Este cuaderno de R ilustra cómo descargar datos de propiedades de suelos a cualquier profundidad desde la plataforma SoilGrids.
Dichos datos están en estructura Raster con resolución espacial de 250m.
El uso de R para descargar datos de SoilGrids ofrece varias ventajas sobre el uso de un navegador web:
SoilGrids ofrece tres servicios principales para acceder a los datos:
En este cuaderno utilizaremos el servicio WebDAV, que nos permite descargar datos específicos para nuestra región de interés de manera eficiente.
Primero vamos a limpiar nuestro espacio de trabajo.
rm(list=ls())
Luego instalamos las librerías desde la consola, no desde el cuaderno.
##it is assummed that you already installed terra, ggplot2, tidyterra, sf, and leaflet
##paquetes= c('XML','rgdal', 'dplyr','devtools', 'stars', 'mapview', 'RColorBrewer')
##install.packages(paquetes)
## in addition, use either 1 or 2 options below
##option1##
#devtools::install_github("JoshOBrien/gdalUtilities")
##option2##
#devtools::install_github('gearslaboratory/gdalUtils')
Vamos a llamar las librerías.
library(terra)
library(ggplot2)
library(tidyterra)
library(sf)
library(leaflet)
library(RColorBrewer)
library(gdalUtilities)
library(XML)
library(dplyr)
SoilGrids es un sistema de cartografía digital de suelos a escala global que utiliza información de perfiles de suelo de todo el mundo y datos de covariables para modelar la distribución espacial de las propiedades del suelo.
SoilGrids es una colección de mapas de propiedades del suelo producidos mediante aprendizaje automático (machine learning) con una resolución de 250 metros.
Nota importante: Para Colombia, es recomendable comparar los datos de SoilGrids con los mapas nacionales producidos por el Instituto Geográfico Agustín Codazzi (IGAC), ya que los mapas nacionales suelen tener mayor precisión al estar basados en información de suelos más detallada a nivel local.
url = "https://files.isric.org/soilgrids/latest/data/" # Ruta al servidor webDAV
# Variables disponibles: soc, phh2o, clay, silt, sand, cec, bdod, cfvo, nitrogen, ocd
voi = "soc" # carbono orgánico del suelo
depth = "15-30cm" # profundidades disponibles: 0-5cm, 5-15cm, 15-30cm, 30-60cm, 60-100cm, 100-200cm
quantile = "mean" # opciones: mean, Q0.05, Q0.5, Q0.95
# Concatenamos las cadenas de texto
(variable = paste(url, voi, sep=""))
## [1] "https://files.isric.org/soilgrids/latest/data/soc"
(layer = paste(variable, depth, quantile, sep="_")) # capa de interés
## [1] "https://files.isric.org/soilgrids/latest/data/soc_15-30cm_mean"
(vrt_layer = paste(layer, '.vrt', sep=""))
## [1] "https://files.isric.org/soilgrids/latest/data/soc_15-30cm_mean.vrt"
Explicación del resultado: El código construye la URL completa del archivo VRT (Virtual Raster) que apunta a los datos de carbono orgánico del suelo (SOC) en la profundidad de 15-30 cm, usando el valor medio de las predicciones. Este formato VRT permite acceder eficientemente a subconjuntos de datos globales sin necesidad de descargar el archivo completo.
Vamos a leer un geopackage de Colombia y después seleccionamos nuestro departamento de interés.
(col = st_read("DeptoColombia.gpkg"))
## Reading layer `DeptoColombia' from data source
## `C:\Users\usuagro\Documents\GB\Proyect5\Proyect5\DeptoColombia.gpkg'
## using driver `GPKG'
## Simple feature collection with 32 features and 11 fields
## Geometry type: MULTIPOLYGON
## Dimension: XY
## Bounding box: xmin: -81.84153 ymin: -4.228429 xmax: -66.87033 ymax: 15.91247
## Geodetic CRS: WGS 84
## Simple feature collection with 32 features and 11 fields
## Geometry type: MULTIPOLYGON
## Dimension: XY
## Bounding box: xmin: -81.84153 ymin: -4.228429 xmax: -66.87033 ymax: 15.91247
## Geodetic CRS: WGS 84
## First 10 features:
## ID_0 ISO NAME_0 ID_1 NAME_1 ID_2 NAME_2 TYPE_2
## 1 53 COL Colombia 5 Bolívar 163 Achí Municipio
## 2 53 COL Colombia 18 La Guajira 653 Barrancas Municipio
## 3 53 COL Colombia 29 Tolima 966 Alpujarra Municipio
## 4 53 COL Colombia 27 Santander 855 Aguada Municipio
## 5 53 COL Colombia 6 Boyacá 199 Almeida Municipio
## 6 53 COL Colombia 26 San Andrés y Providencia 852 n.a. (1) <NA>
## 7 53 COL Colombia 17 Huila 616 Acevedo Municipio
## 8 53 COL Colombia 2 Antioquia 9 Abejorral Municipio
## 9 53 COL Colombia 19 Magdalena 663 Aracataca Municipio
## 10 53 COL Colombia 25 Risaralda 838 Apía Municipio
## ENGTYPE_2 NL_NAME_2 VARNAME_2 geom
## 1 Municipality <NA> <NA> MULTIPOLYGON (((-74.9564 10...
## 2 Municipality <NA> <NA> MULTIPOLYGON (((-72.9464 10...
## 3 Municipality <NA> <NA> MULTIPOLYGON (((-75.968 2.9...
## 4 Municipality <NA> <NA> MULTIPOLYGON (((-73.9762 5....
## 5 Municipality <NA> <NA> MULTIPOLYGON (((-73.556 4.8...
## 6 <NA> <NA> <NA> MULTIPOLYGON (((-81.83986 1...
## 7 Municipality <NA> <NA> MULTIPOLYGON (((-76.1585 1....
## 8 Municipality <NA> <NA> MULTIPOLYGON (((-75.9337 5....
## 9 Municipality <NA> <NA> MULTIPOLYGON (((-74.4607 9....
## 10 Municipality <NA> <NA> MULTIPOLYGON (((-76.0129 4....
Vamos a extraer nuestro departamento de interés.
cordoba <- col %>%
filter(NAME_1 == "Córdoba")
cordoba
## Simple feature collection with 1 feature and 11 fields
## Geometry type: MULTIPOLYGON
## Dimension: XY
## Bounding box: xmin: -76.5189 ymin: 7.3516 xmax: -74.7731 ymax: 9.448473
## Geodetic CRS: WGS 84
## ID_0 ISO NAME_0 ID_1 NAME_1 ID_2 NAME_2 TYPE_2 ENGTYPE_2 NL_NAME_2
## 1 53 COL Colombia 7 Córdoba 322 Ayapel Municipio Municipality <NA>
## VARNAME_2 geom
## 1 <NA> MULTIPOLYGON (((-76.5183 7....
Transformamos a la proyección Interrupted Goode Homolosine (IGH), que es la proyección utilizada por SoilGrids.
igh='+proj=igh +lat_0=0 +lon_0=0 +datum=WGS84 +units=m +no_defs'
cordoba_igh <- st_transform(cordoba, igh)
Obtenemos el bounding box (cuadro delimitador) de nuestra área de interés:
(bbox <- st_bbox(cordoba_igh))
## xmin ymin xmax ymax
## -8541357.2 818376.4 -8352761.5 1051799.2
Definimos los límites en el formato requerido por GDAL (upper left y lower right).
ulx = bbox$xmin # x mínima (esquina superior izquierda)
uly = bbox$ymax # y máxima (esquina superior izquierda)
lrx = bbox$xmax # x máxima (esquina inferior derecha)
lry = bbox$ymin # y mínima (esquina inferior derecha)
(bb <- c(ulx, uly, lrx, lry))
## xmin ymax xmax ymin
## -8541357.2 1051799.2 -8352761.5 818376.4
Definimos las rutas para la descarga de datos:
sg_url="/vsicurl/https://files.isric.org/soilgrids/latest/data/"
datos = 'soc/soc_15-30cm_mean.vrt'
file = "soc_igh_15_30.tif" # Nombre del archivo de salida
IMPORTANTE: Ejecuta este código solo la primera vez. Después coméntalo para evitar descargas repetidas innecesarias.
# DESCOMENTAR PARA PRIMER USO
# DESPUÉS, COMENTAR DE NUEVO
gdal_translate(paste0(sg_url,datos), file,
tr=c(250,250),
projwin=bb,
projwin_srs=igh)
Leemos el archivo descargado y aplicamos el factor de conversión. Según la documentación de SoilGrids, los valores de SOC están en unidades mapeadas y deben dividirse por 10 para obtener gramos por kilogramo (g/kg).
(cordoba_soc <- terra::rast(file)/10)
## class : SpatRaster
## size : 935, 755, 1 (nrow, ncol, nlyr)
## resolution : 250, 250 (x, y)
## extent : -8541500, -8352750, 818250, 1052000 (xmin, xmax, ymin, ymax)
## coord. ref. : Interrupted_Goode_Homolosine
## source(s) : memory
## varname : soc_igh_15_30
## name : soc_igh_15_30
## min value : 7.8
## max value : 183.3
Primero generamos un histograma para visualizar la distribución de los valores de carbono orgánico del suelo.
terra::hist(cordoba_soc,
main="Distribución del Carbono Orgánico del Suelo",
xlab="SOC (g/kg)",
ylab="Frecuencia",
col="#8B7355") # Color tierra
Un resumen estadístico de los datos:
summary(cordoba_soc)
## soc_igh_15_30
## Min. : 7.80
## 1st Qu.: 18.90
## Median : 26.00
## Mean : 30.53
## 3rd Qu.: 36.80
## Max. :178.10
## NA's :10020
Cambiamos el nombre del atributo para que sea más claro:
(names(cordoba_soc) <- "soc")
## [1] "soc"
Extraemos los valores válidos (sin NA) para crear la paleta de colores:
valores <- values(cordoba_soc, na.rm=TRUE)
Creamos una paleta de colores geomorfológica (tonos tierra a verde oscuro):
# Paleta geomorfológica: desde tonos claros (bajo SOC) a oscuros (alto SOC)
# Simula la transición de suelos pobres en materia orgánica a suelos ricos
orangecyan <- colorNumeric(
palette = c("#F4E4C1", "#D4A574", "#8B7355", "#6B8E23", "#2F4F2F"),
domain = valores,
na.color = "transparent"
)
Ahora vamos a visualizar el contenido de carbono orgánico en el departamento de Córdoba con un mapa interactivo:
# Para Córdoba: longitud ≈ -75.5, latitud ≈ 8, zoom ≈ 10
leaflet::leaflet(cordoba) %>%
addTiles() %>%
setView(-75.5, 8, 10) %>%
addPolygons(color = "#8B4513", weight = 2.0, smoothFactor = 0.5,
opacity = 0.8, fillOpacity = 0.05) %>%
addRasterImage(cordoba_soc,
colors = c("#F4E4C1", "#D4A574", "#8B7355", "#6B8E23", "#2F4F2F"),
opacity = 0.7) %>%
addLegend(pal = orangecyan,
values = valores,
title = "Carbono Orgánico<br>del Suelo (SOC)<br>[g/kg]",
position = "bottomright")
En esta sección utilizamos el paquete tidyterra para
crear una visualización estática más profesional y personalizable.
# Convertir a formato sf para overlay
cordoba_sf <- st_as_sf(cordoba)
# Crear visualización con ggplot2 y tidyterra
ggplot() +
geom_spatraster(data = cordoba_soc) +
geom_sf(data = cordoba_sf, fill = NA, color = "#8B4513", linewidth = 1.2) +
scale_fill_gradientn(
colors = c("#F4E4C1", "#D4A574", "#8B7355", "#6B8E23", "#2F4F2F"),
name = "SOC (g/kg)",
na.value = "transparent"
) +
labs(
title = "Carbono Orgánico del Suelo - Departamento de Córdoba",
subtitle = "Profundidad: 15-30 cm | Fuente: SoilGrids 250m",
caption = "Elaborado por: Julian Santiago Gonzalez Malpica"
) +
theme_minimal() +
theme(
plot.title = element_text(size = 16, face = "bold", hjust = 0.5),
plot.subtitle = element_text(size = 12, hjust = 0.5, color = "gray40"),
plot.caption = element_text(size = 9, color = "gray50"),
legend.position = "right",
legend.key.height = unit(1.5, "cm"),
panel.grid = element_line(color = "gray90", linewidth = 0.3),
axis.text = element_text(size = 9)
) +
coord_sf()
## <SpatRaster> resampled to 500532 cells.
En esta sección generamos un conjunto de muestras aleatorias del dataset de SOC, lo cual es útil para: - Análisis estadísticos - Validación de modelos - Estudios de campo - Análisis de correlación con otras variables
# Establece una semilla para reproducibilidad
# CAMBIAR AQUÍ: Puedes usar cualquier número entero
set.seed(123456)
# Convertimos el raster a proyección geográfica (WGS84)
geog = "+proj=longlat +datum=WGS84"
(geog.soc = project(cordoba_soc, geog))
## class : SpatRaster
## size : 960, 844, 1 (nrow, ncol, nlyr)
## resolution : 0.002187792, 0.002187792 (x, y)
## extent : -76.53678, -74.69029, 7.349996, 9.450277 (xmin, xmax, ymin, ymax)
## coord. ref. : +proj=longlat +datum=WGS84 +no_defs
## source(s) : memory
## name : soc
## min value : 8.394538
## max value : 182.589554
# CAMBIAR AQUÍ: Ajusta el número de puntos de muestreo según tu necesidad
# Muestreo aleatorio de 2000 puntos
(samples <- terra::spatSample(geog.soc, 2000, "random", as.points=TRUE))
## class : SpatVector
## geometry : points
## dimensions : 2000, 1 (geometries, attributes)
## extent : -76.5335, -74.69138, 7.35109, 9.449183 (xmin, xmax, ymin, ymax)
## coord. ref. : +proj=longlat +datum=WGS84 +no_defs
## names : soc
## type : <num>
## values : 29.71
## 37.94
## 17.74
Convertimos las muestras a formato sf para facilitar su
manipulación:
(muestras <- sf::st_as_sf(samples))
## Simple feature collection with 2000 features and 1 field
## Geometry type: POINT
## Dimension: XY
## Bounding box: xmin: -76.5335 ymin: 7.35109 xmax: -74.69138 ymax: 9.449183
## Geodetic CRS: GEOGCRS["unknown",
## DATUM["World Geodetic System 1984",
## ELLIPSOID["WGS 84",6378137,298.257223563,
## LENGTHUNIT["metre",1]],
## ID["EPSG",6326]],
## PRIMEM["Greenwich",0,
## ANGLEUNIT["degree",0.0174532925199433],
## ID["EPSG",8901]],
## CS[ellipsoidal,2],
## AXIS["longitude",east,
## ORDER[1],
## ANGLEUNIT["degree",0.0174532925199433,
## ID["EPSG",9122]]],
## AXIS["latitude",north,
## ORDER[2],
## ANGLEUNIT["degree",0.0174532925199433,
## ID["EPSG",9122]]]]
## First 10 features:
## soc geometry
## 1 29.70628 POINT (-75.31271 9.320103)
## 2 37.94474 POINT (-75.81153 9.359483)
## 3 17.73541 POINT (-75.40241 9.175709)
## 4 43.51871 POINT (-75.71527 8.932864)
## 5 27.22719 POINT (-74.92547 8.952554)
## 6 NA POINT (-75.97561 9.289474)
## 7 39.88127 POINT (-76.14845 8.611258)
## 8 13.40279 POINT (-75.54681 8.685643)
## 9 16.54341 POINT (-75.94061 8.000864)
## 10 88.07214 POINT (-76.12438 7.790836)
Eliminamos los valores NA (muestras que cayeron fuera del área con datos):
nmuestras <- na.omit(muestras)
Extraemos las coordenadas y valores de SOC:
longit <- st_coordinates(nmuestras)[,1]
latit <- st_coordinates(nmuestras)[,2]
soc <- nmuestras$soc
Resumen estadístico de las muestras:
summary(soc)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 10.25 19.33 26.10 30.40 36.22 138.03
length(soc)
## [1] 1682
# Calculamos cuántas muestras se perdieron por caer en áreas sin datos
muestras_perdidas <- 2000 - length(soc)
cat("Muestras con datos válidos:", length(soc), "\n")
## Muestras con datos válidos: 1682
cat("Muestras sin datos (NA):", muestras_perdidas, "\n")
## Muestras sin datos (NA): 318
Creamos un data frame con las muestras:
id <- seq(1, length(soc), 1)
(sitios <- data.frame(id, longit, latit, soc))
## id longit latit soc
## 1 1 -75.31271 9.320103 29.70628
## 2 2 -75.81153 9.359483 37.94474
## 3 3 -75.40241 9.175709 17.73541
## 4 4 -75.71527 8.932864 43.51871
## 5 5 -74.92547 8.952554 27.22719
## 6 6 -76.14845 8.611258 39.88127
## 7 7 -75.54681 8.685643 13.40279
## 8 8 -75.94061 8.000864 16.54341
## 9 9 -76.12438 7.790836 88.07214
## 10 10 -75.12019 9.088197 15.43511
## 11 11 -75.01080 9.446995 14.47740
## 12 12 -75.21864 7.585184 17.18873
## 13 13 -75.80278 9.048817 45.14080
## 14 14 -76.15939 8.053371 17.03923
## 15 15 -76.47662 8.051184 37.10542
## 16 16 -75.03705 8.057747 15.64432
## 17 17 -76.35191 7.779897 26.23966
## 18 18 -75.87279 8.700958 35.94440
## 19 19 -76.05219 7.556742 42.43592
## 20 20 -75.05237 7.618001 28.25255
## 21 21 -75.99530 7.372968 114.50206
## 22 22 -75.62338 9.035690 36.65998
## 23 23 -75.17269 7.836780 19.28768
## 24 24 -76.06750 8.171512 14.04875
## 25 25 -75.52274 8.869418 20.13382
## 26 26 -74.99986 8.051184 16.40576
## 27 27 -75.68464 7.607062 56.19049
## 28 28 -75.81372 9.215089 46.44375
## 29 29 -75.99968 7.359841 99.99400
## 30 30 -75.12456 9.077258 18.18007
## 31 31 -74.85546 8.821286 61.60587
## 32 32 -75.26021 9.250094 30.08397
## 33 33 -76.30816 8.690019 36.59639
## 34 34 -75.23176 9.394488 17.33454
## 35 35 -76.31253 7.876160 36.54565
## 36 36 -76.04562 7.902414 31.78607
## 37 37 -75.29521 9.182272 35.72442
## 38 38 -75.63651 8.954742 57.69430
## 39 39 -76.47443 8.403418 37.71477
## 40 40 -75.17269 7.357653 28.73750
## 41 41 -75.44836 9.296037 18.34413
## 42 42 -75.07862 8.580629 31.24746
## 43 43 -75.34115 9.394488 19.86845
## 44 44 -75.14206 8.344348 30.20000
## 45 45 -74.79858 9.449183 22.70000
## 46 46 -75.31928 8.659390 26.57494
## 47 47 -76.42849 8.073061 25.68927
## 48 48 -75.59713 7.445165 33.31372
## 49 49 -75.79403 8.278714 14.24524
## 50 50 -76.30378 7.512987 84.00249
## 51 51 -74.81390 9.164770 18.56395
## 52 52 -75.98218 7.464855 54.95287
## 53 53 -75.74371 8.427484 29.47605
## 54 54 -76.38254 7.694573 46.77526
## 55 55 -75.94717 8.751277 43.25720
## 56 56 -76.39348 8.125568 26.71153
## 57 57 -74.87515 9.241343 12.95794
## 58 58 -76.41317 7.795212 25.28840
## 59 59 -75.81590 7.585184 33.30376
## 60 60 -75.50961 7.919916 15.20293
## 61 61 -76.32566 8.836601 34.37433
## 62 62 -75.55775 7.561118 25.29725
## 63 63 -74.82483 7.690198 18.95585
## 64 64 -75.59494 9.230404 23.56649
## 65 65 -75.27990 9.383549 14.57718
## 66 66 -76.25346 7.716451 32.30333
## 67 67 -75.41773 7.922104 21.25891
## 68 68 -75.71964 9.226028 41.03026
## 69 69 -74.92329 8.574066 43.34637
## 70 70 -75.70870 7.889287 16.13618
## 71 71 -76.50068 7.959296 27.82693
## 72 72 -75.35428 8.744714 24.42528
## 73 73 -75.50743 7.854282 16.84308
## 74 74 -76.37817 7.738329 49.89487
## 75 75 -74.82265 8.136507 46.13801
## 76 76 -75.08081 7.618001 22.57127
## 77 77 -76.28409 8.652826 26.05977
## 78 78 -76.37817 7.898038 36.61701
## 79 79 -76.06969 8.617822 31.53890
## 80 80 -75.50743 9.438244 24.03780
## 81 81 -74.89703 8.108066 20.94312
## 82 82 -75.81590 8.961305 47.93019
## 83 83 -74.79858 8.611258 27.70127
## 84 84 -74.86859 8.024930 40.00053
## 85 85 -74.83796 8.784094 56.50644
## 86 86 -74.80514 8.810347 83.07249
## 87 87 -74.82265 8.125568 46.55940
## 88 88 -76.44818 8.147446 34.42247
## 89 89 -75.56212 8.294028 17.37979
## 90 90 -74.96485 7.723015 20.93943
## 91 91 -75.05237 8.676892 78.30000
## 92 92 -75.29521 8.650639 17.53524
## 93 93 -76.01062 8.792845 47.95288
## 94 94 -75.43085 7.653005 25.81042
## 95 95 -76.41755 7.418911 56.80454
## 96 96 -75.09612 8.972244 25.46110
## 97 97 -76.09157 9.291662 27.08016
## 98 98 -75.30615 9.339793 19.42419
## 99 99 -75.38053 7.550179 22.98730
## 100 100 -75.37397 8.550000 19.55404
## 101 101 -75.87498 8.482179 12.93191
## 102 102 -75.94498 8.449362 27.86039
## 103 103 -75.42429 7.797400 31.55199
## 104 104 -75.43960 8.731587 25.50596
## 105 105 -76.16158 8.232770 24.62671
## 106 106 -76.24034 7.508611 34.54353
## 107 107 -75.61025 8.633136 22.03021
## 108 108 -75.90123 8.996310 47.92190
## 109 109 -75.41991 8.320282 23.05327
## 110 110 -75.81590 8.215268 13.10514
## 111 111 -75.12237 9.184460 15.92438
## 112 112 -74.84453 7.604874 22.11992
## 113 113 -75.41116 8.735963 20.40539
## 114 114 -76.19877 8.799409 14.92600
## 115 115 -76.38473 7.563306 60.26749
## 116 116 -74.85328 7.351090 53.48166
## 117 117 -76.04562 7.808339 22.76107
## 118 118 -76.22940 7.534864 29.56427
## 119 119 -75.48336 8.440611 25.78408
## 120 120 -76.01718 8.657202 31.27940
## 121 121 -75.85966 9.256657 21.56142
## 122 122 -74.90360 9.171333 25.26814
## 123 123 -75.99312 8.009615 32.38187
## 124 124 -76.27534 8.149634 22.16796
## 125 125 -75.92967 8.267775 11.10089
## 126 126 -75.99749 8.558751 14.95948
## 127 127 -75.42648 7.889287 16.21392
## 128 128 -76.00624 8.103691 25.30105
## 129 129 -76.28190 7.604874 26.85649
## 130 130 -75.73496 7.580808 81.37021
## 131 131 -76.45912 8.379352 41.24933
## 132 132 -75.98437 9.072883 43.21841
## 133 133 -75.53806 9.324479 36.45521
## 134 134 -75.44617 8.615634 22.35200
## 135 135 -76.47224 8.013991 33.20508
## 136 136 -76.38473 8.086188 29.80935
## 137 137 -75.18582 8.116817 11.63851
## 138 138 -75.75027 9.066319 64.05708
## 139 139 -75.71089 8.031493 14.26646
## 140 140 -75.30177 8.773155 16.47591
## 141 141 -75.23395 8.471240 26.75854
## 142 142 -75.51837 7.666132 21.66603
## 143 143 -74.98236 9.431681 16.65412
## 144 144 -75.67807 7.742705 21.19402
## 145 145 -75.06549 9.245718 16.05729
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## 991 991 -75.13113 8.103691 20.45538
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## 995 995 -75.18363 7.974611 19.66827
## 996 996 -76.40005 8.458113 19.75743
## 997 997 -74.95829 7.412348 46.18487
## 998 998 -75.42429 9.048817 23.43327
## 999 999 -76.12438 7.954921 21.74113
## 1000 1000 -76.22065 7.729578 36.31503
## 1001 1001 -74.81390 8.237146 31.87206
## 1002 1002 -76.04781 7.655193 40.95618
## 1003 1003 -75.13331 8.265587 16.54504
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## 1099 1099 -74.88172 8.149634 17.02110
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## 1474 1474 -75.29959 9.206338 22.64710
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## 1476 1476 -75.91654 9.368235 27.68876
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## 1503 1503 -74.89703 8.600319 45.53068
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## 1505 1505 -76.48099 7.753644 24.62711
## 1506 1506 -75.13769 9.072883 19.64466
## 1507 1507 -75.19238 7.806151 44.67292
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## 1509 1509 -76.14407 8.309343 22.89381
## 1510 1510 -75.12019 7.366404 36.65660
## 1511 1511 -75.15519 9.158206 23.04481
## 1512 1512 -75.01517 8.954742 26.51771
## 1513 1513 -75.39366 7.379531 33.62188
## 1514 1514 -74.94954 7.834592 14.83457
## 1515 1515 -76.06313 7.442977 66.60061
## 1516 1516 -76.09157 7.950545 65.64711
## 1517 1517 -75.34115 8.479991 15.11097
## 1518 1518 -75.83778 8.412169 23.02009
## 1519 1519 -76.25128 8.482179 38.43941
## 1520 1520 -74.92110 7.696761 19.96815
## 1521 1521 -74.92985 8.335597 27.74280
## 1522 1522 -75.27552 9.182272 26.84275
## 1523 1523 -75.48117 8.276526 16.03973
## 1524 1524 -74.98236 8.460301 47.63713
## 1525 1525 -74.95829 7.620188 16.26665
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## 1527 1527 -75.33897 9.160394 13.13918
## 1528 1528 -75.13550 7.738329 14.36683
## 1529 1529 -74.91453 9.250094 18.84212
## 1530 1530 -75.71308 7.793024 25.02224
## 1531 1531 -75.99968 9.145080 36.66647
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## 1533 1533 -75.86622 8.602507 23.16379
## 1534 1534 -75.15082 8.884732 24.55332
## 1535 1535 -75.03049 9.341981 18.16883
## 1536 1536 -76.22065 8.379352 35.51750
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## 1539 1539 -75.40022 8.267775 11.87062
## 1540 1540 -75.16613 9.405427 14.58766
## 1541 1541 -75.68901 7.838968 19.85151
## 1542 1542 -75.40460 8.073061 24.71277
## 1543 1543 -75.20989 9.293850 26.15186
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## 1545 1545 -75.73058 8.948178 49.11057
## 1546 1546 -76.46568 8.543437 23.91713
## 1547 1547 -74.94735 8.068686 22.72158
## 1548 1548 -75.48336 7.392658 85.75941
## 1549 1549 -75.01736 8.051184 16.35220
## 1550 1550 -76.31691 8.254648 37.89213
## 1551 1551 -75.03924 8.199953 16.00379
## 1552 1552 -76.31472 7.554555 73.33015
## 1553 1553 -75.29521 9.053192 18.67991
## 1554 1554 -76.04781 8.512808 33.14134
## 1555 1555 -75.36960 7.939606 17.38439
## 1556 1556 -75.08518 9.175709 13.70553
## 1557 1557 -74.88391 8.311531 25.52898
## 1558 1558 -75.41991 9.344169 28.46518
## 1559 1559 -75.26021 7.508611 27.15524
## 1560 1560 -74.93860 8.755653 76.87488
## 1561 1561 -75.39585 8.696582 21.45784
## 1562 1562 -75.95592 9.247906 45.66822
## 1563 1563 -74.90360 8.980995 51.35890
## 1564 1564 -76.44599 8.046808 38.96456
## 1565 1565 -75.85310 8.849728 22.17683
## 1566 1566 -75.49430 8.576254 16.82937
## 1567 1567 -75.43742 8.755653 33.16401
## 1568 1568 -76.50506 7.867409 41.38834
## 1569 1569 -75.19238 7.639879 23.48929
## 1570 1570 -75.13769 9.061944 25.97303
## 1571 1571 -76.18564 7.425475 72.52258
## 1572 1572 -74.75483 8.869418 50.66947
## 1573 1573 -76.21846 8.683456 16.61765
## 1574 1574 -76.00406 7.504235 53.15662
## 1575 1575 -74.92329 7.558930 43.61558
## 1576 1576 -74.93422 8.197766 13.37321
## 1577 1577 -75.62994 8.178075 14.64268
## 1578 1578 -75.43085 9.156019 20.56091
## 1579 1579 -76.43067 8.370601 31.08283
## 1580 1580 -76.11126 8.108066 14.18861
## 1581 1581 -75.50524 9.315728 30.19745
## 1582 1582 -75.86622 9.068507 53.27569
## 1583 1583 -75.43742 8.420920 16.11209
## 1584 1584 -75.84216 7.701137 38.75747
## 1585 1585 -75.97561 8.403418 21.72030
## 1586 1586 -75.67370 7.895850 12.78211
## 1587 1587 -74.94735 7.488921 27.54790
## 1588 1588 -75.42867 9.405427 29.33595
## 1589 1589 -75.36741 8.690019 24.69741
## 1590 1590 -76.02812 8.143071 14.67793
## 1591 1591 -76.10251 9.201962 38.24831
## 1592 1592 -75.70214 8.541249 17.03362
## 1593 1593 -76.32785 7.692386 37.23574
## 1594 1594 -75.96686 8.928488 23.83062
## 1595 1595 -75.76340 8.690019 48.90523
## 1596 1596 -74.82046 8.237146 37.50281
## 1597 1597 -76.20533 8.698770 19.96984
## 1598 1598 -75.21645 7.683634 23.20924
## 1599 1599 -76.43943 8.545625 20.63773
## 1600 1600 -75.25145 8.991934 30.46904
## 1601 1601 -76.50068 7.421099 77.89492
## 1602 1602 -76.19439 7.900226 28.30267
## 1603 1603 -75.66932 9.398864 29.22232
## 1604 1604 -75.61682 8.007428 16.57249
## 1605 1605 -75.50305 7.591747 23.46616
## 1606 1606 -75.68901 8.552188 17.56372
## 1607 1607 -75.71089 7.554555 31.32004
## 1608 1608 -76.38254 8.576254 24.29790
## 1609 1609 -75.82028 7.987738 20.06705
## 1610 1610 -75.43523 9.072883 34.22544
## 1611 1611 -75.22958 9.026939 29.02472
## 1612 1612 -75.81372 9.131953 53.77287
## 1613 1613 -75.86185 7.869597 27.70122
## 1614 1614 -76.51819 7.672695 94.58137
## 1615 1615 -75.96249 7.830216 29.69020
## 1616 1616 -75.60150 7.908977 20.51739
## 1617 1617 -74.91235 9.147268 10.57047
## 1618 1618 -76.23377 8.690019 49.79582
## 1619 1619 -76.28847 7.618001 29.14223
## 1620 1620 -75.11362 7.712076 19.32926
## 1621 1621 -76.37817 7.392658 86.22446
## 1622 1622 -76.17908 8.418733 24.57798
## 1623 1623 -75.54243 9.037878 20.16363
## 1624 1624 -75.33459 8.357474 16.36431
## 1625 1625 -75.27552 8.488742 19.41858
## 1626 1626 -74.99548 7.416724 47.75975
## 1627 1627 -75.66276 8.285277 27.79326
## 1628 1628 -75.31928 7.992113 20.13199
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## 1630 1630 -75.58837 7.981174 20.21615
## 1631 1631 -76.40223 8.574066 24.74866
## 1632 1632 -74.78327 9.425117 35.82970
## 1633 1633 -76.36067 7.539240 73.32922
## 1634 1634 -76.27315 8.580629 28.09310
## 1635 1635 -74.99330 8.197766 14.08192
## 1636 1636 -75.11800 8.795033 25.35253
## 1637 1637 -74.86422 8.770967 42.49812
## 1638 1638 -74.97360 7.587371 22.88523
## 1639 1639 -75.37397 9.005061 22.47174
## 1640 1640 -75.60150 7.657381 26.35739
## 1641 1641 -74.80952 8.348723 28.89093
## 1642 1642 -76.06531 7.797400 36.21469
## 1643 1643 -75.51399 7.462667 38.66615
## 1644 1644 -75.64526 8.670329 14.11207
## 1645 1645 -75.62557 7.904601 15.17042
## 1646 1646 -75.76340 8.615634 18.17611
## 1647 1647 -75.19020 8.031493 15.31400
## 1648 1648 -75.12456 8.186827 11.06841
## 1649 1649 -75.19676 8.840977 31.42736
## 1650 1650 -75.19020 8.027118 16.65754
## 1651 1651 -75.97561 9.110075 27.56363
## 1652 1652 -76.43286 8.541249 14.87028
## 1653 1653 -75.23176 8.882545 24.82857
## 1654 1654 -75.60369 7.526113 40.37266
## 1655 1655 -74.77452 8.261212 30.50645
## 1656 1656 -74.88828 7.928667 19.41807
## 1657 1657 -74.86422 8.547812 32.19085
## 1658 1658 -76.09157 7.788648 41.78369
## 1659 1659 -75.51618 9.044441 19.65776
## 1660 1660 -75.53587 8.399043 13.42074
## 1661 1661 -75.59931 9.206338 24.87223
## 1662 1662 -75.60806 8.158385 28.33183
## 1663 1663 -76.13970 8.088376 23.96947
## 1664 1664 -76.13970 9.153831 52.79066
## 1665 1665 -75.95374 9.341981 43.91915
## 1666 1666 -76.35410 8.016179 34.12669
## 1667 1667 -75.05893 7.530489 28.73641
## 1668 1668 -75.01299 7.644254 22.25146
## 1669 1669 -76.05000 9.158206 37.93252
## 1670 1670 -76.37160 8.412169 34.60609
## 1671 1671 -74.99111 8.460301 46.39294
## 1672 1672 -75.43304 8.241521 12.25632
## 1673 1673 -74.92329 8.357474 23.28105
## 1674 1674 -75.11144 7.653005 30.78077
## 1675 1675 -75.78090 7.661756 32.68599
## 1676 1676 -75.15300 9.379174 13.74164
## 1677 1677 -76.01281 7.519550 92.45084
## 1678 1678 -76.30816 8.952554 51.54703
## 1679 1679 -75.97780 7.775522 25.25772
## 1680 1680 -75.90342 8.464676 18.84040
## 1681 1681 -75.03486 8.812535 61.39713
## 1682 1682 -76.02812 9.013812 26.27451
Visualización interactiva de los puntos de muestreo con agrupamiento (clustering):
# Creamos paleta de colores para los marcadores según valor de SOC
pal_markers <- colorNumeric(
palette = c("#F4E4C1", "#D4A574", "#8B7355", "#6B8E23", "#2F4F2F"),
domain = sitios$soc
)
m <- leaflet() %>%
addTiles() %>%
addCircleMarkers(
data = sitios, # 👈 importante
lng = ~longit,
lat = ~latit,
radius = 5,
fillColor = ~pal_markers(soc), # 👈 sin "sitios$"
color = "#8B4513",
weight = 1,
opacity = 0.8,
fillOpacity = 0.7,
popup = paste(
"<b>ID:</b>", sitios$id, "<br>",
"<b>SOC:</b>", round(sitios$soc, 2), "g/kg<br>",
"<b>Longitud:</b>", round(sitios$longit, 4), "<br>",
"<b>Latitud:</b>", round(sitios$latit, 4)
),
clusterOptions = markerClusterOptions()
) %>%
addLegend(
pal = pal_markers,
values = sitios$soc,
title = "SOC (g/kg)",
position = "bottomright"
)
m
El parámetro clusterOptions = markerClusterOptions()
agrupa los marcadores cercanos cuando el zoom está alejado, mejorando la
legibilidad del mapa. Al hacer clic en un cluster, el mapa hace zoom
para mostrar los puntos individuales.
La función sf::st_write() guarda los datos espaciales en
diversos formatos. En este caso usamos GeoPackage (GPKG), que es: - Un
formato abierto y estándar - Eficiente para datos vectoriales -
Compatible con múltiples software GIS - Puede almacenar múltiples capas
en un solo archivo
# Asegúrate de que la carpeta "data" exista o cambia la ruta
sf::st_write(nmuestras, "data/soc_cordoba.gpkg", driver = "GPKG",
append = FALSE)
## Deleting layer `soc_cordoba' using driver `GPKG'
## Writing layer `soc_cordoba' to data source `data/soc_cordoba.gpkg' using driver `GPKG'
## Writing 1682 features with 1 fields and geometry type Point.
¿Qué hace append = FALSE?
El parámetro append = FALSE indica que si el archivo ya
existe, debe ser sobrescrito completamente. Si usáramos
append = TRUE, se agregarían los datos al archivo existente
sin eliminar el contenido previo. Usar FALSE asegura que
siempre tenemos la versión más reciente de nuestros datos.
Importante: Recuerda llevar el archivo
soc_cordoba.gpkg a clase o compartirlo con tu equipo de
trabajo.
Este trabajo está basado en:
Lizarazo, I. 2025. How to download soil data from SoilGrids. Disponible en: https://rpubs.com/ials2un/downloadSoilGrids
Adaptación para el departamento de Córdoba: - Autor: Julian Santiago Gonzalez Malpica - Fecha: Noviembre 6, 2025 - Variables analizadas: Carbono Orgánico del Suelo (SOC), profundidad 15-30 cm - Área de estudio: Departamento de Córdoba, Colombia
Fuente de datos: - SoilGrids 250m v2.0. ISRIC - World Soil Information. https://www.isric.org/explore/soilgrids
Cita sugerida: Gonzalez Malpica, J.S. 2025. Análisis de carbono orgánico del suelo en el departamento de Córdoba usando datos de SoilGrids. Trabajo de curso.
# Información de la sesión de R (útil para reproducibilidad)
sessionInfo()
## R version 4.5.1 (2025-06-13 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows 10 x64 (build 19045)
##
## Matrix products: default
## LAPACK version 3.12.1
##
## locale:
## [1] LC_COLLATE=Spanish_Colombia.utf8 LC_CTYPE=Spanish_Colombia.utf8
## [3] LC_MONETARY=Spanish_Colombia.utf8 LC_NUMERIC=C
## [5] LC_TIME=Spanish_Colombia.utf8
##
## time zone: America/Bogota
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] dplyr_1.1.4 XML_3.99-0.19 gdalUtilities_1.2.5
## [4] RColorBrewer_1.1-3 leaflet_2.2.3 sf_1.0-21
## [7] tidyterra_0.7.2 ggplot2_4.0.0 terra_1.8-80
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.10 generics_0.1.4 tidyr_1.3.1 class_7.3-23
## [5] KernSmooth_2.23-26 digest_0.6.37 magrittr_2.0.4 evaluate_1.0.5
## [9] grid_4.5.1 fastmap_1.2.0 jsonlite_2.0.0 e1071_1.7-16
## [13] DBI_1.2.3 purrr_1.2.0 crosstalk_1.2.2 scales_1.4.0
## [17] codetools_0.2-20 jquerylib_0.1.4 cli_3.6.5 rlang_1.1.6
## [21] units_1.0-0 withr_3.0.2 cachem_1.1.0 yaml_2.3.10
## [25] tools_4.5.1 vctrs_0.6.5 R6_2.6.1 png_0.1-8
## [29] proxy_0.4-27 lifecycle_1.0.4 classInt_0.4-11 htmlwidgets_1.6.4
## [33] pkgconfig_2.0.3 pillar_1.11.1 bslib_0.9.0 gtable_0.3.6
## [37] glue_1.8.0 data.table_1.17.8 Rcpp_1.1.0 xfun_0.54
## [41] tibble_3.3.0 tidyselect_1.2.1 rstudioapi_0.17.1 knitr_1.50
## [45] farver_2.1.2 htmltools_0.5.8.1 rmarkdown_2.30 labeling_0.4.3
## [49] compiler_4.5.1 S7_0.2.0
Colores utilizados: - Se empleó una paleta
geomorfológica que simula la transición natural de suelos: -
#F4E4C1: Suelos arenosos claros (bajo contenido orgánico) -
#D4A574: Suelos arcillosos - #8B7355: Suelos
con contenido medio de materia orgánica - #6B8E23: Suelos
fértiles con alto contenido orgánico - #2F4F2F: Suelos muy
ricos en materia orgánica