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Ben Amar Charaf Eddine 8 April 2019
summary: the final project came with a goal of aplying the methods and the concepts we learned in class,during the course of Geomatics in this semester and ally those techniques on the domain of conservation management.in my project i will follow the first path of the work Multispecies preliminary conservation assessments from distribution data" and I will use the ConR package to realize that.my work will based on the question of “how it is the situation of an organism from geographicly dustributed data?”the path 1 oblige us to use the ConR package because it helps with on the large georaphical parametres by supplying libraries to execute process that deals with that.
library(sf)## Linking to GEOS 3.5.1, GDAL 2.1.3, PROJ 4.9.2library(raster)## Loading required package: splibrary(tidyverse)## ── Attaching packages ─────────────────────────────────────────────────── tidyverse 1.2.1 ──## ✔ ggplot2 3.1.0 ✔ purrr 0.3.2
## ✔ tibble 2.1.1 ✔ dplyr 0.8.0.1
## ✔ tidyr 0.8.3 ✔ stringr 1.4.0
## ✔ readr 1.3.1 ✔ forcats 0.4.0## ── Conflicts ────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ tidyr::extract() masks raster::extract()
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ✖ dplyr::select() masks raster::select()#install.packages("ConR")
library(sp)
library(ConR)#install.packages("rgbif")
library(rgbif)library(dplyr)
equ_gbif <- occ_download_get(key = "0045549-181108115102211", overwrite = TRUE) %>%
occ_download_import(equ_gbif_download, na.strings = c("", NA))## Download file size: 2.99 MB## On disk at /cloud/project/0045549-181108115102211.zipequ_gbif## # A tibble: 87,271 x 45
## gbifID datasetKey occurrenceID kingdom phylum class order family genus
## * <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 1.99e9 ad43e954-… MH306193 Animal… Chord… Amph… Anura Strab… Pris…
## 2 1.99e9 ad43e954-… MH306194 Animal… Chord… Amph… Anura Strab… Pris…
## 3 1.99e9 50c9509d-… https://www… Animal… Chord… Amph… Anura Phyll… Call…
## 4 1.99e9 50c9509d-… https://www… Animal… Chord… Amph… Anura Strab… Pris…
## 5 1.99e9 50c9509d-… https://www… Animal… Chord… Amph… Anura Lepto… Lept…
## 6 1.99e9 50c9509d-… https://www… Animal… Chord… Amph… Anura Hylid… Tepu…
## 7 1.99e9 50c9509d-… https://www… Animal… Chord… Amph… Anura Strab… Pris…
## 8 1.99e9 50c9509d-… https://www… Animal… Chord… Amph… Anura Hylid… Oste…
## 9 1.99e9 50c9509d-… https://www… Animal… Chord… Amph… Anura Dendr… Amee…
## 10 1.99e9 50c9509d-… https://www… Animal… Chord… Amph… Anura Strab… Pris…
## # … with 87,261 more rows, and 36 more variables: species <chr>,
## # infraspecificEpithet <chr>, taxonRank <chr>, scientificName <chr>,
## # countryCode <chr>, locality <chr>, publishingOrgKey <chr>,
## # decimalLatitude <dbl>, decimalLongitude <dbl>,
## # coordinateUncertaintyInMeters <dbl>, coordinatePrecision <lgl>,
## # elevation <dbl>, elevationAccuracy <dbl>, depth <dbl>,
## # depthAccuracy <dbl>, eventDate <chr>, day <int>, month <int>,
## # year <int>, taxonKey <int>, speciesKey <int>, basisOfRecord <chr>,
## # institutionCode <chr>, collectionCode <chr>, catalogNumber <chr>,
## # recordNumber <chr>, identifiedBy <chr>, dateIdentified <chr>,
## # license <chr>, rightsHolder <chr>, recordedBy <chr>, typeStatus <chr>,
## # establishmentMeans <chr>, lastInterpreted <chr>, mediaType <chr>,
## # issue <chr>library(tidyverse)
equ_gbif %>% drop_na(kingdom) %>% count(kingdom, sort = TRUE)## # A tibble: 1 x 2
## kingdom n
## <chr> <int>
## 1 Animalia 87271equ_gbif %>% filter(taxonRank == "SPECIES") %>% count(species) %>% arrange(desc(n))## # A tibble: 568 x 2
## species n
## <chr> <int>
## 1 Dendropsophus triangulum 4631
## 2 Dendropsophus carnifex 3764
## 3 Atelopus ignescens 2763
## 4 Pristimantis w-nigrum 2331
## 5 Pristimantis curtipes 1796
## 6 Pristimantis achatinus 1784
## 7 Pristimantis unistrigatus 1574
## 8 Rhinella margaritifera 1557
## 9 Epipedobates machalilla 1473
## 10 Hypsiboas punctatus 1408
## # … with 558 more rowslibrary(tidyverse)
equ_gbif %>% count(taxonRank)## # A tibble: 6 x 2
## taxonRank n
## <chr> <int>
## 1 FAMILY 739
## 2 GENUS 8278
## 3 ORDER 102
## 4 SPECIES 78093
## 5 SUBSPECIES 57
## 6 VARIETY 2equ_gbif %>% count(species, sort = TRUE) %>% drop_na(species) %>% filter(n > 500) %>%
ggplot(aes(x = reorder(species, n), y = n, fill = species)) + geom_bar(stat = "identity",
show.legend = FALSE) + labs(x = "SPECIES", y = "Number of Occurrence Records (observations)") +
coord_flip()
equ_gbif %>% filter(species == " Pristimantis lanthanites")## # A tibble: 0 x 45
## # … with 45 variables: gbifID <int>, datasetKey <chr>, occurrenceID <chr>,
## # kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
## # genus <chr>, species <chr>, infraspecificEpithet <chr>,
## # taxonRank <chr>, scientificName <chr>, countryCode <chr>,
## # locality <chr>, publishingOrgKey <chr>, decimalLatitude <dbl>,
## # decimalLongitude <dbl>, coordinateUncertaintyInMeters <dbl>,
## # coordinatePrecision <lgl>, elevation <dbl>, elevationAccuracy <dbl>,
## # depth <dbl>, depthAccuracy <dbl>, eventDate <chr>, day <int>,
## # month <int>, year <int>, taxonKey <int>, speciesKey <int>,
## # basisOfRecord <chr>, institutionCode <chr>, collectionCode <chr>,
## # catalogNumber <chr>, recordNumber <chr>, identifiedBy <chr>,
## # dateIdentified <chr>, license <chr>, rightsHolder <chr>,
## # recordedBy <chr>, typeStatus <chr>, establishmentMeans <chr>,
## # lastInterpreted <chr>, mediaType <chr>, issue <chr>Pristimantis <- equ_gbif %>% dplyr::filter(genus == "Pristimantis") %>%
select(decimalLatitude, decimalLongitude, species)
print(Pristimantis)## # A tibble: 20,781 x 3
## decimalLatitude decimalLongitude species
## <dbl> <dbl> <chr>
## 1 -0.03 -78.7 <NA>
## 2 -0.03 -78.7 <NA>
## 3 0.0530 -78.8 Pristimantis achatinus
## 4 -0.0156 -78.7 Pristimantis appendiculatus
## 5 -4.60 -78.8 <NA>
## 6 -2.07 -78.2 Pristimantis ganonotus
## 7 -1.10 -76.7 Pristimantis diadematus
## 8 -4.46 -78.8 Pristimantis katoptroides
## 9 -0.231 -78.4 Pristimantis unistrigatus
## 10 -0.728 -77.7 Pristimantis galdi
## # … with 20,771 more rowsEOO.results <- EOO.computing(Pristimantis, export_shp = T)## [1] "Skipping 3616 occurrences because of missing coordinates for c(\"Pristimantis vertebralis\", \"Pristimantis lanthanites\", \"Pristimantis peruvianus\", \"Pristimantis altamazonicus\", \"Pristimantis variabilis\", \"Pristimantis unistrigatus\", \"Pristimantis achatinus\", \"Pristimantis croceoinguinis\", \"Pristimantis actites\", \"Pristimantis calcarulatus\", \"Pristimantis chloronotus\", \"Pristimantis duellmani\", \"Pristimantis celator\", \"Pristimantis caprifer\", \"Pristimantis yantzaza\", \"Pristimantis curtipes\", \"Pristimantis w-nigrum\", \"Pristimantis conspicillatus\", NA, \"Pristimantis walkeri\", \n\"Pristimantis rosadoi\", \"Pristimantis eremitus\", \"Pristimantis ornatissimus\", \"Pristimantis lymani\", \"Pristimantis glandulosus\", \"Pristimantis devillei\", \"Pristimantis librarius\", \"Pristimantis lacrimosus\", \"Pristimantis malkini\", \"Pristimantis surdus\", \"Pristimantis ockendeni\", \"Pristimantis quaquaversus\", \"Pristimantis acuminatus\", \"Pristimantis petersi\", \"Pristimantis ventrimarmoratus\", \"Pristimantis waoranii\", \"Pristimantis galdi\", \"Pristimantis floridus\", \"Pristimantis labiosus\", \"Pristimantis leoni\", \n\"Pristimantis orcesi\", \"Pristimantis crenunguis\", \"Pristimantis chalceus\", \"Pristimantis versicolor\", \"Pristimantis pugnax\", \"Pristimantis latidiscus\", \"Pristimantis martiae\", \"Pristimantis cryophilius\", \"Pristimantis riveti\", \"Pristimantis nyctophylax\", \"Pristimantis festae\", \"Pristimantis crucifer\", \"Pristimantis buckleyi\", \"Pristimantis subsigillatus\", \"Pristimantis trachyblepharis\", \"Pristimantis bisignatus\", \"Pristimantis thymelensis\", \"Pristimantis ocreatus\", \"Pristimantis supernatis\", \"Pristimantis prolatus\", \n\"Pristimantis altamnis\", \"Pristimantis vidua\", \"Pristimantis truebae\", \"Pristimantis spinosus\", \"Pristimantis cajamarcensis\", \"Pristimantis percultus\", \"Pristimantis colodactylus\", \"Pristimantis proserpens\", \"Pristimantis nigrogriseus\", \"Pristimantis leucopus\", \"Pristimantis balionotus\", \"Pristimantis incomptus\", \"Pristimantis phoxocephalus\", \"Pristimantis calcaratus\", \"Pristimantis quinquagesimus\", \"Pristimantis tenebrionis\", \"Pristimantis pteridophilus\", \"Pristimantis rubicundus\", \"Pristimantis kichwarum\", \n\"Pristimantis pycnodermis\", \"Pristimantis atratus\", \"Pristimantis inusitatus\", \"Pristimantis eriphus\", \"Pristimantis ignicolor\", \"Pristimantis orestes\", \"Pristimantis exoristus\", \"Pristimantis pecki\", \"Pristimantis cryptomelas\", \"Pristimantis condor\", \"Pristimantis bromeliaceus\", \"Pristimantis acerus\", \"Pristimantis gladiator\", \"Pristimantis modipeplus\", \"Pristimantis diadematus\", \"Pristimantis aureolineatus\", \"Pristimantis metabates\", \"Pristimantis luteolateralis\", \"Pristimantis paululus\", \"Pristimantis ernesti\", \n\"Pristimantis ruidus\", \"Pristimantis parvillus\", \"Pristimantis muricatus\", \"Pristimantis delius\", \"Pristimantis cremnobates\", \"Pristimantis appendiculatus\", \"Pristimantis achuar\", \"Pristimantis ganonotus\", \"Pristimantis pseudoacuminatus\")"## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis apiculatus is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis aureolineatus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis balionotus is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis bicantus is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis carvalhoi is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis citriogaster is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis colomai is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis dissimulatus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis ernesti is not computed
## because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis eugeniae is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis fenestratus is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis frater is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis ganonotus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis hamiotae is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis hectus is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis ignicolor is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis inusitatus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis katoptroides is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis kirklandi is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis laticlavius is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis latro is not computed
## because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis loustes is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis luscombei is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis matidiktyo is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis miktos is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis nimbus is not computed
## because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis ocellatus is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis ocreatus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis pastazensis is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis philipi is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis prometeii is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis rosadoi is not computed
## because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis scolodiscus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis simonbolivari is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis skydmainos is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis waoranii is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis yantzaza is not
## computed because there is only 1 unique occurrencesummary(EOO.results)## Length Class Mode
## Pristimantis acerus 2 -none- list
## Pristimantis achatinus 2 -none- list
## Pristimantis achuar 2 -none- list
## Pristimantis actites 2 -none- list
## Pristimantis acuminatus 2 -none- list
## Pristimantis altamazonicus 2 -none- list
## Pristimantis altamnis 2 -none- list
## Pristimantis apiculatus 1 -none- numeric
## Pristimantis appendiculatus 2 -none- list
## Pristimantis atratus 2 -none- list
## Pristimantis aureolineatus 1 -none- numeric
## Pristimantis balionotus 1 -none- numeric
## Pristimantis baryecuus 2 -none- list
## Pristimantis bicantus 1 -none- numeric
## Pristimantis bromeliaceus 2 -none- list
## Pristimantis buckleyi 2 -none- list
## Pristimantis cajamarcensis 2 -none- list
## Pristimantis calcaratus 2 -none- list
## Pristimantis calcarulatus 2 -none- list
## Pristimantis caprifer 2 -none- list
## Pristimantis carvalhoi 1 -none- numeric
## Pristimantis celator 2 -none- list
## Pristimantis chalceus 2 -none- list
## Pristimantis chloronotus 2 -none- list
## Pristimantis citriogaster 1 -none- numeric
## Pristimantis colodactylus 2 -none- list
## Pristimantis colomai 1 -none- numeric
## Pristimantis condor 2 -none- list
## Pristimantis conspicillatus 2 -none- list
## Pristimantis cremnobates 2 -none- list
## Pristimantis crenunguis 2 -none- list
## Pristimantis croceoinguinis 2 -none- list
## Pristimantis crucifer 2 -none- list
## Pristimantis cryophilius 2 -none- list
## Pristimantis cryptomelas 2 -none- list
## Pristimantis curtipes 2 -none- list
## Pristimantis delius 2 -none- list
## Pristimantis devillei 2 -none- list
## Pristimantis diadematus 2 -none- list
## Pristimantis dissimulatus 1 -none- numeric
## Pristimantis duellmani 2 -none- list
## Pristimantis eremitus 2 -none- list
## Pristimantis eriphus 2 -none- list
## Pristimantis ernesti 1 -none- numeric
## Pristimantis eugeniae 1 -none- numeric
## Pristimantis fenestratus 1 -none- numeric
## Pristimantis festae 2 -none- list
## Pristimantis floridus 2 -none- list
## Pristimantis frater 1 -none- numeric
## Pristimantis galdi 2 -none- list
## Pristimantis ganonotus 1 -none- numeric
## Pristimantis gentryi 2 -none- list
## Pristimantis gladiator 2 -none- list
## Pristimantis glandulosus 2 -none- list
## Pristimantis hamiotae 1 -none- numeric
## Pristimantis hectus 1 -none- numeric
## Pristimantis ignicolor 1 -none- numeric
## Pristimantis illotus 2 -none- list
## Pristimantis incanus 2 -none- list
## Pristimantis incomptus 2 -none- list
## Pristimantis inusitatus 1 -none- numeric
## Pristimantis katoptroides 1 -none- numeric
## Pristimantis kichwarum 2 -none- list
## Pristimantis kirklandi 1 -none- numeric
## Pristimantis labiosus 2 -none- list
## Pristimantis lacrimosus 2 -none- list
## Pristimantis lanthanites 2 -none- list
## Pristimantis laticlavius 1 -none- numeric
## Pristimantis latidiscus 2 -none- list
## Pristimantis latro 1 -none- numeric
## Pristimantis leoni 2 -none- list
## Pristimantis leucopus 2 -none- list
## Pristimantis librarius 2 -none- list
## Pristimantis lividus 2 -none- list
## Pristimantis loustes 1 -none- numeric
## Pristimantis luscombei 1 -none- numeric
## Pristimantis luteolateralis 2 -none- list
## Pristimantis lymani 2 -none- list
## Pristimantis malkini 2 -none- list
## Pristimantis martiae 2 -none- list
## Pristimantis matidiktyo 1 -none- numeric
## Pristimantis miktos 1 -none- numeric
## Pristimantis modipeplus 2 -none- list
## Pristimantis muricatus 2 -none- list
## Pristimantis nigrogriseus 2 -none- list
## Pristimantis nimbus 1 -none- numeric
## Pristimantis nyctophylax 2 -none- list
## Pristimantis ocellatus 1 -none- numeric
## Pristimantis ockendeni 2 -none- list
## Pristimantis ocreatus 1 -none- numeric
## Pristimantis orcesi 2 -none- list
## Pristimantis orestes 2 -none- list
## Pristimantis ornatissimus 2 -none- list
## Pristimantis orphnolaimus 2 -none- list
## Pristimantis parvillus 2 -none- list
## Pristimantis pastazensis 1 -none- numeric
## Pristimantis paululus 2 -none- list
## Pristimantis peruvianus 2 -none- list
## Pristimantis petersi 2 -none- list
## Pristimantis philipi 1 -none- numeric
## Pristimantis phoxocephalus 2 -none- list
## Pristimantis prolatus 2 -none- list
## Pristimantis prometeii 1 -none- numeric
## Pristimantis proserpens 2 -none- list
## Pristimantis pseudoacuminatus 2 -none- list
## Pristimantis pteridophilus 2 -none- list
## Pristimantis pugnax 2 -none- list
## Pristimantis pycnodermis 2 -none- list
## Pristimantis pyrrhomerus 2 -none- list
## Pristimantis quaquaversus 2 -none- list
## Pristimantis quinquagesimus 2 -none- list
## Pristimantis riveti 2 -none- list
## Pristimantis rosadoi 1 -none- numeric
## Pristimantis rubicundus 2 -none- list
## Pristimantis scolodiscus 1 -none- numeric
## Pristimantis simonbolivari 1 -none- numeric
## Pristimantis skydmainos 1 -none- numeric
## Pristimantis sobetes 2 -none- list
## Pristimantis spinosus 2 -none- list
## Pristimantis subsigillatus 2 -none- list
## Pristimantis supernatis 2 -none- list
## Pristimantis surdus 2 -none- list
## Pristimantis tenebrionis 2 -none- list
## Pristimantis thymalopsoides 2 -none- list
## Pristimantis thymelensis 2 -none- list
## Pristimantis trachyblepharis 2 -none- list
## Pristimantis trepidotus 2 -none- list
## Pristimantis truebae 2 -none- list
## Pristimantis unistrigatus 2 -none- list
## Pristimantis variabilis 2 -none- list
## Pristimantis ventrimarmoratus 2 -none- list
## Pristimantis verecundus 2 -none- list
## Pristimantis versicolor 2 -none- list
## Pristimantis vertebralis 2 -none- list
## Pristimantis vidua 2 -none- list
## Pristimantis w-nigrum 2 -none- list
## Pristimantis walkeri 2 -none- list
## Pristimantis waoranii 1 -none- numeric
## Pristimantis yantzaza 1 -none- numericlibrary(rnaturalearth)library(sp)
#world countries
sp::plot(ne_countries(country='ecuador'), border="black",
main="EOO for Pristimantis lanthanites - Convex Hull")
sp::plot(EOO.results[[7]][[2]], col="orange", add=TRUE)
#install.packages("alphahull")
library(alphahull)EOO.results2 <- EOO.computing(Pristimantis, method.range = "alpha.hull",
export_shp = T, alpha=3) ## [1] "Skipping 3616 occurrences because of missing coordinates for c(\"Pristimantis vertebralis\", \"Pristimantis lanthanites\", \"Pristimantis peruvianus\", \"Pristimantis altamazonicus\", \"Pristimantis variabilis\", \"Pristimantis unistrigatus\", \"Pristimantis achatinus\", \"Pristimantis croceoinguinis\", \"Pristimantis actites\", \"Pristimantis calcarulatus\", \"Pristimantis chloronotus\", \"Pristimantis duellmani\", \"Pristimantis celator\", \"Pristimantis caprifer\", \"Pristimantis yantzaza\", \"Pristimantis curtipes\", \"Pristimantis w-nigrum\", \"Pristimantis conspicillatus\", NA, \"Pristimantis walkeri\", \n\"Pristimantis rosadoi\", \"Pristimantis eremitus\", \"Pristimantis ornatissimus\", \"Pristimantis lymani\", \"Pristimantis glandulosus\", \"Pristimantis devillei\", \"Pristimantis librarius\", \"Pristimantis lacrimosus\", \"Pristimantis malkini\", \"Pristimantis surdus\", \"Pristimantis ockendeni\", \"Pristimantis quaquaversus\", \"Pristimantis acuminatus\", \"Pristimantis petersi\", \"Pristimantis ventrimarmoratus\", \"Pristimantis waoranii\", \"Pristimantis galdi\", \"Pristimantis floridus\", \"Pristimantis labiosus\", \"Pristimantis leoni\", \n\"Pristimantis orcesi\", \"Pristimantis crenunguis\", \"Pristimantis chalceus\", \"Pristimantis versicolor\", \"Pristimantis pugnax\", \"Pristimantis latidiscus\", \"Pristimantis martiae\", \"Pristimantis cryophilius\", \"Pristimantis riveti\", \"Pristimantis nyctophylax\", \"Pristimantis festae\", \"Pristimantis crucifer\", \"Pristimantis buckleyi\", \"Pristimantis subsigillatus\", \"Pristimantis trachyblepharis\", \"Pristimantis bisignatus\", \"Pristimantis thymelensis\", \"Pristimantis ocreatus\", \"Pristimantis supernatis\", \"Pristimantis prolatus\", \n\"Pristimantis altamnis\", \"Pristimantis vidua\", \"Pristimantis truebae\", \"Pristimantis spinosus\", \"Pristimantis cajamarcensis\", \"Pristimantis percultus\", \"Pristimantis colodactylus\", \"Pristimantis proserpens\", \"Pristimantis nigrogriseus\", \"Pristimantis leucopus\", \"Pristimantis balionotus\", \"Pristimantis incomptus\", \"Pristimantis phoxocephalus\", \"Pristimantis calcaratus\", \"Pristimantis quinquagesimus\", \"Pristimantis tenebrionis\", \"Pristimantis pteridophilus\", \"Pristimantis rubicundus\", \"Pristimantis kichwarum\", \n\"Pristimantis pycnodermis\", \"Pristimantis atratus\", \"Pristimantis inusitatus\", \"Pristimantis eriphus\", \"Pristimantis ignicolor\", \"Pristimantis orestes\", \"Pristimantis exoristus\", \"Pristimantis pecki\", \"Pristimantis cryptomelas\", \"Pristimantis condor\", \"Pristimantis bromeliaceus\", \"Pristimantis acerus\", \"Pristimantis gladiator\", \"Pristimantis modipeplus\", \"Pristimantis diadematus\", \"Pristimantis aureolineatus\", \"Pristimantis metabates\", \"Pristimantis luteolateralis\", \"Pristimantis paululus\", \"Pristimantis ernesti\", \n\"Pristimantis ruidus\", \"Pristimantis parvillus\", \"Pristimantis muricatus\", \"Pristimantis delius\", \"Pristimantis cremnobates\", \"Pristimantis appendiculatus\", \"Pristimantis achuar\", \"Pristimantis ganonotus\", \"Pristimantis pseudoacuminatus\")"## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis apiculatus is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis aureolineatus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis balionotus is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis bicantus is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis carvalhoi is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis citriogaster is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis colomai is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis dissimulatus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis ernesti is not computed
## because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis eugeniae is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis fenestratus is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis frater is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis ganonotus is not
## computed because there is less than 3 unique occurrences## Warning in tri.mesh(X): success: collinearities reduced through jitter## Warning in tri.mesh(X): dataset started with 3 colinear points, jitter
## added!## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis hamiotae is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis hectus is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis ignicolor is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis inusitatus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis katoptroides is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis kirklandi is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis laticlavius is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis latro is not computed
## because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis loustes is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis luscombei is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis matidiktyo is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis miktos is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis nimbus is not computed
## because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis ocellatus is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis ocreatus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis pastazensis is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis philipi is not computed
## because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis prometeii is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis rosadoi is not computed
## because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis scolodiscus is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis simonbolivari is not
## computed because there is less than 3 unique occurrences## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis skydmainos is not
## computed because there is only 1 unique occurrence## Warning in tri.mesh(X): success: collinearities reduced through jitter## Warning in tri.mesh(X): dataset started with 3 colinear points, jitter
## added!## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis waoranii is not
## computed because there is only 1 unique occurrence## Warning in .EOO.comp(x, Name_Sp = ifelse(ncol(XY) > 2,
## as.character(unique(x$tax)), : EOO for Pristimantis yantzaza is not
## computed because there is only 1 unique occurrencesummary(EOO.results2)## Length Class Mode
## Pristimantis acerus 2 -none- list
## Pristimantis achatinus 2 -none- list
## Pristimantis achuar 2 -none- list
## Pristimantis actites 2 -none- list
## Pristimantis acuminatus 2 -none- list
## Pristimantis altamazonicus 2 -none- list
## Pristimantis altamnis 2 -none- list
## Pristimantis apiculatus 1 -none- numeric
## Pristimantis appendiculatus 2 -none- list
## Pristimantis atratus 2 -none- list
## Pristimantis aureolineatus 1 -none- numeric
## Pristimantis balionotus 1 -none- numeric
## Pristimantis baryecuus 2 -none- list
## Pristimantis bicantus 1 -none- numeric
## Pristimantis bromeliaceus 2 -none- list
## Pristimantis buckleyi 2 -none- list
## Pristimantis cajamarcensis 2 -none- list
## Pristimantis calcaratus 2 -none- list
## Pristimantis calcarulatus 2 -none- list
## Pristimantis caprifer 2 -none- list
## Pristimantis carvalhoi 1 -none- numeric
## Pristimantis celator 2 -none- list
## Pristimantis chalceus 2 -none- list
## Pristimantis chloronotus 2 -none- list
## Pristimantis citriogaster 1 -none- numeric
## Pristimantis colodactylus 2 -none- list
## Pristimantis colomai 1 -none- numeric
## Pristimantis condor 2 -none- list
## Pristimantis conspicillatus 2 -none- list
## Pristimantis cremnobates 2 -none- list
## Pristimantis crenunguis 2 -none- list
## Pristimantis croceoinguinis 2 -none- list
## Pristimantis crucifer 2 -none- list
## Pristimantis cryophilius 2 -none- list
## Pristimantis cryptomelas 2 -none- list
## Pristimantis curtipes 2 -none- list
## Pristimantis delius 2 -none- list
## Pristimantis devillei 2 -none- list
## Pristimantis diadematus 2 -none- list
## Pristimantis dissimulatus 1 -none- numeric
## Pristimantis duellmani 2 -none- list
## Pristimantis eremitus 2 -none- list
## Pristimantis eriphus 2 -none- list
## Pristimantis ernesti 1 -none- numeric
## Pristimantis eugeniae 1 -none- numeric
## Pristimantis fenestratus 1 -none- numeric
## Pristimantis festae 2 -none- list
## Pristimantis floridus 2 -none- list
## Pristimantis frater 1 -none- numeric
## Pristimantis galdi 2 -none- list
## Pristimantis ganonotus 1 -none- numeric
## Pristimantis gentryi 2 -none- list
## Pristimantis gladiator 2 -none- list
## Pristimantis glandulosus 2 -none- list
## Pristimantis hamiotae 1 -none- numeric
## Pristimantis hectus 1 -none- numeric
## Pristimantis ignicolor 1 -none- numeric
## Pristimantis illotus 2 -none- list
## Pristimantis incanus 2 -none- list
## Pristimantis incomptus 2 -none- list
## Pristimantis inusitatus 1 -none- numeric
## Pristimantis katoptroides 1 -none- numeric
## Pristimantis kichwarum 2 -none- list
## Pristimantis kirklandi 1 -none- numeric
## Pristimantis labiosus 2 -none- list
## Pristimantis lacrimosus 2 -none- list
## Pristimantis lanthanites 2 -none- list
## Pristimantis laticlavius 1 -none- numeric
## Pristimantis latidiscus 2 -none- list
## Pristimantis latro 1 -none- numeric
## Pristimantis leoni 2 -none- list
## Pristimantis leucopus 2 -none- list
## Pristimantis librarius 2 -none- list
## Pristimantis lividus 2 -none- list
## Pristimantis loustes 1 -none- numeric
## Pristimantis luscombei 1 -none- numeric
## Pristimantis luteolateralis 2 -none- list
## Pristimantis lymani 2 -none- list
## Pristimantis malkini 2 -none- list
## Pristimantis martiae 2 -none- list
## Pristimantis matidiktyo 1 -none- numeric
## Pristimantis miktos 1 -none- numeric
## Pristimantis modipeplus 2 -none- list
## Pristimantis muricatus 2 -none- list
## Pristimantis nigrogriseus 2 -none- list
## Pristimantis nimbus 1 -none- numeric
## Pristimantis nyctophylax 2 -none- list
## Pristimantis ocellatus 1 -none- numeric
## Pristimantis ockendeni 2 -none- list
## Pristimantis ocreatus 1 -none- numeric
## Pristimantis orcesi 2 -none- list
## Pristimantis orestes 2 -none- list
## Pristimantis ornatissimus 2 -none- list
## Pristimantis orphnolaimus 2 -none- list
## Pristimantis parvillus 2 -none- list
## Pristimantis pastazensis 1 -none- numeric
## Pristimantis paululus 2 -none- list
## Pristimantis peruvianus 2 -none- list
## Pristimantis petersi 2 -none- list
## Pristimantis philipi 1 -none- numeric
## Pristimantis phoxocephalus 2 -none- list
## Pristimantis prolatus 2 -none- list
## Pristimantis prometeii 1 -none- numeric
## Pristimantis proserpens 2 -none- list
## Pristimantis pseudoacuminatus 2 -none- list
## Pristimantis pteridophilus 2 -none- list
## Pristimantis pugnax 2 -none- list
## Pristimantis pycnodermis 2 -none- list
## Pristimantis pyrrhomerus 2 -none- list
## Pristimantis quaquaversus 2 -none- list
## Pristimantis quinquagesimus 2 -none- list
## Pristimantis riveti 2 -none- list
## Pristimantis rosadoi 1 -none- numeric
## Pristimantis rubicundus 2 -none- list
## Pristimantis scolodiscus 1 -none- numeric
## Pristimantis simonbolivari 1 -none- numeric
## Pristimantis skydmainos 1 -none- numeric
## Pristimantis sobetes 2 -none- list
## Pristimantis spinosus 2 -none- list
## Pristimantis subsigillatus 2 -none- list
## Pristimantis supernatis 2 -none- list
## Pristimantis surdus 2 -none- list
## Pristimantis tenebrionis 2 -none- list
## Pristimantis thymalopsoides 2 -none- list
## Pristimantis thymelensis 2 -none- list
## Pristimantis trachyblepharis 2 -none- list
## Pristimantis trepidotus 2 -none- list
## Pristimantis truebae 2 -none- list
## Pristimantis unistrigatus 2 -none- list
## Pristimantis variabilis 2 -none- list
## Pristimantis ventrimarmoratus 2 -none- list
## Pristimantis verecundus 2 -none- list
## Pristimantis versicolor 2 -none- list
## Pristimantis vertebralis 2 -none- list
## Pristimantis vidua 2 -none- list
## Pristimantis w-nigrum 2 -none- list
## Pristimantis walkeri 2 -none- list
## Pristimantis waoranii 1 -none- numeric
## Pristimantis yantzaza 1 -none- numeric#
sp::plot(EOO.results2[[7]][[2]], col="green", main="EOO for Pristimantis lanthanites - Alpha Hull")
sp::plot(ne_countries(country='ecuador'), border="black", add=TRUE)
`
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