calc_light_merged throws deprecated error

Open spencer-tassone opened this issue 1 year ago • 1 comments

Brief problem description

I am trying to use the calc_light_merged function to model PAR based on observed PAR and the smoothed PAR produced with calc_light. However, the calc_light_merged function produces an error caused by a function that is deprecated in dplyr (rename_vars). Is there a work around for this issue?

# 1. Load libraries ----
library(tidyverse)
library(nasapower)
library(streamMetabolizer)

# 2. Download shortwave radiation from NASA POWER ----
nasa_par <- get_power(
  community = 'ag',
  pars = c('ALLSKY_SFC_PAR_TOT'), # All Sky Surface PAR Total (W/m^2) 
  temporal_api = 'hourly',
  lonlat = c(-78.6, 38.7),
  dates = '2010-09-19')

# 3. Some data wrangling to create the 2-column data frame needed for calc_light_merged ----
nasa_par_df <- nasa_par %>%
  mutate(dateTime = make_datetime(year = YEAR,
                                  month = MO,
                                  day = DY,
                                  hour = HR),
         solar.time = calc_solar_time(dateTime, -78.6), # throws a warning but still works
         light = convert_SW_to_PAR(ALLSKY_SFC_PAR_TOT)) %>% 
  select(solar.time, light) %>% 
  data.frame()
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `solar.time = calc_solar_time(dateTime, -78.6)`.
#> Caused by warning in `lookup_timezone()`:
#> ! Google timezone lookup now requires an API key; see http://g.co/dev/maps-no-account or provide the timezone

max_PAR_value <- max(nasa_par_df$light, na.rm = TRUE)

# 4. Apply calc_light_merged ----
light_mod <- nasa_par_df %>%
  mutate(light = calc_light_merged(PAR.obs = nasa_par_df,
                                   solar.time = solar.time,
                                   latitude = 38.7,
                                   longitude = -78.6,
                                   max.PAR = max_PAR_value))
#> Error in `mutate()`:
#> ℹ In argument: `light = calc_light_merged(...)`.
#> Caused by error:
#> ! error in evaluating the argument 'object' in selecting a method for function 'deunitted': `rename_vars()` was deprecated in dplyr 0.8.4 and is now defunct.
#> ℹ Please use `tidyselect::vars_rename()` instead.

^{Created on 2024-10-22 with reprex v2.1.1}

devtools::session_info()
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#>  version  R version 4.4.1 (2024-06-14 ucrt)
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#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
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#> 
#> ──────────────────────────────────────────────────────────────────────────────

^{Created on 2024-10-22 with reprex v2.1.1}

Oct 22 '24 19:10 spencer-tassone

Spencer,

If it were me I would simply use the calc_light function. We are working on a paper that shows that using such idealized light is not much of a problem. Then when you go to predict that day’s GPP, use the —real-- light from NASA. This way you also main independence of not using light to predict something estimated from the same light.

As for the error. 1. Try outside of a big tidyverse function to make sure you get the error outside of mutate. Then if brave you can make the recommended fix in the calc_light_merged function, see if now works, and get a pull request.

But I would use calc_light.

Bob

On Oct 22, 2024, at 1:38 PM, Spencer Tassone, Ph.D. @.***> wrote:

Brief problem description

I am trying to use the calc_light_merged function to model PAR based on observed PAR and the smoothed PAR produced with calc_light. However, the calc_light_merged function produces an error caused by a function that is deprecated in dplyr (rename_vars). Is there a work around for this issue?

1. Load libraries ----

library(tidyverse) library(nasapower) library(streamMetabolizer)

2. Download shortwave radiation from NASA POWER ----

nasa_par <- get_power( community = 'ag', pars = c('ALLSKY_SFC_PAR_TOT'), # All Sky Surface PAR Total (W/m^2) temporal_api = 'hourly', lonlat = c(-78.6, 38.7), dates = '2010-09-19')

3. Some data wrangling to create the 2-column data frame needed for calc_light_merged ----

nasa_par_df <- nasa_par %>% mutate(dateTime = make_datetime(year = YEAR, month = MO, day = DY, hour = HR), solar.time = calc_solar_time(dateTime, -78.6), # throws a warning but still works light = convert_SW_to_PAR(ALLSKY_SFC_PAR_TOT)) %>% select(solar.time, light) %>% data.frame() #> Warning: There was 1 warning in mutate(). #> ℹ In argument: solar.time = calc_solar_time(dateTime, -78.6). #> Caused by warning in lookup_timezone(): #> ! Google timezone lookup now requires an API key; see http://g.co/dev/maps-no-account or provide the timezone

max_PAR_value <- max(nasa_par_df$light, na.rm = TRUE)

4. Apply calc_light_merged ----

light_mod <- nasa_par_df %>% mutate(light = calc_light_merged(PAR.obs = nasa_par_df, solar.time = solar.time, latitude = 38.7, longitude = -78.6, max.PAR = max_PAR_value)) #> Error in mutate(): #> ℹ In argument: light = calc_light_merged(...). #> Caused by error: #> ! error in evaluating the argument 'object' in selecting a method for function 'deunitted': rename_vars() was deprecated in dplyr 0.8.4 and is now defunct. #> ℹ Please use tidyselect::vars_rename() instead. Created on 2024-10-22 with reprex v2.1.1 https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Freprex.tidyverse.org%2F&data=05%7C02%7Cbob.hall%40flbs.umt.edu%7Cca0d90c1329a4e105ce708dcf2d12915%7C68407ce503da49ffaf0a724be0d37c9d%7C0%7C0%7C638652227355026839%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=H5Jihx58yr01SSKzpJjBwV%2B84YPjBcbAoiVlDQoNXFw%3D&reserved=0 devtools::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.4.1 (2024-06-14 ucrt) #> os Windows 11 x64 (build 22631) #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate English_United States.utf8 #> ctype English_United States.utf8 #> tz America/New_York #> date 2024-10-22 #> pandoc 3.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.1) #> cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.1) #> devtools 2.4.5 2022-10-11 [1] CRAN (R 4.4.1) #> digest 0.6.36 2024-06-23 [1] CRAN (R 4.4.1) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.4.1) #> evaluate 0.24.0 2024-06-10 [1] CRAN (R 4.4.1) #> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.1) #> fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.1) #> glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.1) #> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.1) #> htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.1) #> httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.1) #> knitr 1.48 2024-07-07 [1] CRAN (R 4.4.1) #> later 1.3.2 2023-12-06 [1] CRAN (R 4.4.1) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.1) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.1) #> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.1) #> mime 0.12 2021-09-28 [1] CRAN (R 4.4.0) #> miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.1) #> pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.4.1) #> pkgload 1.4.0 2024-06-28 [1] CRAN (R 4.4.1) #> profvis 0.3.8 2023-05-02 [1] CRAN (R 4.4.1) #> promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.1) #> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.1) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.1) #> Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.1) #> remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.1) #> reprex 2.1.1 2024-07-06 [1] CRAN (R 4.4.1) #> rlang 1.1.4 2024-06-04 [1] CRAN (R 4.4.1) #> rmarkdown 2.27 2024-05-17 [1] CRAN (R 4.4.1) #> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.1) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.1) #> shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.1) #> stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0) #> stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.1) #> urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.4.1) #> usethis 2.2.3 2024-02-19 [1] CRAN (R 4.4.1) #> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.1) #> withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.1) #> xfun 0.45 2024-06-16 [1] CRAN (R 4.4.1) #> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.1) #> yaml 2.3.9 2024-07-05 [1] CRAN (R 4.4.1) #> #> [1] C:/Users/stassone/AppData/Local/Programs/R/R-4.4.1/library #> #> ────────────────────────────────────────────────────────────────────────────── Created on 2024-10-22 with reprex v2.1.1 https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Freprex.tidyverse.org%2F&data=05%7C02%7Cbob.hall%40flbs.umt.edu%7Cca0d90c1329a4e105ce708dcf2d12915%7C68407ce503da49ffaf0a724be0d37c9d%7C0%7C0%7C638652227355047958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=stjile04PdssIz0zXqQgmp%2FR90VXi6MbqR3%2Fgy7GOCg%3D&reserved=0 — Reply to this email directly, view it on GitHub https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FDOI-USGS%2FstreamMetabolizer%2Fissues%2F434&data=05%7C02%7Cbob.hall%40flbs.umt.edu%7Cca0d90c1329a4e105ce708dcf2d12915%7C68407ce503da49ffaf0a724be0d37c9d%7C0%7C0%7C638652227355058500%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=xy%2B%2Bkxb%2ByVOTeLRYclUiOdE%2BCY4Xw3ZSlXTyigJtWgo%3D&reserved=0, or unsubscribe https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAC4CU5QXFK2N7LKK3SQIILLZ42SUXAVCNFSM6AAAAABQNHPLZWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGYYDMMZRG43DQNI&data=05%7C02%7Cbob.hall%40flbs.umt.edu%7Cca0d90c1329a4e105ce708dcf2d12915%7C68407ce503da49ffaf0a724be0d37c9d%7C0%7C0%7C638652227355068586%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=mlyn%2F4yZXQTT%2Bfm7DDKyuPaEniGKHUhV0dM00OuqcDc%3D&reserved=0. 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Oct 23 '24 14:10 robohall