## ----results='hide', message=FALSE, warning=FALSE, eval=TRUE------------------
library(chmsflow)
library(recodeflow)
library(dplyr)


## ----warning=FALSE------------------------------------------------------------
cycle1 <- recode_meds_cycles1to2(cycle1, cycle1_meds, c("any_htn_med", "diab_med"))


## ----warning=FALSE------------------------------------------------------------
cycle1_diab_data <- recode_after_meds(
  cycle1,
  c("lab_hba1", "diab_a1c", "diab_med", "ccc_51", "diab_status")
)
head(select(cycle1_diab_data, clinicid, diab_status))


## ----warning=FALSE------------------------------------------------------------
cycle1_htn_data <- recode_after_meds(
  cycle1,
  c(
    # Blood pressure (raw + adjusted)
    "bpmdpbps", "bpmdpbpd", "sbp_adj_mmhg", "dbp_adj_mmhg",
    # Medication inputs (merged in Step 1)
    "any_htn_med", "ccc_32",
    # Diabetes chain (input to htn functions)
    "lab_hba1", "diab_a1c", "ccc_51", "diab_med", "diab_status",
    # CVD chain
    "ccc_61", "ccc_63", "ccc_81", "cvd_status",
    # CKD chain
    "lab_bcre", "pgdcgt", "clc_sex", "clc_age", "gfr_ml_min", "ckd_status",
    # Hypertension outcomes
    "htn_status", "htn_adj_status", "htn_control_status", "htn_control_adj_status"
  )
)
head(select(cycle1_htn_data, clinicid, htn_status, htn_adj_status))


## ----warning=FALSE------------------------------------------------------------
cycle3 <- recode_meds_cycles3to6(cycle3, cycle3_meds, c("any_htn_med", "diab_med"))


## ----warning=FALSE------------------------------------------------------------
cycle3_diab_data <- recode_after_meds(
  cycle3,
  c("lab_hba1", "diab_a1c", "diab_med", "ccc_51", "diab_status")
)
head(select(cycle3_diab_data, clinicid, diab_status))


## ----warning=FALSE------------------------------------------------------------
cycle3_htn_data <- recode_after_meds(
  cycle3,
  c(
    # Blood pressure (raw + adjusted)
    "bpmdpbps", "bpmdpbpd", "sbp_adj_mmhg", "dbp_adj_mmhg",
    # Medication inputs (merged in Step 1)
    "any_htn_med", "ccc_32",
    # Diabetes chain (input to htn functions)
    "lab_hba1", "diab_a1c", "ccc_51", "diab_med", "diab_status",
    # CVD chain
    "ccc_61", "ccc_63", "ccc_81", "cvd_status",
    # CKD chain
    "lab_bcre", "pgdcgt", "clc_sex", "clc_age", "gfr_ml_min", "ckd_status",
    # Hypertension outcomes
    "htn_status", "htn_adj_status", "htn_control_status", "htn_control_adj_status"
  )
)
head(select(cycle3_htn_data, clinicid, htn_status, htn_adj_status))


## ----warning=FALSE------------------------------------------------------------
# Single medication classification
is_beta_blocker("C07AA05", 1) # returns 1
is_ace_inhibitor("C09AA02", 1) # returns 1
is_diabetes_med("A10BA02", 1) # returns 1


## ----warning=FALSE------------------------------------------------------------
# Classification using cycles 1--2 wide-format columns
is_ace_med_cycles1to2(atc_101a = "C09AA02", mhr_101b = 1) # returns 1
is_ace_med_cycles1to2(atc_101a = "C09AA02", mhr_101b = 6) # returns 0 (not taken recently)


## ----warning=FALSE------------------------------------------------------------
cycle3_meds |>
  mutate(ace_med = is_ace_inhibitor(meucatc, npi_25b)) |>
  aggregate_meds_by_person(variables = "ace_med")