)
+
+	base_map %>% plot_map()
+	return(base_map)
+}
+
+
 #' Use azizka/speciesgeocodeR/ and WWF data to encode locations for habitat and biome
 #'
 #' Uses info from http://omap.africanmarineatlas.org/BIOSPHERE/data/note_areas_sp/Ecoregions_Ecosystems/WWF_Ecoregions/WWFecoregions.htm to convert codes to more readable text
@@ -352,6 +399,7 @@ get_datelife_biggest <- function(taxon) {
   clade.name<- rotl::tnrs_match_names(taxon)$unique_name[1]
   datelife_biggest <- NULL
   try(datelife_biggest <- datelife::datelife_search(input=clade.name, get_spp_from_taxon=TRUE, summary_format="phylo_biggest"))
+
   return(datelife_biggest)
 }
 

R/eoldata.R

@@ -56,9 +56,9 @@ eol_data <- function(species) {
 #'
 #' @param eol_df A data frame produced by the function eol_data
 #' @return A data frame of one row with columns: behavior circadian rhythm, developmental mode, visual system, and wing morphology
-#' @export
 #' 
 #' This works for a single species but not for the multi-species data frame produced by get_eol
+#' @export
 eol_traits <- function(eol_df){
   df2 <- subset(eol_df, select = c(species, trait, value))
   #remove duplicate rows
@@ -75,9 +75,8 @@ eol_traits <- function(eol_df){
 #'
 #' @param eol_df A data frame produced by the function eol_data
 #' @return A data frame of one row with columns: behavior circadian rhythm, developmental mode, visual system, and wing morphology
-#' @export
 #'
-#' This one works for the full data frame produced by get_eol - maybe rework it with pipes? 
+#' @export
 eol_traits2 <- function(eol_df){
 	#select the columns we want
 	df2 <- subset(eol_df, select = c(species, trait, value))

R/runanalysis.R

@@ -11,9 +11,11 @@ run_chapter2 <- function(taxon) {
   genbank_count <- get_genbank_count(taxon)
   otol <- get_otol(taxon)
   eol <- get_eol(taxon)
-  eol_tbl <- eol_traits2(eol)
-  location_realm_biome <- get_location_realm_biome(taxon)
-  return(list(wikipedia_summary=wikipedia_summary, datelife_biggest=datelife_biggest, pubmed=pubmed, genbank_count_by_gene=genbank_count_by_gene, genbank_count=genbank_count , otol=otol, location_realm_biome=location_realm_biome, eol=eol, eol_tbl=eol_tbl))
+  #eol_tbl <- eol_traits2(eol)
+#  location_realm_biome <- get_location_realm_biome(taxon)
+  #return(list(wikipedia_summary=wikipedia_summary, datelife_biggest=datelife_biggest, pubmed=pubmed, genbank_count_by_gene=genbank_count_by_gene, genbank_count=genbank_count , otol=otol, location_realm_biome=location_realm_biome, eol=eol, eol_tbl=eol_tbl))
+  return(list(wikipedia_summary=wikipedia_summary, datelife_biggest=datelife_biggest, pubmed=pubmed, genbank_count_by_gene=genbank_count_by_gene, genbank_count=genbank_count , otol=otol, eol=eol))
+
 }
 
 #' Create a file of results

inst/rmd/summary.Rmd

@@ -63,7 +63,7 @@ if(nrow(pubmed.df)>0) {
 
 Here is information about realms (biogeographic regions) by species; frequency of record in each realm.
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, eval=FALSE}
 realm <- all_results$location_realm_biome$realm
 for (i in sequence(nrow(realm))) {
   realm[i,] <- realm[i,]/sum(realm[i,], na.rm=TRUE)
@@ -75,7 +75,7 @@ pander::pander(data.frame(realm))
 
 Here is information about biomes by species; frequency of records in each biome.
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, eval=FALSE}
 biome <- all_results$location_realm_biome$biome
 for (i in sequence(nrow(biome))) {
   biome[i,] <- biome[i,]/sum(biome[i,], na.rm=TRUE)