Introduction

In cstidy: Helpful Functions for Cleaning Surveillance Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(data.table)
library(magrittr)

csfmt_rts_data_v1

csfmt_rts_data_v1 (vignette("csfmt_rts_data_v1", package = "cstidy")) is a data format for real-time surveillance.

d <- cstidy::generate_test_data()
cstidy::set_csfmt_rts_data_v1(d)

# Looking at the dataset
d[]

Smart assignment

csfmt_rts_data_v1 does smart assignment for time and geography.

When the variables in bold are assigned using :=, the listed variables will be automatically imputed.

location_code:

• granularity_geo
• country_iso3

isoyear:

• granularity_time
• isoweek
• isoyearweek
• season
• seasonweek
• calyear
• calmonth
• calyearmonth
• date

isoyearweek:

• granularity_time
• isoyear
• isoweek
• season
• seasonweek
• calyear
• calmonth
• calyearmonth
• date

date:

• granularity_time
• isoyear
• isoweek
• isoyearweek
• season
• seasonweek
• calyear
• calmonth
• calyearmonth

d <- cstidy::generate_test_data()[1:5]
cstidy::set_csfmt_rts_data_v1(d)

# Looking at the dataset
d[]

# Smart assignment of time columns (note how granularity_time, isoyear, isoyearweek, date all change)
d[1,isoyearweek := "2021-01"]
d

# Smart assignment of time columns (note how granularity_time, isoyear, isoyearweek, date all change)
d[2,isoyear := 2019]
d

# Smart assignment of time columns (note how granularity_time, isoyear, isoyearweek, date all change)
d[4:5,date := as.Date("2020-01-01")]
d

# Smart assignment fails when multiple time columns are set
d[1,c("isoyear","isoyearweek") := .(2021,"2021-01")]
d

# Smart assignment of geo columns
d[1,c("location_code") := .("norge")]
d

# Collapsing down to different levels, and healing the dataset 
# (so that it can be worked on further with regards to real time surveillance)
d[, .(deaths_n = sum(deaths_n), location_code = "norge"), keyby=.(granularity_time)] %>%
  cstidy::set_csfmt_rts_data_v1(create_unified_columns = FALSE) %>%
  print()

# Collapsing to different levels, and removing the class csfmt_rts_data_v1 because
# it is going to be used in new output/analyses
d[, .(deaths_n = sum(deaths_n), location_code = "norge"), keyby=.(granularity_time)] %>%
  cstidy::remove_class_csfmt_rts_data() %>%
  print()

Summary

We need a way to easily summarize the data structure of a dataset.

cstidy::generate_test_data() %>%
  cstidy::set_csfmt_rts_data_v1() %>%
  summary()

Identifying data structure of one column

We need a way to easily summarize the data structure of one column inside a dataset.

cstidy::generate_test_data() %>%
  cstidy::set_csfmt_rts_data_v1() %>%
  cstidy::identify_data_structure("deaths_n") %>%
  plot()

cstidy documentation built on May 31, 2023, 7:25 p.m.