Update due to climatereanalyzer switch to Copernicus daily data (#27)

* Make daily temp region codes consistent with documentation

* Fixing due to  switch to Copernicus data

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hockeystick
 Title: Download and Visualize Essential Climate Change Data
-Version: 0.8.2
+Version: 0.8.3
 Authors@R: 
     person(given = "Hernando",
            family = "Cortina",

NEWS.md

@@ -77,3 +77,7 @@
 # hockeystick 0.8.2
 
 * Update new get_dailytemp() urls
+
+# hockeystick 0.8.3
+
+* Update to reflect climatereanalyzer switch to Copernicus data

R/daily_temp.R

@@ -11,9 +11,9 @@
 #' @param mean_start (numeric) Start year for historic mean, defaults to 1979.
 #' @param mean_end (numeric) End year for historic mean, defaults to 2000.
 #'
-#' @return Invisibly returns a tibble with the daily 2-meter air or sea surface temperatures since 1979 as well as historic mean by day-of-year and current anomaly versus mean.
+#' @return Invisibly returns a tibble with the daily 2-meter air or sea surface temperatures since 1940 as well as historic mean by day-of-year and current anomaly versus mean.
 #'
-#' `get_dailytemp` invisibly returns a tibble with the daily temperatures since 1979 as well as mean by day-of-year and anomaly. Default to world data, but region can be selected among six options.
+#' `get_dailytemp` invisibly returns a tibble with the daily temperatures since 1940 as well as mean by day-of-year and anomaly. Default to world data, but region can be selected among six options.
 #'
 #' Region options include world air (default), Northern Hemisphere air, Southern Hemisphere air, Tropics air, Arctic air, Antarctic air, World sea surface and North Atlantic sea surface and is stored in attribute of output.
 #' The historic daily mean-by-day period defaults to 1979-2000. This range can be optionally modified.
@@ -48,19 +48,20 @@
 #' \itemize{
 #' \item ClimateReanalyzer.org: \url{https://climatereanalyzer.org/clim/t2_daily/}
 #'
-#' Notes: The "Daily 2-meter Air Temperature" page shows area-weighted daily means calculated from the 2-meter air temperature variable from the Climate Forecast System version 2 and Climate Forecast System Reanalysis, which are publicly available products of the NOAA National Centers for Environmental Prediction.
-#' Sea surface is from NOAA Optimum Interpolation SST (OISST) version 2.1. OISST is a 0.25°x0.25° gridded dataset that provides estimates of temperature based on a blend of satellite, ship, and buoy observations. The dataset spans 1 January 1982 to present with a 1 to 2-day lag from the current day.
+#' Notes: daily mean surface air temperature (2-meter height) estimates from the ECMWF Reanalysis version 5 (ERA5) for the period January 1940 to present. ERA5 is a state-of-the-art numerical climate/weather modeling framework that ingests surface, radiosonde, and satellite observations to estimate the state of the atmosphere through time.
+#' ERA5 files have a horizontal grid resolution of 0.25° x 0.25° (about 31km x 31km at 45°N). Each daily temperature represents an average across all model gridcells within the defined latitude/longitude bounds for the selected domain. The means are area-weighted to account for the convergence of longitude lines at the poles
 #'
 #' }
 #'
 #' @export
 
 get_dailytemp <- function(use_cache = TRUE, write_cache = getOption("hs_write_cache"),
                           region = 'W',
-                          mean_start = if(region == 'WS' | region == 'AS') 1982 else 1979,
+                          mean_start = if(region %in% c('WS','NS', 'ws', 'ns')) 1982 else 1979,
                           mean_end = 2000) {
 
   hs_path <- tools::R_user_dir("hockeystick", "cache")
+  region <- toupper(region)
 
   if (use_cache) {
     if (file.exists(file.path(hs_path, 'dailytemp.rds')))
@@ -72,17 +73,17 @@ get_dailytemp <- function(use_cache = TRUE, write_cache = getOption("hs_write_ca
   }
 
   file_url <- switch(region,
-                      W='https://climatereanalyzer.org/clim/t2_daily/json_cfsr/cfsr_world_t2_day.json',       # World Air
-                     NH='https://climatereanalyzer.org/clim/t2_daily/json_cfsr/cfsr_nh_t2_day.json',          # Northern Hemi Air
-                     SH='https://climatereanalyzer.org/clim/t2_daily/json_cfsr/cfsr_sh_t2_day.json',          # Southern Hemi Air
-                     AR='https://climatereanalyzer.org/clim/t2_daily/json_cfsr/cfsr_arctic_t2_day.json',      # Arctic Air
-                     AN='https://climatereanalyzer.org/clim/t2_daily/json_cfsr/cfsr_antarctic_t2_day.json',   # #Antarctic Air
-                     TR='https://climatereanalyzer.org/clim/t2_daily/json_cfsr/cfsr_tropics_t2_day.json',     # Tropics Air
-                     WS='https://climatereanalyzer.org/clim/sst_daily/json/oisst2.1_world2_sst_day.json',     # World Sea
-                     AS='https://climatereanalyzer.org/clim/sst_daily/json/oisst2.1_natlan1_sst_day.json')    # North Atlantic Sea
+                      W = 'https://climatereanalyzer.org/clim/t2_daily/json/era5_world_t2_day.json',       # World Air
+                     NW = 'https://climatereanalyzer.org/clim/t2_daily/json/era5_nh_t2_day.json',          # Northern Hemi Air
+                     SW = 'https://climatereanalyzer.org/clim/t2_daily/json/era5_sh_t2_day.json',          # Southern Hemi Air
+                     AR = 'https://climatereanalyzer.org/clim/t2_daily/json/era5_arctic_t2_day.json',      # Arctic Air
+                     AN = 'https://climatereanalyzer.org/clim/t2_daily/json/era5_antarctic_t2_day.json',   # #Antarctic Air
+                     TR = 'https://climatereanalyzer.org/clim/t2_daily/json/era5_tropics_t2_day.json',     # Tropics Air
+                     WS = 'https://climatereanalyzer.org/clim/sst_daily/json/oisst2.1_world2_sst_day.json',     # World Sea
+                     NS = 'https://climatereanalyzer.org/clim/sst_daily/json/oisst2.1_natlan1_sst_day.json')    # North Atlantic Sea
 
                      connected <- .isConnected(file_url)
-  if (!connected) {message("Retrieving remote data requires internet connectivity."); return(invisible(NULL))}
+  if (!connected) {message("Retrieving remote data requires internet connectivity.\nAvailable regions are: W, NW, SW, AR, AN, TR, WS, NS."); return(invisible(NULL))}
 
   dl <- tempfile()
   download.file(file_url, dl)
@@ -93,22 +94,38 @@ get_dailytemp <- function(use_cache = TRUE, write_cache = getOption("hs_write_ca
                             } )
   if (is.null(temp_json)) return(invisible(NULL))
 
-leap_years <- seq.int(1980, 2032, 4)
+leap_years <- seq.int(1940, 2032, 4)
 
+if (region!='WS' && region!='NS') {
 
 suppressWarnings(
-daily_temperature <- as_tibble(temp_json) |>
-  separate_wider_delim('data', delim=',', names_sep = '') |>
+daily_temperature <- as_tibble(temp_json) |> head(-3) |>
+  separate_wider_delim('data', delim=', ', names_sep = '') |>
   mutate(data1 = parse_number(data1),
          data366 = parse_number(data366, na = 'NA)')) |>
-  head(-3) |> mutate_all(as.numeric) |>
+  select(-data_source) |> mutate_all(as.numeric) |>
   pivot_longer(2:367, names_to = 'day_of_year') |>
   rename(year = name,
          temp = value) |>
   mutate(day_of_year = parse_number(day_of_year)) |>
   filter(!(day_of_year==60 & year %in% leap_years)) |>
   drop_na()
-)
+) }      else {
+
+  suppressWarnings(
+  daily_temperature <- as_tibble(temp_json) |> head(-3) |> tail(-1) |>
+      separate_wider_delim('data', delim=',', names_sep = '') |>
+    mutate(data1 = parse_number(data1),
+             data366 = parse_number(data366, na = 'NA)')) |>
+    mutate_all(as.numeric) |>
+      pivot_longer(2:367, names_to = 'day_of_year') |>
+      rename(year = name,
+             temp = value) |>
+      mutate(day_of_year = parse_number(day_of_year)) |>
+      filter(!(day_of_year==60 & year %in% leap_years)) |>
+      drop_na()
+  ) }
+
 
 
 daily_temperature <- daily_temperature |> group_by(year) |>
@@ -119,13 +136,13 @@ daily_temperature <- daily_temperature |> group_by(year) |>
   ungroup()
 
 dates <- data.frame(day_of_year=1:365,
-                    dummy_date=seq(as.Date('1975-01-01'), as.Date('1975-12-31'), by = '1 days'))
+                    dummy_date=seq(as.Date('1925-01-01'), as.Date('1925-12-31'), by = '1 days'))
 
 daily_temperature <- left_join(daily_temperature, dates, by='day_of_year')
 
 colnames(daily_temperature)[4] <- paste0(mean_start,'-',mean_end,' mean')
 
-if (region == 'WS' | region == 'AS') daily_temperature <- daily_temperature |> filter(year!=1981)
+if (region == 'WS' | region == 'NS') daily_temperature <- daily_temperature |> filter(year!=1981)
 
 attr(daily_temperature, "hs_daily_region") <- region
 
@@ -137,7 +154,7 @@ invisible(daily_temperature)
 
 #' Download and plot essential climate data
 #'
-#' Plots the daily temperatures and anomaly since 1979 retrieved using `get_dailytemp()` with ggplot2. The output ggplot2 object may be further modified.
+#' Plots the daily temperatures since 1940 and current anomaly data retrieved using `get_dailytemp()` with ggplot2. The output ggplot2 object may be further modified.
 #'
 #'
 #' @name plot_dailytemp
@@ -188,49 +205,51 @@ colnames(dataset)[4] <- 'mean_temp'
 
 region <- attr(dataset, "hs_daily_region")
 
-subtitle_lab <- '2-meter temperature since 1979 and mean'
+subtitle_lab <- '2-meter temperature since 1940 and mean'
 
-if (region == 'WS' ||region == 'AS') subtitle_lab <- 'Sea surface temperature since 1982 and mean'
+if (region == 'WS' ||region == 'NS') subtitle_lab <- 'Sea surface temperature since 1982 and mean'
 
 if (title_lab == "Daily Average Air Temperature") {
 
-    if (region == 'WS' | region == 'AS') title_lab <- 'Daily Average Sea Surface Temperature'
+    if (region == 'WS' | region == 'NS') title_lab <- 'Daily Average Sea Surface Temperature'
 
     region <- switch(region,
-                     W = 'World',
-                     NH = 'Northern Hemisphere',
-                     SH = 'Southern Hemisphere',
+                      W = 'World',
+                     NW = 'Northern Hemisphere',
+                     SW = 'Southern Hemisphere',
                      AR = 'Arctic',
                      AN = 'Antarctic',
                      TR = 'Tropics',
                      WS = 'World (60S-60N)',
-                     AS = 'North Atlantic')
+                     NS = 'North Atlantic')
 
     title_lab <- paste(region, title_lab)}
 
+# Color code notes: 'A': all years, 'M': mean, 'L': latest.
+
 plot <- ggplot(dataset) +
-    geom_line(aes(x = dummy_date, y = temp, group = year), alpha = 0.7, color = 'grey') +
+    geom_line(aes(x = dummy_date, y = temp, group = year, color = 'A'), alpha = 0.7) +
     scale_fill_gradientn(name = 'Anomaly (C\U00B0)', colors = RColorBrewer::brewer.pal(9, 'YlOrRd'), labels = scales::label_number(accuracy = 0.1)) +
     geom_line(aes(dummy_date, mean_temp, color = 'M'), linetype = 'dashed', linewidth = 1.1) +
     scale_y_continuous(n.breaks = 9) +
     theme_bw(base_size = 12) +
-    scale_x_date(name = 'Day of year', breaks = c(as.Date('1975-01-01'), as.Date('1975-04-01'),
-                                                  as.Date('1975-07-01'), as.Date('1975-10-01'), as.Date('1975-12-31')),
+    scale_x_date(name = 'Day of year', breaks = c(as.Date('1925-01-01'), as.Date('1925-04-01'),
+                                                  as.Date('1925-07-01'), as.Date('1925-10-01'), as.Date('1925-12-31')),
                  date_labels = '%b%est', date_minor_breaks = '1 month') +
     labs(title = title_lab, subtitle = subtitle_lab,
          y = 'Temperature (C\U00B0)',
          caption = paste0('Source: Climate Change Institute, University of Maine\nClimateReanalyzer.org as of ', latest),
          color = NULL) +
-    scale_color_manual(values = c('firebrick', 'black', 'grey'), labels = c(current_year, meanperiod), breaks = c('L', 'M')) +
+    scale_color_manual(values = c('firebrick', 'black', 'grey'), labels = c(current_year, meanperiod, 'All years'), breaks = c('L', 'M', 'A')) +
     geom_line(data = filter(dataset, year == current_year),
               aes(dummy_date, temp, color = 'L'), linewidth = 1.3) +
     theme(legend.position = "top") + theme(legend.key.size = unit(0.5, 'cm'),
                                          legend.margin = margin(5, 0, 0, 0))
 
 if (anomaly) {
-  subtitle_lab <- '2-meter temperature since 1979, mean, and current anomaly'
+  subtitle_lab <- '2-meter temperature since 1940, mean, and current anomaly'
 
-  if (region == 'World (60S-60N)' | region == 'North Atlantic' | region == 'WS' | region == 'AS')
+  if (region == 'World (60S-60N)' | region == 'North Atlantic' | region == 'WS' | region == 'NS')
       subtitle_lab <- 'Sea surface temperature since 1982, mean, and current anomaly'
 
   plot <- plot +
@@ -242,6 +261,7 @@ if (anomaly) {
               fill = temp_anom)) +
           geom_line(data = filter(dataset, year == current_year),
             aes(dummy_date, temp, color='L'), linewidth = 1.3) +
+    geom_line(aes(dummy_date, mean_temp, color = 'M'), linetype = 'dashed', linewidth = 1.2) +
   labs(subtitle = subtitle_lab) }
 
   if (print) suppressMessages( print(plot) )

R/globalvars.R

@@ -2,4 +2,4 @@
 utils::globalVariables(c('average', 'trend', 'year','Year', 'J-D', 'gmsl', 'method', 'month', 'name',
                          'age_ice', 'co2', 'land_use_change_co2', 'temp', 'value', 'size', 'measure','RevisedMajorHurricanes', 'RevisedACE',
                          'cumco2', 'country', 'data1', 'data366', 'day_of_year', 'dummy_date', 'linew', 'mean_temp', 'temp_anom',
-                         'hurr_type', 'ice_region'))
+                         'hurr_type', 'ice_region', 'data_source'))

README.Rmd

@@ -53,7 +53,7 @@ remotes::install_github("cortinah/hockeystick")
 
 ## Downloading and viewing global heating data
 
-New: Plot daily global temperatures since 1979 and current anomaly:
+New: Plot daily global temperatures since 1940 and current anomaly:
 
 ```{r dailytemp, fig.retina=2, message=FALSE, out.width='60%', fig.asp=1.03}
 library(hockeystick)

README.md

@@ -69,7 +69,7 @@ remotes::install_github("cortinah/hockeystick")
 
 ## Downloading and viewing global heating data
 
-New: Plot daily global temperatures since 1979 and current anomaly:
+New: Plot daily global temperatures since 1940 and current anomaly:
 
 ``` r
 library(hockeystick)

inst/WORDLIST

@@ -15,6 +15,7 @@ ClimateReanalyzer
 Cowtan
 Delaygue
 Dlugokencky
+ECMWF
 ERSST
 ESRL
 ESS
@@ -49,7 +50,6 @@ NOAA's
 NOAA’s
 NSIDC
 Neukom
-OISST
 ORCID
 OWID
 Organisation
@@ -91,7 +91,7 @@ edX
 et
 ggplot
 github
-gridded
+gridcells
 hs
 https
 icecurves