check_data: Checks data are correctly described for models

In anovir: Analysis of Virulence

Description

Function checking 'time', 'censor' and 'infected treatment' columns in data.frame are correctly specified for the likelihood functions in this package.

Usage

check_data(
  data = data,
  time = time,
  censor = censor,
  infected_treatment = infected_treatment
)

Arguments

data	Name of data.frame to be checked
time	Name of column with time of event data (death or censoring); requires time > 0 and numeric.
censor	Name of column containing censor status; '1' censored, '0' uncensored or died during experiment (needs to be numeric)
infected_treatment	Name of column for infection treatment status; '1' a treatment exposed to infection, '0' treatment not exposed to infection (needs to be numeric). NB Different likelihood models make different assumptions as to whether all the individuals in an infected treatment are infected or not (c.f. nll_exposed_infected)

Details

An error message is also given if data contain rows 'NA'; these need removing.

NB error messages triggered on 1st encounter with a fault. Correct and check revised data for other faults.

Value

Message, 'Checks completed' or error message

Examples

# view head of data.frame to be checked
  head(data_blanford, 3)

# specify data.frame and names of columns for;
  # time, censor status, infection status
  check_data(data = data_blanford,
             time = t,
             censor = censor,
             infected_treatment = inf)

# create data.frame 't_zero' with t = 0 in first row of data.frame
t_zero <- data_blanford
t_zero[1, 8] <- 0
head(t_zero, 3)

check_data(data = t_zero,
           time = t,
           censor = censor,
           infected_treatment = inf)

# correct '0' and make first row of column 'censor' = NA
  t_zero[1, 8] <- 1 ; t_zero[1, 5] <- NA ; head(t_zero, 3)

check_data(data = t_zero,
           time = t,
           censor = censor,
           infected_treatment = inf)

# remove row(s) with 'NA'
  t_zero_II <- na.omit(t_zero) # NB applies to whole data.frame
  check_data(data = t_zero_II,
           time = t,
           censor = censor,
           infected_treatment = inf)

anovir documentation built on Oct. 24, 2020, 9:08 a.m.