The goal of {epikit} is to provide miscellaneous functions for applied epidemiologists. This is a product of the R4EPIs project; learn more at https://r4epis.netlify.com.
Installation
You can install {epikit} from CRAN (see details for the latest version):
install.packages("epikit") Click here for alternative installation options
If there is a bugfix or feature that is not yet on CRAN, you can install it via the {drat} package:
You can also install the in-development version from GitHub using the {remotes} package (but there’s no guarantee that it will be stable):
# install.packages("remotes")
remotes::install_github("R4EPI/epikit") The {epikit} was primarily designed to house convenience functions for applied epidemiologists to use in tidying their reports. The functions in {epikit} come in a few categories:
Age categories
A couple of functions are dedicated to constructing age categories and partitioning them into separate chunks.
-
age_categories()takes in a vector of numbers and returns formatted age categories. -
group_age_categories()will take a data frame with different age categories in columns (e.g. years, months, weeks) and combine them into a single column, selecting the column with the lowest priority.
library("knitr")
library("magrittr")
set.seed(1)
x <- sample(0:100, 20, replace = TRUE)
y <- ifelse(x < 2, sample(48, 20, replace = TRUE), NA)
df <- data.frame(
age_years = age_categories(x, upper = 80),
age_months = age_categories(y, upper = 16, by = 6)
)
df %>%
group_age_categories(years = age_years, months = age_months)
#> age_years age_months age_category
#> 1 60-69 <NA> 60-69 years
#> 2 30-39 <NA> 30-39 years
#> 3 0-9 16+ 16+ months
#> 4 30-39 <NA> 30-39 years
#> 5 80+ <NA> 80+ years
#> 6 40-49 <NA> 40-49 years
#> 7 10-19 <NA> 10-19 years
#> 8 80+ <NA> 80+ years
#> 9 50-59 <NA> 50-59 years
#> 10 50-59 <NA> 50-59 years
#> 11 80+ <NA> 80+ years
#> 12 80+ <NA> 80+ years
#> 13 20-29 <NA> 20-29 years
#> 14 50-59 <NA> 50-59 years
#> 15 70-79 <NA> 70-79 years
#> 16 0-9 <NA> 0-9 years
#> 17 70-79 <NA> 70-79 years
#> 18 70-79 <NA> 70-79 years
#> 19 80+ <NA> 80+ years
#> 20 30-39 <NA> 30-39 yearsQuick proportions with conficence intervals
There are three functions that will provide quick statistics for different rates based on binomial estimates of proportions from binom::binom.wilson()
attack_rate(10, 50)
#> cases population ar lower upper
#> 1 10 50 20 11.24375 33.03711
case_fatality_rate(2, 50)
#> deaths population cfr lower upper
#> 1 2 50 4 1.103888 13.46009
mortality_rate(40, 50000)
#> deaths population mortality per 10 000 lower upper
#> 1 40 50000 8 5.87591 10.89109In addition, it’s possible to rapidly calculate Case fatality rate from a linelist, stratified by different groups (e.g. gender):
library("outbreaks")
case_fatality_rate_df(ebola_sim_clean$linelist,
outcome == "Death",
group = gender,
add_total = TRUE,
mergeCI = TRUE
)
#> # A tibble: 3 × 5
#> gender deaths population cfr ci
#> <fct> <int> <int> <dbl> <chr>
#> 1 f 1291 2280 56.6 (54.58--58.64)
#> 2 m 1273 2247 56.7 (54.59--58.69)
#> 3 Total 2564 4527 56.6 (55.19--58.08)Inline functions
The inline functions make it easier to print estimates with confidence intervals in reports with the correct number of digits.
-
fmt_ci()formats confidence intervals from three numbers. (e.g.fmt_ci(50, 10, 80)produces 50.00% (CI 10.00–80.00) -
fmt_pci()formats confidence intervals from three fractions, multiplying by 100 beforehand.
The _df suffixes (fmt_ci_df(), fmt_pci_df()) will print the confidence intervals for data stored in data frames. These are designed to work with the outputs of the rates functions. For example, fmt_ci_df(attack_rate(10, 50)) will produce 20.00% (CI 11.24–33.04). All of these suffixes will have three options e, l, and u. These refer to estimate, lower, and upper column positions or names.
-
fmt_count()will count a condition in a data frame and present the number and percent ofTRUEvalues. For example, if you wanted to count the number of women patients from Rokupa hospital, you would write:fmt_count(ebola_sim_clean$linelist, gender == "f", hospital == "Rokupa Hospital")and it would produce: 210 (3.6%)
Confidence interval manipulation
The confidence interval manipulation functions take in a data frame and combine their confidence intervals into a single character string much like the inline functions do. There are two flavors:
-
merge_ci_df()andmerge_pci_df()will merge just the values of the confidence interval and leave the estimate alone. Note: this WILL remove the lower and upper columns. -
unite_ci()merges both the confidence interval and the estimate into a single character column. This generally has more options thanmerge_ci()
This is useful for reporting models:
fit <- lm(100/mpg ~ disp + hp + wt + am, data = mtcars)
df <- data.frame(v = names(coef(fit)), e = coef(fit), confint(fit), row.names = NULL)
names(df) <- c("variable", "estimate", "lower", "upper")
print(df)
#> variable estimate lower upper
#> 1 (Intercept) 0.740647656 -0.774822875 2.256118188
#> 2 disp 0.002702925 -0.002867999 0.008273849
#> 3 hp 0.005274547 -0.001400580 0.011949674
#> 4 wt 1.001303136 0.380088737 1.622517536
#> 5 am 0.155814790 -0.614677730 0.926307310
# unite CI has more options
unite_ci(df, "slope (CI)", estimate, lower, upper, m100 = FALSE, percent = FALSE)
#> variable slope (CI)
#> 1 (Intercept) 0.74 (-0.77--2.26)
#> 2 disp 0.00 (-0.00--0.01)
#> 3 hp 0.01 (-0.00--0.01)
#> 4 wt 1.00 (0.38--1.62)
#> 5 am 0.16 (-0.61--0.93)
# merge_ci just needs to know where the estimate is
merge_ci_df(df, e = 2)
#> variable estimate ci
#> 1 (Intercept) 0.740647656 (-0.77--2.26)
#> 2 disp 0.002702925 (-0.00--0.01)
#> 3 hp 0.005274547 (-0.00--0.01)
#> 4 wt 1.001303136 (0.38--1.62)
#> 5 am 0.155814790 (-0.61--0.93)Give me a break
If you need a quick function to determine the number of breaks you need for a grouping or color scale, you can use find_breaks(). This will always start from 1, so that you can include zero in your scale when you need to.
find_breaks(100) # four breaks from 1 to 100
#> [1] 1 26 51 76
find_breaks(100, snap = 20) # four breaks, snap to the nearest 20
#> [1] 1 41 81
find_breaks(100, snap = 20, ceiling = TRUE) # include the highest number
#> [1] 1 41 81 100Pull together population counts
To quickly pull together population counts for use in surveys or demographic pyramids the gen_population() function can help. If you only know the proportions in each group the function will convert this to counts for you - whereas if you have counts, you can type those in directly. The default proportions are based on Doctors Without Borders general emergency intervention standard values.
# get population counts based on proportion, stratified
gen_population(groups = c("0-4","5-14","15-29","30-44","45+"),
strata = c("Male", "Female"),
proportions = c(0.079, 0.134, 0.139, 0.082, 0.067))
#> Warning in gen_population(groups = c("0-4", "5-14", "15-29", "30-44", "45+"), : Given proportions (or counts) is not the same as
#> groups multiplied by strata length, they will be repeated to match
#> # A tibble: 10 × 4
#> groups strata proportions n
#> <fct> <fct> <dbl> <dbl>
#> 1 0-4 Male 0.079 79
#> 2 5-14 Male 0.134 134
#> 3 15-29 Male 0.139 139
#> 4 30-44 Male 0.082 82
#> 5 45+ Male 0.067 67
#> 6 0-4 Female 0.079 79
#> 7 5-14 Female 0.134 134
#> 8 15-29 Female 0.139 139
#> 9 30-44 Female 0.082 82
#> 10 45+ Female 0.067 67Type in counts directly to get the groups in a data frame.
# get population counts based on counts, stratified - type out counts
# for each group and strata
gen_population(groups = c("0-4","5-14","15-29","30-44","45+"),
strata = c("Male", "Female"),
counts = c(20, 10, 30, 40, 0, 0, 40, 30, 20, 20))
#> # A tibble: 10 × 4
#> groups strata proportions n
#> <fct> <fct> <dbl> <dbl>
#> 1 0-4 Male 0.0952 20
#> 2 5-14 Male 0.0476 10
#> 3 15-29 Male 0.143 30
#> 4 30-44 Male 0.190 40
#> 5 45+ Male 0 0
#> 6 0-4 Female 0 0
#> 7 5-14 Female 0.190 40
#> 8 15-29 Female 0.143 30
#> 9 30-44 Female 0.0952 20
#> 10 45+ Female 0.0952 20Table modification
These functions all modify the appearance of a table displayed in a report and work best with the knitr::kable() function.
-
rename_redundant()renames redundant columns with a single name. (e.g.hopitalized_percentandconfirmed_percentcan both be renamed to%) -
augment_redundant()is similar torename_redundant(), but it modifies the redundant column names (e.g.hospitalized_nandconfirmed_ncan becomehospitalized (n)andconfirmed (n)) -
merge_ci()combines estimate, lower bound, and upper bound columns into a single column.
df <- data.frame(
`a n` = 1:6,
`a prop` = round((1:6) / 6, 2),
`a deff` = round(pi, 2),
`b n` = 6:1,
`b prop` = round((6:1) / 6, 2),
`b deff` = round(pi * 2, 2),
check.names = FALSE
)
knitr::kable(df)| a n | a prop | a deff | b n | b prop | b deff |
|---|---|---|---|---|---|
| 1 | 0.17 | 3.14 | 6 | 1.00 | 6.28 |
| 2 | 0.33 | 3.14 | 5 | 0.83 | 6.28 |
| 3 | 0.50 | 3.14 | 4 | 0.67 | 6.28 |
| 4 | 0.67 | 3.14 | 3 | 0.50 | 6.28 |
| 5 | 0.83 | 3.14 | 2 | 0.33 | 6.28 |
| 6 | 1.00 | 3.14 | 1 | 0.17 | 6.28 |
df %>%
rename_redundant("%" = "prop", "Design Effect" = "deff") %>%
augment_redundant(" (n)" = " n$") %>%
knitr::kable()| a (n) | % | Design Effect | b (n) | % | Design Effect |
|---|---|---|---|---|---|
| 1 | 0.17 | 3.14 | 6 | 1.00 | 6.28 |
| 2 | 0.33 | 3.14 | 5 | 0.83 | 6.28 |
| 3 | 0.50 | 3.14 | 4 | 0.67 | 6.28 |
| 4 | 0.67 | 3.14 | 3 | 0.50 | 6.28 |
| 5 | 0.83 | 3.14 | 2 | 0.33 | 6.28 |
| 6 | 1.00 | 3.14 | 1 | 0.17 | 6.28 |
