Cody Markelz - Miracle Mile Species 1

I have started checking off all the conifer species that occur in the Miracle Mile. I recently found some Pacific Yew (Taxus brevifolia) on a trail run with a friend. This was also my first post to iNaturalist. A good time to take a look at the data.

Load the libraries.

library(rinat)
library(tidyverse)

Load the data.

TrailRun1 <- read.csv("~/DATA/data/TrailRun_PacYew.csv")
glimpse(TrailRun1)

Rows: 7,077
Columns: 10
$ X              <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, …
$ timestamp      <chr> "2022-02-27 16:41:35", "2022-02-27 16:41:43", "2022-02-…
$ position_lat   <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,…
$ position_long  <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,…
$ distance       <int> 0, 21, 24, 28, 32, 36, 41, 41, 51, 55, 59, 64, 68, 72, …
$ altitude       <dbl> NA, 791.2, 790.8, 790.6, 790.4, 790.4, 790.0, 789.6, 78…
$ cadence        <int> NA, 87, 86, 85, 84, 84, 85, 87, 87, 87, 87, 85, 85, 84,…
$ speed          <dbl> NA, 2.58, 2.58, 2.92, 2.92, 3.34, 3.34, 3.78, 3.78, 4.0…
$ temperature    <int> NA, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 24, 24,…
$ vertical_speed <dbl> NA, -0.02, -0.04, -0.06, -0.06, -0.08, -0.10, -0.10, -0…

Make a Northern California polygon for iNaturalist, pull in the data and take look.

bounds <- c(40.194, -124.4323, 42.0021, -120)
species <- c("taxus brevifolia")
pacyew_iNat <- get_inat_obs(query = species, bounds = bounds, maxresults = 1000, quality = "research")
dim(pacyew_iNat)

[1] 285  37

I had one of the newest observations of this species in the data set. My username is rjcmarkelz.

glimpse(pacyew_iNat)

Rows: 285
Columns: 37
$ scientific_name                  <chr> "Taxus brevifolia", "Taxus brevifolia…
$ datetime                         <chr> "2024-03-14 09:53:00 -0700", "2024-02…
$ description                      <chr> "", "", "", "", "", "", "", "", "", "…
$ place_guess                      <chr> "Willow Creek, CA, USA", "Shasta-Trin…
$ latitude                         <dbl> 40.90617, 41.13873, 41.23730, 41.1107…
$ longitude                        <dbl> -123.7070, -122.1695, -122.2685, -123…
$ tag_list                         <chr> "", "", "", "", "", "", "", "", "", "…
$ common_name                      <chr> "Pacific yew", "Pacific yew", "Pacifi…
$ url                              <chr> "https://www.inaturalist.org/observat…
$ image_url                        <chr> "https://inaturalist-open-data.s3.ama…
$ user_login                       <chr> "colmanbc", "taradurb", "herbaljunkie…
$ id                               <int> 202457147, 200553158, 197615086, 1933…
$ species_guess                    <chr> "Taxus brevifolia", "Pacific yew", "P…
$ iconic_taxon_name                <chr> "Plantae", "Plantae", "Plantae", "Pla…
$ taxon_id                         <int> 55209, 55209, 55209, 55209, 55209, 55…
$ num_identification_agreements    <int> 1, 2, 3, 2, 2, 2, 1, 2, 2, 1, 2, 2, 2…
$ num_identification_disagreements <int> 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ observed_on_string               <chr> "2024/03/14 9:53 AM", "2024-02-24 13:…
$ observed_on                      <chr> "2024-03-14", "2024-02-24", "2023-09-…
$ time_observed_at                 <chr> "2024-03-14 16:53:00 UTC", "2024-02-2…
$ time_zone                        <chr> "Pacific Time (US & Canada)", "Pacifi…
$ positional_accuracy              <int> 218, 4, 179, 100, 5005, 4, 9, 10, 4, …
$ public_positional_accuracy       <int> 218, 4, 179, 100, 5005, 4, 9, 10, 4, …
$ geoprivacy                       <chr> "", "", "", "", "", "", "", "", "", "…
$ taxon_geoprivacy                 <chr> "open", "open", "open", "open", "open…
$ coordinates_obscured             <chr> "false", "false", "false", "false", "…
$ positioning_method               <chr> "", "", "gps", "", "", "", "", "", ""…
$ positioning_device               <chr> "", "", "gps", "", "", "", "", "", ""…
$ user_id                          <int> 4765474, 4070907, 7728335, 2101146, 3…
$ user_name                        <chr> "colmanbc", "Tara Durboraw", "", "Zan…
$ created_at                       <chr> "2024-03-14 22:04:15 UTC", "2024-02-2…
$ updated_at                       <chr> "2024-03-15 01:08:03 UTC", "2024-02-2…
$ quality_grade                    <chr> "research", "research", "research", "…
$ license                          <chr> "CC-BY-NC", "", "CC-BY-NC", "CC-BY-NC…
$ sound_url                        <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ oauth_application_id             <int> NA, 3, 2, 3, 333, 3, 3, 3, NA, NA, NA…
$ captive_cultivated               <chr> "false", "false", "false", "false", "…

head(pacyew_iNat$user_login, 10)

 [1] "colmanbc"      "taradurb"      "herbaljunkies" "zanethebrain" 
 [5] "paige15"       "mikhela"       "danjuel"       "zanethebrain" 
 [9] "mikhela"       "mikhela"

Here is my image that I uploaded. I had a species confirmation from the community within 12 hours.

Quick map to show all the observations.

maps::map(database = "state", region = "california")
points(TrailRun1[ , c("position_long", "position_lat")], pch = ".", col = "red", cex = 3)
points(pacyew_iNat[ , c("longitude", "latitude")], pch = ".", col = "blue", cex = 3)

Make a quick plot to show the overlay of the run data and the coordinates of the image I took shown as a red dot.

tr_plot1 <- ggplot(TrailRun1, aes(x = position_long, y = position_lat)) +
                    coord_quickmap() + geom_point() +
                    ylab("Latitude") + xlab("Longitude") + 
                 geom_point(aes(x=-122.1683, y=41.120),color="red", size = 5)
tr_plot1