InterVA: Provide InterVA4 analysis on the data input.
In InterVA4: Replicate and Analyse 'InterVA4'

Description Usage Arguments Details Value Author(s) References See Also Examples

This function implements the algorithm in the InterVA4 software. It produces individual cause of death and population cause-specific mortality fractions.

InterVA(Input, HIV, Malaria, directory = NULL, filename = "VA_result",
  output = "classic", append = FALSE, groupcode = FALSE,
  replicate = FALSE, replicate.bug1 = FALSE, replicate.bug2 = FALSE,
  write = TRUE, ...)

`Input`	A matrix input, or data read from csv files in the same format as required by InterVA4. Sample input is included as data(SampleInput).
`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).
`directory`	The directory to store the output from InterVA4. It should either be an existing valid directory, or a new folder to be created. If no path is given, the current working directory will be used.
`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 InterVA4; or "extended": deliminated 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.
`replicate`	A logical value indicating whether or not the calculation should replicate original InterVA4 software (version 4.02) exactly. If replicate = F, causes with small probability are not dropped out of calculation in intermediate steps, and a possible bug in original InterVA4 implementation is fixed. If replicate=T, then the output values will be exactly as they would be from calling the InterVA4 program (version 4.02). If replicate=F, the output values will be the same as calling the InterVA4 program (version 4.03). Since version 1.7.3, setting replicate to be FALSE also includes changes to data checking rules and pre-set conditional probabilities to be the same as the official version 4.03 software. Since version 1.6, two control variables are added to control the two bugs respectively. Setting this to TRUE will overwrite both to TRUE.
`replicate.bug1`	This logical indicator controls whether or not the bug in InterVA4.2 involving the symptom "skin_les" will be replicated or not. It is suggested to set to FALSE.
`replicate.bug2`	This logical indicator controls whether the causes with small probability are dropped out of calculation in intermediate steps or not. It is suggested to set to FALSE.
`write`	A logical value indicating whether or not the output (including errors and warnings) will be saved to file.
`...`	not used

InterVA performs the same tasks as the InterVA4. The output is saved in a .csv file specified by user. The calculation is based on the conditional and prior distribution of 68 CODs. The function also could save the full probability distibution of each individual to file. All information about each individual is saved to a va class object.

Be careful if the input file does not match InterVA 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's wrong match of symptom from warning, please change in the input to correct orders.

`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
`wholeprob`	full distribution of causes of death

Zehang Li, Tyler McCormick, Sam Clark

http://www.interva.net/

InterVA.plot

data(SampleInput)
## to get easy-to-read version of causes of death make sure the column
## orders match interVA4 standard input this can be monitored by checking
## the warnings of column names

sample.output1 <- InterVA(SampleInput, HIV = "h", Malaria = "l", write=FALSE, replicate = FALSE)

## to get causes of death with group code for further usage
sample.output2 <- InterVA(SampleInput, HIV = "h", Malaria = "l", write=FALSE,
    replicate = FALSE, groupcode = TRUE)