Add OBIS EOV notebook & update env

[laurabrenskelle]

Adding dplyr and gh R packages

[MathewBiddle]

This could be submitted with the new notebook to make it a little clearer as to why we're adding new packages (related to #218). It's also fine as a separate PR.

[MathewBiddle]

closes #218

[MathewBiddle]

Folks will need to update their r-vctrs package with this change:

Error: package or namespace load failed for 'robis' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace 'vctrs' 0.6.1 is already loaded, but >= 0.6.4 is required
Traceback:

1. library(robis)
2. tryCatch({
 .     attr(package, "LibPath") <- which.lib.loc
 .     ns <- loadNamespace(package, lib.loc)
 .     env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
 . }, error = function(e) {
 .     P <- if (!is.null(cc <- conditionCall(e))) 
 .         paste(" in", deparse(cc)[1L])
 .     else ""
 .     msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
 .         sQuote(package), P, conditionMessage(e))
 .     if (logical.return && !quietly) 
 .         message(paste("Error:", msg), domain = NA)
 .     else stop(msg, call. = FALSE, domain = NA)
 . })
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. value[[3L]](cond)
6. stop(msg, call. = FALSE, domain = NA)

>conda list | grep vctrs
r-vctrs                   0.6.1             r41ha856d6a_0    conda-forge
>conda install r-vctrs
  added / updated specs:
    - r-vctrs


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    r-vctrs-0.6.5              |    r41ha856d6a_0         1.2 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         1.2 MB

The following packages will be UPDATED:

  r-vctrs                               0.6.1-r41ha856d6a_0 --> 0.6.5-r41ha856d6a_0


Proceed ([y]/n)? y


Downloading and Extracting Packages
                                                                                                                                                                                                                               
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Not sure if that's something to specify in the environment file or not.

[laurabrenskelle]

Interesting. I guess I didn't run into that because I had to uninstall and reinstall the environment with the new added packages so I think that automatically updated the other packages in the process.

[MathewBiddle]

For some reason, map_leaflet() doesn't make a map appear in the notebook. I have to save it then view it.

library(htmlwidgets)
# use the built in leaflet capability from robis to map the occurrences
m <- map_leaflet(mangrove_occ,
            provider_tiles = "Esri.WorldGrayCanvas",
            popup = function(x) { x["scientificName"] },
            )

saveWidget(m, file="test.html")

[MathewBiddle]

I've been playing around with this notebook and was thinking it would be cool to couple it with the obisindicators package to, at least, give a heatmap of how many occurrences we have for each EOV. Unfortunately the R binding for H3 (https://github.com/crazycapivara/h3-r/) and obisindicators are not available to install via conda , so I'm not sure where to go.

Here is the snippet of code that should make the heatmap:

h3_indicators <- function(occ, resolution = 9) {
  ## Compute all indicators on the grid resolution of interest for the points in the identified polygons

  occ <- occ %>%
    group_by(decimalLongitude, decimalLatitude, species, date_year) %>%  # remove duplicate rows
    filter(!is.na(species))  %>%
    summarize(records = n(), .groups = "drop") %>%
    collect()

  # return h3 cell index for occurrences in polygon
  occ_h3 <- occ %>%
    mutate(cell = h3::geo_to_h3(data.frame(decimalLatitude, decimalLongitude), res = RES))
  
  # group by cell index and compute indicators
  idx <- obisindicators::calc_indicators(occ_h3)
  
  # convert hexagon ids to spatial features
  # NOTE: DATELINEOFFSET is inv proportional to hex_res b/c we need to look
  #       further from the dateline as hex sizes get bigger.
  dl_offset <- 60  # 60 is enough for hex_res >= 1. res 0 is weird; don't use it.
  hex_sf <- purrr::map_df(idx$cell, h3::h3_to_geo_boundary_sf) %>%
    sf::st_wrap_dateline(c(
      "WRAPDATELINE=YES",
      glue::glue("DATELINEOFFSET={dl_offset}")
    )) %>%
    dplyr::mutate(hexid = idx$cell)
  
  # merge geometry into indicator table
  grid <- hex_sf %>%
    inner_join(idx, by = c("hexid" = "cell"))
  
  return(grid)
}

# Compute indicators at some resolution
grid <- h3_indicators(mangrove_occ, res=4)

# Number of records, log10 scale, Geographic projection
gmap_indicator(grid, "n", label = "# of records", trans = "log10", crs=4326)

[MathewBiddle]

I messed this up. I somehow changed the base branch in this PR, which then closed the request. I'm working on figuring out what went wrong.

[MathewBiddle]

and it wont let me reopen the PR. I think I can start it over again from your main