Constants

The data are in this folder:

onedrive <- "~/Library/CloudStorage/OneDrive-OxfordUniversityClinicalResearchUnit/"

Packages

library(readr)

Functions

hist2 <- function(..., col = 4, n = 100, alpha = .2, main = NA) {
  hist(..., n = n, main = main, col = adjustcolor(col, alpha), border = col,
       ylab = "frequency")
}

Loading the data

st <- read_csv(paste0(onedrive, "GitHub/OUCRU-Modelling/scrub-typhus/Rickettsia_ELISA.csv"))

The data look like this:

st
## # A tibble: 1,037 × 14
##      No. SAMPLE_ID AGE_MIN AGE_MAX GENDER   DAY MONTH  YEAR  WARD E_Day E_Month
##    <dbl> <chr>       <dbl>   <dbl>  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>   <dbl>
##  1     1 HC040033      1.5     1.5      1    23     2  2010    11    11      12
##  2     2 HC040048      0.5     0.5      0    26     2  2010    11    11      12
##  3     3 HC040078     27      28.0      0     3     2  2010    11    11      12
##  4     4 HC040144     45      46.0      0     4     2  2010    11    11      12
##  5     5 HC040146     47      48.0      0     4     2  2010    11    11      12
##  6     6 HC050055     29      30.0      0     3     3  2010    11    11      12
##  7     7 HC050074     22      23.0      0    18     3  2010    11    11      12
##  8     8 HC050086     28.2    29.2      1    25     3  2010    11    11      12
##  9     9 HC050151     53      54.0      1    16     3  2010    11    11      12
## 10    10 HC050157     56      57.0      0    17     3  2010    11    11      12
## # ℹ 1,027 more rows
## # ℹ 3 more variables: E_Year <dbl>, Scrub_Typhus <dbl>, Typhus <dbl>

The last 3 variables:

st[, 12:14]
## # A tibble: 1,037 × 3
##    E_Year Scrub_Typhus Typhus
##     <dbl>        <dbl>  <dbl>
##  1   2017        0.011  0.215
##  2   2017        0.006  0.21 
##  3   2017        0.097  0.163
##  4   2017        0.081  0.18 
##  5   2017        0.053  0.504
##  6   2017       -0.033  0.132
##  7   2017        0.473  0.152
##  8   2017        0.058  0.261
##  9   2017       -0.002  0.016
## 10   2017        0.033  0.432
## # ℹ 1,027 more rows

Analysis

hist2(st$Scrub_Typhus, xlab = "value", main = "scrub typhus")

hist2(st$Typhus, xlab = "value", main = "typhus")