Write talk for national EAFMWG webinar, adding new slides (zooplankto…

…n!) plus another option for ignoring some.

data-raw/depth/depth.R

@@ -44,4 +44,8 @@ a <- H5Fopen("S102_S111sample/S102/102CA0024600N07100W.h5")
 # https://www.charts.gc.ca/data-gestion/index-eng.html
 #  in the Bathymetry tab. OpenData link looks best.
 
-# Kelsey going to help me.
+# Kelsey going to help me. Cole made suggestions, added to Issue #48.
+
+# From:
+# https://open.canada.ca/data/en/dataset/e6e11b99-f0cc-44f7-f5eb-3b995fb1637e/resource/34d89346-527b-4723-9140-f4782cc384fb
+# canada_west_coast_DEM_original.gdb. zip - 7 Gb file, taking an hour to download.

talks/bccm.Rmd

@@ -63,23 +63,30 @@ bccm_data
 ```
 
 ## Downloading data locally
-The data are saved as a `sf` (simple feature) in a separate GitHub repository `pacea-data` (https://github.com/pbs-assess/pacea-data).
+The data are saved as `sf` (simple feature) objects in a separate GitHub repository `pacea-data` (https://github.com/pbs-assess/pacea-data).
 
 \
-There are built in functions to download specific variables:
-```{r bccmdataDLprompt, eval=FALSE}
-bccm_avg100mtoBot_ph()
 
-pacea would like to download and store these data in the directory:
+One-time download to local machine (will take several minutes):
+```{r bccm_all, eval=FALSE}
+bccm_all_variables()
+
+Downloading all BCCM data may take many minutes. Files will be downloaded to pacea_cache directory:
 C:\Users\TAIT\AppData\Local/pacea/Cache
-Is that okay?
+Would you like to continue?
 1: Yes
 2: No
 
 Selection:
 ```
 
+## Example information
+
+Average of pH from 100 m to sea bottom:
+
 ```{r bccm data head, eval=FALSE}
+> bccm_avg100mtoBot_ph()
+
 Simple feature collection with 33642 features and 324 fields
 Geometry type: POLYGON
 Dimension:     XY
@@ -98,29 +105,17 @@ Projected CRS: NAD83 / BC Albers
 # i 320 more variables: ...
 ```
 
-## Downloading data locally
-\
-Or all variables (will take several minutes):
-```{r bccm_all, eval=FALSE}
-bccm_all_variables()
 
-Downloading all BCCM data may take many minutes. Files will be downloaded to pacea_cache directory:
-C:\Users\TAIT\AppData\Local/pacea/Cache
-Would you like to continue?
-1: Yes
-2: No
 
-Selection:
-```
 
-```{asis, echo = long_talk}
+```{asis, echo = more_details}
 ## Help file
 ```
-```{r bccmhelp, eval = FALSE, echo = long_talk}
+```{r bccmhelp, eval = FALSE, echo = more_details}
 ?bccm_surface_oxygen
 ```
 
-```{r bccmhelp2, eval = FALSE, echo = long_talk}
+```{r bccmhelp2, eval = FALSE, echo = more_details}
 BCCM environmental variable data
 
 Description
@@ -151,7 +146,7 @@ Format
 ## Built in plotting
 
 ```{r bccmplot}
-plot(bccm_surface_temperature(), months.plot = c("April", "july"), years.plot = c(2013, 2016, 2019))
+plot(bccm_surface_temperature(), months.plot = c("april", "july"), years.plot = c(2013, 2016, 2019))
 ```
 
 ## Built in plotting

talks/buoys.Rmd

@@ -27,7 +27,7 @@ knitr::include_graphics(paste0(here::here(),
                                "/man/figures/buoys_map.png"))
 ```
 
-```{asis, echo = long_talk}
+```{asis}
 ## Sea surface temperature data from buoys
 
 Extensive data processing to calculate daily mean SST:
@@ -42,6 +42,8 @@ Extensive data processing to calculate daily mean SST:
 
 - Switch from DFO data stream to ECCC data stream when appropriate
 
+- Time zones and daylight savings time
+
 - Still working on fixing a few outliers in the high-resolution data (hard to automate)
 ```
 

talks/indices.Rmd

@@ -90,15 +90,15 @@ Continuing the help...
      should be considered an estimate.
 ```
 
-```{asis, echo = long_talk}
+```{asis, echo = more_details}
 ## Climatic and oceanographic indices
 
 So for some analyses you may want to restrict values to a specified time period
 (for which values should not change in future `pacea` updates), for example
 
   \
 ```
-```{r onilocal, eval = long_talk, echo = long_talk}
+```{r onilocal, eval = long_talk, echo = more_details}
 oni_fix <- dplyr::filter(oni,
                          year < 2023 | year == 2023 & month < 3)
 tail(oni_fix)       # Will always end with February 2023
@@ -143,17 +143,17 @@ plot(oni,
      lwd = 2)
 ```
 
-```{asis, echo = long_talk}
+```{asis, echo = more_details}
 ## Technical aside regarding `plot()`
 
 The object `oni` has the class `pacea_index`:  \
 ```
 
-```{asis, eval = long_talk, echo = long_talk}
+```{asis, eval = long_talk, echo = more_details}
 class(oni)
 ```
 
-```{asis, echo = long_talk}
+```{asis, echo = more_details}
   \
 which ensures that `plot(oni)`
 automatically uses our specialised function `plot.pacea_index(oni)`, giving

talks/introduction.Rmd

@@ -13,7 +13,7 @@
 
 - DFO's Competitive Science Research Fund for funding (project 21-FS-03-13).
 
-```{asis, echo = long_talk}
+```{asis, echo = explain_assessment}
 ## What is a stock assessment?
 
 - Collect data from surveys and commercial fisheries, including ages of fish
@@ -23,12 +23,12 @@
 Pacific Hake assessment from 2023, estimate the historical population size:
 ```
 
-```{r hakeintro, echo = FALSE, eval = long_talk}
+```{r hakeintro, echo = FALSE, eval = explain_assessment}
 plot(hake_biomass,
      y_max = 3.5)
 ```
 
-```{asis, echo=long_talk}
+```{asis, echo = explain_assessment}
 ## What is a stock assessment?
 
 Advice often in the form of 'decision tables' that indicate probabilities of future events given
@@ -114,7 +114,7 @@ approach data matrix R-package. R package version 0.1 https://github.com/duplise
 
 ## Why an R package?
 
-- R is the programming language most widely used by stock assessment scientists.
+- R is the computer programming language most widely used by stock assessment scientists.
 
 - An R package is the standard way to share code (and data).
 
@@ -128,7 +128,7 @@ approach data matrix R-package. R package version 0.1 https://github.com/duplise
 - Include vignettes that walk users through various features.
 
 - All data (except one type) is saved within the package, no further downloading
-  required.
+  required, so not relying on external websites being functional.
 
 ## Why an R package on GitHub?
 
@@ -148,6 +148,18 @@ knitr::include_graphics(paste0(here::here(),
 - 'codecov' is the amount of the code that is covered by unit tests, which help weed
   out bugs.
 
+## Spatial domain
+
+Started thinking about ecosystem assessment regions like in gslea:
+
+```{r gslea, echo=FALSE, out.width="50%"}
+knitr::include_graphics(paste0(here::here(),
+                               "/talks/talks-manual-figures/gslmap.plain-1.png"))
+```
+
+But it became non-trivial to decide on regions, and we decided to explicitly include
+spatial data.
+
 ## `pacea` objects
 
 Currently, pacea contains:
@@ -163,3 +175,5 @@ Currently, pacea contains:
    and those related to El Niño
 
 - estimates of abundances for Harbour Seals and Pacific Hake
+
+- zooplankton biomass anomalies for the Strait of Georgia

talks/oisst.Rmd

@@ -54,14 +54,14 @@ Geodetic CRS:  WGS 84
 # i Use `print(n = ...)` to see more rows
 ```
 
-```{asis, echo = long_talk}
+```{asis, echo = more_details}
 ## Help file
 ```
-```{r oissthelp, eval=FALSE, echo=long_talk}
+```{r oissthelp, eval = FALSE, echo = more_details}
 ?oisst_month
 ```
 
-```{r oissthelp2, eval=FALSE, echo=long_talk}
+```{r oissthelp2, eval = FALSE, echo = more_details}
 Description
   Simple features objects of NOAAs Optimal Interpolation SST
 

talks/pacea-talk.Rmd

@@ -42,6 +42,8 @@ or click the knit button in RStudio
 Note the first slide below creates the title slide (on page 2), from a
    powerpoint slide saved as .png.
 
+See the long_talk = FALSE and other options in first chunk.
+
 When talk is finished save the .pdf with a new name
 (e.g. pacea-release-talk-dfo.pdf, pacea-release-talk-uvic.pdf) and commit the
 .pdf, so we can just keep the single set of .Rmd code. Also link the pdf talk
@@ -78,8 +80,12 @@ orchid
 -->
 
 ```{r, setup, include = FALSE}
-long_talk <- FALSE    # if FALSE then chunks with eval=long_talk will not be
-                      # evaluated, as we are writing a shorter version
+long_talk <- TRUE    # if FALSE then chunks with eval=long_talk will not be
+                     # evaluated, as we are writing a shorter version
+explain_assessment <- FALSE  # set to TRUE for two slides explaining stock assessment
+
+more_details <- FALSE        # set to TRUE for some of the more detailed slides
+                             # (setting FALSE for national EAFM talk)
 
 knitr::opts_chunk$set(
   collapse = TRUE,
@@ -116,7 +122,7 @@ colorize <- function(x, color){
 
 ```{r coverpage, echo=FALSE, out.width = "100%"}
 knitr::include_graphics(paste0(here::here(),
-                               "/talks/talks-manual-figures/pacea-title-slide-sidney.png"))
+                               "/talks/talks-manual-figures/pacea-title-slide-eafmwg-national.png"))
 ```
 
 ```{r introduction, child = "introduction.Rmd"}

talks/populations.Rmd

@@ -13,6 +13,10 @@ Currently, we have estimates of:
 
 - Pacific Herring (coming soon)
 
+\
+
+Also have zooplankton biomass anomalies for the Strait of Georgia.
+
 ## Hake biomass
 
 The hake biomass time series is saved as a `tibble` object in `pacea`:
@@ -100,3 +104,31 @@ Or just plot estimates for a single region:
 plot(harbour_seals,
      region = "SOG")
 ```
+
+## Zooplankton in the Strait of Georgia
+
+Biomass anomalies of zooplankton biomass from 1996 onwards from
+
+Perry et al. (2021), as extended by Kelly Young each year for DFO's
+
+State of the Pacific Ocean Report.
+```{r zooplankton}
+zooplankton_sog
+```
+
+## Zooplankton in the Strait of Georgia
+
+Default plot of anomalies of total biomass:
+```{r zooplot}
+plot(zooplankton_sog)
+```
+
+```{asis, echo = long_talk}
+## Zooplankton in the Strait of Georgia
+
+Or plot anomalies for a specific species group:
+```
+```{r zooplot2, echo = long_talk, eval = long_talk}
+plot(zooplankton_sog,
+     species_group = "cladocera")
+```

talks/summary.Rmd

@@ -39,7 +39,9 @@ Please:
 
  - understand the limitations of the data
 
-```{asis, echo = long_talk}
+ - cite `pacea` and the original sources for any data you use
+
+```{asis, echo = more_details}
 ## Recommended guidelines for users
 
 To check when you last installed `pacea`
@@ -52,12 +54,12 @@ Compare that with the updates in the NEWS file (and you can also check dates of
 https://github.com/pbs-assess/pacea/commits/main)
 ```
 
-```{r installedscreenshot, echo=FALSE, out.width="30%", eval = long_talk}
+```{r installedscreenshot, echo=FALSE, out.width="30%", eval = more_details}
 knitr::include_graphics(paste0(here::here(),
                                "/talks/talks-manual-figures/github-commits.png"))
 ```
 
-```{asis, echo = long_talk}
+```{asis, echo = more_details}
 ## Recommended guidelines for users
 
  - any problems, make a minimum working example (usually makes you figure it out yourself)
@@ -70,24 +72,56 @@ knitr::include_graphics(paste0(here::here(),
      a new `Issue` (allows others to see, and maybe answer, your question)
 ```
 
-## Recommended guidelines for users
+## Current uses of pacea (that we know about)
 
- - cite `pacea` and the original sources for any data you use
+ - Spiny Dogfish: understanding declines over the past 20 years
+
+ - shrimp: impact of including environmental variables on predicting distributions
+
+ - humpback whales and porpoises: environmental covariates in species distribution models
+
+ - Pacific Saury assessment: finding links between two basin-scale indices and process errors, directly supporting Canada's North Pacific Fisheries
+   Commission commitments
+
+## Lessons learned (applicable to other regions)
+
+ - is possible to amaglamate different ecosystem information into one place
 
- - let us know of any applications (so we understand the uptake and how much
+ - not an off-the-side-of-your-desk project
+
+ - is being used by DFO scientists (and others)
+
+ - infrastructure of the package could be utilised in other regions if
+   interested
+
+   (e.g. my monthly download of OISST data is for all Canadian waters, the data processing,
+   storing and plotting functions could be adopted)
+
+## Summary
+
+<!-- - let us know of any applications (so we understand the uptake and how much
    effort to devote to maintaining it)
 
    - you could be out on a survey and wondering how warm the water is
         compared to previous years
 
     - Chris Rooper: looking at Pacific Saury process errors from a stock assessment
  using the indices (PDO etc.). ``It made my life easier today."
+-->
+ - https://github.com/pbs-assess/pacea
+
+ - installation:
+   \textcolor{red}{\texttt{remotes::install\_github("pbs-assess/pacea")}}
+
+\
 
 \begin{center}
 \includegraphics[width = 1cm]{"../man/figures/logo.png"}\\
 \emph{We wrangle the data so you don't have to}
 \end{center}
 
+\
+
 ```{r citation, eval=FALSE}
 citation("pacea")