#' Fix Dead Records for Transition Matrix Data
#'
#' @param Plant.Surveys.TM.largest.parent Transition matrix data.
#' @export
fixDeadRecords <- function(Plant.Surveys.TM.largest.parent) {
plants_measured_dead_year <- Plant.Surveys.TM.largest.parent %>%
filter(DeadMissingbyEndofYear==1, !(is.na(SizewClones_t)))
# make sure for plants that were measured in the spring/summer but dead by fall/winter there is another year where the plant is in the dead stage
plants_dead_year <- Plant.Surveys.TM.largest.parent %>%
filter(DeadMissingbyEndofYear==1, is.na(SizewClones_t))
# make extra year surveys for these plants
need_dead_survey <- plants_measured_dead_year %>%
filter(!(PlantID %in% plants_dead_year$PlantID)) %$%
PlantID
Plant.Surveys.TM.largest.parent %<>%
filter(PlantID %in% need_dead_survey) %>%
group_by(PlantID) %>%
filter(FecundityYear == max(FecundityYear)) %>%
mutate(
FecundityYear = FecundityYear + 1,
SizewClones_t = NA,
Fruit_Flowers_t = NA,
CA_t = NA,
ME_t = NA,
Old_Moth_Evidence_t = NA,
stage = "dead"
) %>%
rbind.fill(Plant.Surveys.TM.largest.parent)
# remove extra dead records
Plant.Surveys.TM.largest.parent %<>%
arrange(PlantID, FecundityYear) %>%
group_by(PlantID) %>%
mutate(prev_stage = lag(stage, default="NA")) %>%
filter(prev_stage!="dead")
Plant.Surveys.TM.largest.parent %>% dplyr::select(-prev_stage)
}
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