Get started • motus

This is a quick introduction to downloading Motus data. Definitely check out the various articles for more details!

Let’s get started by loading the packages we’ll use (see also Chapter 2 - Installing packages.)

library(motus)
library(dplyr)
library(lubridate)

Now we’ll download some data. Here we’re downloading project 176 (sample data, use user name and password ‘motus.sample’). You can use your own project number or receiver name.

We use the tagme() function to download the data

sql_motus <- tagme(176, dir = "./data/")

## Checking for new data in project 176

## Updating metadata

## activity:     1 new batch records to check

## batchID  1977125 (#     1 of      1): got    156 activity records

## Downloaded 156 activity records

## nodeData:     0 new batch records to check

## Fetching deprecated batches

## Total deprecated batches: 6
## New deprecated batches: 0

tagme() includes several options. Here we’re using:

new = FALSE means the data base already exists, if it doesn’t, change FALSE to TRUE
dir = "./data/" means the data base will be stored in the data folder inside your current working directory

tagme() stores a project-176.motus SQLite data base in ./data/.

We can access parts of the data base by referencing the SQL object we created, sql_motus

Here, we’ll retrieve the alltags view from the SQLite database using the tbl() function from the dplyr package

tbl_alltags <- tbl(sql_motus, "alltags")

Next, we can convert this to a data frame (a flat file; see Converting to flat data in Chapter 3)

Convert to flat (collect()) and create a date/time column time from the numeric timestamps, ts.

df_alltags <- tbl_alltags %>%
  collect() %>%
  mutate(time = as_datetime(ts))

If you want to save this flat file, you can export as RDS (see Exporting detections in Chapter 3)

saveRDS(df_alltags, "my_motus_data.rds")

Use caution when producing a flat file as using the full suite of fields can use a lot of memory. This can slow R down considerably when dealing with large datasets.

Workflow summary

For your own data we suggest creating a script (or scripts) with the following workflow:

Download/update your data (see Chapter 2 - Installing packages, Chapter 3 - Accessing detections data)
Select variables of interest for the table you are working with (typically alltags) (see Chapter 3 - Accessing detections data, Chapter 4 - Tag and receiver deployments)
Initial cleaning (see Chapter 4 - Tag and receiver deployments and Chapter 5 - Data cleaning)
Output the resulting data as an .rds file (see Exporting detections in Chapter 3). We suggest using RDS instead of CSV, because the RDS format preserves the underlying structure of the data (e.g. times stay as times). If you want to export your data to another program, then a CSV format might be preferred.

What next? Check out the walkthrough starting with Chapter 1 - Introduction (Explore all articles)