Getting started with getTBinR

Sam Abbott

2018-05-16

Using the package

First load the package. We also load several other packages to help quickly explore the data.

library(getTBinR)
library(ggplot2)
library(knitr)
library(magrittr)
library(dplyr)

Getting TB burden data

Get TB burden data with a single function call. This will download the data if it has never been accessed and then save a local copy to R’s temporary directory (see tempdir()). If a local copy exists from the current seesion then this will be loaded instead.

tb_burden <- get_tb_burden()
#> Loading data from: /tmp/Rtmp96NayL/TB_burden.rds
#> Loading data from: /tmp/Rtmp96NayL/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Joining, by = c("country", "iso2", "iso3", "iso_numeric", "year")

tb_burden
#> # A tibble: 3,634 x 91
#>    country  iso2  iso3  iso_numeric g_whoregion  year e_pop_num e_inc_100k
#>    <chr>    <chr> <chr>       <int> <chr>       <int>     <int>      <dbl>
#>  1 Afghani… AF    AFG             4 Eastern Me…  2000  20093756        190
#>  2 Afghani… AF    AFG             4 Eastern Me…  2001  20966463        189
#>  3 Afghani… AF    AFG             4 Eastern Me…  2002  21979923        189
#>  4 Afghani… AF    AFG             4 Eastern Me…  2003  23064851        189
#>  5 Afghani… AF    AFG             4 Eastern Me…  2004  24118979        189
#>  6 Afghani… AF    AFG             4 Eastern Me…  2005  25070798        189
#>  7 Afghani… AF    AFG             4 Eastern Me…  2006  25893450        189
#>  8 Afghani… AF    AFG             4 Eastern Me…  2007  26616792        189
#>  9 Afghani… AF    AFG             4 Eastern Me…  2008  27294031        189
#> 10 Afghani… AF    AFG             4 Eastern Me…  2009  28004331        189
#> # ... with 3,624 more rows, and 83 more variables: e_inc_100k_lo <dbl>,
#> #   e_inc_100k_hi <dbl>, e_inc_num <int>, e_inc_num_lo <int>,
#> #   e_inc_num_hi <int>, e_inc_num_f014 <int>, e_inc_num_f014_lo <int>,
#> #   e_inc_num_f014_hi <int>, e_inc_num_f15plus <int>,
#> #   e_inc_num_f15plus_lo <int>, e_inc_num_f15plus_hi <int>,
#> #   e_inc_num_f <int>, e_inc_num_f_lo <int>, e_inc_num_f_hi <int>,
#> #   e_inc_num_m014 <int>, e_inc_num_m014_lo <int>,
#> #   e_inc_num_m014_hi <int>, e_inc_num_m15plus <int>,
#> #   e_inc_num_m15plus_lo <int>, e_inc_num_m15plus_hi <int>,
#> #   e_inc_num_m <int>, e_inc_num_m_lo <int>, e_inc_num_m_hi <int>,
#> #   e_inc_num_014 <int>, e_inc_num_014_lo <int>, e_inc_num_014_hi <int>,
#> #   e_inc_num_15plus <int>, e_inc_num_15plus_lo <int>,
#> #   e_inc_num_15plus_hi <int>, e_tbhiv_prct <dbl>, e_tbhiv_prct_lo <dbl>,
#> #   e_tbhiv_prct_hi <dbl>, e_inc_tbhiv_100k <dbl>,
#> #   e_inc_tbhiv_100k_lo <dbl>, e_inc_tbhiv_100k_hi <dbl>,
#> #   e_inc_tbhiv_num <int>, e_inc_tbhiv_num_lo <int>,
#> #   e_inc_tbhiv_num_hi <int>, e_mort_exc_tbhiv_100k <dbl>,
#> #   e_mort_exc_tbhiv_100k_lo <dbl>, e_mort_exc_tbhiv_100k_hi <dbl>,
#> #   e_mort_exc_tbhiv_num <int>, e_mort_exc_tbhiv_num_lo <int>,
#> #   e_mort_exc_tbhiv_num_hi <int>, e_mort_tbhiv_100k <dbl>,
#> #   e_mort_tbhiv_100k_lo <dbl>, e_mort_tbhiv_100k_hi <dbl>,
#> #   e_mort_tbhiv_num <int>, e_mort_tbhiv_num_lo <int>,
#> #   e_mort_tbhiv_num_hi <int>, e_mort_100k <dbl>, e_mort_100k_lo <dbl>,
#> #   e_mort_100k_hi <dbl>, e_mort_num <int>, e_mort_num_lo <int>,
#> #   e_mort_num_hi <int>, cfr <dbl>, cfr_lo <dbl>, cfr_hi <dbl>,
#> #   c_newinc_100k <dbl>, c_cdr <dbl>, c_cdr_lo <dbl>, c_cdr_hi <dbl>,
#> #   source_rr_new <chr>, source_drs_coverage_new <chr>,
#> #   source_drs_year_new <chr>, e_rr_pct_new <dbl>, e_rr_pct_new_lo <dbl>,
#> #   e_rr_pct_new_hi <dbl>, e_mdr_pct_rr_new <int>, source_rr_ret <chr>,
#> #   source_drs_coverage_ret <chr>, source_drs_year_ret <chr>,
#> #   e_rr_pct_ret <dbl>, e_rr_pct_ret_lo <dbl>, e_rr_pct_ret_hi <dbl>,
#> #   e_mdr_pct_rr_ret <int>, e_inc_rr_num <int>, e_inc_rr_num_lo <int>,
#> #   e_inc_rr_num_hi <int>, e_rr_in_notified_pulm <int>,
#> #   e_rr_in_notified_pulm_lo <int>, e_rr_in_notified_pulm_hi <int>

Searching for variable definitions

The WHO provides a large, detailed, data dictionary for use with the TB burden data. However, searching through this dataset can be tedious. To streamline this process getTBinR provides a search function to find the definition of a single or multiple variables. Again if not previously used this function will download the data dictionary to the temporary directory, but in subsequent uses will load a local copy.

vars_of_interest <- search_data_dict(var = c("country",
                                             "e_inc_100k",
                                             "e_inc_100k_lo",
                                             "e_inc_100k_hi"))
#> Loading data from: /tmp/Rtmp96NayL/TB_data_dict.rds
#> 4 results found for your variable search for country, e_inc_100k, e_inc_100k_lo, e_inc_100k_hi

knitr::kable(vars_of_interest)
variable_name dataset code_list definition
country Country identification Country or territory name
e_inc_100k Estimates Estimated incidence (all forms) per 100 000 population
e_inc_100k_hi Estimates Estimated incidence (all forms) per 100 000 population, high bound
e_inc_100k_lo Estimates Estimated incidence (all forms) per 100 000 population, low bound

We might also want to search the variable definitions for key phrases, for example mortality.

defs_of_interest <- search_data_dict(def = c("mortality"))
#> Loading data from: /tmp/Rtmp96NayL/TB_data_dict.rds
#> 9 results found for your definition search for mortality

knitr::kable(defs_of_interest)
variable_name dataset code_list definition
e_mort_100k Estimates Estimated mortality of TB cases (all forms) per 100 000 population
e_mort_100k_hi Estimates Estimated mortality of TB cases (all forms) per 100 000 population, high bound
e_mort_100k_lo Estimates Estimated mortality of TB cases (all forms) per 100 000 population, low bound
e_mort_exc_tbhiv_100k Estimates Estimated mortality of TB cases (all forms, excluding HIV) per 100 000 population
e_mort_exc_tbhiv_100k_hi Estimates Estimated mortality of TB cases (all forms, excluding HIV), per 100 000 population, high bound
e_mort_exc_tbhiv_100k_lo Estimates Estimated mortality of TB cases (all forms, excluding HIV), per 100 000 population, low bound
e_mort_tbhiv_100k Estimates Estimated mortality of TB cases who are HIV-positive, per 100 000 population
e_mort_tbhiv_100k_hi Estimates Estimated mortality of TB cases who are HIV-positive, per 100 000 population, high bound
e_mort_tbhiv_100k_lo Estimates Estimated mortality of TB cases who are HIV-positive, per 100 000 population, low bound

Finally we could both search for a known variable and for key phrases in variable definitions.

vars_defs_of_interest <- search_data_dict(var = c("country"),
                                     def = c("mortality"))
#> Loading data from: /tmp/Rtmp96NayL/TB_data_dict.rds
#> 1 results found for your variable search for country
#> 9 results found for your definition search for mortality

knitr::kable(vars_defs_of_interest)
variable_name dataset code_list definition
country Country identification Country or territory name
e_mort_100k Estimates Estimated mortality of TB cases (all forms) per 100 000 population
e_mort_100k_hi Estimates Estimated mortality of TB cases (all forms) per 100 000 population, high bound
e_mort_100k_lo Estimates Estimated mortality of TB cases (all forms) per 100 000 population, low bound
e_mort_exc_tbhiv_100k Estimates Estimated mortality of TB cases (all forms, excluding HIV) per 100 000 population
e_mort_exc_tbhiv_100k_hi Estimates Estimated mortality of TB cases (all forms, excluding HIV), per 100 000 population, high bound
e_mort_exc_tbhiv_100k_lo Estimates Estimated mortality of TB cases (all forms, excluding HIV), per 100 000 population, low bound
e_mort_tbhiv_100k Estimates Estimated mortality of TB cases who are HIV-positive, per 100 000 population
e_mort_tbhiv_100k_hi Estimates Estimated mortality of TB cases who are HIV-positive, per 100 000 population, high bound
e_mort_tbhiv_100k_lo Estimates Estimated mortality of TB cases who are HIV-positive, per 100 000 population, low bound

Mapping Global Incidence Rates

To start exploring the WHO TB data we map global TB incidence rates in 2016. Mapping data can help identify spatial patterns.

getTBinR::map_tb_burden(metric = "e_inc_100k",
                        year = 2016)
#> Loading data from: /tmp/Rtmp96NayL/TB_burden.rds
#> Loading data from: /tmp/Rtmp96NayL/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Joining, by = c("country", "iso2", "iso3", "iso_numeric", "year")
#> Loading data from: /tmp/Rtmp96NayL/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k
#> Warning: Removed 12 rows containing missing values (geom_path).

Plotting Incidence Rates for All Countries

To showcase how quickly we can go from no data to plotting informative graphs we quickly explore incidence rates for all countries in the WHO data.

getTBinR::plot_tb_burden_overview(metric = "e_inc_100k",
                                  interactive = FALSE)
#> Loading data from: /tmp/Rtmp96NayL/TB_burden.rds
#> Loading data from: /tmp/Rtmp96NayL/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Joining, by = c("country", "iso2", "iso3", "iso_numeric", "year")
#> Loading data from: /tmp/Rtmp96NayL/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k

Another way to compre incidence rates in countries is to look at the annual percentage change (currently only available in the development version of the package). The plot below only shows countries with a maximum incidence rate above 5 per 100,000.

higher_burden_countries <- tb_burden %>% 
  group_by(country) %>% 
  summarise(e_inc_100k = min(e_inc_100k)) %>% 
  filter(e_inc_100k > 5) %>% 
  pull(country) %>% 
  unique

getTBinR::plot_tb_burden_overview(metric = "e_inc_100k",
                                  interactive = FALSE,
                                  annual_change = TRUE,
                                  countries = higher_burden_countries)
#> Loading data from: /tmp/Rtmp96NayL/TB_burden.rds
#> Loading data from: /tmp/Rtmp96NayL/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Joining, by = c("country", "iso2", "iso3", "iso_numeric", "year")
#> Loading data from: /tmp/Rtmp96NayL/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k