Closed lime-n closed 4 years ago
I am trying to prepare a dataframe of species observation for abundance and occurrence data using habitat covariates.
When using this code:
library(auk) occ_wide <- format_unmarked_occu(occ, site_id = "site", response = "species_observed", site_covs = c("n_observations", "latitude", "longitude", "pland_00_water", "pland_11_wetland", "pland_12_cropland", "pland_13_urban"), obs_covs = c("time_observations_started", "duration_minutes", "effort_distance_km", "number_observers", "protocol_type", "pland_11_wetland"))
I get this error:
Error in format_unmarked_occu(pract, site_id = "site", response = "species_observed", : Site-level covariates must be constant across sites
What does this mean and how can I overcome this error?
a reproducible code:
structure(list(site = c("L10018668_obs439702_2020", "L10018668_obs439702_2020", "L10018668_obs439702_2020", "L10018668_obs439702_2020", "L10024459_obs1462591_2020", "L10024459_obs1462591_2020"), closure_id = c("2020", "2020", "2020", "2020", "2020", "2020"), n_observations = c(4L, 4L, 4L, 4L, 6L, 6L), checklist_id = c("S62823384", "S62823384", "S62823384", "S62823384", "S62830871", "S62830871"), observer_id = c("obs439702", "obs439702", "obs439702", "obs439702", "obs1462591", "obs1462591" ), sampling_event_identifier = c("S62823384", "S62823384", "S62823384", "S62823384", "S62830871", "S62830871"), scientific_name = c("Calidris canutus", "Calidris canutus", "Calidris canutus", "Calidris canutus", "Calidris canutus", "Calidris canutus"), observation_count = c(0, 0, 0, 0, 0, 0), species_observed = c(0L, 0L, 0L, 0L, 0L, 0L), state_code = c("AU-VIC", "AU-VIC", "AU-VIC", "AU-VIC", "AU-NSW", "AU-NSW"), locality_id = c("L10018668", "L10018668", "L10018668", "L10018668", "L10024459", "L10024459" ), latitude = c(-37.0209359, -37.0209359, -37.0209359, -37.0209359, -34.785917, -34.785917), longitude = c(145.1458832, 145.1458832, 145.1458832, 145.1458832, 150.750221, 150.750221), protocol_type = c("Stationary", "Stationary", "Stationary", "Stationary", "Traveling", "Traveling" ), all_species_reported = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE), observation_date = structure(c(18262, 18262, 18262, 18262, 18262, 18262), class = "Date"), year = c(2020, 2020, 2020, 2020, 2020, 2020), day_of_year = c(1, 1, 1, 1, 1, 1 ), time_observations_started = c(8.71666666666667, 8.71666666666667, 8.71666666666667, 8.71666666666667, 14.8166666666667, 14.8166666666667 ), duration_minutes = c(30, 30, 30, 30, 59, 59), effort_distance_km = c(0, 0, 0, 0, 0.805, 0.805), number_observers = c(1, 1, 1, 1, 1, 1), pland_00_water = c(NA, NA, NA, NA, 0.032258064516129, NA), pland_01_evergreen_needleleaf = c(NA, NA, NA, NA, NA, NA), pland_02_evergreen_broadleaf = c(NA, NA, NA, NA, NA, 0.129032258064516), pland_03_deciduous_needleleaf = c(NA, NA, NA, NA, NA, NA), pland_04_deciduous_broadleaf = c(NA, NA, NA, NA, NA, NA), pland_05_mixed_forest = c(NA, NA, NA, NA, NA, NA), pland_06_closed_shrubland = c(NA, NA, NA, NA, NA, NA), pland_07_open_shrubland = c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_), pland_08_woody_savanna = c(NA, NA, NA, NA, NA, NA), pland_09_savanna = c(NA, NA, NA, NA, NA, NA), pland_10_grassland = c(NA, NA, NA, NA, NA, NA), pland_11_wetland = c(NA, NA, NA, NA, NA, NA), pland_12_cropland = c(NA, NA, NA, NA, NA, NA), pland_13_urban = c(NA, NA, NA, 0.125, NA, NA), pland_14_mosiac = c(NA, NA, NA, NA, NA, NA), pland_15_barren = c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_), id = c(57262, 57262, 57262, 57262, 85293, 85293), elevation_median = c(150.127420697893, 150.127420697893, 150.127420697893, 150.127420697893, 17.1925210271563, 17.1925210271563), elevation_sd = c(5.25428441050561, 5.25428441050561, 5.25428441050561, 5.25428441050561, 7.86367063800502, 7.86367063800502 )), row.names = c(NA, -6L), class = c("tbl_df", "tbl", "data.frame" ))
closing because addressed here: https://github.com/CornellLabofOrnithology/ebird-best-practices/issues/8#issuecomment-674951896
I am trying to prepare a dataframe of species observation for abundance and occurrence data using habitat covariates.
When using this code:
I get this error:
What does this mean and how can I overcome this error?
a reproducible code: