Prepares input for estimate_liability

Prepares input for estimate_liability

prepare_LTFHPlus_input(
  .tbl,
  CIP,
  age_col,
  aoo_col,
  CIP_merge_columns = c("sex", "birth_year", "age"),
  CIP_cip_col = "cip",
  status_col = "status",
  use_fixed_case_thr = F,
  fam_id_col = "fam_id",
  personal_id_col = "pid",
  interpolation = NULL,
  bst.params = list(max_depth = 10, base_score = 0, nthread = 4, min_child_weight = 10),
  min_CIP_value = 1e-05,
  xgboost_itr = 50
)

Arguments

.tbl

contains family and personal ids and role with a family.

CIP

tibble with population representative cumulative incidence proportions. CIP values should be merged by CIP_columns.

age_col

name of column with age

aoo_col

name of column with age of onset

CIP_merge_columns

The columns the CIPs are subset by, e.g. CIPs by birth_year, sex.

CIP_cip_col

name of column with CIP values

status_col

Column that contains the status of each family member

use_fixed_case_thr

Should the threshold be fixed for cases? Can be used if CIPs are detailed, e.g. stratified by birth_year and sex.

fam_id_col

Column that contains the family ID

personal_id_col

Column that contains the personal ID

interpolation

type of interpolation, defaults to NULL.

bst.params

list of parameters to pass on to xgboost

min_CIP_value

minimum cip value to allow, too low values may lead to numerical instabilities.

xgboost_itr

Number of iterations to run xgboost for.