Paed parameters that need to be extracted

[mwalte10]

ART distribution: https://github.com/mrc-ide/leapfrog/blob/clean/R/spectrum-inputs.R#L239-L248
Rates of MTCT: https://github.com/mrc-ide/leapfrog/blob/clean/R/spectrum-inputs.R#L275-L302
Mortality RR by age: https://github.com/mrc-ide/leapfrog/blob/clean/R/spectrum-inputs.R#L275-L302
ART distribution by age: https://github.com/mrc-ide/leapfrog/blob/clean/R/spectrum-inputs.R#L313-L321
Transition between cd4 categories at 14 to 15: https://github.com/mrc-ide/leapfrog/blob/clean/R/spectrum-inputs.R#L313-L321

[mwalte10]

Whether cotrim was input as a percentage or a number should be added here.

leapfrog/R/read-spectrum.R

Lines 292 to 324 in b579d26

	dp_read_childart <- function(dp) {
	dp <- get_dp_data(dp)
	dpy <- get_dp_years(dp)
	indicator_names <- c("childart_ctx",
	"childart_art0to14",
	"childart_art0to4",
	"childart_art5to9",
	"childart_art10to14")
	if (exists_dptag(dp, "<ChildTreatInputs MV3>")) {
	childart <- dpsub(dp, "<ChildTreatInputs MV3>", 2:6, dpy$time_data_idx)
	} else {
	stop("Child ART input tag not recognized. Function probably needs update for this .DP file.")
	}
	childart <- sapply(childart, as.numeric)
	dimnames(childart) <- list(indicator = indicator_names, year = dpy$proj_years)
	childart[childart == -9999] <- NA_real_
	if (exists_dptag(dp, "<ChildARTByAgeGroupPerNum MV2>")) {
	childart_ispercent <- dpsub(dp, "<ChildARTByAgeGroupPerNum MV2>", 2:6, dpy$time_data_idx)
	} else {
	stop("Child ART input tag not recognized. Function probably needs update for this .DP file.")
	}
	childart_ispercent <- sapply(childart_ispercent, as.logical)
	dimnames(childart_ispercent) <- list(indicator = indicator_names, year = dpy$proj_years)
	list(childart = childart,
	childart_ispercent = childart_ispercent)
	}

@jeffeaton

[jeffeaton]

Whether cotrim was input as a percentage or a number should be added here.

leapfrog/R/read-spectrum.R

Lines 292 to 324 in b579d26

	dp_read_childart <- function(dp) {
	dp <- get_dp_data(dp)
	dpy <- get_dp_years(dp)
	indicator_names <- c("childart_ctx",
	"childart_art0to14",
	"childart_art0to4",
	"childart_art5to9",
	"childart_art10to14")
	if (exists_dptag(dp, "<ChildTreatInputs MV3>")) {
	childart <- dpsub(dp, "<ChildTreatInputs MV3>", 2:6, dpy$time_data_idx)
	} else {
	stop("Child ART input tag not recognized. Function probably needs update for this .DP file.")
	}
	childart <- sapply(childart, as.numeric)
	dimnames(childart) <- list(indicator = indicator_names, year = dpy$proj_years)
	childart[childart == -9999] <- NA_real_
	if (exists_dptag(dp, "<ChildARTByAgeGroupPerNum MV2>")) {
	childart_ispercent <- dpsub(dp, "<ChildARTByAgeGroupPerNum MV2>", 2:6, dpy$time_data_idx)
	} else {
	stop("Child ART input tag not recognized. Function probably needs update for this .DP file.")
	}
	childart_ispercent <- sapply(childart_ispercent, as.logical)
	dimnames(childart_ispercent) <- list(indicator = indicator_names, year = dpy$proj_years)
	list(childart = childart,
	childart_ispercent = childart_ispercent)
	}

@jeffeaton

Thanks very much. This function returns a list of two tables, where the first table val$childart is the values entered for cotrim and child ART by age, and the second table val$childart_ispercent has the same dimension and reflects whether each number is a number or percent.

I think that the cotrim as a percentage is the first row of the output of the second table. However, there was an error in the code and it was mostly returning NA values. That is fixed in PR #54.

Can you please merge that and check if the percentage flag makes sense now, or still looks funny?

[jeffeaton]

@mwalte10 -- what is status on this issue now?