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Compute empirical mortality rate

Source: R/compute_mortality_rate.R
compute_mortality_rate.Rd

Calculate the empirical mortality rate over a given interval.

Usage

compute_mortality_rate(
  lifelihoodData,
  interval_width,
  max_time = NULL,
  min_sample_size = 1,
  groupby = NULL
)

Arguments

lifelihoodData

lifelihoodData object created with lifelihoodData().

interval_width

The interval width used to calculate the mortality rate. For instance, if the time unit for deaths in the original dataset is days and interval_width is set to 10, the mortality rate will be calculated every 10 days for each group.

max_time

The maximum time for calculating the mortality rate. If set to NULL, the time of the last observed death is used.

min_sample_size

The minimum number of individuals alive at the beggining of a time interval for computing the observed mortality rate

groupby

covariate(s) over which mortality rate should be computed (default is NULL).

  • If NULL, calculates a single overall mortality rate.

  • If "all", calculates mortality rate over each combination of covariates listed in thelifelihoodData object provided.

  • Otherwise must be a character ("covariate1") or a character vector (c("covariate1", "covariate2")).

Value

A dataframe with 3 columns: Interval (time interval, based on interval_width value), Group (identifier of a given subgroup, or "Overall" if groupby = NULL), and MortalityRate (mortality rate at this time).

Examples

library(lifelihood)
library(tidyverse)

df <- fakesample |>
  mutate(
    geno = as.factor(geno),
    type = as.factor(type)
  )

clutchs <- c(
  "clutch_start1", "clutch_end1", "clutch_size1",
  "clutch_start2", "clutch_end2", "clutch_size2"
)

dataLFH <- lifelihoodData(
  df = df,
  sex = "sex",
  sex_start = "sex_start",
  sex_end = "sex_end",
  maturity_start = "mat_start",
  maturity_end = "mat_end",
  clutchs = clutchs,
  death_start = "death_start",
  death_end = "death_end",
  covariates = c("geno", "type"),
  model_specs = c("gam", "lgn", "wei")
)

mort_df <- compute_mortality_rate(dataLFH, interval_width = 2)
head(mort_df)
#>   Interval_start Interval_end Mean_Interval MortalityRate
#> 1              0            2             1     0.2307692
#> 2              2            4             3     0.0000000
#> 3              4            6             5     0.1000000
#> 4              6            8             7     0.0000000
#> 5              8           10             9     0.0000000
#> 6             10           12            11     0.0000000

mort_df <- compute_mortality_rate(
  dataLFH,
  interval_width = 2,
  groupby = NULL,
  max_time = 170
)
head(mort_df)
#>   Interval_start Interval_end Mean_Interval MortalityRate
#> 1              0            2             1     0.2307692
#> 2              2            4             3     0.0000000
#> 3              4            6             5     0.1000000
#> 4              6            8             7     0.0000000
#> 5              8           10             9     0.0000000
#> 6             10           12            11     0.0000000