InterVA5 {InterVA5}

Provide InterVA5 analysis on the data input.

Description

This function implements the algorithm in the InterVA5 software. It produces individual cause of death (COD) and population cause-specific mortality fractions. The output is saved in a .csv file specified by user. The calculation is based on the conditional and prior distribution of 61 CODs. The function can also save the full probability distibution of each individual to file. All information about each individual is saved to a va class object.

Usage

InterVA5(
  Input,
  HIV,
  Malaria,
  write = TRUE,
  directory = NULL,
  filename = "VA5_result",
  output = "classic",
  append = FALSE,
  groupcode = FALSE,
  sci = NULL,
  returnCheckedData = FALSE,
  ...
)

Arguments

Input

A matrix input, or data read from csv files in the same format as required by InterVA5. Sample input is included as data(RandomVA5).

HIV

An indicator of the level of prevalence of HIV. The input should be one of the following: "h"(high),"l"(low), or "v"(very low).

Malaria

An indicator of the level of prevalence of Malaria. The input should be one of the following: "h"(high),"l"(low), or "v"(very low).

write

A logical value indicating whether or not the output (including errors and warnings) will be saved to file. If the value is set to TRUE, the user must also provide a value for the parameter "directory".

directory

The directory to store the output from InterVA5. It should either be an existing valid directory, or a new folder to be created. If no path is given and the parameter for "write" is true, then the function stops and and error message is produced.

filename

The filename the user wish to save the output. No extension needed. The output is in .csv format by default.

output

"classic": The same deliminated output format as InterVA5; or "extended": delimited output followed by full distribution of cause of death proability.

append

A logical value indicating whether or not the new output should be appended to the existing file.

groupcode

A logical value indicating whether or not the group code will be included in the output causes.

sci

A data frame that contains the symptom-cause-information (aka Probbase) that InterVA uses to assign a cause of death.

returnCheckedData

A logical indicating if the checked data (i.e., the data that have been modified by the consistency checks) should be returned.

...

not used

Details

Be careful if the input file does not match InterVA5 input format strictly. The function will run normally as long as the number of symptoms are correct. Any inconsistent symptom names will be printed in console as warning. If there is a wrong match of symptom from warning, please change the input to the correct order.

Value

ID

identifier from batch (input) file

MALPREV

selected malaria prevalence

HIVPREV

selected HIV prevalence

PREGSTAT

most likely pregnancy status

PREGLIK

likelihood of PREGSTAT

PRMAT

likelihood of maternal death

INDET

indeterminate outcome

CAUSE1

most likely cause

LIK1

likelihood of 1st cause

CAUSE2

second likely cause

LIK2

likelihood of 2nd cause

CAUSE3

third likely cause

LIK3

likelihood of 3rd cause

COMCAT

most likely circumstance of mortality

COMNUM

likelihood of COMCAT

wholeprob

full distribution of causes of death

Author(s)

Jason Thomas, Zehang Li, Tyler McCormick, Sam Clark

References

http://www.interva.net/

See Also

InterVA5.plot

Examples

data(RandomVA5)
# only fit first 5 observations for a quick illustration
RandomVA5 <- RandomVA5[1:5, ]

## to get easy-to-read version of causes of death make sure the column
## orders match interVA5 standard input this can be monitored by checking
## the warnings of column names

sample.output1 <- InterVA5(RandomVA5, HIV = "h", Malaria = "l", write = FALSE, 
    directory = tempdir(), filename = "VA5_result", output = "extended", append = FALSE)

## Not run: 
## to get causes of death with group code for further usage
sample.output2 <- InterVA5(RandomVA5, HIV = "h", Malaria = "l", 
    write = FALSE, directory = "VA test", filename = "VA5_result_wt_code", output = "classic", 
    append = FALSE, groupcode = TRUE)

## End(Not run)