Merge branch 'main' into dev-andy

.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$

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 ",

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).
 

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")
+
+  }
+
+}

README.Rmd

@@ -4,10 +4,13 @@ output: github_document
 
 <!--
 README.md is generated from README.Rmd. Please edit that file. Build with
+-->
 
+```{r, include = FALSE, eval = FALSE}
 load_all()
 rmarkdown::render("README.Rmd")
-
+```
+<!--
 which builds the .html that can be viewed locally (but isn't pushed to GitHub;
 GitHub uses README.md to make the page you see on GitHub).
 
@@ -30,6 +33,7 @@ library(tibble)
 <!-- badges: start -->
 [![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)
 <!-- badges: end -->
 
@@ -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."
-  <https://github.com/pbs-assess/pacea>.
+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.
+  <https://github.com/pbs-assess/pacea>, <https://zenodo.org/doi/10.5281/zenodo.13840804>
 
 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.
 

README.md

@@ -1,10 +1,8 @@
 
 <!--
 README.md is generated from README.Rmd. Please edit that file. Build with
-
-load_all()
-rmarkdown::render("README.Rmd")
-
+-->
+<!--
 which builds the .html that can be viewed locally (but isn't pushed to GitHub;
 GitHub uses README.md to make the page you see on GitHub).
 
@@ -18,6 +16,7 @@ the .png file. See notes below (and Issue #44).
 
 [![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)
 <!-- badges: end -->
 
@@ -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
 #>    <dbl> <dbl> <dbl>   <dbl>
 #>  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.” <https://github.com/pbs-assess/pacea>.
+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. <https://github.com/pbs-assess/pacea>,
+<https://zenodo.org/doi/10.5281/zenodo.13840804>
 
 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.

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)

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

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"
 )

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).