More edits, manually including some things (color in table and short …

…hotssea_data), update title slide.

talks/bccm-short.Rmd

@@ -6,9 +6,9 @@ Physical biogeochemical oceanographic model
 
 - Regional Ocean Modelling Systen (ROMS)
 
-- Curvilinear grid at 3km x 3km resolution
+- curvilinear grid at 3km x 3km resolution
 
-- We interpolate to regular grids
+- we interpolate to regular grids
 
 \
 Model output provided by Angelica Peña at the Institute of Ocean Sciences (Fisheries and
@@ -25,23 +25,25 @@ Original mapping:
 
 - clipped to Canada's Pacific Exclusive Economic Zone
 
-- Inshore (2 km x 2 km) and offshore (6 km x 6 km)
+- inshore (2 km x 2 km) and offshore (6 km x 6 km)
 
 - 40,480 cells
 
-- Monthly from 1993-2019
+- monthly from 1993-2019
 
-New additional mapping:
+New additional mapping `r colorize("(request from Lisa last year)", "red")`:
 
 - `r colorize("covers full domain (into US waters)", "red")`
 
 - `r colorize("2 km x 2km grid throughout", "red")`
 
 - `r colorize("161,025 cells", "red")`
 
-- Monthly from 1993-2019
+- monthly from 1993-2019
 
-- `r colorize("New grid also used for HOTSSea outputs, and has interpolated
+- huge filesizes required hosting outputs on Zenodo not GitHub
+
+- `r colorize("new grid also used for HOTSSea outputs, and has interpolated
   depths", "red")`
 
 
@@ -89,8 +91,12 @@ plot(bccm_primaryproduction())
 plot(bccm_primaryproduction_full())
 ```
 
+<!--
+pdf was getting locked and could refresh pacea-talk.pdf, can with this not -->
+<!-- done. COuld do it manually.
 ## Built in plotting - monthly primary production through 2018
+-->
 
-```{r bccmplot2}
+```{r bccmplot2, echo = FALSE, eval = FALSE}
 plot(bccm_primaryproduction_full(), months = 1:12)
 ```

talks/hotssea.Rmd

@@ -13,11 +13,34 @@ Development*, in press)](https://doi.org/10.5194/gmd-2024-58).
   etc. functions can be used)
 
 ## Available variables
+
 HOTSSea objects in pacea are (40 in total):
-```{r hotssea}
+```{r hotssea, eval = FALSE}
 hotssea_data
+                              data_name
+1          hotssea_surface_salinity_min
+2         hotssea_surface_salinity_mean
+3          hotssea_surface_salinity_max
+4          hotssea_surface_salinity_std
+5       hotssea_surface_temperature_min
+6      hotssea_surface_temperature_mean
+7       hotssea_surface_temperature_max
+8       hotssea_surface_temperature_std
+9        hotssea_avg0to30m_salinity_min
+10      hotssea_avg0to30m_salinity_mean
+11       hotssea_avg0to30m_salinity_max
+12       hotssea_avg0to30m_salinity_std
+13    hotssea_avg0to30m_temperature_min
+14   hotssea_avg0to30m_temperature_mean
+15    hotssea_avg0to30m_temperature_max
+16    hotssea_avg0to30m_temperature_std
+17     hotssea_avg30to150m_salinity_min
+18    hotssea_avg30to150m_salinity_mean
+19     hotssea_avg30to150m_salinity_max
+20     hotssea_avg30to150m_salinity_std
 ```
 
+
 ## Example plot
 
 ```{r hotsseaplot, echo = FALSE}

talks/indices-short.Rmd

@@ -4,12 +4,34 @@
 
 Various climate and oceanographic indices are currently included in pacea:
 
-```{r indicestable, echo=FALSE}
-
+```{r indicestable, echo=FALSE, eval=FALSE}
+# Used to create tex that is copied below and red added to
 kableExtra::kable(pacea_indices, "latex", booktabs = TRUE) %>%
   kableExtra::kable_styling(latex_options = c("scale_down", "striped"))
 ```
 
+\begin{table}
+\centering
+\resizebox{\ifdim\width>\linewidth\linewidth\else\width\fi}{!}{
+\begin{tabular}{lllrr}
+\toprule
+Object & Description & Resolution & Start year & End year\\
+\midrule
+\cellcolor{gray!10}{pdo} & \cellcolor{gray!10}{Pacific Decadal Oscillation} & \cellcolor{gray!10}{monthly} & \cellcolor{gray!10}{1854} & \cellcolor{gray!10}{\textcolor{red}{2024}}\\
+npi\_monthly & North Pacific Index (monthly) & monthly & 1899 & \textcolor{red}{2024}\\
+\cellcolor{gray!10}{npi\_annual} & \cellcolor{gray!10}{North Pacific Index (annual)} & \cellcolor{gray!10}{annual} & \cellcolor{gray!10}{1899} & \cellcolor{gray!10}{\textcolor{red}{2024}}\\
+alpi & Aleutian Low Pressure Index & annual & 1900 & \textcolor{red}{2022}\\
+\cellcolor{gray!10}{oni} & \cellcolor{gray!10}{Oceanic Niño Index} & \cellcolor{gray!10}{monthly} & \cellcolor{gray!10}{1950} & \cellcolor{gray!10}{\textcolor{red}{2024}}\\
+\addlinespace
+npgo & North Pacific Gyre Oscillation & monthly & 1950 & \textcolor{red}{2024}\\
+\cellcolor{gray!10}{ao} & \cellcolor{gray!10}{Arctic Oscillation} & \cellcolor{gray!10}{monthly} & \cellcolor{gray!10}{1950} & \cellcolor{gray!10}{\textcolor{red}{2024}}\\
+soi & Southern Oscillation Index & monthly & 1951 & \textcolor{red}{2024}\\
+\cellcolor{gray!10}{\textcolor{red}{bi}} & \cellcolor{gray!10}{\textcolor{red}{North Pacific Bifurcation Index}} & \cellcolor{gray!10}{\textcolor{red}{annual}} & \cellcolor{gray!10}{\textcolor{red}{1967}} & \cellcolor{gray!10}{\textcolor{red}{2024}}\\
+mei & Multivariate El Niño Southern Oscillation Index & monthly & 1979 & \textcolor{red}{2024}\\
+\bottomrule
+\end{tabular}}
+\end{table}
+
 ## New index
 
 Now includes Mike Malick's North Pacific Current Bifurcation Index:

talks/introduction-short.Rmd

@@ -3,34 +3,39 @@
 
 ## Motivation
 
+\centering pacea: An R package of Pacific ecosystem information to help facilitate an
+ecosystem approach to fisheries management
+\
+
 - push to include ecosystem information in advice to fisheries managers
 
-- availability of data and model output is the leading impediment
+- leading impediment: availability of data and model output
   - where to find it, wrangling it (e.g netCDF into R), understanding it
   - Open Data is great, but have to convert raw data into
   `r colorize("usable information", "red")`
 
-- Primary audience is DFO stock assessment scientists, but usable by anyone
+- primary audience is DFO stock assessment scientists, but usable by anyone
   (with a minimal working knowledge of R)
 
-\
-
-\centering pacea: An R package of Pacific ecosystem information to help facilitate an
-ecosystem approach to fisheries management
 
 ## Availability
 
-- Hosted free on Github at https://github.com/pbs-assess/pacea
+- hosted free on GitHub at https://github.com/pbs-assess/pacea
+
+- easy installation:
 
-- Easy installation:
+\
+
+\centering \textcolor{red}{\texttt{remotes::install\_github("pbs-assess/pacea")}}
 
-\textcolor{red}{\texttt{remotes::install\_github("pbs-assess/pacea")}}
+\
 
-- All vignettes are rendered on github for easy learning, custom plotting files,
+- all vignettes are rendered on GitHub for easy learning, custom plotting files,
   help for everything, fully open source
 
-- All data (except oceanographic model output) is saved within the package, no further downloading
-  required, so not relying on external websites being functional
+- all data (except oceanographic model output) is saved within the package
+  - no further downloading required
+  - not relying on external websites being functional
 
 ## `pacea` objects (climatic/oceanographic)
 

talks/populations-short.Rmd

@@ -2,7 +2,7 @@
 
 ## Zooplankton in the Strait of Georgia (new)
 
-Biomass anomalies of zooplankton biomass from 1996 onwards from
+Anomalies of zooplankton biomass from 1996 onwards from
 
 Perry et al. (2021), as extended by Kelly Young each year for DFO's
 
@@ -18,7 +18,7 @@ Default plot of anomalies of total biomass:
 plot(zooplankton_sog)
 ```
 
-## Zooplankton in the Strait of Georgia
+## Zooplankton in the Strait of Georgia (new)
 
 Or plot anomalies for a specific species group: