Risaralda
Valentina Diez
2026-03-14
###Cargar paquetes
library(grateful) # Facilitate Citation of R Packages## Warning: package 'grateful' was built under R version 4.4.3library(readxl) # Read Excel Files## Warning: package 'readxl' was built under R version 4.4.3library(readr) ## Warning: package 'readr' was built under R version 4.4.3library(sf) # Simple Features for R## Warning: package 'sf' was built under R version 4.4.3## Linking to GEOS 3.13.0, GDAL 3.10.1, PROJ 9.5.1; sf_use_s2() is TRUElibrary(mapview) # Interactive Viewing of Spatial Data in R## Warning: package 'mapview' was built under R version 4.4.3library(readr) # No used functions found
library(camtrapR) # Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses ## Warning: package 'camtrapR' was built under R version 4.4.3library(unmarked) # hierarchical models of animal occurrence and abundance ## Warning: package 'unmarked' was built under R version 4.4.3library(DT) # datatable## Warning: package 'DT' was built under R version 4.4.3library(kableExtra) # Construct Complex Table with 'kable' and Pipe Syntax## Warning: package 'kableExtra' was built under R version 4.4.3library(tidyverse) # Easily Install and Load the 'Tidyverse'## Warning: package 'tidyverse' was built under R version 4.4.3## Warning: package 'ggplot2' was built under R version 4.4.3## Warning: package 'tidyr' was built under R version 4.4.3## Warning: package 'dplyr' was built under R version 4.4.3## Warning: package 'lubridate' was built under R version 4.4.3## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.2.0 ✔ purrr 1.0.2
## ✔ forcats 1.0.0 ✔ stringr 1.5.1
## ✔ ggplot2 4.0.2 ✔ tibble 3.2.1
## ✔ lubridate 1.9.5 ✔ tidyr 1.3.2## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::group_rows() masks kableExtra::group_rows()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(glue)
library(terra)## terra 1.7.83
##
## Adjuntando el paquete: 'terra'
##
## The following object is masked from 'package:glue':
##
## trim
##
## The following object is masked from 'package:tidyr':
##
## extractlibrary(elevatr)## Warning: package 'elevatr' was built under R version 4.4.3## elevatr v0.99.0 NOTE: Version 0.99.0 of 'elevatr' uses 'sf' and 'terra'. Use
## of the 'sp', 'raster', and underlying 'rgdal' packages by 'elevatr' is being
## deprecated; however, get_elev_raster continues to return a RasterLayer. This
## will be dropped in future versions, so please plan accordingly.###Abrir los datos que obtuvimos de Wildlifeinsights
cameras<- read_csv("C:/Users/valen/OneDrive/Escritorio/Curso fototrampeo/DatosRisaralda/data/cameras.csv")## Rows: 131 Columns: 7
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (4): camera_name, make, model, serial_number
## dbl (3): project_id, camera_id, year_purchased
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.images <- read_csv("C:/Users/valen/OneDrive/Escritorio/Curso fototrampeo/DatosRisaralda/data/images_2000367.csv")## Rows: 17390 Columns: 28
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (16): deployment_id, image_id, filename, location, identified_by, wi_ta...
## dbl (4): project_id, is_blank, number_of_objects, cv_confidence
## lgl (7): uncertainty, animal_recognizable, individual_id, individual_anima...
## dttm (1): timestamp
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.deployments <- read_csv("C:/Users/valen/OneDrive/Escritorio/Curso fototrampeo/DatosRisaralda/data/deployments.csv")## Rows: 162 Columns: 29
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (15): deployment_id, placename, bait_type, feature_type, feature_type_m...
## dbl (5): project_id, longitude, latitude, camera_id, quiet_period
## lgl (7): bait_description, height_other, orientation_other, plot_treatment...
## dttm (2): start_date, end_date
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.View(cameras)#enlazar 3 tablas
data1 <- cameras |> left_join(deployments) # join first two tables## Joining with `by = join_by(project_id, camera_id, camera_name)`by <- join_by("deployment_id") # join by "Deployment ID"
# join by "Deployment ID" and # lets put together genus and species
data <- left_join(data1, images, by) |>
filter(subproject_name=="Ucumari") |>
mutate(binomial=paste(genus, species) )##hacer mapa, con internet me puedo acercar y ver bien los datos
datos_distinct <- data |> distinct(longitude, latitude, deployment_id, camera_name) |> as.data.frame()
projlatlon <- "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"
datos_sf <- st_as_sf(x = datos_distinct,
coords = c("longitude",
"latitude"),
crs = projlatlon)
mapview(datos_sf)##Extraer covariables de sitio con una imagen de satelite
# let make a 3K buffer around the points
datos_sf_buff <- st_buffer(datos_sf, 3000)
# get elevation raster from AWS using the 3K buffer
elevation_detailed <- rast(get_elev_raster(datos_sf_buff, z = 9, clip="bbox", neg_to_na=TRUE))## Mosaicing & Projecting## Clipping DEM to bbox## Note: Elevation units are in meters.slope_map<-terrain(elevation_detailed, v="slope", unit='degrees', neighbors=8)
aspect_map<-terrain(elevation_detailed, v="aspect", unit='degrees', neighbors=8)
roughness_map <- terrain(elevation_detailed, v = c("roughness"))
# Load forest map... it is huge!
# forest_type <- rast("C:/CodigoR/CameraTrapCesar/posts/2026-01-01-wildlifeinsights-to-detections/raster/2017_coverage_lclu.tif")
# cut the huge forest map to 3K buffer
# forest_type_cropped <- crop(forest_type, elevation_detailed)
# lets remove the huge map from memory to save RAM
# rm(forest_type)
per_tree_cov <- rast("C:/Users/valen/OneDrive/Escritorio/Curso fototrampeo/MOD44B_Perc_TreeCov_2017_065.tif")
# cut the huge tree cover map to 3K buffer
per_tree_cov_cropped <- crop(per_tree_cov, elevation_detailed)
# lets remove the huge map from memory to save RAM
rm(per_tree_cov)
# Forest Integrity Index
FLII2017 <- rast("C:/Users/valen/OneDrive/Escritorio/Curso fototrampeo/FLII_2017.tif")
# cut the huge FLII map to 3K buffer
FLII2017_cropped <- crop(FLII2017, elevation_detailed)
# lets remove the huge map from memory to save RAM
rm(FLII2017)
# extract covs using points (datos_sf) and add to sites
# covs <- cbind(sites, terra::extract(SiteCovsRast, sites))
elev <- terra::extract(elevation_detailed, datos_sf)
# forest_typ <- terra::extract(forest_type_cropped, datos_sf)
tree_cov <- terra::extract(per_tree_cov_cropped, datos_sf)
slope <- terra::extract(slope_map, datos_sf)
aspect <- terra::extract(aspect_map, datos_sf)
roughness <- terra::extract(roughness_map, datos_sf)
flii <- terra::extract(FLII2017_cropped, datos_sf)
#### make a table of cameras dropping geometry
sites <- datos_sf %>%
mutate(
lat = st_coordinates(.)[, 1],
lon = st_coordinates(.)[, 2]
) %>%
st_drop_geometry() |>
as.data.frame()
### Add the covariates to the table
# remove decimals convert to factor
# sites$forest_typ <- factor(forest_typ[,2])
sites$elev <- elev[,2]
sites$tree_cov <- tree_cov[,2]
sites$slope <- slope[,2]
sites$aspect <- aspect[,2]
sites$roughness <- roughness[,2]
sites$flii <- flii[,2]
mapview(per_tree_cov_cropped)+ mapview(elevation_detailed) + mapview(datos_sf)###Estas Covariables hacen un buffer alrededor de los puntos, necesita concexión a internet
# filter first year and make uniques to get a table of cameras and operation dates
CToperation <- data |>
# filter(samp_year == 2021) |> # multi-season data
group_by(deployment_id) |>
mutate(minStart = min(start_date), maxEnd = max(end_date)) |>
distinct(longitude, latitude, minStart, maxEnd) |> #, samp_year) |>
ungroup() |>
as.data.frame()
# camera operation matrix for
# multi-season data. Season1
camop <- cameraOperation(
CTtable = CToperation, # Tabla de operación
stationCol = "deployment_id", # Columna que define la estación
setupCol = "minStart", # Columna fecha de colocación
retrievalCol = "maxEnd", # Columna fecha de retiro
# sessionCol = "samp_year", # multi-season column
# hasProblems= T, # Hubo fallos de cámaras
dateFormat = "%Y-%m-%d"
) # , #, # Formato de las fechas## Warning: There are spaces in CTtable[, setupCol], but not in dateFormat## Warning: There are spaces in CTtable[, retrievalCol], but not in dateFormat# cameraCol="CT")
# sessionCol= "samp_year")
# Plot camera operation as image
image(t(camop))
#que veo ahi la diferencia en los tiempos de muestreo etre las camaras
desde que las coloque, las rayas que estan en blanco y se extienden es
porque no tomaron datos, entonces hay que
# Generar las historias de detección ---------------------------------------
## remove plroblem species
# ind <- which(datos_PCF$Species=="Marmosa sp.")
# datos_PCF <- datos_PCF[-ind,]
DetHist_list_UCU <- lapply(unique(data$binomial), FUN = function(x) {
detectionHistory(
recordTable = data, # Tabla de registros
camOp = camop, # Matriz de operación de cámaras
stationCol = "deployment_id",
speciesCol = "binomial",
recordDateTimeCol = "timestamp",
recordDateTimeFormat = "%Y-%m-%d %H:%M:%S",
species = x, # la función reemplaza x por cada una de las especies
occasionLength = 1, # Colapso de las historias a días
day1 = "survey",# "station", # inicie en la fecha de cada survey
datesAsOccasionNames = FALSE, # pone fecha en columna
includeEffort = TRUE,
scaleEffort = FALSE,
unmarkedMultFrameInput = TRUE,
timeZone = "America/Bogota"
)
})## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted## Warning:
## At 6 stations there were records after camera operation date range: CT-UC-02-08, CT-UC-01-26, CT-UC-01-17, CT-UC-01-15, CT-UC-01-08, CT-UC-01-07## Warning:
##
## 17 records (out of 610) were removed because they were taken after the end of the last occasion, e.g.:
## CT-UC-02-08: 2017-03-18 06:58:29
## CT-UC-02-08: 2017-03-18 07:44:32
## CT-UC-02-08: 2017-03-18 13:53:44
## CT-UC-01-26: 2017-01-27 03:13:18
## CT-UC-01-26: 2017-01-27 03:13:27
## CT-UC-01-26: 2017-01-27 03:13:34## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted## Warning:
## At 1 stations there were records before camera operation date range: CT-UC-01-03## Warning:
## At 6 stations there were records after camera operation date range: CT-UC-02-15, CT-UC-01-26, CT-UC-01-25, CT-UC-01-16, CT-UC-01-11, CT-UC-01-07## Warning: 91 records (out of 6562) were removed because they were taken before day1 (if a date was specified), within the buffer period, or before occasionStartTime on the 1st day, e.g.:
## CT-UC-01-03: 2017-01-03 18:36:58
## CT-UC-01-03: 2017-01-03 18:37:01
## CT-UC-01-03: 2017-01-03 18:37:00
## CT-UC-01-03: 2017-01-03 18:37:01
## CT-UC-01-03: 2017-01-03 18:37:03
## CT-UC-01-03: 2017-01-03 18:37:03## Warning:
##
## 116 records (out of 6562) were removed because they were taken after the end of the last occasion, e.g.:
## CT-UC-02-15: 2017-03-20 01:45:54
## CT-UC-02-15: 2017-03-20 01:45:56
## CT-UC-02-15: 2017-03-20 01:46:00
## CT-UC-02-15: 2017-03-20 01:48:20
## CT-UC-02-15: 2017-03-20 01:46:02
## CT-UC-01-26: 2017-01-27 04:57:05## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted## Warning:
## At 3 stations there were records after camera operation date range: CT-UC-02-21, CT-UC-01-26, CT-UC-01-07## Warning:
##
## 28 records (out of 292) were removed because they were taken after the end of the last occasion, e.g.:
## CT-UC-02-21: 2017-03-19 21:20:13
## CT-UC-02-21: 2017-03-19 21:20:28
## CT-UC-02-21: 2017-03-19 21:20:37
## CT-UC-02-21: 2017-03-19 21:20:43
## CT-UC-02-21: 2017-03-19 21:21:13
## CT-UC-02-21: 2017-03-19 21:39:23## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted## Warning:
## At 1 stations there were records after camera operation date range: CT-UC-02-18## Warning:
##
## 3 records (out of 75) were removed because they were taken after the end of the last occasion, e.g.:
## CT-UC-02-18: 2017-03-18 23:51:28
## CT-UC-02-18: 2017-03-18 23:55:42
## CT-UC-02-18: 2017-03-18 23:55:43## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted## Warning:
## At 1 stations there were records after camera operation date range: CT-UC-01-08## Warning:
##
## 1 records (out of 255) were removed because they were taken after the end of the last occasion, e.g.:
## CT-UC-01-08: 2017-01-27 11:41:08## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted## Warning:
## At 1 stations there were records after camera operation date range: CT-UC-01-13## Warning:
##
## 1 records (out of 217) were removed because they were taken after the end of the last occasion, e.g.:
## CT-UC-01-13: 2017-01-27 11:58:13## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted## Warning:
## At 1 stations there were records after camera operation date range: CT-UC-02-08## Warning:
##
## 4 records (out of 65) were removed because they were taken after the end of the last occasion, e.g.:
## CT-UC-02-08: 2017-03-18 06:41:00
## CT-UC-02-08: 2017-03-18 06:58:37
## CT-UC-02-08: 2017-03-18 06:58:39
## CT-UC-02-08: 2017-03-18 06:58:44## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted## Warning:
## At 5 stations there were records after camera operation date range: CT-UC-02-13, CT-UC-01-31, CT-UC-01-13, CT-UC-01-12, CT-UC-01-10## Warning:
##
## 21 records (out of 34) were removed because they were taken after the end of the last occasion, e.g.:
## CT-UC-02-13: 2017-03-18 10:25:14
## CT-UC-01-31: 2017-01-27 09:48:47
## CT-UC-01-31: 2017-01-27 09:48:49
## CT-UC-01-31: 2017-01-27 09:48:52
## CT-UC-01-13: 2017-01-27 07:53:15
## CT-UC-01-13: 2017-01-27 07:53:23## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted## Warning:
## At 1 stations there were records after camera operation date range: CT-UC-02-10## Warning:
##
## 4 records (out of 78) were removed because they were taken after the end of the last occasion, e.g.:
## CT-UC-02-10: 2017-03-18 08:35:37
## CT-UC-02-10: 2017-03-18 13:14:59
## CT-UC-02-10: 2017-03-18 13:15:02
## CT-UC-02-10: 2017-03-18 13:15:08## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted## Warning:
## At 1 stations there were records after camera operation date range: CT-UC-01-07## Warning:
##
## 1 records (out of 3) were removed because they were taken after the end of the last occasion, e.g.:
## CT-UC-01-07: 2017-01-29 01:31:09## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted
## Warning: 'unmarkedMultFrameInput' is defined, but I cannot find session IDs in
## the rownames of camOp. Check the row names format and maybe run
## camtrapR:::deparseCamOpRownames(camOp) to see if it can be interpreted# names
names(DetHist_list_UCU) <- unique(data$binomial)
# Finalmente creamos una lista nueva donde estén solo las historias de detección
ylist_UCU <- lapply(DetHist_list_UCU, FUN = function(x) x$detection_history)
# y el esfuerzo de muestreo
effortlist_UCU <- lapply(DetHist_list_UCU, FUN = function(x) x$effort)
### Danta, venado
# which(names(ylist_UCU) == "Tapirus pinchaque")
#> integer(0)
# which(names(ylist_UCU) == "Mazama rufina")
#> [1] 5###Se obtiene la historia de detección, saca para todas las especies como fueron los registros, si se detecto o no ### Listado de especies extraer
names(DetHist_list_UCU) # name of each list entry## [1] "Bos taurus" "NA NA"
## [3] "Aburria aburri" "Didelphis marsupialis"
## [5] "Tapirus pinchaque" "Sciurus NA"
## [7] "Grallaria NA" "Eira barbara"
## [9] "Mazama rufina" "Puma concolor"
## [11] "Leopardus pardalis" "Dasypus novemcinctus"
## [13] "Leopardus wiedii" "Cuniculus taczanowskii"
## [15] "Nasuella olivacea" "Penelope perspicax"
## [17] "Momotus aequatorialis" "Mustela felipei"
## [19] "Dasyprocta leporina" "Nothoprocta pentlandii"
## [21] "Herpailurus yagouaroundi" "Leptotila NA"
## [23] "Formicarius analis" "Formicarius NA"
## [25] "Canis familiaris" "Sciurus granatensis"
## [27] "Columba NA" "Penelope montagnii"
## [29] "Nasua nasua" "Odontophorus columbianus"
## [31] "Turdus NA" "Leptotila verreauxi"
## [33] "Odontophorus gujanensis" "Aramides cajaneus"
## [35] "Tamandua mexicana" "Neogale frenata"
## [37] "Dasyprocta fuliginosa" "Odontophorus NA"
## [39] "Tinamus major" "Bassaricyon neblina"
## [41] "Odontophorus hyperythrus" "Dasyprocta punctata"
## [43] "Tinamus NA" "Momotus momota"
## [45] "Cyanocorax NA" "Alouatta seniculus"
## [47] "Pyroderus scutatus" "Didelphis virginiana"
## [49] "Leopardus NA" "Tremarctos ornatus"
## [51] "Leopardus tigrinus" "Didelphis albiventris"
## [53] "Didelphis NA"#> [1] "Bos taurus" "NA NA"
#> [3] "Aburria aburri" "Didelphis marsupialis"
#> [5] "Tapirus pinchaque" "Sciurus NA"
#> [7] "Grallaria NA" "Eira barbara"
#> [9] "Mazama rufina" "Puma concolor"
#> [11] "Leopardus pardalis" "Dasypus novemcinctus"
#> [13] "Leopardus wiedii" "Cuniculus taczanowskii"
#> [15] "Nasuella olivacea" "Penelope perspicax"
#> [17] "Momotus aequatorialis" "Mustela felipei"
#> [19] "Dasyprocta leporina" "Nothoprocta pentlandii"
#> [21] "Herpailurus yagouaroundi" "Leptotila NA"
#> [23] "Formicarius analis" "Formicarius NA"
#> [25] "Canis familiaris" "Sciurus granatensis"
#> [27] "Columba NA" "Penelope montagnii"
#> [29] "Nasua nasua" "Odontophorus columbianus"
#> [31] "Turdus NA" "Leptotila verreauxi"
#> [33] "Odontophorus gujanensis" "Aramides cajaneus"
#> [35] "Tamandua mexicana" "Neogale frenata"
#> [37] "Dasyprocta fuliginosa" "Odontophorus NA"
#> [39] "Tinamus major" "Bassaricyon neblina"
#> [41] "Odontophorus hyperythrus" "Dasyprocta punctata"
#> [43] "Tinamus NA" "Momotus momota"
#> [45] "Cyanocorax NA" "Alouatta seniculus"
#> [47] "Pyroderus scutatus" "Didelphis virginiana"
#> [49] "Leopardus NA" "Tremarctos ornatus"
#> [51] "Leopardus tigrinus" "Didelphis albiventris"
#> [53] "Didelphis NA"#Ahora tomaremos un dato especiefico para un modelo de danta
y_sp <- ylist_UCU$"Tapirus pinchaque"
head(y_sp)## o1 o2 o3 o4 o5 o6 o7 o8 o9 o10 o11 o12 o13 o14 o15 o16 o17 o18 o19
## CT-UC-02-24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## CT-UC-02-23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## CT-UC-02-22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## CT-UC-02-21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## CT-UC-02-18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## CT-UC-02-17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## o20 o21 o22 o23 o24 o25 o26 o27 o28 o29 o30 o31 o32 o33 o34 o35 o36
## CT-UC-02-24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## CT-UC-02-23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## CT-UC-02-22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## CT-UC-02-21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## CT-UC-02-18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## CT-UC-02-17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## o37 o38 o39 o40 o41 o42 o43 o44 o45 o46 o47 o48 o49 o50 o51 o52 o53
## CT-UC-02-24 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
## CT-UC-02-23 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
## CT-UC-02-22 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
## CT-UC-02-21 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
## CT-UC-02-18 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
## CT-UC-02-17 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
## o54 o55 o56 o57 o58 o59 o60 o61 o62 o63 o64 o65 o66 o67 o68 o69 o70
## CT-UC-02-24 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0
## CT-UC-02-23 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0
## CT-UC-02-22 1 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0
## CT-UC-02-21 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
## CT-UC-02-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## CT-UC-02-17 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 1 0
## o71 o72 o73 o74 o75 o76 o77 o78 o79 o80 o81 o82 o83 o84 o85 o86 o87
## CT-UC-02-24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## CT-UC-02-23 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
## CT-UC-02-22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## CT-UC-02-21 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
## CT-UC-02-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## CT-UC-02-17 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0
## o88 o89 o90 o91 o92 o93 o94 o95 o96 o97 o98 o99 o100 o101
## CT-UC-02-24 0 0 0 0 0 0 NA NA NA NA NA NA NA NA
## CT-UC-02-23 0 0 0 0 0 0 0 1 0 NA NA NA NA NA
## CT-UC-02-22 0 0 0 0 0 0 NA NA NA NA NA NA NA NA
## CT-UC-02-21 0 0 1 0 0 0 NA NA NA NA NA NA NA NA
## CT-UC-02-18 0 0 0 0 0 0 NA NA NA NA NA NA NA NA
## CT-UC-02-17 0 0 0 1 0 0 NA NA NA NA NA NA NA NA#> o1 o2 o3 o4 o5 o6 o7 o8 o9 o10 o11 o12 o13 o14 o15 o16 o17 o18 o19
#> CT-UC-02-24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> CT-UC-02-23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> CT-UC-02-22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> CT-UC-02-21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> CT-UC-02-18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> CT-UC-02-17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> o20 o21 o22 o23 o24 o25 o26 o27 o28 o29 o30 o31 o32 o33 o34 o35 o36
#> CT-UC-02-24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> CT-UC-02-23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> CT-UC-02-22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> CT-UC-02-21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> CT-UC-02-18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> CT-UC-02-17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> o37 o38 o39 o40 o41 o42 o43 o44 o45 o46 o47 o48 o49 o50 o51 o52 o53
#> CT-UC-02-24 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
#> CT-UC-02-23 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
#> CT-UC-02-22 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
#> CT-UC-02-21 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
#> CT-UC-02-18 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
#> CT-UC-02-17 NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0
#> o54 o55 o56 o57 o58 o59 o60 o61 o62 o63 o64 o65 o66 o67 o68 o69 o70
#> CT-UC-02-24 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0
#> CT-UC-02-23 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0
#> CT-UC-02-22 1 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0
#> CT-UC-02-21 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
#> CT-UC-02-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> CT-UC-02-17 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 1 0
#> o71 o72 o73 o74 o75 o76 o77 o78 o79 o80 o81 o82 o83 o84 o85 o86 o87
#> CT-UC-02-24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> CT-UC-02-23 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
#> CT-UC-02-22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> CT-UC-02-21 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
#> CT-UC-02-18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> CT-UC-02-17 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0
#> o88 o89 o90 o91 o92 o93 o94 o95 o96 o97 o98 o99 o100 o101
#> CT-UC-02-24 0 0 0 0 0 0 NA NA NA NA NA NA NA NA
#> CT-UC-02-23 0 0 0 0 0 0 0 1 0 NA NA NA NA NA
#> CT-UC-02-22 0 0 0 0 0 0 NA NA NA NA NA NA NA NA
#> CT-UC-02-21 0 0 1 0 0 0 NA NA NA NA NA NA NA NA
#> CT-UC-02-18 0 0 0 0 0 0 NA NA NA NA NA NA NA NA
#> CT-UC-02-17 0 0 0 1 0 0 NA NA NA NA NA NA NA NA#leer datos de precipitación
# read de precipitation data
rainfall_total <- read_csv("C:/Users/valen/OneDrive/Escritorio/Curso fototrampeo/descargaDhime.csv")## Rows: 757 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (5): NombreEstacion, Variable, Parametro, Unidad, NivelAprobacion
## dbl (2): CodigoEstacion, Valor
## dttm (1): Fecha
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.sampling_start <- min(CToperation$minStart)
Sampling_end <- max(CToperation$maxEnd)
# extracts dates of start and end to match the precipitation dates
rainfall_selected <- rainfall_total |> filter(Fecha >= sampling_start, Fecha<=Sampling_end)
# put selected precipitation values on columns an repeated 49 times in rows
rainfall_mat <- matrix(rainfall_selected$Valor,
nrow=49, ncol=101, byrow=TRUE)
#show table
datatable(head(y_sp))###leer datos de precipitación con los datos de ocurrencia
library(unmarked)
umf <- unmarkedFrameOccu(y= y_sp,
siteCovs=data.frame(tree_cov=sites$tree_cov,
elev=sites$elev,
slope=sites$slope,
aspect=sites$aspect,
roughness=sites$roughness,
flii=sites$flii),
obsCovs=list(rain=rainfall_mat)
)
summary(umf)## unmarkedFrame Object
##
## 49 sites
## Maximum number of observations per site: 101
## Mean number of observations per site: 44.63
## Sites with at least one detection: 45
##
## Tabulation of y observations:
## 0 1 <NA>
## 1965 222 2762
##
## Site-level covariates:
## tree_cov elev slope aspect
## Min. : 2.00 Min. :1820 Min. : 3.792 Min. : 0.4294
## 1st Qu.:11.00 1st Qu.:1998 1st Qu.: 7.663 1st Qu.:164.5982
## Median :20.00 Median :2127 Median :12.657 Median :199.8469
## Mean :23.71 Mean :2140 Mean :13.926 Mean :206.3143
## 3rd Qu.:34.00 3rd Qu.:2254 3rd Qu.:17.225 3rd Qu.:255.9186
## Max. :54.00 Max. :2724 Max. :32.342 Max. :359.4761
## roughness flii
## Min. : 40.0 Min. :6.153
## 1st Qu.: 75.0 1st Qu.:8.834
## Median :111.0 Median :9.364
## Mean :117.4 Mean :9.029
## 3rd Qu.:150.0 3rd Qu.:9.626
## Max. :235.0 Max. :9.865
##
## Observation-level covariates:
## rain
## Min. : 0.000
## 1st Qu.: 0.000
## Median : 3.300
## Mean : 8.904
## 3rd Qu.:11.200
## Max. :95.200#> unmarkedFrame Object
#>
#> 49 sites
#> Maximum number of observations per site: 101
#> Mean number of observations per site: 44.63
#> Sites with at least one detection: 45
#>
#> Tabulation of y observations:
#> 0 1 <NA>
#> 1965 222 2762
#>
#> Site-level covariates:
#> tree_cov elev slope aspect
#> Min. : 2.00 Min. :1820 Min. : 3.792 Min. : 0.4294
#> 1st Qu.:11.00 1st Qu.:1998 1st Qu.: 7.663 1st Qu.:164.5982
#> Median :20.00 Median :2127 Median :12.657 Median :199.8469
#> Mean :23.71 Mean :2140 Mean :13.926 Mean :206.3143
#> 3rd Qu.:34.00 3rd Qu.:2254 3rd Qu.:17.225 3rd Qu.:255.9186
#> Max. :54.00 Max. :2724 Max. :32.342 Max. :359.4761
#> roughness flii
#> Min. : 40.0 Min. :6.153
#> 1st Qu.: 75.0 1st Qu.:8.834
#> Median :111.0 Median :9.364
#> Mean :117.4 Mean :9.029
#> 3rd Qu.:150.0 3rd Qu.:9.626
#> Max. :235.0 Max. :9.865
#>
#> Observation-level covariates:
#> rain
#> Min. : 0.000
#> 1st Qu.: 0.000
#> Median : 3.300
#> Mean : 8.904
#> 3rd Qu.:11.200
#> Max. :95.200###lo que se ve en el plot es donde aparecio la foto de la danta en los dias