land4health

Extract remote sensing metrics for spatial health analysis 🛰️, integrating vector-borne disease data. Easily compute areal and zonal statistics for infectious disease modeling in spatial epidemiology 🦠🏥

https://github.com/harmonize-tools/land4health

Science Score: 44.0%

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Low similarity (18.3%) to scientific vocabulary

Keywords

geography geohealth harmonize health-geography innovalab rgee rspatial spatial-epidemiology zonal-statistics

Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: harmonize-tools
License: other
Language: R
Default Branch: main
Homepage: https://harmonize-tools.github.io/land4health/
Size: 9.46 MB

Statistics

Stars: 4
Watchers: 3
Forks: 3
Open Issues: 16
Releases: 1

Topics

geography geohealth harmonize health-geography innovalab rgee rspatial spatial-epidemiology zonal-statistics

Created over 1 year ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# land4health: Remote Sensing Metrics for Spatial Health Analysis 


[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![R-CMD-check](https://github.com/harmonize-tools/land4health/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/harmonize-tools/land4health/actions/workflows/R-CMD-check.yaml)
[![HTML-Docs](https://img.shields.io/badge/docs-HTML-informational)](https://harmonize-tools.github.io/land4health/)
[![License](https://img.shields.io/badge/license-MIT-green)](./LICENSE)
[![test-coverage.yaml](https://github.com/harmonize-tools/land4health/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/harmonize-tools/land4health/actions/workflows/test-coverage.yaml)
[![Codecov test coverage](https://codecov.io/gh/harmonize-tools/land4health/graph/badge.svg)](https://app.codecov.io/gh/harmonize-tools/land4health)


Calculate and extract remote sensing metrics for spatial health analysis 🛰️.
This package offers R users a quick and easy way to obtain areal or zonal statistics of key indicators and covariates, ideal for modeling infectious diseases 🦠 within the framework of spatial epidemiology 🏥.

## 1. Installation

You can install CRAN version of  land4health with: 

```r
install.packages("land4health")
```

or you can install the development version with:
```r
# install.packages("pak")
pak::pak("harmonize-tools/land4health")
```


```{r message=FALSE,warning=FALSE}
library(land4health)
ee_Initialize(quiet = TRUE)
```

```r
── Welcome to land4health ────────────────────────────────────────────────────
A tool of Harmonize Project to calculate and extract Remote Sensing Metrics
for Spatial Health Analysis. Currently,`land4health` supports metrics in the
following categories:
• Accesibility
• Climate
• Enviroment
• and more!
For a complete list of available metrics, use the `l4h_list_metrics()`
function.

──────────────────────────────────────────────────────────────────────────────
Attaching core land4health packages:
→ rgee v1.1.7
→ sf v1.0.21
```
## 2. List of available metrics

```{r}
l4h_list_metrics()
```

## 3. Example: Calculate Forest Loss in a Custom Region

This example demonstrates how to calculate forest loss between 2005 and 2020 using a custom polygon and Earth Engine.

```{r example, message=FALSE, warning=FALSE}
library(geoidep)

# Downloading the adminstration limits of Loreto provinces
provinces_loreto <- get_provinces(show_progress = FALSE) |>
  subset(nombdep == "LORETO")

# Run forest loss calculation
result <- provinces_loreto |>
  l4h_forest_loss(from = '2005-01-01', to = '2020-01-01', sf = TRUE)
head(result)
```

```{r area,fig.dpi=300, fig.height= 5,fig.width= 12}
# Visualization with ggplot2
library(ggplot2)
ggplot(data = st_drop_geometry(result), aes(x = date, y = value)) +
  geom_area(fill = "#FDE725FF", alpha = 0.8) +
  facet_wrap(~nombprov) +
  theme_minimal()
```

```{r mapa,fig.dpi=300, fig.height= 14,fig.width= 15}
# Spatial visualization
ggplot(data = result) +
  geom_sf(aes(fill = value), color = NA) +
  scale_fill_viridis_c(name = "Forest loss mean \n(km²)") +
  theme_minimal(base_size = 15) +
  facet_wrap(date ~ .)
```

## 4. Example: Extract time series of climate variables 

```{r,message=FALSE, warning=FALSE}
etp_ts <- provinces_loreto |>
  l4h_sebal_modis(
    from = "2005-01-01",
    to = "2022-12-31",
    by = "month"
  )
```

```{r ts,fig.dpi=300, fig.height= 5,fig.width= 12}
etp_ts |>
  st_drop_geometry() |>
  ggplot(aes(x = date, y = value, col = value)) +
  geom_line() +
  scale_color_viridis_c("ETP (mm)",option = "viridis") +
  theme_minimal() +
  facet_wrap(~nombprov, ncol = 4)
```

Owner

Name: Harmonize Tools
Login: harmonize-tools
Kind: organization

Repositories: 1
Profile: https://github.com/harmonize-tools

Harmonizing multi-scale spatiotemporal data for health in climate change hotspots.

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "land4health" in publications use:'
type: software
license: MIT
title: 'land4health: Remote Sensing Metrics for Spatial Health Analysis'
version: 0.1.0
identifiers:
- type: url
  value: https://harmonize-tools.github.io/land4health/
abstract: Calculate and extract remote sensing metrics for spatial analysis in the
  field of health. This package offers R users a quick and straightforward way to
  obtain areal or zonal statistics of key environmental indicators, covariates, and
  vector-borne disease data ideal for modeling infectious diseases within the framework
  of spatial epidemiology.
authors:
- family-names: Barja
  given-names: Antony
  email: antony.barja@upch.pe
  orcid: https://orcid.org/0000-0001-5921-2858
- family-names: Ferreyra
  given-names: Yomali
  email: yomali.ferreyra@upch.pe
  orcid: https://orcid.org/0000-0002-5184-9595
repository-code: https://github.com/harmonize-tools/land4health
url: https://github.com/harmonize-tools/land4health/
contact:
- family-names: Barja
  given-names: Antony
  email: antony.barja@upch.pe
  orcid: https://orcid.org/0000-0001-5921-2858
keywords:
- geography
- geohealth
- harmonize
- health-geography
- rgee
- rspatial
- spatial-epidemiology
- zonal-statistics
references:
- type: software
  title: cli
  abstract: 'cli: Helpers for Developing Command Line Interfaces'
  notes: Imports
  url: https://cli.r-lib.org
  repository: https://CRAN.R-project.org/package=cli
  authors:
  - family-names: Csárdi
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    email: gabor@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.cli
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  authors:
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  - family-names: FitzJohn
    given-names: Rich
  year: '2025'
  doi: 10.32614/CRAN.package.progress
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  abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
  notes: Imports
  url: https://lifecycle.r-lib.org/
  repository: https://CRAN.R-project.org/package=lifecycle
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  year: '2025'
  doi: 10.32614/CRAN.package.lifecycle
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
  url: https://tidyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
  - family-names: Girlich
    given-names: Maximilian
  year: '2025'
  doi: 10.32614/CRAN.package.tidyr
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
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    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
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    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2025'
  doi: 10.32614/CRAN.package.dplyr
- type: software
  title: rgee
  abstract: 'rgee: R Bindings for Calling the ''Earth Engine'' API'
  notes: Imports
  url: https://github.com/r-spatial/rgee/
  repository: https://CRAN.R-project.org/package=rgee
  authors:
  - family-names: Aybar
    given-names: Cesar
    email: csaybar@gmail.com
    orcid: https://orcid.org/0000-0003-2745-9535
  year: '2025'
  doi: 10.32614/CRAN.package.rgee
- type: software
  title: sf
  abstract: 'sf: Simple Features for R'
  notes: Imports
  url: https://r-spatial.github.io/sf/
  repository: https://CRAN.R-project.org/package=sf
  authors:
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    given-names: Edzer
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    orcid: https://orcid.org/0000-0001-8049-7069
  year: '2025'
  doi: 10.32614/CRAN.package.sf
- type: software
  title: reticulate
  abstract: 'reticulate: Interface to ''Python'''
  notes: Imports
  url: https://rstudio.github.io/reticulate/
  repository: https://CRAN.R-project.org/package=reticulate
  authors:
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    given-names: Kevin
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  doi: 10.32614/CRAN.package.reticulate
- type: software
  title: glue
  abstract: 'glue: Interpreted String Literals'
  notes: Imports
  url: https://glue.tidyverse.org/
  repository: https://CRAN.R-project.org/package=glue
  authors:
  - family-names: Hester
    given-names: Jim
    orcid: https://orcid.org/0000-0002-2739-7082
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    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2025'
  doi: 10.32614/CRAN.package.glue
- type: software
  title: httr2
  abstract: 'httr2: Perform HTTP Requests and Process the Responses'
  notes: Imports
  url: https://httr2.r-lib.org
  repository: https://CRAN.R-project.org/package=httr2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.httr2
- type: software
  title: ows4R
  abstract: 'ows4R: Interface to OGC Web-Services (OWS)'
  notes: Imports
  url: https://eblondel.github.io/ows4R/
  repository: https://CRAN.R-project.org/package=ows4R
  authors:
  - family-names: Blondel
    given-names: Emmanuel
    email: emmanuel.blondel1@gmail.com
    orcid: https://orcid.org/0000-0002-5870-5762
  year: '2025'
  doi: 10.32614/CRAN.package.ows4R
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
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    given-names: JJ
    email: jj@posit.co
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    given-names: Yihui
    email: xie@yihui.name
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    given-names: Yihui
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    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
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    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 3.0.0'
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 4.1.0'

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cli * imports
dplyr * imports
tidyr * imports

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