diff --git a/.Rbuildignore b/.Rbuildignore index e295b477..93e69b5a 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -15,6 +15,7 @@ data-raw/* R/plot-buoy-sst.R ^R/plot-buoy-sst\.R$ R/plot-buoy-sst*.R +^R-temp/$ notes/* ^README\.Rmd$ diff --git a/DESCRIPTION b/DESCRIPTION index dbebaff4..8f4653b3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -30,6 +30,9 @@ Authors@R: c( email = "chris.rooper@dfo-mpo.gc.ca", role = c("aut"), comment = c(ORCID = "0000-0003-2315-1269")), + person(c("K.", "L."), "Flynn", + email = "kelsey.flynn@dfo-mpo.gc.ca", + role = c("aut")), person("Kelsey", "Flynn", role = c("ctb")), person("Jessica", "Nephin ", diff --git a/NEWS.md b/NEWS.md index 1d81d168..8d87ffea 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,6 +5,18 @@ Developers: for some general tips for writing good bullets see https://style.tid ## Updates by date +* 2024-09-25 Update citation info (increment year to 2024, add Kelsey Flynn as + co-author) and obtain a DOI. See README or run `citation("pacea")`. + +* 2024-09-20 Monthly updates for: `buoy_sst`, and indices `ao`, `mei`, `npgo`, `oni`, `pdo`, and `soi`. + +* 2024-08-21 Monthly update for: `oisst_7day` and `oisst_month`. + +* 2024-08-06 Monthly update for: `oisst_7day`, `oisst_month` (both updated two + weeks earlier), `buoy_sst`, and indices `ao`, `oni`, `pdo`, and `soi`. + +* 2024-06-10 Monthly update for May: `oisst_7day`, `oisst_month` (both updated 2024-05-20), `buoy_sst`, and indices `ao`, `oni`, `pdo`, and `soi`. + * 2024-05-08 Added Pacific Herring stock assessment results, including new plotting functions (see `populations` vignette linked from README). diff --git a/R-temp/ecosystem-summary.R b/R-temp/ecosystem-summary.R new file mode 100644 index 00000000..05a33b23 --- /dev/null +++ b/R-temp/ecosystem-summary.R @@ -0,0 +1,102 @@ +##' Some example ideas for a species-specific Ecosystem Summary. Currently +##' ignored in .Rbuildignore as developing. +##' +##' Doing a herring example for now, based on Jennifer's manuscript. +##' Figure 11 gives the indicators that were identified in one or more +##' pressure-respose model. The ones we already have in pacea are: +##' * PDO +##' * SST_Spring - Mar-May, 1982-2019. Satellite measured sea surface temperature, +##' from AVHRR satellite +##' https://www.avl.class.noaa.gov/release/data_available/avhrr/index.htm - +##' website not working, 24/9/24. +##' ##' * SST_Summer - Apr-Jul, 1982-2019 +##' * SST_Fall - Sept-Nov, 1981-2019 + +##' * Upwelling (maybe not) +##' +##' +##' Do not have +##' * copepdods and total zooplankton in HG +##' * humpback whales +##' * Steller SeaLion +##' * hakeAcoustic_B - could get +##' * Arrowtooth, dogfish, cod, IPHC catch rates +##' * herring-related +##' @param species species of interest, might need stock also. Could save the +##' list of desired variables as a data list object, to then apply to the +##' relevant calculation and plotting functions. +##' @return +##' @export +##' @author Andrew Edwards +##' @examples +##' \dontrun{ +##' +##' } +ecosystem_summary <- function(species = "herring-example"){ + + par(mfcol = c(4, 2)) + years <- range(dplyr::filter(herring_recruitment, + region == "HG") %>% + select(year)) + + x_lim = c(lubridate::dmy(paste0("0101", min(years))), # day-month-year + lubridate::dmy(paste0("0101", max(years)))) + + plot(herring_recruitment, + region = "HG", + xlim = x_lim) + + plot(pdo, + xlim = x_lim) + + # For quickness for now, let's just look at buoy data for buoys within the + # study area defined in the manuscript. + # For now just eyeballing which buoys to use, easiest to id by names: + names_hg <- c("Central Dixon Entrance", + "South Moresby", # is maybe just outside, but relevant? + "North Hecate Strait", + "South Hecate Strait", + "West Sea Otter", + "East Dellwood Knolls") # also maybe just outside + + stn_id_hg <- dplyr::filter(buoy_metadata, + name %in% names_hg)$stn_id # not necessarily in + # same order as stn_id_hg. Though think + # will be given how I first listed the + # names above. TODO + + buoy_sst_hg <- dplyr::filter(buoy_sst, + stn_id %in% stn_id_hg) # generalise variable + # names at some point to not be HG + # specific TODO + + # Usual style of plot: + #for(i in 1:length(stn_id_hg)){ + # plot(buoy_sst_hg, + # stn_id = stn_id_hg[1]) %>% print() + #} + + # Want to calculate mean for each time period + buoy_sst_hg_spring <- list() + for(i in 1:length(stn_id_hg)){ + buoy_sst_hg_spring[[i]] <- + dplyr::filter(buoy_sst_hg, + stn_id %in% stn_id_hg[i], + lubridate::month(date) %in% c(3, 4, 5)) %>% + dplyr::mutate(year = lubridate::year(date)) %>% + dplyr::group_by(year) %>% + summarise(mean = mean(sst, + na.rm = TRUE)) + + # TODO add a check for how many days in the period, like in quality control + # for buoy_sst. + + plot(buoy_sst_hg_spring[[i]], + xlim = range(years), + main = paste0("Mean spring SST, ", + names_hg[i]), + type = "o") + + } + +} diff --git a/README.Rmd b/README.Rmd index eebdd1fa..4aad846d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -4,10 +4,13 @@ output: github_document +```{r, include = FALSE, eval = FALSE} load_all() rmarkdown::render("README.Rmd") - +``` + [![R-CMD-check](https://github.com/pbs-assess/pacea/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pbs-assess/pacea/actions/workflows/R-CMD-check.yaml) [![codecov](https://codecov.io/gh/pbs-assess/pacea/graph/badge.svg?token=93afkFJUVL)](https://codecov.io/gh/pbs-assess/pacea) +[![DOI](https://zenodo.org/badge/417554147.svg)](https://zenodo.org/doi/10.5281/zenodo.13840804) ![Visitors](https://api.visitorbadge.io/api/visitors?path=https%3A%2F%2Fgithub.com%2Fpbs-assess%2Fpacea&label=VISITORS&countColor=%23263759&style=flat&labelStyle=lower) @@ -345,15 +349,19 @@ This work is strongly motivated by, and based on, the [GSLea](https://github.com ## Citation -If you use `pacea` in your work then please cite it as +If you use `pacea` in your work then please cite it as (NOTE this has been +updated since the original release): -Edwards A.M., Tai T.C., Watson J., Peña M.A., Hilborn A., Hannah C.G., and Rooper - C.N. (2023). "pacea: An R package of Pacific ecosystem information to - help facilitate an ecosystem approach to fisheries management." - . +Edwards A.M., Tai T.C., Watson J., Peña M.A., Hilborn A., Hannah C.G., Rooper + C.N., and Flynn K.L. (2024). pacea: An R package of Pacific ecosystem information to + help facilitate an ecosystem approach to fisheries management. + , You may wish to add the date you installed it (using `pacea_installed()`). Use -`citation("pacea")` to get a version for LaTeX and R Markdown bibliographies. +`citation("pacea")` to get a version for LaTeX and R Markdown +bibliographies. Although the DOI badge at the top of this page ends in ...805, +the ...804 DOI is preferable because that will not change with any future +updates to the GitHub tag. So ...804 seems simpler and more consistent to use (thanks!). Also let us know of any applications. This will help us devote effort into maintaining `pacea`. @@ -366,7 +374,7 @@ and Oceans Canada (project 21-FS-03-13). We thank the following for contributing ideas, example code for ROMS output, model output, and/or helping with ideas and coding issues: -- Kelsey Flynn, Jessica Nephin, Lindsay Davidson, Strahan Tucker, +- Jessica Nephin, Lindsay Davidson, Strahan Tucker, Brianna Wright, Patrick Thompson, Matt Grinnell, Sean Anderson, Philina English, Chris Grandin, Jennifer Boldt, Kelly Young, and others. diff --git a/README.md b/README.md index 28887201..f0673ba7 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,8 @@ + @@ -42,7 +41,7 @@ to get you started. Currently, pacea contains: -- 205,179 calculations of daily sea surface temperature based on data +- 206,901 calculations of daily sea surface temperature based on data from 19 buoys. **Updated monthly.** - outputs from the spatial British Columbia continental margin (BCCM) @@ -70,7 +69,7 @@ Currently, pacea contains: record, that incorporates observations from different platforms (satellites, ships, buoys, and Argo floats): - - provided as weekly and monthly means from Sep 1981 to Apr 2024. + - provided as weekly and monthly means from Sep 1981 to Jul 2024. **Updated monthly.** - 9 climatic and oceanographic indices, such as the Pacific Decadal @@ -201,7 +200,7 @@ example: ``` r oni -#> # A tibble: 890 × 4 +#> # A tibble: 895 × 4 #> year month value anomaly #> #> 1 1950 1 24.7 -1.53 @@ -214,7 +213,7 @@ oni #> 8 1950 8 26.0 -0.42 #> 9 1950 9 25.8 -0.39 #> 10 1950 10 25.6 -0.44 -#> # ℹ 880 more rows +#> # ℹ 885 more rows ``` **What climatic and oceanographic indices are currently available, and @@ -339,16 +338,21 @@ colleagues for the Gulf of St Lawrence. ## Citation -If you use `pacea` in your work then please cite it as +If you use `pacea` in your work then please cite it as (NOTE this has +been updated since the original release): Edwards A.M., Tai T.C., Watson J., Peña M.A., Hilborn A., Hannah C.G., -and Rooper C.N. (2023). “pacea: An R package of Pacific ecosystem -information to help facilitate an ecosystem approach to fisheries -management.” . +Rooper C.N., and Flynn K.L. (2024). pacea: An R package of Pacific +ecosystem information to help facilitate an ecosystem approach to +fisheries management. , + You may wish to add the date you installed it (using `pacea_installed()`). Use `citation("pacea")` to get a version for LaTeX -and R Markdown bibliographies. +and R Markdown bibliographies. Although the DOI badge at the top of this +page ends in …805, the …804 DOI is preferable because that will not +change with any future updates to the GitHub tag. So …804 seems simpler +and more consistent to use (thanks!). Also let us know of any applications. This will help us devote effort into maintaining `pacea`. @@ -361,10 +365,9 @@ Fisheries and Oceans Canada (project 21-FS-03-13). We thank the following for contributing ideas, example code for ROMS output, model output, and/or helping with ideas and coding issues: -- Kelsey Flynn, Jessica Nephin, Lindsay Davidson, Strahan Tucker, - Brianna Wright, Patrick Thompson, Matt Grinnell, Sean Anderson, - Philina English, Chris Grandin, Jennifer Boldt, Kelly Young, and - others. +- Jessica Nephin, Lindsay Davidson, Strahan Tucker, Brianna Wright, + Patrick Thompson, Matt Grinnell, Sean Anderson, Philina English, + Chris Grandin, Jennifer Boldt, Kelly Young, and others. And a big thanks to Carley Colclough for expertly designing the pacea logo. diff --git a/data-raw/buoys/buoy-sst.R b/data-raw/buoys/buoy-sst.R index 49b91e66..56e1208e 100644 --- a/data-raw/buoys/buoy-sst.R +++ b/data-raw/buoys/buoy-sst.R @@ -100,6 +100,8 @@ dfo_data # 3.666 million rows when removing pre-1991 . Every few minutes h # so keeping with with_tz. # 9/11/2023 update: 3.797 million rows # 29/1/2024 update: 3.811 million rows + # 6/8/2024 update: 3.839 million rows + # 20/9/2024 update: 3.845 million rows summary(dfo_data) # Earliest is 1987, so not adding tons of data, yet not really worth # excluding 1987-1991 for our purposes (Andrea did since @@ -174,6 +176,7 @@ dfo_daily_mean # 158,012 rows up to 2023-08-23 # 158,638 2023-11-09 # 159,407 2023-02-17 # max(dfo_daily_mean$date) +# 160,467 2024-07-30 # Before doing two-hour quality control had less, not sure how many (can test by # changing num_two_hour_intervals_required) diff --git a/data-raw/coastwide-indices/coastwide-indices.R b/data-raw/coastwide-indices/coastwide-indices.R index 48a5f8b3..8541080e 100644 --- a/data-raw/coastwide-indices/coastwide-indices.R +++ b/data-raw/coastwide-indices/coastwide-indices.R @@ -457,8 +457,17 @@ if(check_index_changed(soi, soi_new)){ #NGPO # Useful background: -# http://www.o3d.org/npgo/ -download.file("http://www.o3d.org/npgo/npgo.php", +# http://www.o3d.org/npgo/ # Timed out on 10-06-2024, no time to dig +# into. Did once on 6-08-2024 then worked the second time (had looked on +# browser also, though doubt that mattered). Did download but looks like format +# has changed: download file is just html. But 'Download Index' link from https://www.o3d.org/npgo/ has not +# been updated since the latest already in pacea, though that isn't exactly +# what we used. So something has changed, but don't worry now as looks like +# data not updated anyway. +# 20-09-2024: changing filename to "https://www.o3d.org/npgo/data/NPGO.txt" +# which has been updated to August 2024. It used to be "http://www.o3d.org/npgo/npgo.php" + +download.file("http://www.o3d.org/npgo/data/NPGO.txt", destfile="npgo.txt", mode="wb", quiet = FALSE) @@ -480,7 +489,7 @@ npgo_new <-read.table("npgo.txt", stopifnot(npgo_new[1, 1:2] == c(1950, 1)) # Check still starts in January 1950 class(npgo_new) <- c("pacea_index", - class(npgo_new)) + class(npgo_new)) attr(npgo_new, "axis_name") <- "North Pacific Gyre Oscillation" @@ -496,7 +505,6 @@ if(check_index_changed(npgo, npgo_new)){ npgo <- npgo_new usethis::use_data(npgo, overwrite = TRUE) - plot(npgo) # TODO maybe update when plotting functions finalised } # ENSO MEI https://www.psl.noaa.gov/enso/mei @@ -605,6 +613,7 @@ tail(ao) tail(ao_new) check_index_changed(ao, ao_new) + if(check_index_changed(ao, ao_new)){ expect_equal(ao, ao_new[1:nrow(ao), ]) # See note at top if fails. Not tested diff --git a/data/ao.rda b/data/ao.rda index b150166d..f077528a 100644 Binary files a/data/ao.rda and b/data/ao.rda differ diff --git a/data/buoy_sst.rda b/data/buoy_sst.rda index 9e41d170..454245fe 100644 Binary files a/data/buoy_sst.rda and b/data/buoy_sst.rda differ diff --git a/data/mei.rda b/data/mei.rda index beda1c74..2be863cf 100644 Binary files a/data/mei.rda and b/data/mei.rda differ diff --git a/data/npgo.rda b/data/npgo.rda index 10ff14d0..11eadaef 100644 Binary files a/data/npgo.rda and b/data/npgo.rda differ diff --git a/data/oisst_7day.rda b/data/oisst_7day.rda index 590370d9..af5a6fea 100644 Binary files a/data/oisst_7day.rda and b/data/oisst_7day.rda differ diff --git a/data/oisst_month.rda b/data/oisst_month.rda index ceae7172..960f5eb8 100644 Binary files a/data/oisst_month.rda and b/data/oisst_month.rda differ diff --git a/data/oni.rda b/data/oni.rda index f6d49a2c..1176fcda 100644 Binary files a/data/oni.rda and b/data/oni.rda differ diff --git a/data/pdo.rda b/data/pdo.rda index 8485dd93..7160f4bf 100644 Binary files a/data/pdo.rda and b/data/pdo.rda differ diff --git a/data/soi.rda b/data/soi.rda index a746b217..88a42e81 100644 Binary files a/data/soi.rda and b/data/soi.rda differ diff --git a/inst/CITATION b/inst/CITATION index 13eaa656..1e81eccf 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -4,7 +4,8 @@ citHeader("To cite pacea in publications please use:") bibentry( bibtype = "misc", title = "pacea: An R package of Pacific ecosystem information to help facilitate an ecosystem approach to fisheries management", - author = "A. M. Edwards and T. C. Tai and J. Watson and M. A. Peña and A. Hilborn and C. G. Hannah and C. N. Rooper", - url = "https://github.com/pbs-assess/pacea", - year = "2023" + author = + "A. M. Edwards and T. C. Tai and J. Watson and M. A. Peña and A. Hilborn and C. G. Hannah and C. N. Rooper and K. L. Flynn", + url = "https://github.com/pbs-assess/pacea, https://zenodo.org/doi/10.5281/zenodo.13840804", + year = "2024" ) diff --git a/man/figures/README-north-hecate-temp.png b/man/figures/README-north-hecate-temp.png index 3f57ae38..53fd9822 100644 Binary files a/man/figures/README-north-hecate-temp.png and b/man/figures/README-north-hecate-temp.png differ diff --git a/man/figures/README-oni.png b/man/figures/README-oni.png index 282f1880..61d4cdd7 100644 Binary files a/man/figures/README-oni.png and b/man/figures/README-oni.png differ diff --git a/man/figures/README-pdo.png b/man/figures/README-pdo.png index 679f43ff..c1ef13b0 100644 Binary files a/man/figures/README-pdo.png and b/man/figures/README-pdo.png differ diff --git a/vignettes/buoys.Rmd b/vignettes/buoys.Rmd index bd2891aa..9198bad6 100644 --- a/vignettes/buoys.Rmd +++ b/vignettes/buoys.Rmd @@ -59,7 +59,7 @@ knitr::include_graphics(paste0(here::here(), (built with code in data-raw/buoys/buoys-map.R), and also shown at -https://github.com/IOS-OSD-DPG/Pacific_SST_Monitoring#eccc-buoy-data . +[https://github.com/IOS-OSD-DPG/Pacific_SST_Monitoring#eccc-buoy-data](https://github.com/IOS-OSD-DPG/Pacific_SST_Monitoring#eccc-buoy-data). Some of the recent data are also plotted on that website, by Andrea Hilborn, Charles Hannah and Lu Guan, which is automatically updated roughly every @@ -98,7 +98,7 @@ Plot data from a single buoy for all years, the default is for buoy C46205: plot(buoy_sst) ``` -The red lines gives the current year. Since `buoy_sst` has class `pacea_buoy`, +The red line gives the current year. Since `buoy_sst` has class `pacea_buoy`, `plot(buoy_sst)` function calls our tailored `plot.pacea_buoy()` function. The gap in the red line at the start of the year indicates missing data (or days that get excluded due to our protocols). diff --git a/vignettes/buoys.html b/vignettes/buoys.html index eef00655..d00db6b2 100644 --- a/vignettes/buoys.html +++ b/vignettes/buoys.html @@ -340,7 +340,7 @@

Buoy Sea Surface Temperature Data

Andrew Edwards

-

Last rendered on 09 November, 2023

+

Last rendered on 20 September, 2024

@@ -390,12 +390,12 @@

Daily average sea surface temperature from buoys

#> 19 Levels: Central Dixon Entrance East Dellwood Knolls ... West Sea Otter

The locations of the buoys are given by

-

(built with code in data-raw/buoys/buoys-map.R), and also shown at https://github.com/IOS-OSD-DPG/Pacific_SST_Monitoring#eccc-buoy-data .

+

(built with code in data-raw/buoys/buoys-map.R), and also shown at https://github.com/IOS-OSD-DPG/Pacific_SST_Monitoring#eccc-buoy-data.

Some of the recent data are also plotted on that website, by Andrea Hilborn, Charles Hannah and Lu Guan, which is automatically updated roughly every week (so look there for a quick glance at recent conditions). For pacea we have, with Andrea, adapted some of that code to include the data and create plotting functions in our package.

The wrangling of data is taken care of within pacea, and includes using protocols to remove certain flagged data, dealing with timezones and pesky daylight savings time changes, and averaging over a day (the original raw data are even higher resolution). We are still refining this to remove outliers – this has to be somewhat manual.

The sst value are saved in a tibble, which also has class pacea_buoy

buoy_sst
-#> # A tibble: 202,927 × 3
+#> # A tibble: 206,901 × 3
 #>    date       stn_id   sst
 #>    <date>     <fct>  <dbl>
 #>  1 1988-08-05 C46004  12.8
@@ -408,17 +408,17 @@ 
Daily average sea surface temperature from buoys

 #>  8 1988-08-12 C46004  12.7
 #>  9 1988-08-13 C46004  12.8
 #> 10 1988-08-14 C46004  12.9
-#> # ℹ 202,917 more rows
+#> # ℹ 206,891 more rows
 tail(buoy_sst)
 #> # A tibble: 6 × 3
 #>   date       stn_id   sst
 #>   <date>     <fct>  <dbl>
-#> 1 2023-11-03 C46304 10.3 
-#> 2 2023-11-04 C46304 10.6 
-#> 3 2023-11-05 C46304 10.6 
-#> 4 2023-11-06 C46304 10.3 
-#> 5 2023-11-07 C46304 10.3 
-#> 6 2023-11-08 C46304  9.87
+#> 1 2024-09-14 C46304 17.0 +#> 2 2024-09-15 C46304 16.8 +#> 3 2024-09-16 C46304 16.2 +#> 4 2024-09-17 C46304 15.0 +#> 5 2024-09-18 C46304 15.4 +#> 6 2024-09-19 C46304 15.3

with stn_id specifying each buoy as described above in buoy_metadata, and date based on UTC -8 hours (i.e. Pacific Standard Time, not changing due to daylight savings), and sst is the mean SST (deg C) for that day at that station; see ?buoy_sst for full details.

To see the ranges of dates for each buoy, use dplyr functions in the usual way:

buoy_ranges <- buoy_sst %>%
@@ -430,42 +430,37 @@ 
Daily average sea surface temperature from buoys

 #>    stn_id start      end       
 #>    <fct>  <date>     <date>    
 #>  1 C46004 1988-08-05 2023-06-17
-#>  2 C46036 1987-09-23 2023-11-08
-#>  3 C46131 1992-10-20 2023-11-08
-#>  4 C46132 1994-09-07 2023-11-08
+#>  2 C46036 1987-09-23 2024-07-09
+#>  3 C46131 1992-10-20 2024-09-19
+#>  4 C46132 1994-09-07 2024-09-19
 #>  5 C46134 2001-02-20 2016-12-08
-#>  6 C46145 1991-04-17 2023-11-08
-#>  7 C46146 1992-03-14 2023-11-08
-#>  8 C46147 1993-06-17 2023-11-08
-#>  9 C46181 1988-12-07 2023-11-08
-#> 10 C46183 1991-05-15 2023-11-08
-#> 11 C46184 1987-09-21 2023-11-08
-#> 12 C46185 1991-09-13 2023-11-08
-#> 13 C46204 1989-09-08 2023-11-08
-#> 14 C46205 1988-11-23 2023-11-08
-#> 15 C46206 1988-11-23 2023-11-08
+#>  6 C46145 1991-04-17 2024-09-19
+#>  7 C46146 1992-03-14 2024-09-19
+#>  8 C46147 1993-06-17 2024-09-19
+#>  9 C46181 1988-12-07 2024-09-19
+#> 10 C46183 1991-05-15 2023-12-11
+#> 11 C46184 1987-09-21 2024-05-28
+#> 12 C46185 1991-09-13 2024-09-19
+#> 13 C46204 1989-09-08 2024-01-21
+#> 14 C46205 1988-11-23 2024-09-19
+#> 15 C46206 1988-11-23 2024-09-19
 #> 16 C46207 1989-10-18 2022-09-07
 #> 17 C46208 1990-07-12 2023-08-03
-#> 18 C46303 2019-10-01 2023-11-08
-#> 19 C46304 2019-10-02 2023-11-08
+#> 18 C46303 2019-10-01 2024-07-26 +#> 19 C46304 2019-10-02 2024-09-19

Plot data from a single buoy for all years, the default is for buoy C46205:

plot(buoy_sst)
-

-

The red lines gives the current year. Since buoy_sst has class pacea_buoy, plot(buoy_sst) function calls our tailored plot.pacea_buoy() function. The gap in the red line at the start of the year indicates missing data (or days that get excluded due to our protocols).

+

+

The red line gives the current year. Since buoy_sst has class pacea_buoy, plot(buoy_sst) function calls our tailored plot.pacea_buoy() function. The gap in the red line at the start of the year indicates missing data (or days that get excluded due to our protocols).

To see data from each buoy in turn:

for(i in 1:nrow(buoy_metadata)){
   plot(buoy_sst,
        stn_id = buoy_metadata[i, ]$stn_id) %>% print()
 }
-

-
#> Warning: Removed 215 rows containing missing values (`geom_line()`).
-

-
#> Warning: Removed 123 rows containing missing values (`geom_line()`).
-

-
#> Warning: Removed 274 rows containing missing values (`geom_line()`).
-

-
#> Warning: Removed 156 rows containing missing values (`geom_line()`).
-

+

+
#> Warning: Removed 33 rows containing missing values or values outside the scale range
+#> (`geom_line()`).
+

We might adapt Andrea Hilborn’s code (saved below in the .Rmd) to produce a panel plot of all buoys at once, to give a figure resembling that at https://github.com/IOS-OSD-DPG/Pacific_SST_Monitoring/blob/main/figures/current/Daily_mean_buoy_overview_2023.png. But for pacea users the individual buoys are probably sufficient.