{fifo} is a re-imagined fork of {extractOz} that is under active development providing a unified interface to extract data from georeferenced Australian data sets using GPS points, i.e., latitude and longitude coordinates, that include all the data that the original {extractOz} supports and more:
{fifo} is named after a work arrangement commonly used in Australian mining where an employer will temporarily transport employees to a work location or site of work, typically a mine, and transport them back for a period of rest.
{fifo}
xy rather than x as the primary function argument to provide the geo-locations of interest;locations rather than names to denote the named geo-locations of the paired lon lat values to avoid confusion with base R functionality;data.frame, including {sf}, objects for extraction rather than requiring a list of lon and lat values;The preferred method is to install through R-Universe like so:
# Enable this universe
options(
repos = c(
adamhsparks = "https://adamhsparks.r-universe.dev",
CRAN = "https://cloud.r-project.org"
)
)
# Install
install.packages("fifo")
Load the packages necessary to execute the examples that follow.
library(fifo)
## Registered S3 method overwritten by 'data.table':
## method from
## print.data.table colorDF
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
locs <- list(
Merredin = c(x = 118.28, y = -31.48),
Corrigin = c(x = 117.87, y = -32.33),
Tamworth = c(x = 150.84, y = -31.07)
)
See the help for extract_ae_zone for more help on how to use this function.
z <- extract_ae_zone(xy = locs)
See the help for extract_soil_order for more help on how to use this function.
s <- extract_daas_soil_order(xy = locs)
Using the previously used list of GPS points, fetch weather data from SILO for 2020.
This example uses a locally-stored API key found in the .Renviron file.
See the help for extract_patched_point for more help on how to use this function.
three_sites <-
extract_patched_point(
xy = locs,
start_date = "20200101",
end_date = "20201231",
api_key = Sys.getenv("SILO_API_KEY")
)
## You have requested station observation data but some rows in this
## dataset have data codes for interpolated data.
## Check the 'data_source' columns and `get_patched_point()` or
## `get_data_drill()` documentation for further details on codes and
## references.
##
## You have requested station observation data but some rows in this
## dataset have data codes for interpolated data.
## Check the 'data_source' columns and `get_patched_point()` or
## `get_data_drill()` documentation for further details on codes and
## references.
Now using dplyr::left_join, create a single data.frame of the location, GPS coordinates, agroecological zone and weather data.
left_join(
z,
three_sites,
by = c(
"location" = "location",
"x" = "x",
"y" = "y"
)
) %>%
left_join(s)
## Joining with `by = join_by(location, x, y)`
## location x y ae_zone station_code station_name
## <char> <num> <num> <char> <char> <char>
## 1: Corrigin 117.87 -32.33 WA Central 010536 Corrigin
## 2: Corrigin 117.87 -32.33 WA Central 010536 Corrigin
## 3: Corrigin 117.87 -32.33 WA Central 010536 Corrigin
## 4: Corrigin 117.87 -32.33 WA Central 010536 Corrigin
## 5: Corrigin 117.87 -32.33 WA Central 010536 Corrigin
## ---
## 1094: Tamworth 150.84 -31.07 NSW NE/Qld SE 055325 Tamworth Airport AWS
## 1095: Tamworth 150.84 -31.07 NSW NE/Qld SE 055325 Tamworth Airport AWS
## 1096: Tamworth 150.84 -31.07 NSW NE/Qld SE 055325 Tamworth Airport AWS
## 1097: Tamworth 150.84 -31.07 NSW NE/Qld SE 055325 Tamworth Airport AWS
## 1098: Tamworth 150.84 -31.07 NSW NE/Qld SE 055325 Tamworth Airport AWS
## distance year day date air_tmax air_tmax_source air_tmin
## <num> <num> <int> <Date> <num> <int> <num>
## 1: 0.3 2020 1 2020-01-01 37.4 25 15.3
## 2: 0.3 2020 2 2020-01-02 23.0 0 16.0
## 3: 0.3 2020 3 2020-01-03 26.0 0 12.5
## 4: 0.3 2020 4 2020-01-04 34.0 0 8.0
## 5: 0.3 2020 5 2020-01-05 38.0 0 12.0
## ---
## 1094: 0.6 2020 27 2020-12-27 29.8 0 15.0
## 1095: 0.6 2020 28 2020-12-28 26.8 0 18.3
## 1096: 0.6 2020 29 2020-12-29 28.9 0 17.5
## 1097: 0.6 2020 30 2020-12-30 29.4 0 14.9
## 1098: 0.6 2020 31 2020-12-31 30.0 0 16.1
## air_tmin_source elev_m et_morton_actual et_morton_actual_source
## <int> <char> <num> <int>
## 1: 25 295.0 m 3.3 26
## 2: 25 295.0 m 6.4 26
## 3: 0 295.0 m 3.4 26
## 4: 0 295.0 m 4.6 26
## 5: 0 295.0 m 7.4 26
## ---
## 1094: 0 394.9 m 5.5 26
## 1095: 0 394.9 m 4.1 26
## 1096: 0 394.9 m 2.6 26
## 1097: 0 394.9 m 6.6 26
## 1098: 0 394.9 m 6.2 26
## et_morton_potential et_morton_potential_source et_morton_wet
## <num> <int> <num>
## 1: 11.0 26 7.2
## 2: 6.4 26 6.4
## 3: 7.3 26 5.4
## 4: 8.4 26 6.5
## 5: 8.8 26 8.1
## ---
## 1094: 6.9 26 6.2
## 1095: 4.9 26 4.5
## 1096: 5.3 26 3.9
## 1097: 6.6 26 6.6
## 1098: 8.1 26 7.1
## et_morton_wet_source et_short_crop et_short_crop_source et_tall_crop
## <int> <num> <int> <num>
## 1: 26 8.0 26 10.4
## 2: 26 4.4 26 4.7
## 3: 26 5.4 26 6.7
## 4: 26 7.0 26 8.9
## 5: 26 7.3 26 9.0
## ---
## 1094: 26 5.3 26 6.3
## 1095: 26 3.5 26 4.2
## 1096: 26 3.8 26 4.8
## 1097: 26 5.2 26 5.9
## 1098: 26 6.0 26 7.1
## et_tall_crop_source evap_comb evap_comb_source evap_morton_lake
## <int> <num> <int> <num>
## 1: 26 9.5 25 8.1
## 2: 26 10.4 0 6.6
## 3: 26 8.0 0 6.2
## 4: 26 8.0 0 7.5
## 5: 26 10.6 0 8.4
## ---
## 1094: 26 5.5 25 6.3
## 1095: 26 3.6 25 4.5
## 1096: 26 2.6 25 4.0
## 1097: 26 4.3 25 6.8
## 1098: 26 5.0 25 7.3
## evap_morton_lake_source evap_pan evap_pan_source evap_syn evap_syn_source
## <int> <num> <int> <num> <int>
## 1: 26 9.5 25 11.1 26
## 2: 26 10.4 0 7.2 26
## 3: 26 8.0 0 8.3 26
## 4: 26 8.0 0 10.1 26
## 5: 26 10.6 0 10.4 26
## ---
## 1094: 26 5.5 25 6.7 26
## 1095: 26 3.6 25 4.5 26
## 1096: 26 2.6 25 5.1 26
## 1097: 26 4.3 25 6.5 26
## 1098: 26 5.0 25 7.5 26
## extracted station_y station_x mslp mslp_source radiation
## <Date> <num> <num> <num> <int> <num>
## 1: 2026-10-07 -32.3292 117.8733 1012.7 25 31.0
## 2: 2026-10-07 -32.3292 117.8733 1010.8 0 27.1
## 3: 2026-10-07 -32.3292 117.8733 1017.2 0 26.8
## 4: 2026-10-07 -32.3292 117.8733 1020.9 0 30.9
## 5: 2026-10-07 -32.3292 117.8733 1015.9 0 30.8
## ---
## 1094: 2026-10-07 -31.0742 150.8362 1015.7 0 24.9
## 1095: 2026-10-07 -31.0742 150.8362 1012.7 0 15.7
## 1096: 2026-10-07 -31.0742 150.8362 1011.4 0 14.0
## 1097: 2026-10-07 -31.0742 150.8362 1014.2 0 26.4
## 1098: 2026-10-07 -31.0742 150.8362 1015.8 0 28.7
## radiation_source rainfall rainfall_source rh_tmax rh_tmax_source rh_tmin
## <int> <num> <int> <num> <int> <num>
## 1: 42 0.0 0 22.6 26 83.5
## 2: 42 0.0 0 71.2 26 100.0
## 3: 42 0.0 0 37.5 26 87.0
## 4: 42 0.0 0 26.3 26 100.0
## 5: 42 0.0 0 33.4 26 100.0
## ---
## 1094: 42 2.0 0 46.5 26 100.0
## 1095: 42 10.2 0 61.9 26 100.0
## 1096: 42 1.0 0 50.0 26 99.6
## 1097: 42 18.8 0 52.7 26 100.0
## 1098: 42 0.0 0 44.5 26 100.0
## rh_tmin_source vp vp_deficit vp_deficit_source vp_source
## <int> <num> <num> <int> <int>
## 1: 26 14.5 32.7 26 25
## 2: 26 20.0 5.2 26 0
## 3: 26 12.6 14.9 26 0
## 4: 26 14.0 22.7 26 0
## 5: 26 22.1 24.1 26 0
## ---
## 1094: 26 19.5 14.3 26 0
## 1095: 26 21.8 9.3 26 0
## 1096: 26 19.9 13.8 26 0
## 1097: 26 21.6 11.6 26 0
## 1098: 26 18.9 15.8 26 0
## daas_soil_order
## <fctr>
## 1: Sodosol
## 2: Sodosol
## 3: Sodosol
## 4: Sodosol
## 5: Sodosol
## ---
## 1094: Dermosol
## 1095: Dermosol
## 1096: Dermosol
## 1097: Dermosol
## 1098: Dermosol
The examples in this README assume that you have stored your API key(s) in your .Renviron file. See Chapter 8 in "What They Forgot to Teach You About R" by Bryan et al. for more on storing details in your .Renviron if you are unfamiliar.
If you are using Linux, you will likely need to install several system-level libraries. For Nectar with a fresh Ubuntu image, you can use the following command to install system libraries to install {pak} and then install {fifo}. In your Linux terminal (not your R console, the "terminal" tab in RStudio should do here in most cases) type:
sudo apt update && sudo apt install libcurl4-openssl-dev libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev libudunits2-dev libxml2-dev
Please note that the {fifo} project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Please note that the {fifo} project has a Contributing guide, please refer to it before contributing to this project.