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Annotate vaccines

annotate_vaccines.Rmd

Introduction

The chronogram package provides a family of functions to annotate a chronogram. These all start cg_annotate_. This vignette explains how to use these annotation functions. Before using this vignette, consult the vignette("assembly").

Setup 

library(chronogram)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(ggplot2)
library(patchwork)

We will use the example pre-built chronogram, introduced in the vignette("assembly"), and add on some example infection data.

data(built_smallstudy)
cg <- built_smallstudy$chronogram
infections_to_add <-  built_smallstudy$infections_to_add

## add to chronogram
cg <- cg_add_experiment(
  cg,
  infections_to_add
)

Vaccine annotation

Annotation is required to allow the selection sub-cohorts of individuals (and corresponding dates) that are relevant to test your biological hypothesis.

For vaccines, use cg_annotate_vaccines_count()

– adds a column which counts the number of vaccines each participant has received over time.

– includes a “star” system, to allow the first few days after a vaccine to be easily identified. For example, 24hrs after the first dose of a vaccine (“1star”) is probably not biologically reflect of that dose’s effect. The user can set the value of days to “star” to suit their analysis.

cg_annotate_vaccines_count() requires that metadata columns follow this pattern:

  • dose_1, dose_2, dose_3, …, dose_i

  • date_dose_1, date_dose_2, date_dose_3, …, date_dose_i

The trailing digit reflects the dose number for both dose_i and date_dose_i.

The {dose} and {date_dose} prefixes should be provided to the function, as shown in the chunk below. You might envisage a study with {sarscov2_dose}, {sarscov2_date_dose}, {influenza_dose} & {influenza_date_dose} for which two runs of cg_annotate_vaccines_count() would be needed.

Worked example 

cg <- cg_annotate_vaccines_count(
  cg,
  ## the prefix to the dose columns: ##
  dose = dose,
  ## the output column name: ##
  dose_counter = dose_number,
  ## the prefix to the date columns: ##
  vaccine_date_stem = date_dose,
  ## use 14d to 'star' after a dose ##
  intermediate_days = 14
)
#> Using stem: date_dose
#> Found vaccine dates
#> date_dose_1
#> 
#> date_dose_2

## plot over time ##
cg %>%
  ggplot(
    aes(
      x = calendar_date,
      y = elig_study_id,
      fill = dose_number
    )
  ) +
  geom_tile(height = 0.5) +
  scale_fill_grey(end = 0.2, start = 0.8) +
  theme_bw()

In the above plot, the character vector dose_number is coerced to a factor. The resulting levels of the factor are counter-intuitive. To improve the plot, you can manually specify the factor:

cg %>%
  mutate(dose_number = factor(dose_number,
    levels = c(
      "0",
      "1star",
      "1",
      "2star",
      "2"
    )
  )) %>%
  ggplot(
    aes(
      x = calendar_date,
      y = elig_study_id,
      fill = dose_number
    )
  ) +
  geom_tile(height = 0.5) +
  scale_fill_grey(end = 0.2, start = 0.8) +
  theme_bw()

The dose_number column is intentionally returned to cg as character vector rather than converting to a factor. There is the possibility for mishandling if a factor: as.numeric(dose_number) == 1, refers to the situation dose == 0, and as.numeric(dose_number) == 2, refers to the situation dose == 1.

Summary

This vignette has provided examples of the cg_annotate family in action. If you are conducting a multi-pathogen study (RSV, flu, covid), then run a set of cg_annotate family functions for each pathogen - and you may wish to prefix the output columns eg RSV_, flu_ & covid_.

SessionInfo 

sessionInfo()
#> R version 4.4.1 (2024-06-14)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] patchwork_1.2.0  ggplot2_3.5.1    dplyr_1.1.4      chronogram_1.0.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] gtable_0.3.5      jsonlite_1.8.8    highr_0.11        compiler_4.4.1   
#>  [5] tidyselect_1.2.1  stringr_1.5.1     tidyr_1.3.1       jquerylib_0.1.4  
#>  [9] systemfonts_1.1.0 scales_1.3.0      textshaping_0.4.0 yaml_2.3.10      
#> [13] fastmap_1.2.0     R6_2.5.1          generics_0.1.3    knitr_1.48       
#> [17] tibble_3.2.1      desc_1.4.3        munsell_0.5.1     lubridate_1.9.3  
#> [21] bslib_0.8.0       pillar_1.9.0      rlang_1.1.4       utf8_1.2.4       
#> [25] stringi_1.8.4     cachem_1.1.0      xfun_0.46         fs_1.6.4         
#> [29] sass_0.4.9        timechange_0.3.0  cli_3.6.3         pkgdown_2.1.0    
#> [33] withr_3.0.1       magrittr_2.0.3    digest_0.6.36     grid_4.4.1       
#> [37] lifecycle_1.0.4   vctrs_0.6.5       evaluate_0.24.0   glue_1.7.0       
#> [41] farver_2.1.2      ragg_1.3.2        fansi_1.0.6       colorspace_2.1-1 
#> [45] purrr_1.0.2       rmarkdown_2.27    tools_4.4.1       pkgconfig_2.0.3  
#> [49] htmltools_0.5.8.1