analysis_scripts/study_duration_summary.R

In camposfa/plhdbR: Tools for working with the Primate Life History Database

# This code creates Table 1 in the manuscript

fert_durations <- fert %>%
  filter(!(Study.Id == "kakamega" & year(Start.Date) < 1997)) %>%
  group_by(Study.Id) %>%
  summarise(min_start = min(Start.Date),
            max_end = max(Stop.Date),
            n = n()) %>%
  mutate(dur = as.duration(max_end - min_start) / dyears(1))

fert_durations <- fert %>%
  filter(!(Study.Id == "kakamega" & year(Start.Date) < 1997)) %>%
  group_by(Study.Id) %>%
  summarise(n = n_distinct(Animal.Id)) %>%
  right_join(fert_durations)

fert_individ_years <- fert %>%
  filter(!(Study.Id == "kakamega" & year(Start.Date) < 1997)) %>%
  mutate(dur = Stop.Date - Start.Date) %>%
  group_by(Study.Id, Animal.Id) %>%
  summarise(ind_dur = sum(dur)) %>%
  ungroup %>%
  group_by(Study.Id) %>%
  summarise(fert_yrs = sum(ind_dur)) %>%
  mutate(fert_yrs = fert_yrs / dyears(1)) %>%
  inner_join(fert_durations)



study_durations <- lh %>%
  group_by(Study.Id) %>%
  dplyr::summarise(min_entry = min(Entry.Date),
                   max_depart = max(Depart.Date),
                   n_rec = n()) %>%
  mutate(dur = as.duration(max_depart - min_entry))

surv_individ_years <- lh %>%
  mutate(dur = Depart.Date - Entry.Date) %>%
  group_by(Study.Id, Animal.Id) %>%
  summarise(ind_dur = sum(dur)) %>%
  ungroup() %>%
  group_by(Study.Id) %>%
  summarise(lh_yrs = sum(ind_dur)) %>%
  mutate(lh_yrs = lh_yrs / dyears(1)) %>%
  inner_join(study_durations) %>%
  mutate(dur = dur / dyears(1))



# ---- new_summaries ------------------------------------------------------

fert_durations <- fert %>%
  filter(!(Study.Id == "kakamega" & year(Start.Date) < 1997) &
           !year(Start.Date) >= 2015) %>%
  mutate(Stop.Date = if_else(year(Stop.Date) >= 2015, as.POSIXct("2014-12-31"), Stop.Date)) %>%
  group_by(Study.Id) %>%
  summarise(min_start = min(Start.Date),
            max_end = max(Stop.Date),
            n_total = n(),
            n = n_distinct(Animal.Id)) %>%
  mutate(dur = as.duration(max_end - min_start) / dyears(1))


# Accrued female-years in adult stage of life
f %>%
  group_by(site) %>%
  summarise(sum_female_years = sum(female_years)) %>%
  View()




study_durations <- lh %>%
  filter(!year(Entry.Date) >= 2015) %>%
  mutate(Depart.Date = if_else(year(Depart.Date) >= 2015, as.POSIXct("2014-12-31"), Depart.Date)) %>%
  group_by(Study.Id) %>%
  dplyr::summarise(min_entry = min(Entry.Date),
                   max_depart = max(Depart.Date),
                   n_rec = n(),
                   n = n_distinct(Animal.Id)) %>%
  mutate(dur = as.duration(max_depart - min_entry))

surv_individ_years <- lh %>%
  filter(!year(Entry.Date) >= 2015) %>%
  mutate(Depart.Date = if_else(year(Depart.Date) >= 2015, as.POSIXct("2014-12-31"), Depart.Date)) %>%
  mutate(dur = Depart.Date - Entry.Date) %>%
  group_by(Study.Id, Animal.Id) %>%
  summarise(ind_dur = sum(dur)) %>%
  ungroup() %>%
  group_by(Study.Id) %>%
  summarise(lh_yrs = sum(ind_dur)) %>%
  mutate(lh_yrs = lh_yrs / dyears(1)) %>%
  inner_join(study_durations) %>%
  mutate(dur = dur / dyears(1))