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access to geographic locations of african health sites from different sources

Home Page: https://wellcomeopenresearch.org/articles/5-157

License: GNU General Public License v3.0

R 100.00%

african-health-sites africa

afrihealthsites's Introduction

afrihealthsites

access to geographic locations of african health facilities from different sources.

See web interface and paper demonstrating these components.

Part of the afrimapr project.

In early development, will change, contact Andy South with questions.

Install afrihealthsites

Install the development version from GitHub :

# install.packages("remotes") # if not already installed

remotes::install_github("afrimapr/afrihealthsites")

First Usage

library(afrihealthsites)
library(sf)

## WHO database 

# with interactive map
sfken <- afrihealthsites("kenya", datasource='who', plot='mapview')

# static map
sfeth <- afrihealthsites("ethiopia", datasource='who', plot='sf')

## healthsites.io

# pre-downloaded data

# with interactive map
sfmali <- afrihealthsites("mali", datasource='healthsites', plot='mapview')

## compare locations from different sources

compare_hs_sources('togo')

# these are defaults
compare_hs_sources('togo', datasources=c('who', 'healthsites'), plot='mapview')

# run a shiny application allowing you to select any country
runviewer()

# live data - requires a free API key from https://healthsites.io/
library(rhealthsites)
#rhealthsites::hs_set_api_key('[requires a free API key from https://healthsites.io/]')

# with interactive map
sfmali <- afrihealthsites("mali", datasource='healthsites_live', plot='mapview')

Find National Master Facility Lists

# all countries list of available MFLs
df <- national_list_avail()

# availability for a single country
national_list_avail("Togo")

# url for data (if available)
national_list_url("Ghana")

# example of reading in data direct from a url and mapping
# will only work for countries where "machine_readable" is TRUE
dfgha <- read.csv(national_list_url("Ghana"))
sfgha <- sf::st_as_sf(dfgha, coords=c("Longitude","Latitude"), crs=4326, na.fail=FALSE)
afrihealthsites('gha',datasource=sfgha, type_column='Type')

specifying countries

The following can be used :

capitalisation (as you would write the country name in normal text e.g. "South Africa"
all lower caps (e.g. "south africa")
3 letter country iso3c code (e.g. "zaf")

sfzaf1 <- afrihealthsites("south africa", datasource='who', plot=FALSE)
sfzaf2 <- afrihealthsites("ZAF", datasource='healthsites', plot='sf')
sfzaf3 <- afrihealthsites("South Africa", datasource='who', plot='mapview')

Research notice

Please note that this repository is participating in a study into sustainability of open source projects. Data will be gathered about this repository for approximately the next 12 months, starting from June 2021.

Data collected will include number of contributors, number of PRs, time taken to close/merge these PRs, and issues closed.

For more information, please visit the informational page or download the participant information sheet.

afrihealthsites's People

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anelda devmachtech yochannah kumarnarendra0619

afrihealthsites's Issues

add ability to search facilities by admin regions [Feature]

Add a function to return health facilities within specified admin regions in specified countries (and from from specified data sources)

[Existing data]KEMRI/WHO import differs from original spreadsheet

Which dataset
KEMRI/WHO

Short description of the error or suggestion
When I import the original spreadsheet with read_excel it and filter Country for 'South Africa' there are 4303 observations but when I import the same dataset via afrihealthsites I find 4288 observations.

> ah_kemri_who_tb <- afrihealthsites(country="south africa", datasource = "who")
> dim(ah_kemri_who_tb)
[1] 4288    8

> kemri_excel <- read_excel('data/raw_data/who-cds-gmp-2019-01-eng.xlsx') %>% filter(Country == 'South Africa')
                                                                                                                 
> dim(kemri_excel)
[1] 4303    8

Suggested actions

I'm trying to figure out what is going on and will report back here.

[Existing data] KEMRI/WHO coordinates

Which dataset
KEMRI-WHO

Short description of the error or suggestion
The dataset is downloaded as SF object. In the original spreadsheet, there are two columns for coordinates called Lat and Long which isn't present in the object that is downloaded via afrihealthsites.

> ah_kemri_who_tb <- afrihealthsites(country="south africa", datasource = "who")
> colnames(ah_kemri_who_tb)
[1] "Country"       "Admin1"        "Facility name" "Facility type" "Ownership"     "LL source"     "geometry"     
[8] "iso3c"

> kemri_excel <- read_excel('data/raw_data/who-cds-gmp-2019-01-eng.xlsx') %>% filter(Country == 'South Africa')
> colnames(kemri_excel)
[1] "Country"       "Admin1"        "Facility name" "Facility type" "Ownership"     "Lat"           "Long"         
[8] "LL source"

Suggested actions
Please is it possible to add the two columns with Lat and Long as per the original Excel file?

[Feature] Use iso3c for country specification

Is your feature request related to a problem? Please describe.
At the moment the query to access country-specific data looks like this:

afrihealthsites("south africa", datasource = "healthsites", plot = FALSE)

The way that we have to specify the country i.e. lower case full name is not very intuitive.

Describe the solution you'd like
Maybe rather specify that one should use the iso3c or another standardised way to extract a country to make it as straight-forward as possible for users?

small [Bug] in UI with admin region selection : object 'mapplot' not found

Happens because map plotting is triggered by country change which also triggers change in admin regions (if option selected).

It's just a temporary error msg that flashes up & is then replaced.

On changing country with region selection enabled, compare_hs_sources() is being called with the admin region selection from the previous country.

Best solution will be to sort out the reactivity chain, but tricky because admin region selection is not always enabled.

https://github.com/afrimapr/afrihealthsites/tree/master/inst/shiny/healthsites_viewer_v03

[Bug] in UI healthsites_viewer_v03 admin region selection - geoboundaries download files not found

same as afrimapr/africovid#1

add table of African national Master Facility Lists [Feature]

add Table1 from the paper and a function to access it. e.g. to allow users to query download URL for a country.
https://wellcomeopenresearch.org/articles/5-157/v1#T1

[Feature] Make app mobile ready

Is your feature request related to a problem? Please describe.
The app can currently be viewed on mobile phones but the experience can be improved

Describe the solution you'd like
See this twitter conversation - https://twitter.com/MapMeuBairro/status/1262703318490664960

Serialization warning R version >= 3.5.0

Hi Andy,

I had this warning when I installed the latest version of the package.

  NB: this package now depends on R (>= 3.5.0)
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects: ‘afrihealthsites/data/sfssd.rda’

I think making the package depends on R (>= 3.5.0) in DESCRIPTION will remove it.
Thanks

library(afrihealthsites)
afrihealthsites("mali")

Error in st_geometry.sf(x) :
attr(obj, "sf_column") does not point to a geometry column.
Did you rename it, without setting st_geometry(obj) <- "newname"?

But when I browse to debug the error doesn't happen.

Can anyone fix please ?