InterVA5: Provide InterVA5 analysis on the data input.
In InterVA5: Replicate and Analyse 'InterVA5'

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

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.

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

`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

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.

`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

Jason Thomas, Zehang Li, Tyler McCormick, Sam Clark

http://www.interva.net/

InterVA5.plot

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)