version 0.72.4

Wycology · May 13, 2021 · 4889f53 · 4889f53
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: chillR
 Type: Package
 Title: Statistical Methods for Phenology Analysis in Temperate Fruit
         Trees
-Version: 0.72.2
-Date: 2021-01-06
+Version: 0.72.4
+Date: 2021-05-13
 Authors@R: 
     person(given = "Eike",
              family = "Luedeling",
@@ -33,7 +33,7 @@ Depends: R (>= 3.5.0)
 Imports: pls, dplyr, rlang, Kendall, fields, sp, readxl, XML, httr,
         grDevices, graphics, jsonlite, stats, utils, RMAWGEN, RCurl,
         R.utils, raster, ggplot2, assertthat, reshape2, plyr, Rcpp,
-        GenSA
+        GenSA, lubridate
 LinkingTo: Rcpp
 Suggests: testthat, knitr, rmarkdown
 VignetteBuilder: knitr
@@ -42,8 +42,8 @@ LazyData: TRUE
 RoxygenNote: 7.1.1
 Encoding: UTF-8
 NeedsCompilation: yes
-Packaged: 2021-01-06 16:05:41 UTC; EL
+Packaged: 2021-05-13 08:21:44 UTC; Eike
 Author: Eike Luedeling [aut, cre] (<https://orcid.org/0000-0002-7316-3631>)
 Maintainer: Eike Luedeling <[email protected]>
 Repository: CRAN
-Date/Publication: 2021-01-06 17:40:14 UTC
+Date/Publication: 2021-05-13 09:42:18 UTC
diff --git a/MD5 b/MD5
@@ -1,5 +1,5 @@
-d457746386db93c0e82f36fbd9b3983e *DESCRIPTION
-629deffecf325076d77af6cae3a2b9e8 *NAMESPACE
+e3727273e33106d1f6433bbdae5c013d *DESCRIPTION
+d49b6d1efd4ce5c1bd5cab77ee2ae013 *NAMESPACE
 2c3732bcc5a9bf44dc8546b620067f2c *R/Date2YEARMODA.R
 bac838ea1d86125368b0203c4b34f774 *R/Empirical_temperature_curve.R
 db123cd9bd4773547581d011bc5140ba *R/PLS_chill_force.R
@@ -33,12 +33,10 @@ dc97e072c946637d8f9fc95b9e9aa61b *R/filter_temperatures.R
 9b328eff5117fe3efc7f9a8cf95589e5 *R/getClimateWizardData.R
 d8f660643b617b2dec1617172c363004 *R/getClimateWizard_scenarios.R
 4deec0fee446626e2151a3f3aed3d2b4 *R/get_last_date.R
-69a64f27ec8482f328bf082ebd6318c9 *R/get_weather.R
-e68f445f52433eeac71688294099ed3f *R/handle_chile_agromet.R
-3156aae43a53569ade8866a02b76df44 *R/handle_cimis.R
-690800799883b00f9c6d30cf5930936c *R/handle_gsod.R
+033fefd8898f54fbd4cc0b8dccefaca9 *R/get_weather.R
+8479dab7c3231c72ad42ec28f61498ad *R/handle_cimis.R
+491e70af50cd9b1876349811ff04afe1 *R/handle_gsod.R
 7d872170a6f9bacc1a3715ddafa9671b *R/handle_ucipm.R
-5ac1a7f105cf2c63fd0ffb49aad44645 *R/handle_wunderground.R
 0b3c267a80549ee4d494ae6c667fc5a0 *R/identify_common_string.R
 ad747f4cff628395e600681ef58e49c1 *R/interpolate_gaps.R
 19f3333da9a21a836a8613f78757edb0 *R/interpolate_gaps_hourly.R
@@ -50,12 +48,13 @@ e446e6b58d584ebe0619979386c88adb *R/make_california_UCIPM_station_list.R
 fdebf7c96c36d211b29cf12d3c1a5371 *R/make_climate_scenario.R
 4dff456409a5e3ffde4119f1e6319b71 *R/make_climate_scenario_from_files.R
 525ca5ef9c198c18f077a9d25695943a *R/make_daily_chill_figures.R
-7c5705596f5b783bd8db87de4d51ea8a *R/make_daily_chill_plot.R
+08a43eac512e5b0956dca8850a8d0588 *R/make_daily_chill_plot.R
 4f973c0eed3ee38bca8e1aa84bad2f54 *R/make_hourly_temps.R
 a1d5d1c4d4e93581bbeaee5ebd89ac7a *R/make_multi_pheno_trend_plot.R
 5438bc5b39c4ac8b3ff7c0c65076c54d *R/make_pheno_trend_plot.R
 de909adb304bf2f0019429ccaa3651d0 *R/ordered_climate_list.R
-85dd8edb895dcbdd1d60dfb34e23b5a0 *R/patch_daily_temperatures.R
+79b42e22bf5c2a620d0ae17955ac047d *R/patch_daily_temperatures.R
+dcf0f3ed394378d01e3f2acc0d3a9c04 *R/patch_daily_temps.R
 028e7c246ca0213c6fdfbaa6d52e5a96 *R/phenologyFitter.R
 f81fc5b2145b11c203b3cf3c9b5208f3 *R/plot_climate_scenarios.R
 b03f11972bbae36d66c08199eea57a04 *R/plot_pheno_results.R
@@ -69,22 +68,22 @@ fecac721becb450fc819054b064b546a *R/select_by_file_extension.R
 ee68a99d334dae5298f1999d9d8bf231 *R/tempResponse_daily_list.R
 2a16036b51396e4331498268b1b25f97 *R/tempResponse_hourtable.R
 5202ac8baf40991b771c4263c4fada1a *R/temp_models.R
-a3141773af4567ed9fe2770c850b6b31 *R/temperature_generation.R
+63be99d652799938f449d4818770cee5 *R/temperature_generation.R
 4fdfa9e62cbe2a48c7d68d7db87e224e *R/temperature_scenario_baseline_adjustment.R
 7d64a33b5fe00024ed52175ec25f315a *R/temperature_scenario_from_records.R
 58b01a0c11e9051037d667f14a32442b *R/test_if_equal.R
-3aae7619cf361b041d148af7bf7f3bd6 *R/weather2chillR.R
-c912040bba5168a09841bc96df65b3e5 *build/vignette.rds
+adad21e8a31582947f71f435b537534e *R/weather2chillR.R
+4773bcc17b68f0e60ae5c3ee008f561d *build/vignette.rds
 bc6c01922610dd0c1f80f97a938f00ef *data/KA_bloom.rda
 1242aa70ce0b9b8f354f4e28db4ccfc9 *data/KA_weather.rda
 3739b578469f1b842feb2eb018b72304 *data/Winters_hours_gaps.rda
 dfe396905139e63e255d9049c1f8fc0d *data/california_stations.rda
 5dfd11770fd123f3c421f261115a32f2 *inst/doc/PhenoFlex.R
 abc91f336779baf8c88868f79a0bb963 *inst/doc/PhenoFlex.Rmd
-4f5c32d38bc9a2bfd50af182fff6641e *inst/doc/PhenoFlex.html
+e93f62d189c45d16040ec6ab581f8282 *inst/doc/PhenoFlex.html
 7c72a0fe6808552265f8f184891d8d74 *inst/doc/hourly_temperatures.R
 757c48876fdf0cae52e8196d2f46c3c7 *inst/doc/hourly_temperatures.Rmd
-df9ebf58f8c479c8ecfff057b1127054 *inst/doc/hourly_temperatures.html
+3d6239c52949646deeabb2f3888a8520 *inst/doc/hourly_temperatures.html
 83fcf726305bc980f0d2c9779373c53d *man/Chilling_Hours.Rd
 f85216497c478b89bfe70c34c7d33f45 *man/ChuineCF.Rd
 47c058abb6819d8fb5d16de3a5805869 *man/ChuineFstar.Rd
@@ -147,12 +146,10 @@ c6102179f537357be111df59428bdfe3 *man/genSeasonList.Rd
 fd83a154fa7b89c009eb7b1d6a0a4fc8 *man/getClimateWizardData.Rd
 9c2bf12d74a17ded902b97d1d2262b49 *man/getClimateWizard_scenarios.Rd
 f81935e7d4e4f39f91824910e76a63fe *man/get_last_date.Rd
-951ea2e3772afb2503628e13f4445ace *man/get_weather.Rd
-b9a2b15b40455bf01ee00284eab5cba7 *man/handle_chile_agromet.Rd
+bf64a89d8704072f00762f4ae1add3c7 *man/get_weather.Rd
 61dd75767b6ac754072a13576054d7e3 *man/handle_cimis.Rd
 213430713471110de1acc578a63c7ba5 *man/handle_gsod.Rd
 609d2110de5685306fef8d94f26f2c67 *man/handle_ucipm.Rd
-c974452bc11b3b23504113739ee8fecd *man/handle_wunderground.Rd
 26a1421a1021c714cb7ad88b6d8774da *man/identify_common_string.Rd
 67534c0df47c70967756ba384510c185 *man/interpolate_gaps.Rd
 1d0d4e75b469fbc4031c61690cd90d89 *man/interpolate_gaps_hourly.Rd
@@ -172,7 +169,8 @@ b200db12c9f5e40fbd82c06ea7ef3744 *man/make_hourly_temps.Rd
 b4e391850a093b56e00ae75797304d9a *man/make_multi_pheno_trend_plot.Rd
 748973fd05666b00f808c7870dfc65a7 *man/make_pheno_trend_plot.Rd
 9a7d22a0ef6b24adf1520fb999299ab6 *man/ordered_climate_list.Rd
-1e3d1078b3591bf038824afa54452fe3 *man/patch_daily_temperatures.Rd
+6a4938a0ca7f6cacea4a74a8d4736c28 *man/patch_daily_temperatures.Rd
+cb4268050a7f62b8ad20027eab0b9884 *man/patch_daily_temps.Rd
 b4a56087eef174f460d88238e0745ba1 *man/phenologyFit.Rd
 5e02249b39862254bb2438c7e6b716e4 *man/phenologyFitter.Rd
 a5c8377acbe4cefccda24e5b975b8d0f *man/plot.bootstrap_phenologyFit.Rd
@@ -200,7 +198,7 @@ feff60c83c9484cf21660ddbb213164c *man/temperature_generation.Rd
 648271dbf2830c2f7626744ea1f0b170 *man/temperature_scenario_baseline_adjustment.Rd
 cdc95ca5b9335d37fa11d6ac6dae81da *man/temperature_scenario_from_records.Rd
 cfebf637248c5bee7ac1337c01eb40c3 *man/test_if_equal.Rd
-a2997d85ccba97506c1e95856c3bc1f3 *man/weather2chillR.Rd
+c11a17ce09ec2a891164ed808cdb91b0 *man/weather2chillR.Rd
 ba3eedd7d0c69cbd2cf4ae7e04968de5 *src/PhenoFlex.cpp
 f8c18a21932b45f82cd095c2fb383e85 *src/RcppExports.cpp
 67d4d5b7b77d8735d8dd272ce64e8d01 *tests/testthat.R

diff --git a/NAMESPACE b/NAMESPACE
@@ -60,11 +60,9 @@ export(getClimateWizardData)
 export(getClimateWizard_scenarios)
 export(get_last_date)
 export(get_weather)
-export(handle_chile_agromet)
 export(handle_cimis)
 export(handle_gsod)
 export(handle_ucipm)
-export(handle_wunderground)
 export(identify_common_string)
 export(interpolate_gaps)
 export(interpolate_gaps_hourly)
@@ -85,6 +83,7 @@ export(make_multi_pheno_trend_plot)
 export(make_pheno_trend_plot)
 export(ordered_climate_list)
 export(patch_daily_temperatures)
+export(patch_daily_temps)
 export(phenologyFit)
 export(phenologyFitter)
 export(plot_PLS)
@@ -151,6 +150,7 @@ importFrom(graphics,strwidth)
 importFrom(graphics,text)
 importFrom(httr,POST)
 importFrom(httr,content)
+importFrom(lubridate,month)
 importFrom(pls,crossval)
 importFrom(pls,explvar)
 importFrom(pls,plsr)

diff --git a/R/get_weather.R b/R/get_weather.R
@@ -8,9 +8,6 @@
 #' Summary of the Day - "GSOD"
 #' (https://data.noaa.gov/dataset/global-surface-summary-of-the-day-gsod)
 #' 
-#' Weather Underground ("Wunderground") airport database - "Wunderground"
-#' (http://www.wunderground.com/)
-#' 
 #' California Irrigation Management Information System (CIMIS) - "CIMIS"
 #' (http://www.cimis.water.ca.gov/)
 #' 
@@ -34,8 +31,8 @@
 #' 'chillRcode' of a weather station in the specified database. See details.
 #' @param time_interval numeric vector with two elements, specifying the start
 #' and end date of the period of interest.
-#' @param database the database to be accessed. Must be "GSOD", "CIMIS",
-#' "Wunderground" or "UCIPM". Since among these, "UCIPM" is the most
+#' @param database the database to be accessed. Must be "GSOD", "CIMIS"
+#' or "UCIPM". Since among these, "UCIPM" is the most
 #' comprehensive one for California, the initial area of interest, this is the
 #' default.
 #' @param station_list if the list of weather stations has already been
@@ -59,8 +56,7 @@
 #' @note Many databases have data quality flags, which may sometimes indicate
 #' that data aren't reliable. These are not considered by this function!
 #' 
-#' see the documentation of the handler functions (e.g. handle_wunderground,
-#' handle_ucipm) for details.
+#' see the documentation of the handler functions (e.g. handle_ucipm) for details.
 #' @author Eike Luedeling
 #' @references The chillR package:
 #' 
@@ -104,8 +100,6 @@ get_weather<-function(location,time_interval=NA,database="UCIPM",station_list=NU
                                              stations_to_choose_from=stations_to_choose_from,end_at_present=end_at_present),
                           CIMIS = handle_cimis("list_stations",location=location,time_interval=time_interval,station_list=station_list,
                                                stations_to_choose_from=stations_to_choose_from,end_at_present=end_at_present),
-                          Wunderground = handle_wunderground("list_stations",location=location,time_interval=time_interval,station_list=station_list,
-                                                             stations_to_choose_from=stations_to_choose_from,end_at_present=end_at_present),
                           UCIPM = handle_ucipm("list_stations",location=location,time_interval=time_interval,station_list=station_list,
                                                stations_to_choose_from=stations_to_choose_from,end_at_present=end_at_present))
       if(is.null(sorted_list)) warning("No valid database specified") else
@@ -122,8 +116,6 @@ get_weather<-function(location,time_interval=NA,database="UCIPM",station_list=NU
                                            end_at_present=end_at_present),
                         CIMIS = handle_cimis("download_weather",location=location,time_interval=time_interval,station_list=station_list,
                                              end_at_present=end_at_present),
-                        Wunderground = handle_wunderground("download_weather",location=location,time_interval=time_interval,station_list=station_list,
-                                                           end_at_present=end_at_present),
                         UCIPM = handle_ucipm("download_weather",location=location,time_interval=time_interval,station_list=station_list,
                                              end_at_present=end_at_present))
     if(is.null(weather)) warning("No valid database specified")