Package 'LARisk'

Cancer incidence table of Korea 2010

Description

A dataset containing the crude incidence rate of death by age, cancer site and gender.

Usage

incid2010

Format

A data frame with 1919 rows and 4 variables:

Site

cancer site

Age

age

Rate_m

crude incidence rate for male

Rate_f

crude incidence rate for female

Source

KOSIS(Ministry of Health and Welfare, Cancer Registration Statistics) https://kosis.kr/

---

Cancer incidence table of Korea 2018

Description

A dataset containing the crude incidence rate of death by age, cancer site and gender.

Usage

incid2018

Format

A data frame with 1919 rows and 4 variables:

Site

cancer site

Age

age

Rate_m

crude incidence rate for male

Rate_f

crude incidence rate for female

Source

KOSIS(Ministry of Health and Welfare, Cancer Registration Statistics) https://kosis.kr/

---

Estimate Lifetime Attributable Risk for one person

Description

LAR is used to estimate lifetime attributable radiation-related cancer risk for data with one person.

Usage

LAR(
  data,
  basedata,
  sim = 300,
  seed = 99,
  current = as.numeric(substr(Sys.Date(), 1, 4)),
  ci = 0.9,
  weight = NULL,
  DDREF = TRUE,
  basepy = 1e+05
)

Arguments

data	data frame containing demographic information and exposure information. See 'Details'.
basedata	a list of the data of lifetime table and incidence rate table. The first element is lifetime table and the second is incidence rate table.
sim	number of iteration of simulation.
seed	a random seed number.
current	a current year. default is year of the system time.
ci	confidence level of the confidence interval.
weight	a list containing the value between 0 and 1 which is a weight on ERR model. See 'Details'.
DDREF	logical. Whether to apply the dose and dose-rate effectiveness factor.
basepy	number of base person-years

Details

The maximum age in LAR is set as 100. If the data contains birth which makes attained age (=current - birth) exceed 100, the result has no useful value.

data should include information which includes gender, year of birth, year of exposure, sites where exposed, exposure rate, distribution of dose and dose parameters of exosed radiation. The name of each variables must be sex, birth, exposure, site, exposure_rate, dosedist, dose1, dose2, dose3.

For some variables, there is a fixed format. sex can have the component 'male' or 'female'. site can have the component 'stomach', 'colon', 'liver', 'lung', 'breast', 'ovary', 'uterus', 'prostate', 'bladder', 'brain/cns', 'thyroid', 'remainder', 'oral', 'oesophagus', 'rectum', 'gallbladder', 'pancreas', 'kidney', 'leukemia'. exposure_rate can have the component 'acute' or 'chronic'. dosedist can have the component 'fixedvalue', 'lognormal', 'normal', 'triangular', 'logtriangular', 'uniform', 'loguniform'.

dose1, dose2, dose3 are parameters of dose distribution. The parameters for each distribution are that:

fixedvalue

dose value (dose1)

lognormal

median (dose1), geometric standard deviation (dose2)

normal

mean (dose1), standard deviation (dose2)

triangular or logtriangular

minimum (dose1), mode (dose2), maximum (dose3)

uniform or loguniform

minimum (dose1), maximum (dose2)

weight

Value

LAR returns an object of "LAR" class.

An object of class "LAR" is a list containing the following components:

LAR

Lifetime attributable risk (LAR) from the time of exposure to the end of the expected lifetime.

F_LAR

Future attributable risk from current to the expected lifetime.

LBR

Lifetime baseline risk.

BFR

Baseline future risk.

LFR

Lifetime fractional risk.

TFR

Total future risk.

current

Current year.

ci

Confidence level.

pinfo

Information of the person.

References

Berrington de Gonzalez, A., Iulian Apostoaei, A., Veiga, L., Rajaraman, P., Thomas, B., Owen Hoffman, F., Gilbert, E. and Land, C. (2012). RadRAT: a radiation risk assessment tool for lifetime cancer risk projection. Journal of Radiological Protection, 32(3), pp.205-222.

National Research Council (NRC) and Committee to Assess Health Risks from Exposure to Low Levels of Ionizing Radiation (2005) Health Risks from Exposure to Low Levels of Ionizing Radiation: BEIR VII Phase 2 (Washington, DC: National Academy of Sciences)

See Also

LAR_batch, LAR_group

Examples

## example with lifetime and incidence rate table in 2010 Korea.
organ2 <- split(organ, organ$ID)[[1]]   ## data of one person.

## defualt
lar1 <- LAR(organ2, basedata = list(life2010, incid2010))
summary(lar1)

## change the weight for ERR and EAR models
weight_list <- list("rectum" = 0.5)
lar2 <- LAR(organ2, basedata = list(life2010, incid2010), weight = weight_list)
summary(lar2)

## change the DDREF option (DDREF=FALSE)
lar3 <- LAR(organ2, basedata = list(life2010, incid2010), DDREF = FALSE)
summary(lar3)

---

Estimate Lifetime Attributable Risk for several people

Description

LAR_batch is used to estimate lifetime attributable radiation-related cancer risk for data with several people.

Usage

LAR_batch(
  data,
  pid,
  basedata,
  sim = 300,
  seed = 99,
  current = as.numeric(substr(Sys.Date(), 1, 4)),
  ci = 0.9,
  weight = NULL,
  DDREF = TRUE,
  basepy = 1e+05
)

Arguments

data	data frame containing demographic information and exposure information. See 'Details'.
pid	a vector which distinguish each person.
basedata	a list of the data of lifetime table and incidence rate table. The first element is lifetime table and the second is incidence rate table.
sim	number of iteration of simulation.
seed	a random seed number.
current	a current year. default is year of the system time.
ci	confidence level of the confidence interval.
weight	a list containing the value between 0 and 1 which is a weight on ERR model. See 'Details'.
DDREF	logical. Whether to apply the dose and dose-rate effectiveness factor.
basepy	number of base person-years

Value

LAR_batch returns an object of multiple classes "LAR_batch", "LAR". An object of class LAR_batch is a list of LAR class objects which names of elements are ID of each person.

References

Berrington de Gonzalez, A., Iulian Apostoaei, A., Veiga, L., Rajaraman, P., Thomas, B., Owen Hoffman, F., Gilbert, E. and Land, C. (2012). RadRAT: a radiation risk assessment tool for lifetime cancer risk projection. Journal of Radiological Protection, 32(3), pp.205-222.

National Research Council (NRC) and Committee to Assess Health Risks from Exposure to Low Levels of Ionizing Radiation (2005) Health Risks from Exposure to Low Levels of Ionizing Radiation: BEIR VII Phase 2 (Washington, DC: National Academy of Sciences)

See Also

LAR, LAR_group

Examples

## example with lifetime and incidence rate table in 2010 Korea.
lar1 <- LAR_batch(nuclear, pid=nuclear$ID, basedata = list(life2010, incid2010))
summary(lar1)

---

Average Estimated Lifetime Attributable Risk by Group

Description

LAR_group is used to estimate lifetime attributable radiation-related cancer risk by group.

Usage

LAR_group(
  data,
  pid,
  group,
  basedata,
  sim = 300,
  seed = 99,
  current = as.numeric(substr(Sys.Date(), 1, 4)),
  ci = 0.9,
  weight = NULL,
  DDREF = TRUE,
  basepy = 1e+05
)

Arguments

data	data frame containing demographic information and exposure information. See 'Details'.
pid	a vector which distinguish each person.
group	a vector or list of vectors which distinguish each group.
basedata	a list of the data of lifetime table and incidence rate table. The first element is lifetime table and the second is incidence rate table.
sim	number of iteration of simulation.
seed	a random seed number.
current	a current year. default is year of the system time.
ci	confidence level of the confidence interval.
weight	a list containing the value between 0 and 1 which is a weight on ERR model. See 'Details'.
DDREF	logical. Whether to apply the dose and dose-rate effectiveness factor.
basepy	number of base person-years

Value

LAR_group returns an object of multiple classes "LAR_group", "LAR". An object of class LAR_group is a list of LAR class objects which names of elements are group of each groups.

References

Berrington de Gonzalez, A., Iulian Apostoaei, A., Veiga, L., Rajaraman, P., Thomas, B., Owen Hoffman, F., Gilbert, E. and Land, C. (2012). RadRAT: a radiation risk assessment tool for lifetime cancer risk projection. Journal of Radiological Protection, 32(3), pp.205-222.

National Research Council (NRC) and Committee to Assess Health Risks from Exposure to Low Levels of Ionizing Radiation (2005) Health Risks from Exposure to Low Levels of Ionizing Radiation: BEIR VII Phase 2 (Washington, DC: National Academy of Sciences)

Examples

## example with lifetime and incidence rate table in 2010 Korea.
lar1 <- LAR_group(nuclear, pid=nuclear$ID, group=nuclear$distance,
                 basedata = list(life2010, incid2010))
summary(lar1)

lar2 <- LAR_group(nuclear, pid=nuclear$ID, group=list(nuclear$sex, nuclear$distance),
                 basedata = list(life2010, incid2010))
summary(lar2)

---

Lifetime table of Korea 2010

Description

A dataset containing the probability of death by age and gender.

Usage

life2010

Format

A data frame with 101 rows and 3 variables:

Age

age

Prob_d_m

probability of death for male

Prob_d_f

probability of death for female

Source

KOSIS(Statistics Korea, Life Tables By Province) https://kosis.kr/

---

Lifetime table of Korea 2018

Description

A dataset containing the probability of death by age and gender.

Usage

life2018

Format

A data frame with 101 rows and 3 variables:

Age

age

Prob_d_m

probability of death for male

Prob_d_f

probability of death for female

Source

KOSIS(Statistics Korea, Life Tables By Province) https://kosis.kr/

---

Simulated data of organ radiation exposure dose

Description

nuclear is simulated dataset for acute exposure event. The scenario assumes that the people exposure the radiation at 2011.

Usage

nuclear

Format

A data frame with 100 observation of 11 variables:

ID

person ID.

sex

gender

birth

birth-year

exposure

exposed year to radiation

site

organ where exposed to radiation

exposure_rate

expsoure rate

dosedist

distribution of dose

dose1

dose parameter

dose2

dose parameter

dose3

dose parameter

distance

distance from the hyper

---

Simulated data of organ radiation exposure dose

Description

organ is simulated dataset from the data of workers at interventional radiology departments.

Usage

organ

Format

A data frame with 971 observation of 11 variables:

ID

person ID.

sex

gender

birth

birth-year

exposure

exposed year to radiation

site

organ where exposed to radiation

exposure_rate

expsoure rate

dosedist

distribution of dose

dose1

dose parameter

dose2

dose parameter

dose3

dose parameter

occup

occupation

References

Lee, W. J., Bang, Y. J., Cha, E. S., Kim, Y. M., & Cho, S. B. (2021). Lifetime cancer risks from occupational radiation exposure among workers at interventional radiology departments. International Archives of Occupational and Environmental Health, 94(1), 139-145.

---

Print estimated Lifetime Attributable Risk for one person

Description

print.LAR is the basic function for printing class "LAR".

Usage

## S3 method for class 'LAR'
print(x, digits = 4, ...)

## S3 method for class 'LAR_batch'
print(x, digits = 4, max.id = 50, ...)

## S3 method for class 'LAR_group'
print(x, digits = 4, max.id = 50, ...)

Arguments

x	'LAR', 'LAR_batch' or 'LAR_group' object.
digits	the number of decimal points to print.
...	further arguments to be passed from or to other methods.
max.id	the number of maximum of printing LAR results.

---

Summarize estimated Lifetime Attributable Risk for one person

Description

summary.LAR is the function for printing class "LAR".

Usage

## S3 method for class 'LAR'
summary(object, digits = 4, ...)

## S3 method for class 'LAR_batch'
summary(object, digits = 4, max.id = 50, ...)

## S3 method for class 'LAR_group'
summary(object, digits = 4, max.id = 50, ...)

Arguments

object	object of class 'LAR_batch' or LAR'.
digits	the number of decimal points to print.
...	further arguments to be passed from or to other methods.
max.id	the number of maximum of printing LAR results.

---

Write a LAR object

Description

Write 'LAR' object to CSV file

Usage

write_LAR(x, filename)

## S3 method for class 'LAR'
write_LAR(x, filename)

## S3 method for class 'LAR_batch'
write_LAR(x, filename)

## S3 method for class 'LAR_group'
write_LAR(x, filename)

Arguments

x	a 'LAR' object.
filename	a string naming the file to save (.csv file)

Methods (by class)

• LAR: write an 'LAR' class object

• LAR_batch: write an 'LAR_batch' class object

• LAR_group: write an 'LAR_group' class object

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