Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----include = FALSE----------------------------------------------------------
### needed libraries
library(mapdata)
library(plotdap)
library(rerddap)
## ----eval = FALSE-------------------------------------------------------------
# install.packages("plotdap")
## ----eval = FALSE-------------------------------------------------------------
# devtools::install_github('ropensci/plotdap')
## ----world, fig.align = 'center', fig.height = 4, fig.width = 5---------------
library(plotdap)
plotdap()
plotdap("base")
## ----southPole, fig.align = 'center', fig.height = 4, fig.width = 5-----------
plotdap("base",
mapTitle = "MODIS South Pole Stereographic",
mapFill = "transparent",
mapColor = "steelblue",
crs = "+proj=stere +lat_0=-90 +lat_ts=-90 +lon_0=-63 +k=1 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs"
)
## ----alaska, fig.align = 'center', fig.height = 4, fig.width = 5--------------
alaska <- "+proj=aea +lat_1=55 +lat_2=65 +lat_0=50 +lon_0=-154 +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs"
plotdap("base", crs = alaska)
## ----echo = FALSE-------------------------------------------------------------
alaska <- "+proj=aea +lat_1=55 +lat_2=65 +lat_0=50 +lon_0=-154 +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs"
## ----usmap, fig.align = 'center', fig.height = 4, fig.width = 5---------------
library(sf)
library(mapdata)
w <- st_as_sf(maps::map("world", plot = FALSE, fill = TRUE))
us <- st_transform(subset(w, ID == "USA"), alaska)
plotdap(mapData = us)
## ----get_viirsSST, eval = FALSE-----------------------------------------------
# sstInfo <- rerddap::info('erdVHsstaWS3day')
# # get latest 3-day composite sst
# viirsSST <- rerddap::griddap(sstInfo,
# latitude = c(41., 31.),
# longitude = c(-128., -115),
# time = c('last','last'),
# fields = 'sst')
#
## ----viirs_hires,echo = TRUE, eval = FALSE------------------------------------
# w <- map("worldHires", xlim = c(-140., -114), ylim = c(30., 42.),
# fill = TRUE, plot = FALSE)
# # map using that outline, temperature color from cmocean
# add_griddap(plotdap(mapData = w), viirsSST, ~sst, fill = "thermal" )
#
## ----world2Hires, fig.align = 'center', fig.height = 3, fig.width = 5, message = FALSE, warning = FALSE----
xpos <- c(135.25, 240.25)
ypos <- c(20.25, 60.25)
zpos <- c(70.02, 70.02)
remove <- c("UK:Great Britain", "France", "Spain", "Algeria", "Mali", "
Burkina Faso", "Ghana", "Togo")
#subset world2Hires with those countries removed
w <- map("world2Hires", plot = FALSE, fill = TRUE, ylim = ypos, xlim = xpos)
w <- map("world2Hires", regions = w$names[!(w$names %in% remove)],
plot = FALSE, fill = TRUE, ylim = ypos, xlim = xpos)
# plot result
plotdap(mapData = w)
## ----cairo, eval = FALSE, echo = TRUE, warning = FALSE, message = FALSE------
# # write plot to disk using the Cairo package
# library(Cairo)
# # (latitude limits) / (longitude limits)
# r <- 85 / 120
# CairoPNG("myPlot.png", height = 400 * r, width = 400, res = 96)
# # alter default margins for base plotting
# # (leaving just enough space for a title)
# par(mar = c(0, 0, 1, 0))
# plotdap("base", mapData = us, mapTitle = "Albers projection of Alaska")
# dev.off()
## ----get_sardines, echo = TRUE, eval = FALSE----------------------------------
# my_url <- 'https://coastwatch.pfeg.noaa.gov/erddap/'
# sardines <- tabledap(
# 'FRDCPSTrawlLHHaulCatch',
# fields = c('latitude', 'longitude', 'time', 'scientific_name',
# 'subsample_count'),
# 'time>=2010-01-01', 'time<=2012-01-01', 'scientific_name="Sardinops sagax"',
# url = my_url)
## ----echo = TRUE, eval = FALSE------------------------------------------------
# p1 <- add_tabledap(
# plotdap(crs = "+proj=robin", mapTitle = "subsample count"),
# sardines,
# ~subsample_count
# )
# p2 <- add_tabledap(
# plotdap(crs = "+proj=robin", mapTitle = "Log subsample count"),
# sardines,
# ~log2(subsample_count)
# )
#
# p1
# p2
#
## ----echo = TRUE, eval = FALSE------------------------------------------------
# p1 <- add_tabledap(
# plotdap(crs = "+proj=robin", mapTitle = "Sardines - change color"),
# sardines,
# ~subsample_count,
# color = "dense",
# )
# p2 <- add_tabledap(
# plotdap(crs = "+proj=robin", mapTitle = "Sardines - change shape and size"),
# sardines,
# ~subsample_count,
# shape = 4,
# size = 1.
# )
# p1
# p2
## ----get_mur, eval = FALSE----------------------------------------------------
# murSST_west <- griddap(
# 'jplMURSST41',
# latitude = c(22, 51),
# longitude = c(-140, -105),
# time = c('last', 'last'),
# fields = 'analysed_sst'
# )
## ----plot_mur, echo = TRUE, eval = FALSE--------------------------------------
# add_griddap(
# plotdap(crs = "+proj=robin"),
# murSST_west,
# ~analysed_sst,
# maxpixels = 50000
# )
## ----get_wind, eval = FALSE---------------------------------------------------
# wind <- griddap(
# 'erdQMwindmday',
# time = c('2016-04-16', '2016-06-16'),
# latitude = c(30, 50),
# longitude = c(210, 240),
# fields = 'y_wind'
# )
## ----echo = TRUE, eval = FALSE------------------------------------------------
# p1 <- add_griddap(
# plotdap(mapTitle = "Mean Meridional Wind"),
# wind,
# ~y_wind,
# fill = "delta",
# time = mean
# )
# my_func <- function(x) var(x, na.rm = TRUE)
# p2 <- add_griddap(
# plotdap(mapTitle = "Variance of Meridional Wind"),
# wind,
# ~y_wind,
# fill = "delta",
# time = my_func
# )
# p1
# p2
#
## ----viirsSST_gridland, echo = TRUE, eval = FALSE-----------------------------
# plotdap(mapTitle = "Grid over Land") %>%
# add_griddap(
# viirsSST,
# ~sst,
# fill = "thermal"
# )
#
## ----viirsSST_landgrid, echo = TRUE, eval = FALSE-----------------------------
# plotdap(mapTitle = "Land Over Grid") %>%
# add_griddap(
# viirsSST,
# ~sst,
# fill = "thermal"
# ) %>%
# print(landmask = TRUE)
## ----maxpix_10, echo = TRUE, eval = FALSE-------------------------------------
# plotdap(mapTitle = "maxpixels = 10,000") %>%
# add_griddap(
# viirsSST,
# ~sst,
# fill = "thermal",
# maxpixels = 10000
# )
## ----maxpix_50, echo = TRUE, eval = FALSE-------------------------------------
# plotdap(mapTitle = "maxpixels = 50,000") %>%
# add_griddap(
# viirsSST,
# ~sst,
# fill = "thermal",
# maxpixels = 50000
# )
## ----maxpix_100, echo = TRUE, eval = FALSE------------------------------------
# plotdap(mapTitle = "maxpixels = 100,000") %>%
# add_griddap(
# viirsSST,
# ~sst,
# fill = "thermal",
# maxpixels = 100000
# )
## ----maxpix_100_mask, echo = TRUE, eval = FALSE-------------------------------
# plotdap(mapTitle = "maxpixels = 100,000, landmask") %>%
# add_griddap(
# viirsSST,
# ~sst,
# fill = "thermal",
# maxpixels = 100000
# ) %>%
# print(landmask = TRUE)
## ----hires--------------------------------------------------------------------
w <- map("worldHires", xlim = c(-130., -114), ylim = c(30., 42.),
fill = TRUE, plot = FALSE)
## ----viirs_hires_mask, echo = TRUE, eval = FALSE------------------------------
# plotdap(mapData = w) %>%
# add_griddap(
# viirsSST,
# ~sst,
# fill = 'thermal',
# maxpixels = 50000
# ) %>%
# print(landmask = TRUE)
## ----soda70_get, echo = TRUE, eval = FALSE------------------------------------
# soda70Info <- rerddap::info('erdSoda331oceanmday')
# xpos <- c(135.25, 240.25)
# ypos <- c(20.25, 60.25)
# zpos <- c(70.02, 70.02)
# tpos <- c('2010-12-15', '2010-12-15')
# soda70 <- rerddap::griddap(soda70Info,
# longitude = xpos,
# latitude = ypos,
# time = tpos,
# depth = zpos,
# fields = 'temp' )
#
## ----soda70, echo= TRUE, eval = FALSE-----------------------------------------
# remove <- c("UK:Great Britain", "France", "Spain", "Algeria", "Mali",
# "Burkina Faso", "Ghana", "Togo")
# #subset world2Hires with those countries removed
# w <- map("mapdata::world2Hires", plot = FALSE, fill = TRUE,
# ylim = ypos, xlim = xpos)
# w <- map("mapdata::world2Hires", regions = w$names[!(w$names %in% remove)],
# plot = FALSE, fill = TRUE, ylim = ypos, xlim = xpos)
# # plot result
# plotdap(mapData = w) %>%
# add_griddap(
# soda70,
# ~temp,
# fill = "thermal"
# ) %>%
# print(landmask = TRUE)
#
## ----overlay, echo = TRUE, eval = FALSE---------------------------------------
# p <- add_griddap(plotdap(),
# murSST_west,
# ~analysed_sst,
# fill = "thermal"
# )
# p1 <- add_tabledap(p,
# sardines,
# ~subsample_count
# )
# print(p1, landmask = TRUE)
## ----modify, fig.align = 'center', fig.height = 4, fig.width = 5--------------
library(ggplot2)
plotdap(crs = "+proj=robin") %>%
add_tabledap(
sardines,
~subsample_count,
size = 1
) %>%
add_ggplot(
labs(
subtitle = "Sardinops sagax samples",
caption = "Sardines are yummy"
),
theme_minimal(),
theme(axis.ticks = element_blank(), axis.text = element_blank())
)
## ----modify2, echo = TRUE, eval = FALSE, timeit = TRUE------------------------
# temp_color <- rerddap::colors$temperature
# plotdap(mapTitle = "Reset colorscale limits") %>%
# add_griddap(
# viirsSST,
# ~sst,
# fill = "thermal"
# ) %>%
# add_ggplot(
# scale_fill_gradientn(colours = temp_color, na.value = NA, limits = c(10, 20)),
# scale_colour_gradientn(colors = temp_color, na.value = NA, limits = c(10, 20)),
# guides(colour = FALSE)
# ) %>%
# print(landmask = TRUE)
## ----eval = FALSE, echo = TRUE------------------------------------------------
# add_tabledap(
# plotdap(crs = "+proj=robin"),
# sardines,
# ~subsample_count,
# color = "dense",
# shape = 4,
# animate = TRUE
# )
## ----eval = FALSE, echo = TRUE------------------------------------------------
# add_griddap(
# plotdap(crs = "+proj=robin"),
# wind, ~y_wind,
# time = identity,
# fill = 'delta',
# animate = TRUE
# )
## ----eval = FALSE, echo = TRUE------------------------------------------------
# p <- add_griddap(
# plotdap(crs = "+proj=robin"),
# wind, ~y_wind,
# time = identity,
# fill = 'delta',
# animate = TRUE
# )
# ylim <- c(30, 50)
# xlim <- c(-150, -120)
# p <- bbox_set(p, xlim, ylim)
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