Predict antimicrobial resistance

Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns se_min and se_max. See Examples for a real live example.

resistance_predict(
  x,
  col_ab,
  col_date = NULL,
  year_min = NULL,
  year_max = NULL,
  year_every = 1,
  minimum = 30,
  model = NULL,
  I_as_S = TRUE,
  preserve_measurements = TRUE,
  info = interactive(),
  ...
)

rsi_predict(
  x,
  col_ab,
  col_date = NULL,
  year_min = NULL,
  year_max = NULL,
  year_every = 1,
  minimum = 30,
  model = NULL,
  I_as_S = TRUE,
  preserve_measurements = TRUE,
  info = interactive(),
  ...
)

# S3 method for resistance_predict
plot(x, main = paste("Resistance Prediction of", x_name), ...)

# S3 method for resistance_predict
ggplot(x, main = paste("Resistance Prediction of", x_name), ribbon = TRUE, ...)

ggplot_rsi_predict(
  x,
  main = paste("Resistance Prediction of", x_name),
  ribbon = TRUE,
  ...
)

Arguments

x	a data.frame containing isolates. Can be left blank for automatic determination, see Examples.
col_ab	column name of `x` containing antimicrobial interpretations (`"R"`, `"I"` and `"S"`)
col_date	column name of the date, will be used to calculate years if this column doesn't consist of years already, defaults to the first column of with a date class
year_min	lowest year to use in the prediction model, dafaults to the lowest year in `col_date`
year_max	highest year to use in the prediction model, defaults to 10 years after today
year_every	unit of sequence between lowest year found in the data and `year_max`
minimum	minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.
model	the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)``, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for all valid options.
I_as_S	a logical to indicate whether values `"I"` should be treated as `"S"` (will otherwise be treated as `"R"`). The default, `TRUE`, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section Interpretation of S, I and R below.
preserve_measurements	a logical to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be `NA`.
info	a logical to indicate whether textual analysis should be printed with the name and `summary()` of the statistical model.
...	arguments passed on to functions
main	title of the plot
ribbon	a logical to indicate whether a ribbon should be shown (default) or error bars

Value

A data.frame with extra class resistance_predict with columns:

year
value, the same as estimated when preserve_measurements = FALSE, and a combination of observed and estimated otherwise
se_min, the lower bound of the standard error with a minimum of 0 (so the standard error will never go below 0%)
se_max the upper bound of the standard error with a maximum of 1 (so the standard error will never go above 100%)
observations, the total number of available observations in that year, i.e. $S + I + R$
observed, the original observed resistant percentages
estimated, the estimated resistant percentages, calculated by the model

Furthermore, the model itself is available as an attribute: attributes(x)$model, see Examples.

Details

Valid options for the statistical model (argument model) are:

"binomial" or "binom" or "logit": a generalised linear regression model with binomial distribution
"loglin" or "poisson": a generalised log-linear regression model with poisson distribution
"lin" or "linear": a linear regression model

Stable Lifecycle

The lifecycle of this function is stable. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.

If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.

Interpretation of R and S/I

In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (https://www.eucast.org/newsiandr/).

R = Resistant
A microorganism is categorised as Resistant when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
S = Susceptible
A microorganism is categorised as Susceptible, standard dosing regimen, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
I = Increased exposure, but still susceptible
A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.

This AMR package honours this new insight. Use susceptibility() (equal to proportion_SI()) to determine antimicrobial susceptibility and count_susceptible() (equal to count_SI()) to count susceptible isolates.

Examples

x <- resistance_predict(example_isolates, 
                        col_ab = "AMX",
                        year_min = 2010,
                        model = "binomial")
plot(x)
# \donttest{
if (require("ggplot2")) {
  ggplot_rsi_predict(x)
}

# using dplyr:
if (require("dplyr")) {
  x <- example_isolates %>%
    filter_first_isolate() %>%
    filter(mo_genus(mo) == "Staphylococcus") %>%
    resistance_predict("PEN", model = "binomial")
  plot(x)

  # get the model from the object
  mymodel <- attributes(x)$model
  summary(mymodel)
}

# create nice plots with ggplot2 yourself
if (require("dplyr") & require("ggplot2")) {

  data <- example_isolates %>%
    filter(mo == as.mo("E. coli")) %>%
    resistance_predict(col_ab = "AMX",
                       col_date = "date",
                       model = "binomial",
                       info = FALSE,
                       minimum = 15)
                       
  ggplot(data)

  ggplot(as.data.frame(data),
         aes(x = year)) +
    geom_col(aes(y = value),
             fill = "grey75") +
    geom_errorbar(aes(ymin = se_min,
                      ymax = se_max),
                  colour = "grey50") +
    scale_y_continuous(limits = c(0, 1),
                       breaks = seq(0, 1, 0.1),
                       labels = paste0(seq(0, 100, 10), "%")) +
    labs(title = expression(paste("Forecast of Amoxicillin Resistance in ",
                                  italic("E. coli"))),
         y = "%R",
         x = "Year") +
    theme_minimal(base_size = 13)
}
# }