Epitweetr

Package ‘epitweetr’
December 1, 2022
Title Early Detection of Public Health Threats from 'Twitter' Data
Version 2.2.13
Description It allows you to automatically monitor trends of tweets by time, place and topic aim-
ing at detecting public health threats early through the detection of signals (e.g. an unusual in-
crease in the number of tweets). It was designed to focus on infectious diseases, and it can be ex-
tended to all hazards or other fields of study by modifying the topics and keywords. More infor-
mation is available in the 'epitweetr' peer-review publication (<https:
//www.eurosurveillance.org/content/10.2807/1560-7917.ES.2022.27.39.2200177>).
License EUPL
URL https://github.com/EU-ECDC/epitweetr
BugReports https://github.com/EU-ECDC/epitweetr/issues
Encoding UTF-8
Imports bit64, dplyr, crul, curl, DT, emayili, future, httpuv, httr,
htmltools, jsonlite, keyring, knitr, lifecycle, ggplot2,
janitor, magrittr, parallel, plotly, processx, rtweet, readxl,
rgdal, rlang, rmarkdown, rnaturalearthdata, openxlsx, plyr,
shiny, sp, stringr, stats, tibble, tidyverse, tidytext,
tokenizers, tools, utils, xtable, xml2
RoxygenNote 7.2.0
Suggests taskscheduleR
VignetteBuilder knitr
NeedsCompilation no
Author Laura Espinosa [aut, fnd, cre]
(<https://orcid.org/0000-0003-0748-9657>, Project manager, author
of the design and concept of the package, and package maintainer),
Francisco Orchard [aut, ctr] (<https://orcid.org/0000-0001-5793-3301>,
Author of the package and original code),
Ariana Wijermans [ctb] (Contributor to the design and concept of the
package),
Thomas Mollet [ctb, fnd] (Business owner of the project, and
contributor to the design and concept of the package),
Adrian Prodan [ctb],
1
2 R topics documented:
Thomas Czernichow [ctb],

Maria Prieto Gonzalez [ctb],
Esther Kissling [ctb],
Michael Höhle [ctb]
Maintainer Laura Espinosa <laura.espinosa@ecdc.europa.eu>
Repository CRAN
Date/Publication 2022-12-01 00:40:03 UTC
R topics documented:
check_all . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
create_map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
create_snapshot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
create_topchart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
create_topwords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
detect_loop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
download_dependencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
ears_t_reweighted . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
epitweetr_app . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
fs_loop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
generate_alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
geolocate_text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
get_aggregates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
get_alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
get_tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
get_todays_sample_tweets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
health_check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
is_detect_running . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
is_fs_running . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
is_search_running . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
json2lucene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
register_detect_runner_task . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
register_fs_monitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
register_fs_runner_task . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
register_search_runner_task . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
save_config . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
search_loop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
search_tweets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
setup_config . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
set_twitter_app_auth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
stop_detect_runner_task . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
stop_fs_runner_task . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
stop_search_runner_task . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
trend_line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
update_geonames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
update_languages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
check_all 3
Index 43
check_all Run automatic sanity checks
Description
It runs a set of automated sanity checks for helping the user to troubleshot issues
Usage
check_all()
Details
This function executes a series of sanity checks, concerning, Java, bitness, task status, dependencies
and Twitter authentication.
Value
Data frame containing the statuses of all realized checks
Examples
if(FALSE){
#importing epitweer
library(epitweetr)
message('Please choose the epitweetr data directory')
setup_config(file.choose())
#running all tests
check_all()
}
create_map Plot the map report on the epitweetr dashboard
Description
Generates a bubble map plot of number of tweets by countries, for one topic
4 create_map
Usage
create_map(
topic = c(),
countries = c(1),
date_min = "1900-01-01",
date_max = "2100-01-01",
with_retweets = FALSE,
location_type = "tweet",
caption = "",
proj = NULL,
forplotly = FALSE
)
Arguments
topic Character(1) containing the topic to use for the report
countries Character vector containing the name of the countries and regions to plot or their
respective indexes on the Shiny app, default: c(1)
date_min Date indicating start of the reporting period, default: "1900-01-01"
date_max Date indicating end of the reporting period, default: "2100-01-01"
with_retweets Logical value indicating whether to include retweets in the time series, default:
FALSE
location_type Character(1) vector indicating the location type. Possible values ’tweet’, ’user’
or ’both’, default: ’tweet’
caption Character(1) vector indicating a caption to print at the bottom of the chart, de-
fault: ""
proj Parameter indicating the CRS (Coordinate Reference System) to use on PROJ4
format CRS-class? If null and all countries are selected +proj=robin is used
(Robinson projection) otherwise the Lambert azimuthal equal-area projection
will be chosen, default: NULL
forplotly Logical(1) parameter indicating whether some hacks are activated to improve
plotly rendering, default: FALSE
Details
Produces a bubble chart map for a particular topic on number of tweets collected based on the
provided parameters. The map will display information at country level if more than one country is
selected, otherwise it will display bubbles at the smallest possible location identified for each tweet
within the period which could be any administrative level or city level.
Tweets associated with a country but with no finer granularity are omitted when displaying a single
country.
When an aggregated zone is requested, all countries in that zone are included.
This functions requires that search_loop and detect_loop have already been run successfully to
show results.
create_snapshot 5
Value
A named list containing two elements: ’chart’ with the ggplot2 figure and ’data’ containing the
dataframe that was used to build the map.
See Also
trend_line create_topwords detect_loop search_loop spTransform,coordinates,is.projected,CRS-class
fortify,geom_polygon,geom_point
Examples
if(FALSE){
#Getting bubble chart for dengue for South America for last 30 days
create_map(
topic = "dengue",
countries = "South America",
date_min = as.Date(Sys.time())-30,
date_max=as.Date(Sys.time())
)
}
create_snapshot Snapshot of your epitweetr installation
Description
Creates a snapshot file of your epitweetr installation folder. This can include all or a subset of the
data files.
Usage
create_snapshot(
destination_dir,
types = c("settings", "dependencies", "machine-learning", "aggregations", "tweets",
"logs"),
tweets_period = get_aggregated_period(),
aggregated_period = get_aggregated_period(),
compress = TRUE,
progress = function(v, m) message(paste(round(v * 100, 2), m))
)
Arguments
destination_dir,
character(1) vector with the path of the destination folder to produce the snap-
shot
6 create_topchart
types, character vector indicating the types of data to include on a snapshot. Some
of: "settings", "dependencies", "machine-learning", "aggregations", "tweets",
"logs"
tweets_period,
date(2) start and end dates to filter tweets to include on snapshot (if selected)
aggregated_period,
date(2) start and end dates to filter time series to include on snapshot (if selected)
compress, logical(1) whether to compress or not the output file
progress, function to report progress during execution.
Details
This function can be used to create a a portable file to move your epitweetr installation in a single
file, to backup your data, to archive your old data or to send information to technical team in
order to reproduce an observed issue. Different kinds of data can be included on the snapshot
depending on the type of parameter. Possible values are: - ’settings’: Including all setting files
of your installation (excluding passwords) - ’dependencies’: All jars and winutils.exe on windows
installations - ’machine-learning’: All trained models and vectors and training data (this can include
tweet text which is personal data) - ’aggregations’: Epitweetr aggregated time series - ’tweets’:
Tweets collected by epitweetr - ’logs’: Log files produced automatically on windows task scheduler
tasks.
Value
Nothing
Examples
if(FALSE){
#importing epitweer
library(epitweetr)
#creating a compressed snapshot for settings and logs
create_snapshot(getwd(), c("settings","dependencies"), compress = TRUE)
}
create_topchart Plot the top elements for a specific series on the epitweetr dashboard
Description
Generates a bar plot of most popular elements in tweets, for one topic. Top elements among ("top-
words", "hashtags", "entities", "contexts", "urls")
create_topchart 7
Usage
create_topchart(
topic,
serie,
country_codes = c(),
date_min = "1900-01-01",
date_max = "2100-01-01",
top = 25
)
Arguments
serie Character(1) name of the series to be used for the report. It should be one of
("topwords", "hashtags", "entities", "contexts", "urls")
country_codes Character vector containing the ISO 3166-1 alpha-2 countries to plot, default:
c()
FALSE
location_type Character(1) this parameter is currently being IGNORED since this report shows
only tweet location and cannot show user or both locations for performance
reasons, default: ’tweet’
top numeric(1) Parameter indicating the number of words to show, default: 25
Details
Produces a bar chart showing the occurrences of the most popular words in the collected tweets
based on the provided parameters. For performance reasons on tweet aggregation, this report only
shows tweet location and ignores the location_type parameter
This functions requires that search_loop and detect_loop have already been run successfully to
show results.
Value
A named list containing two elements: ’chart’ with the ggplot2 figure and ’data’ containing the data
frame that was used to build the map.
See Also
trend_line create_map detect_loop search_loop
8 create_topwords
Examples
if(FALSE){
#Getting topword chart for dengue for France, Chile, Australia for last 30 days
create_topchart(
topic = "dengue",
serie = "topwords",
country_codes = c("FR", "CL", "AU"),
)
}
create_topwords Plot the top words report on the epitweetr dashboard
Description
Generates a bar plot of most popular words in tweets, for one topic
Usage
create_topwords(
topic,
country_codes = c(),
date_min = "1900-01-01",
date_max = "2100-01-01",
top = 25
)
Arguments
country_codes Character vector containing the ISO 3166-1 alpha-2 countries to plot, default:
c()
FALSE
location_type Character(1) this parameter is currently being IGNORED since this report shows
only tweet location and cannot show user or both locations for performance
reasons, default: ’tweet’
top numeric(1) Parameter indicating the number of words to show, default: 25
detect_loop 9
Details
Produces a bar chart showing the occurrences of the most popular words in the collected tweets
based on the provided parameters. For performance reasons on tweet aggregation this report only
shows tweet location and ignores the location_type parameter
This report may be empty for combinations of countries and topics with very few tweets since
for performance reasons, the calculation of top words is an approximation using chunks of 10.000
tweets.
This function requires that search_loop and detect_loop have already been run successfully to
show results.
Value
frame that was used to build the map.
See Also
trend_line create_map detect_loop search_loop
Examples
if(FALSE){
#Getting topword chart for dengue for France, Chile, Australia for last 30 days
create_topwords(
topic = "dengue",
country_codes = c("FR", "CL", "AU"),
)
}
detect_loop Runs the detect loop
Description
Infinite loop ensuring the daily signal detection and email alerts
Usage
detect_loop(data_dir = NA)
10 detect_loop
Arguments
data_dir Path to the ’data directory’ containing application settings, models and collected
tweets. If not provided the system will try to reuse the existing one from last
session call of setup_config or use the EPI_HOME environment variable, de-
fault: NA
Details
The detect loop is composed of three ’one shot tasks’ download_dependencies, update_geonames,
update_languages ensuring the system has all necessary components and data to run the three re-
current tasks generate_alerts
The loop report progress on the ’tasks.json’ file which is read or created by this function.
The recurrent tasks are scheduled to be executed each ’detect span’ minutes, which is a parameter
set on the Shiny app.
If any of these tasks fails it will be retried three times before going to abort status. Aborted tasks
can be relaunched from the Shiny app.
Value
nothing
See Also
download_dependencies
update_geonames
update_languages
detect_loop
generate_alerts
get_tasks
Examples
if(FALSE){
#Running the detect loop
library(epitweetr)
detect_loop()
}
download_dependencies 11
download_dependencies Updates Java dependencies
Description
Download Java dependencies of the application mainly related to Apache SPARK and Lucene,
Usage
download_dependencies(tasks = get_tasks())
Arguments
tasks Task object for reporting progress and error messages, default: get_tasks()
Details
Run a one-shot task consisting of downloading Java and Scala dependencies, this is separated by
the following subtasks
• Download jar dependencies from configuration maven repo to project data folder. This in-
cludes, scala, spark, lucene. Packages to be downloaded are defined in package file ’sbt-
deps.txt’
• Download winutils from configuration URL to project data folder. For more details on winu-
tils please see https://issues.apache.org/jira/browse/HADOOP-13223 and https://
issues.apache.org/jira/browse/HADOOP-16816
The URLs to download the JAR dependencies (maven package manager) and Winutils are on the
configuration tab of the Shiny app.
Normally this function is not called directly by the user but from the detect_loop function.
Value
The list of tasks updated with produced messages
See Also
detect_loop
get_tasks
Examples
if(FALSE){
library(epitweetr)
# setting up the data folder
12 ears_t_reweighted
# geolocating last tweets

tasks <- download_dependencies()
}
ears_t_reweighted algorithm for outbreak detection, extends the EARS algorithm
Description
The simple 7 day running mean version of the Early Aberration Reporting System (EARS) algo-
rithm is extended as follows:
• proper computation of the prediction interval

• downweighting of previous signals, similar to the approach by Farrington (1996)
Usage
ears_t_reweighted(
ts,
alpha = 0.025,
alpha_outlier = 0.05,
k_decay = 4,
no_historic = 7L,
same_weekday_baseline = FALSE
)
Arguments
ts A numeric vector containing the counts of the univariate time series to monitor.
The last time point in ts is investigated
alpha The alpha is used to compute the upper limit of the prediction interval: (1-alpha)
* 100%, default: 0.025
alpha_outlier Residuals beyond 1-alpha_outlier quantile of the the t(n-k-1) distribution are
downweighted, default: 0.05
k_decay Power k in the expression (r_star/r_threshold)^k determining the weight, de-
fault: 4
no_historic Number of previous values i.e -1, -2, ..., no_historic to include when computing
baseline parameters, default: 7
same_weekday_baseline
whether to calculate baseline using same weekdays or any day, default: FALSE
Details
for algorithm details see package vignette.
epitweetr_app 13
Value
A dataframe containing the monitored time point, the upper limit and whether a signal is detected
or not.
Author(s)
Michael Hoehle <https://www.math.su.se/~hoehle>
Examples
if(FALSE){
library(epitweetr)
#Running the modifies version of the ears algorithm for a particular data series
ts <- c(150, 130, 122, 160, 155, 128, 144, 125, 300, 319, 289, 277, 500)
show(ears_t_reweighted(ts))
}
epitweetr_app Run the epitweetr Shiny app
Description
Open the epitweetr Shiny app, used to setup the Data collection & processing pipeline, the Require-
ments & alerts pipeline and to visualise the outputs.
Usage
epitweetr_app(data_dir = NA)
Arguments
tweets. If not provided the system will try to reuse the existing one from last
fault: NA
Details
The epitweetr app is the user entry point to the epitweetr package. This application will help the
user to setup the tweet collection process, manage all settings, see the interactive dashboard visual-
isations, export them to Markdown or PDF, and setup the alert emails.
All its functionality is described on the epitweetr vignette.
Value
The Shiny server object containing the launched application
14 fs_loop
See Also
search_loop
detect_loop
Examples
if(FALSE){
#Running the epitweetr app
library(epitweetr)
epitweetr_app()
}
fs_loop Runs the epitweetr embedded database loop
Description
Infinite loop ensuring that the epitweetr embedded database is running (Lucene + akka-http)
Usage
fs_loop(data_dir = NA)
Arguments
tweets. If not provided, the system will try to reuse the existing one from last
fault: NA
Details
Launches the epitweetr embedded database which is accessed via a REST API located on http:
//localhost:8080. You can test that the database is running by accessing http://localhost:
8080/ping the REST API provide epitweetr a way to send and retrieve data related with tweets and
time series and to trigger geolocation or aggregation The database is implemented using Apache
Lucene indexes allowing epitweetr to access its data as a search engine but also as a tabular database.
health_check called each 60 seconds on a background process to send alerts to the administrator
if some epitweetr components fail.
Value
nothing
generate_alerts 15
See Also
detect_loop
search_loop
health_check
Examples
if(FALSE){
library(epitweetr)
fs_loop()
}
generate_alerts Execute the alert task
Description
Evaluate alerts for the last collected day for all topics and regions and send email alerts to sub-
scribers
Usage
generate_alerts(tasks = get_tasks())
Arguments
tasks Current tasks for reporting purposes, default: get_tasks()
Details
This function calculates alerts for the last aggregated day and then send emails to subscribers.
The alert calculation is based on the country_counts time series which stores alerts by country, hour
and topics.
For each country and region, the process starts by aggregating the last N days. A day is a block of
consecutive 24 hours ending before the hour of the collected last tweet. N is defined by the alert
baseline parameter on the configuration tab of the Shiny application (the default is N=7).
An alert will be produced when the number of tweets observed is above the threshold calculated
by the modified version of the EARS algorithm (for more details see the package vignette). The
behaviour of the alert detection algorithm is modified by the signal false positive rate (alpha), down-
weighting of previous alerts and weekly or daily baseline parameters as defined on the configuration
tab of the Shiny application and the topics file.
A prerequisite to this function is that the search_loop must already have stored collected tweets
in the search folder and that the geotagging and aggregation tasks have already been run. Normally
this function is not called directly by the user but from the detect_loop function.
16 geolocate_text
Value
See Also
detect_loop
Examples
if(FALSE){
library(epitweetr)
# calculating alerts for last day tweets and sending emails to subscribers
generate_alerts()
}
geolocate_text geolocate text in a data frame given a text column and optionally a
language column
Description
extracts geolocaion information on text on a column of the provided data frame and returns a new
data frame with geolocation information
Usage
geolocate_text(df, text_col = "text", lang_col = NULL, min_score = NULL)
Arguments
df A data frame containing at least character column with text, a column with the
language name can be provided to improve geolocation quality
text_col character, name of the column on the data frame containing the text to geolocal-
ize, default:text
lang_col character, name of the column on the data frame containing the language of
texts, default: NULL
min_score, numeric, the minimum score obtained on the Lucene scoring function to accept
matches on GeoNames. It has to be empirically set default: NULL
geolocate_text 17
Details
This function perform a call to the epitweetr database which includes functionality for geolocating
for languages activated and successfully processed on the shiny app.
The geolocation process tries to find the best match in GeoNames database https://www.geonames.
org/ including all local aliases for words.
If no language is associated to the text, all tokens will be sent as a query to the indexed GeoNames
database.
If a language code is associated to the text and this language is trained on epitweetr, entity recog-
nition techniques will be used to identify the best candidate in text to contain a location and only
these tokens will be sent to the GeoNames query.
A custom scoring function is implemented to grant more weight to cities increasing with population
to try to perform disambiguation.
Rules for forcing the geolocation choices of the algorithms and for tuning performance with manual
annotations can be performed on the geotag tab of the Shiny app.
A prerequisite to this function is that the tasks download_dependencies update_geonames and
update_languages has been run successfully.
This function is called from the Shiny app on geolocation evaluation tab but can also be used for
manually evaluating the epitweetr geolocation algorithm.
Value
A new data frame containing the following geolocation columns: geo_code, geo_country_code,
geo_country, geo_name, tags
See Also
update_geonames
detect_loop
Examples
if(FALSE) {
library(epitweetr)
# creating a test dataframe

df <- data.frame(text = c("Me gusta Santiago de Chile es una linda ciudad"), lang = c("es"))
geo <- geolocate_text(df = df, text_col = "text", lang_col="lang")
}
18 get_aggregates
get_aggregates Getting already aggregated time series produced by detect_loop
Description
Read and returns the required aggregated dataset for the selected period and topics defined by the
filter.
Usage
get_aggregates(
dataset = "country_counts",
cache = TRUE,
filter = list(),
top_field = NULL,
top_freq = NULL
)
Arguments
dataset A character(1) vector with the name of the series to request, it must be one of
’country_counts’, ’geolocated’, ’topwords’, ’hashtags’, ’entities’, ’urls’, ’con-
texts’, default: ’country_counts’
cache Whether to use the cache for lookup and storing the returned dataframe, default:
TRUE
filter A named list defining the filter to apply on the requested series, it should be on
the shape of a named list e.g. list(tweet_geo_country_code=list(’FR’, ’DE’))
default: list()
top_field Name of the top field used with top_frequency to enable optimisation for getting
only most frequent elements. It will only keep top 500 items after first 50k lines
on reverse index order
top_freq character, Name of the frequency fields used with top_field to enable optimisa-
tion for getting only most frequent elements. It will only keep top 500 items
after first 50k rows on reverse index order
Details
This function returns data aggregated by epitweetr. The data is found on the ’series’ folder, which
contains Rds files per weekday and type of series. starting on v 1.0.x it will also look on Lucene
indexes situated on fs folder. Names of files and folders are parsed to limit the files to be read.
When using Lucene indexes, filters are directly applied on read. This is an improvement compared
’series’ folder where filters are applied after read. All returned rows are joined in a single dataframe.
If no filter is provided all data series is returned, which can end up with millions of rows depending
on the time series. To limit by period, the filter list must have an element ’period’ containing a date
vector or list with two dates representing the start and end of the request.
get_alerts 19
To limit by topic, the filter list must have an element ’topic’ containing a non-empty character vector
or list with the names of the topics to return.
The available time series are:
• "country_counts" counting tweets and retweets by posted date, hour and country
• "geolocated" counting tweets and retweets by posted date and the smallest possible geolocated
unit (city, administrative level or country)
• "topwords" counting tweets and retweets by posted date, country and the most popular words,
(this excludes words used in the topic search)
The returned dataset can be cached for further calls if requested. Only one dataset per series is
cached.
Value
A data frame containing the requested series for the requested period
See Also
detect_loop fs_loop
Examples
if(FALSE){
# Getting all country tweets between 2020-jan-10 and 2020-jan-31 for all topics
df <- get_aggregates(
filter = list(period = c("2020-01-10", "2020-01-31"))
)
# Getting all country tweets for the topic dengue

df <- get_aggregates(dataset = "country_counts", filter = list(topic = "dengue"))
# Getting all country tweets between 2020-jan-10 and 2020-jan-31 for the topic dengue
df <- get_aggregates(
filter = list(topic = "dengue", period = c("2020-01-10", "2020-01-31"))
)
}
get_alerts Getting signals produced by the task generate_alerts of

detect_loop
Description
Returns a data frame of signals produced by the detect_loop, which are stored on the signal folder.
20 get_alerts
Usage
get_alerts(
topic = character(),
countries = numeric(),
from = "1900-01-01",
until = "2100-01-01",
toptweets = 0,
limit = 0,
duplicates = "all",
progress = function(a, b) {
}
)
Arguments
topic Character vector. When it is not empty it will limit the returned signals to the
provided topics, default: character()
countries Character vector containing the names of countries or regions or a numeric vec-
tor containing the indexes of countries as displayed at the Shiny App to filter the
signals to return., default: numeric()
from Date defining the beginning of the period of signals to return, default: ’1900-01-
01’
until Date defining the end of the period of signals to return, default: ’2100-01-01’
toptweets Integer number of top tweets to be added to the alert. These are obtained from
the tweet index based on topwords and Lucene score, default: 0
limit Maximum number of alerts returned, default: 0
duplicates Character, action to decide what to do with alerts generated on the same day.
Options are "all" (keep all alerts), "first" get only first alert and "last" for getting
only the last alert
progress Function, function to report progress it should receive two parameter a progress
between 0 and 1 and a message, default: empty function
Details
For more details see the package vignette.
Value
a data frame containing the calculated alerts for the period. If no alerts are found then NULL is
returned
See Also
generate_alerts
detect_loop
get_tasks 21
Examples
if(FALSE){
library(epitweetr)
# Getting signals produced for last 30 days for a particular country

get_alerts(
countries = c("Chile", "Australia", "France"),
from = as.Date(Sys.time())-30,
until = as.Date(Sys.time())
)
}
get_tasks Get the detect_loop task status
Description
Reads the status of the detect_loop tasks and updates it with changes requested by the Shiny app
Usage
get_tasks(statuses = list())
Arguments
statuses Character vector for limiting the status of the returned tasks, default: list()
Details
After reading the tasks.json file and parsing it with jsonlite, this function will update the necessary
fields in the tasks for executing and monitoring them.
Value
A named list containing all necessary information to run and monitor the detect loop tasks.
See Also
update_geonames
update_languages
detect_loop
generate_alerts
22 get_todays_sample_tweets
Examples
if(FALSE){
#getting tasks statuses
library(epitweetr)
tasks <- get_tasks()
}
get_todays_sample_tweets
Get a sample of latest tweet geolocations (deprecated)
Description
This function was removed from epitweetr v1.0.1. Please use search_tweets instead
Usage
get_todays_sample_tweets(limit = 1000, text_col = "text", lang_col = "lang")
Arguments
limit Size of the sample, default: 100
text_col Name of the tweet field to geolocate it should be one of the following ("text",
"linked_text", "user_description", "user_location", "place_full_name", "linked_place_full_name"),
default: ’text’
lang_col Name of the tweet variable containing the language to evaluate. It should be one
of the following ("lang", "linked_lang", NA), default: "lang"
Details
This function was removed from epitweetr v1.0.1. Please use search_tweets instead.
Value
Data frame containing the sampled tweets and the geolocation metrics
See Also
update_geonames
update_languages
health_check 23
Examples
if(FALSE){
library(epitweetr)
# geolocating today's tweets

show(get_todays_sample_tweets())
}
health_check Send email to administrator if a failure of epitweetr is detected
Description
It validates if epitweetr is not collecting tweets, aggregating tweets or not calculating alerts
Usage
health_check(send_mail = TRUE, one_per_day = TRUE)
Arguments
send_mail Boolean. Whether an email should be sent to the defined administrator, default:
TRUE
one_per_day Boolean. Whether a limit of one email per day will be applied, default: TRUE
Details
This function sends an email to the defined administrator if epitweetr is not collecting tweets, ag-
gregating tweets or not calculating alerts
Value
A list of health check errors found
Examples
if(FALSE){
#importing epitweetr
library(epitweetr)
#sending the email to the administrator if epitweetr components are not properly working
health_check()
}
24 is_fs_running
is_detect_running Check whether the alert detection task is running
Description
gets the alert detection runner execution status
Usage
is_detect_running()
Details
returns a logical value being TRUE if the alert detection task is actually running
Value
logical Whether the alert detection task is running
Examples
if(FALSE){
library(epitweetr)
is_detect_running()
}
is_fs_running Check whether the database is running
Description
gets the database runner execution status
Usage
is_fs_running()
Details
returns a logical value being TRUE if the database runner is actually running
Value
logical Whether the database is running
is_search_running 25
Examples
if(FALSE){
library(epitweetr)
is_fs_running()
}
is_search_running Check whether the tweet collection task is running
Description
gets the tweet collection execution status
Usage
is_search_running()
Details
returns a logical value being TRUE if the tweet collection is running
Value
logical Whether the tweet collection is running
Examples
if(FALSE){
library(epitweetr)
is_search_running()
}
json2lucene Function used for migrating tweets from to old to the new file system
Description
migrates geolocated tweets from the old to the new file system allowing full text search using
Apache Lucene Indexes
Usage
json2lucene(tasks = get_tasks(), chunk_size = 400)
26 register_detect_runner_task
Arguments
tasks named list, current tasks for logging and updating progress default: get_tasks()
chunk_size, integer, the chunk size for indexing tweets, default: 400
Details
This function can be called manually to perform the migration of tweets between v0.0.x to v2+ It
iterates over existing tweets collected with epitweetr v0.0.x series joins base tweets and geolocated
tweets and then sends themes to the Lucene index via the dedicated REST API. Migrated files will
be moved to search_archive and geo_archive folders. Users can backup and remove these folders
when migration ends to gain disk space. Series folders are maintained for migrated tweets
Value
the updated tasks.
Examples
if(FALSE){
library(epitweetr)
# runnint the migration
json2lucene()
}
register_detect_runner_task
Registers the alert detection task
Description
registers the alert detection task or stops if no configuration has been set or if it is already running
Usage
register_detect_runner_task()
Details
Registers the alert detection task or stops if no configuration has been set or if it is already running.
To generate alerts, this task needs the tweet collection to had successfully run since the last time it
ran. This function will use the task scheduler on windows and will fall back to launching the runner
as a separate process (attached to this session) on Linux.
register_fs_monitor 27
Value
Nothing
Examples
if(FALSE){
library(epitweetr)
register_detect_runner_task()
}
register_fs_monitor Registers the fs_monitor for the current process or exits
Description
registers the fs_monitor (by writing fs.monitor.PID file) for the current process or stops if no con-
figuration has been set or if it is already running
Usage
register_fs_monitor()
Details
Registers the fs_monitor (by writing fs.monitor.PID file) for the current process or stops if no con-
figuration has been set or if it is already running This function has been exported so it can be
properly called from the future package on the database runner, but it is not intended to be directly
called by end users.
Value
Nothing
Examples
if(FALSE){
library(epitweetr)
register_fs_monitor()
}
28 register_search_runner_task
register_fs_runner_task
Registers the epitweetr database task
Description
registers the epitweetr database task or stops if no configuration has been set or if it is already
running
Usage
register_fs_runner_task()
Details
Registers the epitweetr database task or stops if no configuration has been set or if it is already
running. This task need the dependencies, geonames and languages steps to have been success-
fully ran. This can be done on the shiny app configuration page or by manually running the de-
tect_runner_task. This function will try to use the task scheduler on windows and will fall back to
launching the runner as a separate process (attached to this session) on Linux.
Value
Nothing
Examples
if(FALSE){
library(epitweetr)
register_fs_runner_task()
}
register_search_runner_task
Registers the tweet collection task
Description
registers the tweet collection task or stops if no configuration has been set or if it is already running
Usage
register_search_runner_task()
save_config 29
Details
Registers the tweet collextion task or stops if no configuration has been set or if it is already running.
Twitter authentication needs to be previously set on the shiny app or by calling set_twitter_app_auth().
You can test if authentication is working on the shiny app troubleshot page or by calling (with dplyr):
epitweetr::check_all() This function will use the task scheduler on windows and will fall back to
launching the runner as a separate process (attached to this session) on Linux.
Value
Nothing
Examples
if(FALSE){
library(epitweetr)
register_search_runner_task()
}
save_config Save the configuration changes
Description
Permanently saves configuration changes to the data folder (excluding Twitter credentials, but not
SMTP credentials)
Usage
save_config(data_dir = conf$data_dir, properties = TRUE, topics = TRUE)
Arguments
data_dir Path to a directory to save configuration settings, Default: conf$data_dir
properties Whether to save the general properties to the properties.json file, default: TRUE
topics Whether to save topic download plans to the topics.json file, default: TRUE
Details
Permanently saves configuration changes to the data folder (excluding Twitter credentials, but not
SMTP credentials) to save Twitter credentials please use set_twitter_app_auth
Value
Nothing
30 search_loop
See Also
setup_config set_twitter_app_auth
Examples
if(FALSE){
library(epitweetr)
#load configuration
#make some changes
#conf$collect_span = 90
#saving changes
save_config()
}
search_loop Runs the search loop
Description
Infinite loop ensuring the permanent collection of tweets
Usage
search_loop(data_dir = NA)
Arguments
data_dir optional path to the ’data directory’ containing application settings, models and
collected tweets. If not provided it will reuse the last set on the current session.
If not provided the system will try to reuse the existing one from last session call
of setup_config or use the EPI_HOME environment variable, Default: NA
Details
The detect loop is a pure R function designed for downloading tweets from the Twitter search API.
It can handle several topics ensuring that all of them will be downloaded fairly using a round-robin
philosophy and respecting Twitter API rate-limits.
The progress of this task is reported on the ’topics.json’ file which is read or created by this function.
This function will try to collect tweets respecting a ’collect_span’ window in minutes, which is
defined on the Shiny app and defaults to 60 minutes.
To see more details about the collection algorithm please see epitweetr vignette.
In order to work, this task needs Twitter credentials, which can be set on the Shiny app or using
set_twitter_app_auth
search_tweets 31
Value
Nothing
See Also
set_twitter_app_auth
Examples
if(FALSE){
#Running the search loop
library(epitweetr)
search_loop(file.choose())
}
search_tweets perform full text search on tweets collected with epitweetr
Description
perform full text search on tweets collected with epitweetr (tweets migrated from epitweetr v<1.0.x
are also included)
Usage
search_tweets(
query = NULL,
topic = NULL,
from = NULL,
to = NULL,
countries = NULL,
mentioning = NULL,
users = NULL,
hide_users = FALSE,
action = NULL,
max = 100,
by_relevance = FALSE
)
Arguments
query character. The query to be used if a text it will match the tweet text. To see how
to match particular fields please see details, default:NULL
topic character, Vector of topics to include on the search default:NULL
from an object which can be converted to ‘"POSIXlt"’ only tweets posted after or on
this date will be included, default:NULL
32 search_tweets
to an object which can be converted to ‘"POSIXlt"’ only tweets posted before or

on this date will be included, default:NULL
countries character or numeric, the position or name of epitweetr regions to be included
on the query, default:NULL
mentioning character, limit the search to the tweets mentioning the given users, default:NULL
users character, limit the search to the tweets created by the provided users, default:NULL
hide_users logical, whether to hide user names on output replacing them by the USER
keyword, default:FALSE
action character, an action to be performed on the search results respecting the max
parameter. Possible values are ’delete’ or ’anonymise’ , default:NULL
max integer, maximum number of tweets to be included on the search, default:100
by_relevance logical, whether to sort the results by relevance of the matching query or by
indexing order, default:FALSE If not provided the system will try to reuse the
existing one from last session call of setup_config or use the EPI_HOME
environment variable, default: NA
Details
epitweetr translate the query provided by all parameters into a single query that will be executed on
tweet indexes which are weekly indexes. The q parameter should respect the syntax of the Lucene
classic parser https://lucene.apache.org/core/8_5_0/queryparser/org/apache/lucene/queryparser/
classic/QueryParser.html So other than the provided parameters, multi field queries are sup-
ported by using the syntax field_name:value1;value2 AND, OR and -(for excluding terms) are sup-
ported on q parameter. Order by week is always applied before relevance so even if you provide
by_relevance = TRUE all of the matching tweets of the first week will be returned first
Value
a data frame containing the tweets matching the selected filters, the data frame contains the follow-
ing columns: linked_user_location, linked_user_name, linked_user_description, screen_name, cre-
ated_date, is_geo_located, user_location_loc, is_retweet, text, text_loc, user_id, hash, user_description,
linked_lang, linked_screen_name, user_location, totalCount, created_at, topic_tweet_id, topic, lang,
user_name, linked_text, tweet_id, linked_text_loc, hashtags, user_description_loc
See Also
search_loop
detect_loop
Examples
if(FALSE){
library(epitweetr)
df <- search_tweets(
setup_config 33
q = "vaccination",
topic="COVID-19",
countries=c("Chile", "Australia", "France"),
from = Sys.Date(),
to = Sys.Date()
)
df$text
}
setup_config Load epitweetr application settings
Description
Load epitweetr application settings from the designated data directory
Usage
setup_config(
data_dir = if (exists("data_dir", where = conf)) conf$data_dir else if
(Sys.getenv("EPI_HOME") != "") Sys.getenv("EPI_HOME") else file.path(getwd(),
"epitweetr"),
ignore_keyring = FALSE,
ignore_properties = FALSE,
ignore_topics = FALSE,
save_first = list()
)
Arguments
data_dir Path to the directory containing the application settings (it must exist). If not
provided it takes the value of the latest call to setup_config in the current ses-
sion, or the value of the EPI_HOME environment variable or epitweetr sub-
directory in the working directory, default: if (exists("data_dir", where = conf))
conf$data_dir else if (Sys.getenv("EPI_HOME") != "") Sys.getenv("EPI_HOME")
else file.path(getwd(), "epitweetr")
ignore_keyring Whether to skip loading settings from the keyring (Twitter and SMTP creden-
tials), default: FALSE
ignore_properties
Whether to skip loading settings managed by the Shiny app in properties.json
file, Default: FALSE
ignore_topics Whether to skip loading settings defined in the topics.xlsx file and download
plans from topics.json file, default: FALSE
save_first Whether to save current settings before loading new ones from disk, default:
list()
34 set_twitter_app_auth
Details
epitweetr relies on settings and data stored in a system folder, so before loading the dashboard,
collecting tweets or detecting alerts the user has to designate this folder. When a user wants to use
epitweetr from the R console they will need to call this function for initialisation. The ’data_folder’
can also be given as a parameter for program launch functions epitweetr_app, search_loop or
detect_loop, which will internally call this function.
This call will fill (or refresh) a package scoped environment ’conf’ that will store the settings.
Settings stored in conf are:
• General properties of the Shiny app (stored in properties.json)

• Download plans from the Twitter collection process (stored in topics.json merged with data
from the topics.xlsx file
• Credentials for Twitter API and SMTP stored in the defined keyring
When calling this function and the keyring is locked, a password will be prompted to unlock the
keyring. This behaviour can be changed by setting the environment variable ’ecdc_twitter_tool_kr_password’
with the password.
Changes made to conf can be stored permanently (except for ’data_dir’) using:
• save_config, or
• set_twitter_app_auth
Value
Nothing
See Also
save_config set_twitter_app_auth epitweetr_app search_loop detect_loop
Examples
if(FALSE){
library(epitweetr)
#loading system settings
}
set_twitter_app_auth Save Twitter App credentials
Description
Update Twitter authentication tokens in a configuration object
set_twitter_app_auth 35
Usage
set_twitter_app_auth(
app = "",
access_token = "",
access_token_secret = "",
api_key = "",
api_secret = "",
bearer = ""
)
Arguments
app Application name
access_token Access token as provided by Twitter
access_token_secret
Access token secret as provided by Twitter
api_key API key as provided by Twitter
api_secret API secret as provided by Twitter
bearer the bearer token of the application
Details
Update Twitter authentication tokens in configuration object
Value
Nothing
See Also
save_config
Examples
if(FALSE){
#Setting the configuration values
app = "my super app",
access_token = "123456",
access_token_secret = "123456",
api_key = "123456",
api_secret = "123456"
)
bearer = "123456"
)
}
36 stop_fs_runner_task
stop_detect_runner_task
Stops the alert detection task
Description
stops the alert detection task
Usage
stop_detect_runner_task()
Details
Stops the alert detection task if it is already running This function will try also deactivate the re-
spective scheduled task on Windows.
Value
Nothing
Examples
if(FALSE){
library(epitweetr)
stop_detect_runner_task()
}
stop_fs_runner_task Stops the epitweetr database task
Description
stops the epitweetr database task
Usage
stop_fs_runner_task()
Details
Stops the epitweetr database task if it is already running This function will try also deactivate the
respective scheduled task on Windows.
stop_search_runner_task 37
Value
Nothing
Examples
if(FALSE){
library(epitweetr)
stop_fs_runner_task()
}
stop_search_runner_task
Stops the tweet collection task
Description
stops the tweet collection task
Usage
stop_search_runner_task()
Details
Stops the tweet collection task if it is already running This function will try also deactivate the
respective scheduled task on Windows.
Value
Nothing
Examples
if(FALSE){
library(epitweetr)
stop_search_runner_task()
}
38 trend_line
trend_line Plot the trendline report of epitweetr dashboard
Description
Generates a trendline chart of number of tweets by region, for one topic, including alerts using the
reweighted version of the EARS algorithm
Usage
trend_line(
topic,
countries = c(1),
date_type = "created_date",
date_min = "1900-01-01",
date_max = "2100-01-01",
alpha = 0.025,
alpha_outlier = 0.05,
k_decay = 4,
no_historic = 7,
bonferroni_correction = FALSE,
same_weekday_baseline = FALSE
)
Arguments
countries Character vector containing the name of the countries and regions to plot or their
respective indexes on the Shiny app select, default: c(1)
date_type Character vector specifying the time granularity of the report either ’created_weeknum’
or ’created_date’, default: ’created_date’
FALSE
location_type Character(1) vector indicating the location type. Possible values ’tweet’, ’user’
or ’both’, default: ’tweet’
alpha Numeric(1) value indicating the alert detection confidence, default: 0.025
alpha_outlier Numeric(1) value indicating the outliers detection confidence for downweight-
ing, default: 0.05
k_decay Strength of outliers downweighting, default: 4
no_historic Number of observations to build the baseline for signal detection, default: 7
update_geonames 39
bonferroni_correction
Logical value indicating whether to apply the Bonferroni correction for signal
detection, default: FALSE
same_weekday_baseline
Logical value indicating whether to use same day of weeks for building the
baseline or consecutive days, default: FALSE
Details
Produces a multi-region line chart for a particular topic of number of tweets collected based on the
provided parameters. Alerts will be calculated using a modified version of the EARS algorithm that
applies a Farrington inspired downweighting of previous outliers.
Days in this function are considered as contiguous blocks of 24 hours starting for the previous hour
of the last collected tweet.
This function requires search_loop and detect_loop to have already run successfully to show
results.
Value
frame that was used to build the chart.
See Also
create_map create_topwords generate_alerts detect_loop search_loop
Examples
if(FALSE){
#Getting trendline for dengue for South America for the last 30 days
trend_line(
topic = "dengue",
countries = "South America",
)
}
update_geonames Updates the local copy of the GeoNames database
Description
Downloading and indexing a fresh version of the GeoNames database from the provided URL
40 update_geonames
Usage
update_geonames(tasks = get_tasks())
Arguments
tasks Tasks object for reporting progress and error messages, default: get_tasks()
Details
Run a one shot task to download and index a local copy of the GeoNames database. The GeoNames
geographical database covers all countries and contains over eleven million place names that are
available; Creative Commons Attribution 4.0 License.
The URL to download the database from is set on the configuration tab of the Shiny app, in case it
changes.
The indexing is developed in Spark and Lucene
A prerequisite to this function is that the search_loop must already have stored collected tweets in
the search folder and that the task download_dependencies has been successfully run.
Value
See Also
detect_loop
get_tasks
Examples
if(FALSE){
library(epitweetr)
# geolocating last tweets

tasks <- update_geonames()
}
update_languages 41
update_languages Updates local copies of languages
Description
Downloading and indexing a fresh version of language models tagged for update on the Shiny app
configuration tab
Usage
update_languages(tasks = get_tasks())
Arguments
tasks Tasks object for reporting progress and error messages, default: get_tasks()
Details
Run a one shot task to download and index a local fasttext pretrained models. A fasttext model is a
collection of vectors for a language automatically produced scrolling a big corpus of text that can
be used to capture the semantic of a word.
The URL to download the vectors from are set on the configuration tab of the Shiny app.
This task will also update SVM models to predict whether a word is a location that will be used in
the geolocation process.
The indexing is developed in SPARK and Lucene.
A prerequisite to this function is that the search_loop must already have stored collected tweets in
the search folder and that the tasks download_dependencies and update_geonames has been run
successfully.
Value
See Also
update_geonames
detect_loop
get_tasks
42 update_languages
Examples
if(FALSE){
library(epitweetr)
# updating language tasks

tasks <- update_languages()
}
Index
check_all, 3 search_loop, 4, 5, 7, 9, 14, 15, 30, 32, 34,

coordinates, 5 39–41
create_map, 3, 7, 9, 39 search_tweets, 31
create_snapshot, 5 set_twitter_app_auth, 29–31, 34, 34
create_topchart, 6 setup_config, 10, 13, 14, 30, 32, 33
create_topwords, 5, 8, 39 spTransform, 5
stop_detect_runner_task, 36
detect_loop, 4, 5, 7, 9, 9, 10, 11, 14–21, 32, stop_fs_runner_task, 36
34, 39–41 stop_search_runner_task, 37
download_dependencies, 10, 11, 17, 21, 22,
40, 41 trend_line, 5, 7, 9, 38
ears_t_reweighted, 12 update_geonames, 10, 17, 21, 22, 39, 41

epitweetr_app, 13, 34 update_languages, 10, 17, 21, 22, 41
fortify, 5
fs_loop, 14, 19
generate_alerts, 10, 15, 19–21, 39

geolocate_text, 16
geom_point, 5
geom_polygon, 5
get_aggregates, 18
get_alerts, 19
get_tasks, 10, 11, 21, 40, 41
get_todays_sample_tweets, 22
health_check, 14, 15, 23
is.projected, 5
is_detect_running, 24
is_fs_running, 24
is_search_running, 25
json2lucene, 25
register_detect_runner_task, 26
register_fs_monitor, 27
register_fs_runner_task, 28
register_search_runner_task, 28
save_config, 29, 34, 35
43

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Package ‘epitweetr’

Thomas Czernichow [ctb],

check_all Run automatic sanity checks

Data frame containing the statuses of all realized checks

create_map Plot the map report on the epitweetr dashboard

create_snapshot Snapshot of your epitweetr installation

create_topwords Plot the top words report on the epitweetr dashboard

trend_line create_map detect_loop search_loop

detect_loop Runs the detect loop

download_dependencies Updates Java dependencies

# geolocating last tweets

ears_t_reweighted algorithm for outbreak detection, extends the EARS algorithm

• proper computation of the prediction interval

epitweetr_app Run the epitweetr Shiny app

fs_loop Runs the epitweetr embedded database loop

generate_alerts Execute the alert task

The list of tasks updated with produced messages

geolocate_text(df, text_col = "text", lang_col = NULL, min_score = NULL)

# creating a test dataframe

get_aggregates Getting already aggregated time series produced by detect_loop

# Getting all country tweets for the topic dengue

get_alerts Getting signals produced by the task generate_alerts of

# Getting signals produced for last 30 days for a particular country

get_tasks Get the detect_loop task status

# geolocating today's tweets

health_check Send email to administrator if a failure of epitweetr is detected

is_detect_running Check whether the alert detection task is running

is_fs_running Check whether the database is running

is_search_running Check whether the tweet collection task is running

register_fs_monitor Registers the fs_monitor for the current process or exits

save_config Save the configuration changes

search_loop Runs the search loop

search_tweets perform full text search on tweets collected with epitweetr

to an object which can be converted to ‘"POSIXlt"’ only tweets posted before or

setup_config Load epitweetr application settings

• General properties of the Shiny app (stored in properties.json)

set_twitter_app_auth Save Twitter App credentials

stop_fs_runner_task Stops the epitweetr database task

trend_line Plot the trendline report of epitweetr dashboard

update_geonames Updates the local copy of the GeoNames database

The list of tasks updated with produced messages

# geolocating last tweets

update_languages Updates local copies of languages

The list of tasks updated with produced messages

# updating language tasks

check_all, 3 search_loop, 4, 5, 7, 9, 14, 15, 30, 32, 34,

ears_t_reweighted, 12 update_geonames, 10, 17, 21, 22, 39, 41

generate_alerts, 10, 15, 19–21, 39

health_check, 14, 15, 23

save_config, 29, 34, 35

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