Add aware_influxdb in beta
JulioV
parent
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commit
42cee67664
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@ -54,6 +54,10 @@ PHONE_DATA_STREAMS:
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aware_csv:
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FOLDER: data/external/aware_csv
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aware_influxdb:
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DATABASE_GROUP: MY_GROUP
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# Sensors ------
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# https://www.rapids.science/latest/features/phone-accelerometer/
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@ -4,7 +4,7 @@
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- Add a new [Overview](../setup/overview/) page.
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- You can [extend](../datastreams/add-new-data-streams/) RAPIDS with your own [data streams](../datastreams/data-streams-introduction/). Data streams are data collected with other sensing apps besides AWARE (like Beiwe, mindLAMP), and stored in other data containers (databases, files) besides MySQL.
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- Support to analyze Empatica wearable data (thanks to Joe Kim and Brinnae Bent from the [DBDP](https://dbdp.org/))
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- Support to analyze AWARE data stored in [CSV files](../datastreams/aware-csv/) and InfluxDB databases (the latter thanks to Neil Singh)
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- Support to analyze AWARE data stored in [CSV files](../datastreams/aware-csv/) and [InfluxDB](../datastreams/aware-influxdb/) databases (the latter thanks to Neil Singh)
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- Support to analyze data collected over [multiple time zones](../setup/configuration/#multiple-timezones)
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- Support for [sleep intraday features](../features/fitbit-sleep-intraday/) from the core team and also from the community (thanks to Stephen Price)
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- Add RAPIDS new logo
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@ -0,0 +1,18 @@
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# `aware_influxdb (beta)`
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!!! warning
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This data stream is being released in beta while we test it thoroughly.
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This [data stream](../../datastreams/data-streams-introduction) handles iOS and Android sensor data collected with the [AWARE Framework](https://awareframework.com/) and stored in an InfluxDB database.
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## Container
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An InfluxDB database with a table per sensor, each containing the data for all participants.
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The script to connect and download data from this container is at:
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```bash
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src/data/streams/aware_influxdb/container.R
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```
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## Format
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--8<---- "docs/snippets/aware_format.md"
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@ -6,7 +6,7 @@ For example, the `aware_mysql` data stream handles smartphone data (**device**)
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If you want to process a data stream using RAPIDS, make sure that your data is stored in a supported **format** and **container** (see table below).
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If RAPIDS doesn't support your data stream yet (e.g. Beiwe data stored in PostgreSQL, or AWARE data stored in InfluxDB), you can always [implement a new data stream](../add-new-data-streams). If it's something you think other people might be interested on, we will be happy to include your new data stream in RAPIDS, so get in touch!.
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If RAPIDS doesn't support your data stream yet (e.g. Beiwe data stored in PostgreSQL, or AWARE data stored in SQLite), you can always [implement a new data stream](../add-new-data-streams). If it's something you think other people might be interested on, we will be happy to include your new data stream in RAPIDS, so get in touch!.
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!!! hint
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Currently, you can add new data streams for smartphones, Fitbit, and Empatica devices. If you need RAPIDS to process data from **other devices**, like Oura Rings or Actigraph wearables, get in touch. It is a more complicated process that could take a couple of days to implement for someone familiar with R or Python, but we would be happy to work on it together.
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@ -17,6 +17,7 @@ For reference, these are the data streams we currently support:
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|--|--|--|--|--|
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| `aware_mysql`| Phone | AWARE app | MySQL | [link](../aware-mysql)
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| `aware_csv`| Phone | AWARE app | CSV files | [link](../aware-csv)
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| `aware_influxdb` (beta)| Phone | AWARE app | InfluxDB | [link](../aware-influxdb)
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| `fitbitjson_mysql`| Fitbit | JSON (per [Fitbit's API](https://dev.fitbit.com/build/reference/web-api/)) | MySQL | [link](../fitbitjson-mysql)
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| `fitbitjson_csv`| Fitbit | JSON (per [Fitbit's API](https://dev.fitbit.com/build/reference/web-api/)) | CSV files | [link](../fitbitjson-csv)
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| `fitbitparsed_mysql`| Fitbit | Parsed (parsed API data) | MySQL | [link](../fitbitparsed-mysql)
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@ -84,6 +84,7 @@ nav:
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- Phone:
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- aware_mysql: datastreams/aware-mysql.md
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- aware_csv: datastreams/aware-csv.md
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- aware_influxdb (beta): datastreams/aware-influxdb.md
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- Mandatory Phone Format: datastreams/mandatory-phone-format.md
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- Fitbit:
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- fitbitjson_mysql: datastreams/fitbitjson-mysql.md
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@ -0,0 +1,104 @@
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# if you need a new package, you should add it with renv::install(package) so your renv venv is updated
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library(influxdbr)
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library(tidyverse)
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library(yaml)
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#' @description
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#' Auxiliary function to parse the connection credentials from a specifc group in ./credentials.yaml
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#' You can reause most of this function if you are connection to a DB or Web API.
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#' It's OK to delete this function if you don't need credentials, e.g., you are pulling data from a CSV for example.
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#' @param group the yaml key containing the credentials to connect to a database
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#' @preturn dbEngine a database engine (connection) ready to perform queries
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get_db_engine <- function(group){
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# The working dir is aways RAPIDS root folder, so your credentials file is always /credentials.yaml
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credentials <- read_yaml("./credentials.yaml")
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if(!group %in% names(credentials))
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stop(paste("The credentials group",group, "does not exist in ./credentials.yaml. The only groups that exist in that file are:", paste(names(credentials), collapse = ",")))
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#replace with credentials values
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conn_object <- influx_connection(host=credentials[[group]][["host"]],
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user=credentials[[group]][["user"]],
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pass=credentials[[group]][["password"]],
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port= credentials[[group]][["port"]])
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return(conn_object)
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}
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# This file gets executed for each PHONE_SENSOR of each participant
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# If you are connecting to a database the env file containing its credentials is available at "./.env"
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# If you are reading a CSV file instead of a DB table, the @param sensor_container wil contain the file path as set in config.yaml
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# You are not bound to databases or files, you can query a web API or whatever data source you need.
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#' @description
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#' RAPIDS allows users to use the keyword "infer" (previously "multiple") to automatically infer the mobile Operative System a device was running.
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#' If you have a way to infer the OS of a device ID, implement this function. For example, for AWARE data we use the "aware_device" table.
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#'
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#' If you don't have a way to infer the OS, call stop("Error Message") so other users know they can't use "infer" or the inference failed,
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#' and they have to assign the OS manually in the participant file
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#'
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#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
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#' @param device A device ID string
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#' @return The OS the device ran, "android" or "ios"
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infer_device_os <- function(stream_parameters, device){
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dbEngine <- get_db_engine(stream_parameters$SOURCE$DATABASE_GROUP)
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#need to re-fetch the YAML for the DB name
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credentials <- read_yaml("./credentials.yaml")
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message(paste0("Utilizing the Influx query for: ", device))
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#execute query string
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query_object <- influx_select(dbEngine,
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db = credentials[[stream_parameters$SOURCE$DATABASE_GROUP]][["database"]],
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field_keys="device_id,brand",
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measurement="aware_device",
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where= paste0("device_id = '",device,"'"),
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return_xts = FALSE)
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#fetches the table from the query_object, filtering rows with ALL n/a
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#a behavior of influxdbr is that one all NA row will be returned with no matches
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os <- query_object[[1]] %>% filter_all(any_vars(!is.na(.))) %>% select(c('device_id','brand','time'))
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if(nrow(os) > 0)
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return(os %>% mutate(os = ifelse(brand == "iPhone", "ios", "android")) %>% pull(os))
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else
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stop(paste("We cannot infer the OS of the following device id because it does not exist in the aware_device table:", device))
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return(os)
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}
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#' @description
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#' Gets the sensor data for a specific device id from a database table, file or whatever source you want to query
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#'
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#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
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#' @param device A device ID string
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#' @param sensor_container database table or file containing the sensor data for all participants. This is the PHONE_SENSOR[CONTAINER] key in config.yaml
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#' @param columns the columns needed from this sensor (we recommend to only return these columns instead of every column in sensor_container)
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#' @return A dataframe with the sensor data for device
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pull_data <- function(stream_parameters, device, sensor, sensor_container, columns){
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dbEngine <- get_db_engine(stream_parameters$SOURCE$DATABASE_GROUP)
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#need to re-fetch the YAML for the DB name
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credentials <- read_yaml("./credentials.yaml")
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# Letting the user know what we are doing
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message(paste0("Executing an Influx query for: ", device, " ", sensor, ". Extracting ", columns, " from ", sensor_container))
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#execute query string
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query_object <- influx_select(dbEngine,
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db = credentials[[stream_parameters$SOURCE$DATABASE_GROUP]][["database"]],
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field_keys=paste(columns, collapse = ","),
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measurement=sensor_container,
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where= paste0(columns$DEVICE_ID, " = '",device,"'"),
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return_xts=FALSE)
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#fetches the table from the query_object, filtering rows with ALL n/a
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#a behavior of influxdbr is that one all NA row will be returned with no matches
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sensor_data <- query_object[[1]] %>% filter_all(any_vars(!is.na(.))) %>% select(c('time',columns))
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if(nrow(sensor_data) == 0)
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warning(paste("The device '", device,"' did not have data in ", sensor_container))
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return(sensor_data)
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}
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@ -0,0 +1,315 @@
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PHONE_ACCELEROMETER:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_VALUES_0: double_values_0
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DOUBLE_VALUES_1: double_values_1
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DOUBLE_VALUES_2: double_values_2
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_VALUES_0: double_values_0
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DOUBLE_VALUES_1: double_values_1
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DOUBLE_VALUES_2: double_values_2
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_ACTIVITY_RECOGNITION:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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ACTIVITY_NAME: activity_name
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ACTIVITY_TYPE: activity_type
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CONFIDENCE: confidence
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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ACTIVITY_NAME: FLAG_TO_MUTATE
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ACTIVITY_TYPE: FLAG_TO_MUTATE
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CONFIDENCE: FLAG_TO_MUTATE
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MUTATION:
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COLUMN_MAPPINGS:
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ACTIVITIES: activities
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CONFIDENCE: confidence
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SCRIPTS: # List any python or r scripts that mutate your raw data
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- "src/data/streams/mutations/phone/aware/activity_recogniton_ios_unification.R"
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PHONE_APPLICATIONS_CRASHES:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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PACKAGE_NAME: package_name
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APPLICATION_NAME: application_name
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APPLICATION_VERSION: application_version
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ERROR_SHORT: error_short
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ERROR_LONG: error_long
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ERROR_CONDITION: error_condition
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IS_SYSTEM_APP: is_system_app
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_APPLICATIONS_FOREGROUND:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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PACKAGE_NAME: package_name
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APPLICATION_NAME: application_name
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IS_SYSTEM_APP: is_system_app
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_APPLICATIONS_NOTIFICATIONS:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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PACKAGE_NAME: package_name
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APPLICATION_NAME: application_name
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TEXT: text
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SOUND: sound
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VIBRATE: vibrate
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DEFAULTS: defaults
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FLAGS: flags
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_BATTERY:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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BATTERY_STATUS: battery_status
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BATTERY_LEVEL: battery_level
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BATTERY_SCALE: battery_scale
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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BATTERY_STATUS: FLAG_TO_MUTATE
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BATTERY_LEVEL: battery_level
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BATTERY_SCALE: battery_scale
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MUTATION:
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COLUMN_MAPPINGS:
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BATTERY_STATUS: battery_status
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SCRIPTS:
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- "src/data/streams/mutations/phone/aware/battery_ios_unification.R"
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PHONE_BLUETOOTH:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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BT_ADDRESS: bt_address
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BT_NAME: bt_name
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BT_RSSI: bt_rssi
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_CALLS:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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CALL_TYPE: call_type
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CALL_DURATION: call_duration
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TRACE: trace
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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CALL_TYPE: FLAG_TO_MUTATE
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CALL_DURATION: call_duration
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TRACE: trace
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MUTATION:
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COLUMN_MAPPINGS:
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CALL_TYPE: call_type
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SCRIPTS:
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- "src/data/streams/mutations/phone/aware/calls_ios_unification.R"
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PHONE_CONVERSATION:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_ENERGY: double_energy
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INFERENCE: inference
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DOUBLE_CONVO_START: double_convo_start
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DOUBLE_CONVO_END: double_convo_end
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_ENERGY: double_energy
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INFERENCE: inference
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DOUBLE_CONVO_START: double_convo_start
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DOUBLE_CONVO_END: double_convo_end
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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- "src/data/streams/mutations/phone/aware/conversation_ios_timestamp.R"
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PHONE_KEYBOARD:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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PACKAGE_NAME: package_name
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BEFORE_TEXT: before_text
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CURRENT_TEXT: current_text
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IS_PASSWORD: is_password
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_LIGHT:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_LIGHT_LUX: double_light_lux
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ACCURACY: accuracy
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_LOCATIONS:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_LATITUDE: double_latitude
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DOUBLE_LONGITUDE: double_longitude
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DOUBLE_BEARING: double_bearing
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DOUBLE_SPEED: double_speed
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DOUBLE_ALTITUDE: double_altitude
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PROVIDER: provider
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ACCURACY: accuracy
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_LATITUDE: double_latitude
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DOUBLE_LONGITUDE: double_longitude
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DOUBLE_BEARING: double_bearing
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DOUBLE_SPEED: double_speed
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DOUBLE_ALTITUDE: double_altitude
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PROVIDER: provider
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ACCURACY: accuracy
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_LOG:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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LOG_MESSAGE: log_message
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
IOS:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
LOG_MESSAGE: log_message
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
|
||||
PHONE_MESSAGES:
|
||||
ANDROID:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
MESSAGE_TYPE: message_type
|
||||
TRACE: trace
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
|
||||
PHONE_SCREEN:
|
||||
ANDROID:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
SCREEN_STATUS: screen_status
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
IOS:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
SCREEN_STATUS: FLAG_TO_MUTATE
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCREEN_STATUS: screen_status
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
- "src/data/streams/mutations/phone/aware/screen_ios_unification.R"
|
||||
|
||||
PHONE_WIFI_CONNECTED:
|
||||
ANDROID:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
MAC_ADDRESS: mac_address
|
||||
SSID: ssid
|
||||
BSSID: bssid
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
IOS:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
MAC_ADDRESS: mac_address
|
||||
SSID: ssid
|
||||
BSSID: bssid
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
|
||||
PHONE_WIFI_VISIBLE:
|
||||
ANDROID:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
SSID: ssid
|
||||
BSSID: bssid
|
||||
SECURITY: security
|
||||
FREQUENCY: frequency
|
||||
RSSI: rssi
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
|
||||
Loading…
Reference in New Issue