hockeystick 0.8.5 on CRAN (#31)

* Remove unnnecessary fill causing ggplot warning

* Control date labels

* add merged temp carbon function and plots

* tweak temp scatter

* add daily cop

* update daily temp plot

* Update News

* fixed bugs in globalvars and examples

* Update Mauna Loa carbon to http from ftp

* V0.8.5 for CRAN

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hockeystick
 Title: Download and Visualize Essential Climate Change Data
-Version: 0.8.4
+Version: 0.8.5
 Authors@R: 
     person(given = "Hernando",
            family = "Cortina",
@@ -11,7 +11,7 @@ Description: Provides easy access to essential climate change datasets to non-cl
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 URL: https://cortinah.github.io/hockeystick/, https://github.com/cortinah/hockeystick
 BugReports: https://github.com/cortinah/hockeystick/issues
 Imports: ggplot2, lubridate, tools, readr, dplyr, tidyr, patchwork, scales, rvest, tibble, treemapify, RColorBrewer, jsonlite

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2023
+YEAR: 2024
 COPYRIGHT HOLDER: Hernando Cortina

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2023 Hernando Cortina
+Copyright (c) 2024 Hernando Cortina
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NAMESPACE

@@ -5,6 +5,7 @@ export(climate_grid)
 export(emissions_map)
 export(get_carbon)
 export(get_dailytemp)
+export(get_dailytempcop)
 export(get_emissions)
 export(get_hurricanes)
 export(get_icecurves)
@@ -19,7 +20,9 @@ export(hockeystick_cache_delete_all)
 export(hockeystick_cache_details)
 export(hockeystick_cache_list)
 export(hockeystick_update_all)
+export(merge_carbontemp)
 export(plot_carbon)
+export(plot_carbontemp)
 export(plot_dailytemp)
 export(plot_emissions)
 export(plot_emissions_with_land)
@@ -37,6 +40,7 @@ export(plot_temp_scatter)
 export(warming_stripes)
 import(dplyr)
 import(ggplot2)
+import(lubridate)
 import(patchwork)
 import(rvest)
 import(tidyr)

NEWS.md

@@ -1,87 +1,68 @@
 # hockeystick 0.0.0.9000
-
 * Added a `NEWS.md` file to track changes to the package.
 
 # hockeystick 0.1.0
-
 * Five datasets and warming stripes included in package
 
 # hockeystick 0.2.0
-
 * Add climate_grid() and hockeystick_update_all()
 
 # hockeystick 0.3.0
-
 * Add get_icecurves() and plot_icecurves() to visualize current and historic sea ice
 
 # hockeystick 0.3.4
-
 * Don't cache data by default, added write_cache options
 
 # hockeystick 0.4.0
-
 * Add get_temp2k() and plot_temp2k() to visualize global Common Era reconstructed temp
 
 # hockeystick 0.5.0
-
 * Add Atlantic hurricane data, get_hurricanes(), plot_hurricanes(), plot_hurricane_nrg()
 
 # hockeystick 0.5.1
-
 * Update caching approach to comply with CRAN policies
 
 # hockeystick 0.5.2
-
 * Add date/value annotations to charts
 
 # hockeystick 0.6.0
-
 * Add global emissions from GCP: get_emissions(), plot_emissions()
 
 # hockeystick 0.6.1
-
 * Fix leaving example data in cache
 
 # hockeystick 0.6.2
-
 * Update documentation to conform with R version 4.2
 
 # hockeystick 0.6.3
-
 * Add connectivity checks to conform with CRAN requirements
 
 # hockeystick 0.7.0
-
 * Added methane data and cumulative co2 emissions treemap visualization
 
 # hockeystick 0.7.1
-
 * Plot GCP emissions with land use change
 
 # hockeystick 0.7.2
-
 * url-specific connectivity checks
 
 # hockeystick 0.7.3
-
 * Fix climate grid connectivity checks
 
 # hockeystick 0.8.0
-
 * Add daily temperature data from ClimateReanalyzer.org
 
 # hockeystick 0.8.1
-
 * Select hurricane category in get_hurricanes() / Fix daily temp caching
 
 # hockeystick 0.8.2
-
 * Update new get_dailytemp() urls
 
 # hockeystick 0.8.3
-
 * Update to reflect climatereanalyzer switch to Copernicus data
 
 # hockeystick 0.8.4
-
 * Update to plot_temp_scatter() and plot_temp_monthly()
+
+# hockeystick 0.8.5
+* Add plot_carbontemp() and get_dailytemp_cop(), default to Copernicus

R/2kyears_temp.R

@@ -2,7 +2,7 @@
 #'
 #' Retrieves the Common Era Global Surface Temperature Reconstructions.
 #' Source is PAGES2k Consortium and NOAA National Centers for Environmental Information.
-#' \url{https://www.ncei.noaa.gov/access/paleo-search/study/26872)}
+#' \url{https://www.ncei.noaa.gov/access/paleo-search/study/26872}
 #'
 #' @name get_temp2k
 #' @param use_cache (boolean) Return cached data if available, defaults to TRUE. Use FALSE to fetch updated data.
@@ -50,7 +50,7 @@ hs_path <- tools::R_user_dir("hockeystick","cache")
 if (use_cache) {
   if (file.exists(file.path(hs_path,'temp2k.rds'))) return(invisible(readRDS((file.path(hs_path,'temp2k.rds')))))   }
 
-file_url <- 'https://www1.ncdc.noaa.gov/pub/data/paleo/pages2k/neukom2019temp/recons/Full_ensemble_median_and_95pct_range.txt'
+file_url <- 'https://www.ncei.noaa.gov/pub/data/paleo/pages2k/neukom2019temp/recons/Full_ensemble_median_and_95pct_range.txt'
 connected <- .isConnected(file_url)
 if (!connected) {message("Retrieving remote data requires internet connectivity."); return(invisible(NULL))}
 

R/carbon.R

@@ -47,13 +47,13 @@ if (use_cache & !write_cache) {
   if (file.exists(file.path(hs_path,'maunaloa.rds'))) return(invisible(readRDS((file.path(hs_path,'maunaloa.rds')))))
   }
 
-file_url <- 'ftp://aftp.cmdl.noaa.gov/products/trends/co2/co2_mm_mlo.txt'
+file_url <- 'https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_mm_mlo.csv'
 connected <- .isConnected(file_url)
 if (!connected) {message("Retrieving remote data requires internet connectivity."); return(invisible(NULL))}
 
 dl <- tempfile()
 download.file(file_url, dl)
-maunaloa <- suppressMessages( read_table(dl, col_names = FALSE, skip = 63) )
+maunaloa <- suppressMessages( read_csv(dl, col_names = FALSE, skip = 41) )
 colnames(maunaloa) <- c('year', 'month', 'date', 'average', 'trend', 'ndays','stdev','unc')
 maunaloa$date <- ceiling_date(ymd(paste(maunaloa$year, maunaloa$month, '01',sep='-')), unit='month')-1
 

R/daily_temp.R

@@ -1,6 +1,6 @@
 #' Download and plot essential climate data
 #'
-#' Retrieves the daily air or sea-surface temperature data since 1979 from ClimateReanalyzer.org
+#' Retrieves the daily air or sea-surface temperature data since 1940 from ClimateReanalyzer.org
 #' Source is University of Maine Climate Change Institute.
 #' \url{https://climatereanalyzer.org/clim/t2_daily/}
 #'
@@ -158,16 +158,17 @@ invisible(daily_temperature)
 
 #' Download and plot essential climate data
 #'
-#' Plots the daily temperatures since 1940 and current anomaly data 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_dailytempcop()` with ggplot2. The output ggplot2 object may be further modified.
 #'
 #'
 #' @name plot_dailytemp
-#' @param dataset Name of the tibble generated by `get_dailytemp`
+#' @param dataset Name of the tibble generated by `get_dailytempcop` or `get_dailytemp`
 #' @param print (boolean) Display daily temperature ggplot2 chart, defaults to TRUE. Use FALSE to not display chart.
 #' @param anomaly (boolean) Display current anomaly versus historic mean, defaults to TRUE.
 #' @param maxtemp (boolean) Display current deviation versus historic max, defaults to FALSE.
 #' @param current_year (numeric) Year to highlight in alternate color, defaults to current year.
 #' @param title_lab (string) Title to override default chart title. Default title pulls region name from dataset attributes.
+#' @param cop (boolean) Flag for chart caption, TRUE = Copernicus, FALSE =. ClimateReanalyzer.org
 #'
 #' @return Invisibly returns a ggplot2 object with daily temperature anomaly chart
 #'
@@ -180,15 +181,15 @@ invisible(daily_temperature)
 #' @examples
 #' \donttest{
 #' # Fetch temperature anomaly:
-#' dailydata <- get_dailytemp()
+#' dailydata <- get_dailytempcop()
 #' #
 #' # Plot output using package's built-in ggplot2 defaults
 #' plot_dailytemp(dailydata)
 #'
 #' # Don't plot anomaly shading and highight specific year
 #' plot_dailytemp(anomaly = FALSE, current_year = 2012)
 #'
-#' # Or just call plot_temp(), which defaults to get_temp() dataset
+#' # Or just call plot_temp(), which defaults to get_dailytempcop() dataset
 #' plot_dailytemp()
 #'
 #' p <- plot_dailytemp(dailydata, print = FALSE)
@@ -198,9 +199,9 @@ invisible(daily_temperature)
 #'
 #' @export
 
-plot_dailytemp <- function(dataset = get_dailytemp(), print = TRUE, anomaly = FALSE, maxtemp = FALSE,
+plot_dailytemp <- function(dataset = get_dailytempcop(), print = TRUE, anomaly = FALSE, maxtemp = FALSE,
                            current_year = as.numeric(substr(Sys.Date(), 1, 4)),
-                           title_lab = 'Daily Average Air Temperature') {
+                           title_lab = 'Daily Average Air Temperature', cop=TRUE) {
 
   if (is.null(dataset)) return(invisible(NULL))
 
@@ -234,9 +235,12 @@ if (title_lab == "Daily Average Air Temperature") {
 
 # Color code notes: 'A': all years, 'M': mean, 'L': latest.
 
+captionsource <- if (cop) paste0('Source: EU Copernicus Climate Service\ncds.climate.copernicus.eu as of ', latest)
+                    else
+                          paste0('Source: Climate Change Institute, University of Maine\nClimateReanalyzer.org as of ', latest)
+
 plot <- ggplot(dataset) +
     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) +
@@ -245,7 +249,7 @@ plot <- ggplot(dataset) +
                  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),
+         caption = captionsource,
          color = NULL) +
     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),
@@ -273,7 +277,7 @@ if (anomaly) {
   labs(subtitle = subtitle_lab) }
 
 if (maxtemp) {
-  subtitle_lab <- '2-meter temperature since 1979, mean, and deviation from historic max'
+  subtitle_lab <- '2-meter temperature since 1940, mean, and deviation from historic max'
 
   if (region == 'World (60S-60N)' | region == 'North Atlantic' | region == 'WS' | region == 'AS')
     subtitle_lab <- 'Sea surface temperature since 1982, mean, and current anomaly'
@@ -297,3 +301,93 @@ if (maxtemp) {
   if (print) suppressMessages( print(plot) )
   invisible(plot)
 }
+
+
+#' Download and plot essential climate data
+#'
+#' Retrieves the daily air temperature since 1940 from the EU Copernicus Service
+#' \url{https://cds.climate.copernicus.eu/#!/home}
+#'
+#' @name get_dailytempcop
+#' @param use_cache (boolean) Return cached data if available, defaults to TRUE. Use FALSE to fetch updated data.
+#' @param write_cache (boolean) Write data to cache, defaults to FALSE. Use TRUE to write data to cache for later use. Can also be set using options(hs_write_cache=TRUE)
+#' @param region (string) Region selection, defaults to world air temperature. Options are: World Air "W".
+#'
+#' @return Invisibly returns a tibble with the daily 2-meter air temperatures since 1940 as well as historic mean by day-of-year and current anomaly versus mean.
+#'
+#' `get_dailytempcop` invisibly returns a tibble with the daily temperatures since 1940 as well as mean by day-of-year and anomaly.
+#'
+#' Region options include world air (default).
+#' The historic daily mean-by-day period defaults to 1991-2020.
+#'
+#' Data are updated daily.
+#'
+#' @importFrom utils download.file head tail
+#' @importFrom readr parse_number
+#' @import tidyr
+#' @import dplyr
+#'
+#' @examples
+#' \donttest{
+#' # Fetch temp anomaly from cache if available:
+#' dailytemps <- get_dailytempcop()
+#' #
+#' # Force cache refresh:
+#' dailytemps <- get_dailytempcop(use_cache=FALSE)
+#' #
+#' # Review cache contents and last update dates:
+#' hockeystick_cache_details()
+#' #
+#' # Plot output using package's built-in ggplot2 settings
+#' plot_dailytemp(dailytemps) }
+#'
+#' @author Hernando Cortina, \email{hch@@alum.mit.edu}
+#' @references
+#' \itemize{
+#' \item Copernicus: \url{https://cds.climate.copernicus.eu/#!/home}
+#'
+#' 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_dailytempcop <- function(use_cache = TRUE, write_cache = getOption("hs_write_cache"), region = 'W') {
+
+  hs_path <- tools::R_user_dir("hockeystick", "cache")
+
+  if (use_cache) {
+    if (file.exists(file.path(hs_path, 'dailytempcop.rds')))
+
+    {cached_temp <- readRDS((file.path(hs_path, 'dailytempcop.rds')))
+    cached_region <- attr(cached_temp, "hs_daily_region")
+
+    if (region==cached_region) return(invisible(cached_temp)) }
+  }
+
+  file_url <- 'https://sites.ecmwf.int/data/climatepulse/data/series/era5_daily_series_2t_global.csv'
+
+  connected <- .isConnected(file_url)
+  if (!connected) {message("Retrieving remote data requires internet connectivity."); return(invisible(NULL))}
+
+  dl <- tempfile()
+  download.file(file_url, dl)
+  temp_csv <- read.csv(dl, skip = 18)
+
+  colnames(temp_csv) <- c('date', 'temp', '1991-2020 mean', 'temp_anom', 'status' )
+  temp_csv$date <- as.Date(temp_csv$date)
+  temp_csv$year <- lubridate::year(temp_csv$date)
+  temp_csv$dummy_date <- as.Date(paste("1925", lubridate::month(temp_csv$date), lubridate::day(temp_csv$date),sep = '-'))
+
+  temp_csv <- temp_csv |> filter(!is.na(dummy_date))
+  temp_csv <- temp_csv |> group_by(year) |> mutate(day_of_year = row_number()) |> ungroup()
+
+  daily_temperature <- temp_csv |> select(year, day_of_year, date, temp, `1991-2020 mean`, temp_anom, dummy_date) |> as_tibble()
+
+  attr(daily_temperature, "hs_daily_region") <- region
+
+  if (write_cache) saveRDS(daily_temperature, file.path(hs_path, 'dailytempcop.rds'))
+
+  invisible(daily_temperature) }