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use_parquet_file.Rmd
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use_parquet_file.Rmd
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---
title: "resolution"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{resolution}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
```{r setup}
library(obisindicators)
library(dplyr)
library(dggridR) # remotes::install_github("r-barnes/dggridR")
library(sf)
library(arrow)
library(magick)
library(ggplot2)
```
```{r }
# get OBIS records
# obis_20220404.parquet downloaded from https://obis.org/data/access on 2022-04-26
# NOTE: .gitignore prevents this large file from being on Github
open_parquet_file <- function(filepath){
occ_all <- open_dataset(filepath)
# NOTE: there are lots of other fields in the parquet file.
# These could be used in the future.
occ <- occ_all %>%
group_by(
decimalLongitude, decimalLatitude, species, date_year) %>% # remove duplicate rows
filter(!is.na(species)) %>%
summarize(
records = n(),
.groups = "drop") %>%
collect()
# return occ #I'm not sure what this line is supposed to be doing
}
occ <- open_parquet_file("~/Github/global-obis-es50/obis_20220404.parquet")
occ_1960s <- occ %>%
filter(
date_year >= 1960,
date_year <= 1969)
occ_1970s <- occ %>%
filter(
date_year >= 1970,
date_year <= 1979)
occ_1980s <- occ %>%
filter(
date_year >= 1980,
date_year <= 1989)
occ_1990s <- occ %>%
filter(
date_year >= 1990,
date_year <= 1999)
occ_2000s <- occ %>%
filter(
date_year >= 2000,
date_year <= 2009)
occ_2010s <- occ %>%
filter(
date_year >= 2010,
date_year <= 2019)
occ_2020s <- occ %>%
filter(
date_year >= 2020,
date_year <= 2029)
```
## Create function to make grid, calculate metrics for different resolution grid sizes
```{r function}
res_changes <- function(occur, resolution = 9){
dggs <- dgconstruct(projection = "ISEA", topology = "HEXAGON", res = resolution)
occur$cell <- dgGEO_to_SEQNUM(dggs, occur$decimalLongitude, occur$decimalLatitude)[["seqnum"]]
idx <- calc_indicators(occur)
grid <- dgcellstogrid(dggs, idx$cell) %>%
st_wrap_dateline() %>%
rename(cell = seqnum) %>%
left_join(
idx,
by = "cell")
return(grid)
}
```
## plot stuff
```{r}
RES <- 6
grid_1960s <- res_changes(occ_1960s, RES)
grid_1970s <- res_changes(occ_1970s, RES)
grid_1980s <- res_changes(occ_1980s, RES)
grid_1990s <- res_changes(occ_1990s, RES)
grid_2000s <- res_changes(occ_2000s, RES)
grid_2010s <- res_changes(occ_2010s, RES)
grid_2020s <- res_changes(occ_2020s, RES)
map_1960s <- gmap_indicator(grid_1960s, "es", label = "ES(50)")
ggsave(filename = "images/map_obis_es_1960s.png", plot=map_1960s,width=4,height=4,units="in",scale=1)
png_map_1960s <- image_read("images/map_obis_es_1960s.png")
map_1970s <- gmap_indicator(grid_1970s, "es", label = "ES(50)")
ggsave(filename = "images/map_obis_es_1970s.png", plot=map_1970s,width=4,height=4,units="in",scale=1)
png_map_1970s <- image_read("images/map_obis_es_1970s.png")
map_1980s <- gmap_indicator(grid_1980s, "es", label = "ES(50)")
ggsave(filename = "images/map_obis_es_1980s.png", plot=map_1980s,width=4,height=4,units="in",scale=1)
png_map_1980s <- image_read("images/map_obis_es_1980s.png")
map_1990s <- gmap_indicator(grid_1990s, "es", label = "ES(50)")
ggsave(filename = "images/map_obis_es_1990s.png", plot=map_1990s,width=4,height=4,units="in",scale=1)
png_map_1990s <- image_read("images/map_obis_es_1990s.png")
map_2000s <- gmap_indicator(grid_2000s, "es", label = "ES(50)")
ggsave(filename = "images/map_obis_es_2000s.png", plot=map_2000s,width=4,height=4,units="in",scale=1)
png_map_2000s <- image_read("images/map_obis_es_2000s.png")
map_2010s <- gmap_indicator(grid_2010s, "es", label = "ES(50)")
ggsave(filename = "images/map_obis_es_2010s.png", plot=map_2010s,width=4,height=4,units="in",scale=1)
png_map_2010s <- image_read("images/map_obis_es_2010s.png")
map_2020s <- gmap_indicator(grid_2020s, "es", label = "ES(50)")
ggsave(filename = "images/map_obis_es_2020s.png", plot=map_2020s,width=4,height=4,units="in",scale=1)
png_map_2020s <- image_read("images/map_obis_es_2020s.png")
```
## create animated gif
```{r}
img <- c(png_map_1960s, png_map_1970s, png_map_1980s, png_map_1990s, png_map_2000s, png_map_2010s, png_map_2020s)
image_append(image_scale(img, "x200"))
obis_es50_gif <- image_animate(image_scale(img, "1200x1200"), fps = 1, dispose = "previous")
image_write(obis_es50_gif, "images/obis_es50.gif")
```