The goal of mosquitoR is provide to set of tools for analyzing data associated with the Mosquito Alert citizen science system (http://mosquitoalert.com), including Mosquito Alert citizen science data, smart trap data from the Irideon Senscape API, and traditional mosquito trap data.
IMPORTANT: This package is at an early stage of development, and we may introduce “breaking” changes. In addition, please note that while the package contains functions for working with the Irideon Senscape API, it is not developed by Irideon and is not an official Irideon package.
Installation
You can install the development version of mosquitoR from GitHub as follows:
# install.packages("devtools")
devtools::install_github("Mosquito-Alert/mosquitoR")Example
Turn a set of latitude and longitude coordinates into the standardized sampling cell IDs use to organize Mosquito Alert’s anonymous background tracks:
library(mosquitoR)
make_samplingcell_ids(lon=c(2.1686, 2.1032), lat=c(41.3874, 41.2098), mask=0.05)
#> [1] "2.15_41.35" "2.1_41.2"Extract longitudes from a set of sampling cell IDs:
library(mosquitoR)
make_lonlat_from_samplingcell_ids(ids=c("2.15_41.35", "2.10_41.20"), type="lon")
#> [1] "2.15" "2.10"Download smart trap data from the Senscape server using an API key:
library(mosquitoR)
library(lubridate)
#>
#> Attaching package: 'lubridate'
#> The following objects are masked from 'package:base':
#>
#> date, intersect, setdiff, union
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
library(magrittr)
library(keyring)
# first set your API key:
# key_set("SENSCAPE_API_KEY")
SENSCAPE_API_KEY = key_get("SENSCAPE_API_KEY")
# get list of device IDs with names that start with ASPB
ASPB_deviceIds = get_senscape_devices(api_key = SENSCAPE_API_KEY) %>% filter(startsWith(name, "ASPB")) %>% pull(`_id`)
ASPB_deviceIds
#> [1] "5f10762e98fda900151ff680" "5f10767c98fda900151ff681"
#> [3] "5f1076c998fda900151ff683" "5f1076ae98fda900151ff682"
#> [5] "5f1076e798fda900151ff684"
# get all data from these devices within a specified interval
my_data = get_senscape_data(api_key = SENSCAPE_API_KEY, start_datetime = as_datetime("2023-03-08"), end_datetime = as_datetime("2023-03-09"), deviceIds = ASPB_deviceIds)
#> Getting Senscape Data from 2023-03-08 to 2023-03-09
#> | | | 0% | |======================================================================| 100%
my_data
#> # A tibble: 241 × 11
#> `_id` temperature nice_name classification record_time humidity client_name
#> <chr> <dbl> <chr> <chr> <chr> <dbl> <chr>
#> 1 6408cd… 17.0 FILE_167… Culex female 2023-03-08… 61.1 ASPB 3 (Pe…
#> 2 6407d7… 12.3 FILE_167… Test pulse 2023-03-08… 56.4 ASPB 2 (Ho…
#> 3 6407d7… 12.8 FILE_167… Test pulse 2023-03-08… 61.3 ASPB 3 (Pe…
#> 4 6407d7… 12.7 FILE_167… Test pulse 2023-03-08… 60.4 ASPB 1 (Sa…
#> 5 6407d7… 14.0 FILE_167… Test pulse 2023-03-08… 61.1 ASPB 5 (Zo…
#> 6 6407d7… 14.7 FILE_167… Test pulse 2023-03-08… 72.5 ASPB 4 (Le…
#> 7 6407de… 12.6 FILE_167… Test pulse 2023-03-08… 60.3 ASPB 1 (Sa…
#> 8 6407de… 12.8 FILE_167… Test pulse 2023-03-08… 61.4 ASPB 3 (Pe…
#> 9 6407de… 12.2 FILE_167… Test pulse 2023-03-08… 56.5 ASPB 2 (Ho…
#> 10 6407de… 14.1 FILE_167… Test pulse 2023-03-08… 61.1 ASPB 5 (Zo…
#> # ℹ 231 more rows
#> # ℹ 4 more variables: client_type <chr>, processed <chr>, lat <lgl>, lng <lgl>Documentation
Online documentation can be found at https://mosquito-alert.github.io/mosquitoR/.
Contributing
If you want to contribute new functions, fix bugs, add documentation or tests, etc., please do so on the dev branch. We are developing this package using devtools and testthat and doing our best to follow the guidelines and styles laid out in https://r-pkgs.org.