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("../../../static/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 = 10000, quality = "research")
dim(pacyew_iNat)## [1] 155 36I have one of the newest observations of this species in the data set. My username is rjcmarkelz.
glimpse(pacyew_iNat)## Rows: 155
## Columns: 36
## $ scientific_name <chr> "Taxus brevifolia", "Taxus brevifolia…
## $ datetime <chr> "2022-05-02 12:00:07 -0700", "2022-05…
## $ description <chr> "", "", "", "", "", "", "", "", "Male…
## $ place_guess <chr> "Humboldt County, US-CA, US", "Humbol…
## $ latitude <dbl> 40.92736, 40.87794, 40.64852, 40.8820…
## $ longitude <dbl> -123.9770, -123.9668, -123.9937, -124…
## $ 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> "steph_mo", "steph_mo", "drew_meyer",…
## $ id <int> 114957908, 114950484, 114596338, 1126…
## $ species_guess <chr> "Pacific yew", "Pacific yew", "Pacifi…
## $ iconic_taxon_name <chr> "Plantae", "Plantae", "Plantae", "Pla…
## $ taxon_id <int> 55209, 55209, 55209, 55209, 55209, 55…
## $ num_identification_agreements <int> 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1…
## $ num_identification_disagreements <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
## $ observed_on_string <chr> "2022-05-02 12:00:07-07:00", "2022-05…
## $ observed_on <chr> "2022-05-02", "2022-05-02", "2022-05-…
## $ time_observed_at <chr> "2022-05-02 19:00:07 UTC", "2022-05-0…
## $ time_zone <chr> "Pacific Time (US & Canada)", "Pacifi…
## $ positional_accuracy <int> 16, 14, NA, 31, NA, NA, 4, 31, 31, 4,…
## $ public_positional_accuracy <int> 27877, 27877, 27908, 27877, 27877, 27…
## $ geoprivacy <chr> "", "", "", "", "", "", "", "", "obsc…
## $ taxon_geoprivacy <chr> "obscured", "obscured", "obscured", "…
## $ coordinates_obscured <chr> "true", "true", "true", "true", "true…
## $ positioning_method <chr> "", "", "gps", "", "gps", "gps", "", …
## $ positioning_device <chr> "", "", "gps", "", "gps", "gps", "", …
## $ user_id <int> 782696, 782696, 3937945, 5492151, 738…
## $ created_at <chr> "2022-05-03 00:48:07 UTC", "2022-05-0…
## $ updated_at <chr> "2022-05-03 01:33:54 UTC", "2022-05-0…
## $ quality_grade <chr> "research", "research", "research", "…
## $ license <chr> "CC-BY-NC-ND", "CC-BY-NC-ND", "CC-BY-…
## $ sound_url <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
## $ oauth_application_id <int> 3, 3, 2, 3, 2, 2, 3, NA, 3, 3, NA, 3,…
## $ captive_cultivated <chr> "false", "false", "false", "false", "…head(pacyew_iNat$user_login, 100)## [1] "steph_mo" "steph_mo" "drew_meyer"
## [4] "farah49" "cmccarron" "drew_meyer"
## [7] "prickly_sculpin" "johnny9000" "steph_mo"
## [10] "steph_mo" "ventanaphile" "steph_mo"
## [13] "cinnamon3" "drew_meyer" "drew_meyer"
## [16] "shaunnastodola" "shaunnastodola" "shakeyouroncorhynchus"
## [19] "rjcmarkelz" "nathanielreyes" "abudnik"
## [22] "sandragonfruit" "sethberes" "sethberes"
## [25] "abr" "scottdharding" "toadwarrior"
## [28] "goldleaf" "jeffbisbee" "matsonburger"
## [31] "danjuel" "jacquelinerose" "kees_hood"
## [34] "pandabadger" "ventanaphile" "bstar"
## [37] "dblanco" "jenniferlchandler" "lilyboy"
## [40] "morganstickrod" "pedro2aeiou" "griffith"
## [43] "christinags" "gnomewardbound" "dgreenberger"
## [46] "erik-jules" "erik-jules" "erik-jules"
## [49] "erik-jules" "oren_nardi" "tellittothevoid"
## [52] "michaelkauffmann" "justingarwood" "junej"
## [55] "tellittothevoid" "mycobiont" "paradishsu"
## [58] "mandymushii" "wnaylor" "tr94"
## [61] "chrisbrant47" "jrmorris" "alexfern"
## [64] "alexfern" "kalelevin" "rangertyler"
## [67] "olddustytrail" "ishirahhsu" "shakeyouroncorhynchus"
## [70] "watchingitallgrow" "bstar" "justinaceae"
## [73] "justinaceae" "calibas" "fieldbio"
## [76] "lcwimmer1" "caseycroshaw" "ericlearning"
## [79] "justingarwood" "ericlearning" "justingarwood"
## [82] "justingarwood" "gnomewardbound" "erik-jules"
## [85] "simoneysg" "ventanaphile" "morganstickrod"
## [88] "michaelkauffmann" "tyannasb" "sapienshane"
## [91] "sapienshane" "suziesavoie" "tyannasb"
## [94] "tyannasb" "calibas" "tyannasb"
## [97] "michaelkauffmann" "tyannasb" "tyannasb"
## [100] "jrmorris"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() + geom_point(aes(x=-122.1683,y=41.120),color="red", size = 5)
tr_plot1