Distribution of Fucus distichus in San Francisco Estuary

Intercative map showing the distribution of Fucus distichus in San Francisco Estuary. Using data from the citizen science app iNaturalist, “The distribution and temporal dynamics of the estuarine macroalgal communit of San Francisco Bay (Josselyn & West 1985), and”Distribution and Genetic Structure of Fucus distichus 1953 (formely F. gardneri) within Central San Francisco Bay" (Whitaker et al 2017)

Observations from iNaturalist were downloaded on May 15, 2020 at 4:01pm. I filtered for “research grade” observations only. Based on the photos, each observation was then assigned one of three catagories: attached (green), wrack (yellow), or unclear (grey). When you click on the observation you can see what data it was observed on.

Observations from Josselyn & West, 1985: coordinates are an estimate based on the site name. Could not find site “Twin Sisters” that they list in the paper.

Only using the observations from the gentetic analysis from Whitaker et al since their abudance surveys focus in Central SFE (where we also surveyed) and these locations are already captured by iNaturalist observatons. Their populations for genetic analysis broaden the distribution in several cases. They list the coordinates in Table 4 so I was able to use that.

To do: -Add a polygon of where I downloaded the iNat observations from. Example code:

fitBounds(-118.5, 33.8, -118.25, 34.15) %>% addPolygons(c(-118.5, -118.3, -118.25), c(33.8, 33.95, 34.15)) 37.815226, -122.527939 37.783851, -122.512482 38.056139, -122.232022 38.147807, -122.419157 37.405751, -121.926774

-Change the colors
-Add a title

Set up

Data

map.data<-read.csv(
      "https://raw.githubusercontent.com/Cmwegener/thesis/master/data/distribution/fucus_distribution.csv",
    header = TRUE
  )

#removing datapoint that is not longer listed on iNaturalist so I can't verify 
map.data<-map.data[!is.na(map.data$Type),]

Map

pal<-colorFactor(palette=c("green4", "deeppink", "grey48", "deepskyblue3", "yellow"),domain= c("attached", "Josselyn & West, 1985", "unclear", "Whitaker et al, 2017", "wrack"))


map<-leaflet(map.data) %>%
  addTiles() %>%
  addCircleMarkers(
    lng = map.data$longitude,
    lat = map.data$latitude,
    color = pal(map.data$Type),
    popup = map.data$observed_on,
    radius = 0.1,
    opacity=0.5
  ) %>%
  addLegend(
    "bottomright",
    pal = pal ,
    values = ~ Type,
    title = "Type",
    labFormat = labelFormat(),
    opacity = 1
  )

## Warning in validateCoords(lng, lat, funcName): Data contains 1 rows with either
## missing or invalid lat/lon values and will be ignored

map

Save map

saveWidget(map, "map_pic.html", selfcontained = FALSE)