From 850cf46198446aa7eaf8095fd03ccc6e9ade30a8 Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Wed, 16 May 2018 16:33:52 +0100
Subject: [PATCH 01/13] modification to have modup method1

---
 R/modified_update.R | 192 ++++++++++++++++++++++++--------------------
 1 file changed, 103 insertions(+), 89 deletions(-)

diff --git a/R/modified_update.R b/R/modified_update.R
index 86a2579..22841e8 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -10,25 +10,25 @@
 ##'   this off of
 ##'
 ##' @export
-modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use) {
+modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = "method1") {
   year_min <- 2001
   year_max <- 2030
-
+  
   sql <- paste("SELECT *",
                "  FROM touchstone",
                " WHERE touchstone_name = $1",
                sep = "\n")
   touchstone_mod <- DBI::dbGetQuery(con, sql, touchstone_name_mod)
-    i <- touchstone_mod$id != '201510gavi-42'
-    touchstone_mod <- touchstone_mod[which.max(touchstone_mod$version[i]), ]
+  i <- touchstone_mod$id != '201510gavi-42'
+  touchstone_mod <- touchstone_mod[which.max(touchstone_mod$version[i]), ]
   modup_by_itself <- any(touchstone_name_mod == touchstone_use)
   meta <- mu_prepare(con, touchstone_mod$id, modup_by_itself = modup_by_itself)
   meta <- mu_impact_metadata(meta, touchstone_use)
-
+  
   meta$touchstone_mod <-
     as.list(touchstone_mod[c("id", "touchstone_name", "version")])
   meta$touchstone_use <- touchstone_use
-
+  
   meta$group$touchstone_src <- meta$group$touchstone
   touchstone_src_native <- sub("-[0-9]{6}.*", "", meta$group$touchstone_name)
   meta$group$touchstone_name_dest <-
@@ -37,21 +37,22 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use)
     "[%s] %s",
     ifelse(meta$group$activity_type == "routine", "Rout", "SIA"),
     meta$group$vaccine)
-
+  
   ## This is quite slow to run but we can just pull it once:
   fmt <- "SELECT * FROM v_target_pop_%s WHERE YEAR BETWEEN %d AND %d"
   pop <- list(
     total = DBI::dbGetQuery(con, sprintf(fmt, "total", year_min, year_max)),
     routine = DBI::dbGetQuery(con, sprintf(fmt, "routine", year_min, year_max)))
-
-
+  
+  
   index <- meta$group$index
   data <- lapply(index, function(i) mu_build_data(con, i, meta, pop))
-
+  
   data <- rbind_simple(data)
   ## Perform the update itself the update:
-  data$deaths_averted_new <- mu_scale("deaths_averted", data)
-  data$cases_averted_new <- mu_scale("cases_averted", data)
+  data$deaths_averted_new <- mu_scale("deaths_averted", data, method)
+  data$cases_averted_new <- mu_scale("cases_averted", data, method)
+  
   meta$data <- data
   meta
 }
@@ -79,27 +80,27 @@ modified_update_summary_output <- function(con, res, path_meta) {
     x[j] <- tr[[to]][i[j]]
     x
   }
-
+  
   ## TODO: At the moment the metadata handling is very crude; the
   ## inputs are not properly documented or anything.
   meta_files <- c("gavi_country_data.csv", "tr_touchstone.csv",
                   "years_output.csv")
   stopifnot(all(file.exists(file.path(path_meta, meta_files))))
-
-
+  
+  
   ## Start on the meta
   group <- res$group
-
+  
   ## TODO: we need to filter this to only include the "gavi focal model"
   ## for each disease.  This will do for now:
   focal <- DBI::dbReadTable(con, "gavi_focal_model")
   focal$.code <- paste(focal$touchstone, focal$disease, focal$model, sep = "\n")
   group$is_focal <-
     paste(group$touchstone, group$disease, group$model, sep = "\n") %in%
-  focal$.code
-
+    focal$.code
+  
   tr_touchstone <- read_csv("meta/tr_touchstone.csv")
-
+  
   group_out <- data_frame(
     vaccine = group$vaccine,
     ## New columns
@@ -111,10 +112,10 @@ modified_update_summary_output <- function(con, res, path_meta) {
     model = group$model,
     touchstone = group$touchstone_name,
     vaccine_delivery = group$vaccine_delivery)
-
+  
   group_out$touchstone_short <-
     translate_vals(group$touchstone_name, tr_touchstone, "montagu_short")
-
+  
   ## The metadata that we have on countries differs from what the shiny
   ## app has (e.g WHO region of EMR vs EMRO for AFG), so we'll use this:
   ## cmp <- read.csv("../gavi-shiny-app/data_20170117.csv",
@@ -125,7 +126,7 @@ modified_update_summary_output <- function(con, res, path_meta) {
   ## write.csv(country, "meta/shiny/gavi_country_data.csv", row.names = FALSE)
   country <- read_csv(file.path(path_meta, "gavi_country_data.csv"))
   country$global <- NULL
-
+  
   ## Which leaves us with the rest:
   ##
   ## TODO: this should be target_pop_estimated_new which needs to come
@@ -146,17 +147,17 @@ modified_update_summary_output <- function(con, res, path_meta) {
                    cases_averted = "cases_averted_new",
                    fvps = "fvps_new",
                    population = "target_pop_given_new")
-
+  
   dat <- res$data[cols]
   names(dat) <- names(cols)
   tmp <- country[match(dat$country, country$country),
                  setdiff(names(country), "country")]
   dat <- cbind(dat, tmp)
   rownames(dat) <- NULL
-
+  
   dat_updated <- dat
   dat_updated[names(cols_update)] <- res$data[cols_update]
-
+  
   group_out_updated <- group_out
   ## Makeup the suffix from res$touchstone_mod$touchstone_name
   name_suffix <- unlist(strsplit(res$touchstone_mod$touchstone_name, "-"))
@@ -165,26 +166,26 @@ modified_update_summary_output <- function(con, res, path_meta) {
     paste0(sub("-[0-9]{6}.*", "", group_out$touchstone),"-",
            name_suffix )
   stopifnot(all(group_out_updated$touchstone %in%
-                tr_touchstone$montagu))
+                  tr_touchstone$montagu))
   group_out_updated$touchstone_short <-
     translate_vals(group_out_updated$touchstone,
                    tr_touchstone,
                    from = "montagu",
                    to = "montagu_short")
-
+  
   i <- match(res$data$index, res$group$index)
   d1 <- cbind(group_out[i, ], dat)
   d2 <- cbind(group_out_updated[i, ], dat_updated)
   d3 <- rbind(d1, d2)
   rownames(d3) <- NULL
-
+  
   ## Filter output to a set of years per touchstone:
   keep <- read_csv("meta/years_output.csv")
   i <- logical(nrow(d3))
   for (j in seq_len(nrow(keep))) {
     i[d3$touchstone == keep$touchstone[j] &
-      d3$year >= keep$year_from[j] &
-      d3$year <= keep$year_to[j]] <- TRUE
+        d3$year >= keep$year_from[j] &
+        d3$year <= keep$year_to[j]] <- TRUE
   }
   ## Exclude MCV1
   i[d3$vaccine == "MCV1"] <- FALSE
@@ -213,13 +214,13 @@ mu_prepare <- function(con, touchstone_new, modup_by_itself = FALSE) {
     whisker::whisker.render(txt, list(touchstone_new2 = touchstone_new2, 
                                       touchstone_new = touchstone_new))
   }
-
+  
   views <- c("migrate_coverage", "burden_fvps", "impact", "coverage",
              "target_pop_total", "target_pop_routine")
   for (v in views) {
     DBI::dbExecute(con, temporary_view(v, read_sql(v)))
   }
-
+  
   DBI::dbGetQuery(con, read_sql("query_metadata"))
 }
 
@@ -229,14 +230,14 @@ mu_build_data <- function(con, index, meta, pop) {
   year_min <- min(pop$total$year)
   year_max <- max(pop$total$year)
   w <- 4L # 1/2 window for rolling average
-
+  
   ## Process our arguments a bit more:
   x <- meta$group[meta$group$index == index, ]; print(x)
   xd <- meta$impacts[meta$impacts$index == index, ]
   x_deaths <- xd[xd$impact_outcome == "deaths_averted", ]
   x_cases <- xd[xd$impact_outcome == "cases_averted", ]
   x_fvps <- xd[xd$impact_outcome == "fvps_added", ]
-
+  
   sql <- paste("SELECT country",
                "  FROM touchstone_country",
                " WHERE touchstone = $1",
@@ -244,22 +245,22 @@ mu_build_data <- function(con, index, meta, pop) {
                " ORDER BY country",
                sep = "\n")
   countries <- DBI::dbGetQuery(con, sql, list(x$touchstone, x$disease))[[1]]
-
+  
   if (length(countries) == 0L) {
     stop("Import error")
   }
-
+  
   window <- 2 * w + 1
   year_max2 <- year_max + w
   years <- year_min:year_max2
   n_years <- length(years)
-
+  
   dat <- expand.grid(year = years,
                      country = countries,
                      index = index,
                      stringsAsFactors = FALSE)[3:1]
   dat$.code <- paste(dat$country, dat$year, sep = "\r")
-
+  
   merge_in <- function(dat, d, cols) {
     d$.code <- paste(d$country, d$year, sep = "\r")
     i <- match(dat$.code, d$.code)
@@ -272,16 +273,16 @@ mu_build_data <- function(con, index, meta, pop) {
     }
     cbind(dat, keep)
   }
-
+  
   ## 1. impact:
   sql <- paste("SELECT * FROM v_impact",
                " WHERE YEAR BETWEEN 2001 AND $2",
                "   AND impact_estimate_set = $1")
-
+  
   d_deaths_averted <-
     DBI::dbGetQuery(con, sql, list(x_deaths$impact_estimate_set, year_max2))
   dat <- merge_in(dat, d_deaths_averted, c(deaths_averted = "value"))
-
+  
   if (nrow(x_cases) == 0) {
     dat$cases_averted <- NA_real_
   } else {
@@ -289,7 +290,7 @@ mu_build_data <- function(con, index, meta, pop) {
       DBI::dbGetQuery(con, sql, list(x_cases$impact_estimate_set, year_max2))
     dat <- merge_in(dat, d_cases_averted, c(cases_averted = "value"))
   }
-
+  
   if (nrow(x_fvps) > 0) {
     d_fvps_added <-
       DBI::dbGetQuery(con, sql, list(x_fvps$impact_estimate_set, year_max2))
@@ -302,7 +303,7 @@ mu_build_data <- function(con, index, meta, pop) {
     d_fvps <- DBI::dbGetQuery(con, sql, list(x$burden_estimate_set, year_max2))
     dat <- merge_in(dat, d_fvps, c(fvps = "value"))
   }
-
+  
   ## 3. old coverage
   sql <- paste("SELECT * FROM v_coverage",
                " WHERE YEAR BETWEEN 2001 and $2",
@@ -311,23 +312,24 @@ mu_build_data <- function(con, index, meta, pop) {
   dat <-
     merge_in(dat, mu_fix_coverage(d_cov_old),
              c(coverage_old = "coverage", coverage_target = "target"))
-
+  
   ## 4. new coverage
   if (is.na(x$coverage_set_new)) {
-    stop("Import error: no new coverage found")
+    #stop("Import error: no new coverage found")
+    d_cov_new <- d_cov_old
   } else {
     if(meta$touchstone_mod$touchstone_name == meta$group$touchstone_name[meta$group$index == index])  {
       d_cov_new <- d_cov_old
     } else {
       d_cov_new <- DBI::dbGetQuery(con, sql, list(x$coverage_set_new, year_max2))
     }
-    dat <- merge_in(dat, mu_fix_coverage(d_cov_new),
-                    c(coverage_new = "coverage",
-                      coverage_target_new = "target"))
   }
-
-
-
+  dat <- merge_in(dat, mu_fix_coverage(d_cov_new),
+                  c(coverage_new = "coverage",
+                    coverage_target_new = "target"))
+  
+  
+  
   ## 5. population estimates
   pop_total <- pop$total[pop$total$demographic_source == x$demographic_source, ]
   pop_routine <- pop$routine[
@@ -335,9 +337,9 @@ mu_build_data <- function(con, index, meta, pop) {
       pop$routine$demographic_source == x$demographic_source, ]
   dat <- merge_in(dat, pop_total, c(pop_total = "value"))
   dat <- merge_in(dat, pop_routine, c(pop_routine = "value"))
-
+  
   ## 6. Impact rates
-
+  
   ## NOTE: There is some fiddling required here.  We might have cases
   ## where there is nonzero impact but zero fvps.  There are two forms
   ## of this!
@@ -354,8 +356,8 @@ mu_build_data <- function(con, index, meta, pop) {
   ## the coverage_target is not known; those cases I've opted to just
   ## zero the rate calculation but leave the impact in.
   ## (we have such cases for routines as well.)
-
-
+  
+  
   i <- is_blank(dat$fvps) &
     !(is_blank(dat$deaths_averted) & is_blank(dat$cases_averted)) &
     !is_blank(dat$coverage_target)
@@ -365,7 +367,7 @@ mu_build_data <- function(con, index, meta, pop) {
     ## Otherwise use pop_routine.
     dat$fvps[i] <- dat$coverage_old[i] * dat$coverage_target[i]
   }
-
+  
   ## There are cases where we have blank fvps_old, but positive coverage_old
   ## This caused the Inf/-Inf impact rate issue for CHN and TCD
   ## We create synthetic fvps for such cases when applicable.
@@ -378,10 +380,10 @@ mu_build_data <- function(con, index, meta, pop) {
       dat$fvps[i] <- dat$coverage_old[i] * dat$pop_routine[i]
     }
   }
-
+  
   dat <- mu_calculate_rate("deaths", dat, window, n_years)
   dat <- mu_calculate_rate("cases", dat, window, n_years)
-
+  
   ## And another quantity needed
   ##
   ## NOTE: Here, we can run into trouble where the coverage is zero
@@ -390,10 +392,10 @@ mu_build_data <- function(con, index, meta, pop) {
   ## rolling calculation)
   dat$target_pop_estimated <- dat$fvps / dat$coverage_old
   dat$target_pop_estimated[dat$fvps > 0 & is_blank(dat$coverage_old)] <- NA
-
+  
   dat$target_pop_estimated_avg <-
     roll_mean_by(dat$target_pop_estimated, window, n_years)
-
+  
   if (x$activity_type == "routine") {
     dat$target_pop_given <- dat$pop_routine
     dat$target_pop_given_new <- dat$pop_routine
@@ -401,12 +403,12 @@ mu_build_data <- function(con, index, meta, pop) {
     dat$target_pop_given <- dat$coverage_target
     dat$target_pop_given_new <- dat$coverage_target_new
   }
-
+  
   ## We also want new fvps which we compute as coverage * target pop
   v <- if (x$activity_type == "campaign")
     "coverage_target_new" else "pop_routine"
   dat$fvps_new <- dat$coverage_new * dat[[v]]
-
+  
   ## At the moment we can do nothing for MHL, TUV and XK, because we have no routine pop for them
   i <- !is_blank(dat$coverage_new) & is_blank(dat$fvps_new) & dat$year < 2031#& !is_blank(dat$target_pop_estimated)
   if (any(i)) {
@@ -422,18 +424,18 @@ mu_build_data <- function(con, index, meta, pop) {
   ## drop excess temporary things
   dat$.code <- NULL
   dat <- dat[dat$year <= year_max, ]
-
+  
   dat
 }
 
 mu_impact_metadata <- function(meta, touchstone_use) {
   meta <- meta[meta$touchstone_name %in% touchstone_use, ]
   rownames(meta) <- NULL
-
+  
   vary <- c("impact_outcome", "impact_estimate_set", "impact_estimate_recipe",
             "focal_ingredient")
   same <- setdiff(names(meta), vary)
-
+  
   f <- function(y) {
     n <- vapply(y, function(x) length(unique(x)), integer(1))
     stopifnot(all(n[same] == 1))
@@ -443,16 +445,16 @@ mu_impact_metadata <- function(meta, touchstone_use) {
                      meta$vaccine, meta$activity_type, meta$support_type, meta$responsibility,
                      sep = "\r")
   meta_code <- factor(meta_code, unique(meta_code))
-
+  
   i1 <- unname(tapply(seq_along(meta_code), meta_code, min))
   group <- meta[i1, same]
   group$index <- seq_len(nrow(group))
   rownames(group) <- NULL
-
+  
   impacts <- meta[vary]
   impacts$index <- group$index[tapply(meta_code, meta_code)]
   impacts <- impacts[order(impacts$index, impacts$impact_outcome), ]
-
+  
   list(group = group, impacts = impacts)
 }
 
@@ -464,12 +466,24 @@ mu_impact_metadata <- function(meta, touchstone_use) {
 ##' @param d Data: use impact_rate_tot (method 2)
 ##'
 ##' @export
-mu_scale <- function(name, d) {
-  ## This chunck becomes simpler, since only method 2 is used throughout.
-  rate_tot_old <- d[[paste0(name, "_rate_tot")]]
-  fvps_new <- d$fvps_new
-
-  ret <- fvps_new * rate_tot_old
+mu_scale <- function(name, d, method = "method2") {
+  ## This chunck becomes simpler, since only method 2 is used throughout. - Not any more, we need method 1 now.
+  ## This is method 1.
+  if (method != "method2") {
+    # by default use impact_new = impact_old / coverage_old * coverage_new
+    ret <- d[[name]] / d$coverage_old * d$coverage_new
+    
+    # when coverage_old is NA or 0, use impact_rate_tot*fvps_new
+    i <- is.na(d[[name]]) | d[[name]] == 0
+    rate_tot_old <- d[[paste0(name, "_rate_tot")]]
+    fvps_new <- d$fvps_new
+    ret[i] <- fvps_new[i] * rate_tot_old[i]
+  } else {
+    ## This is method 2
+    rate_tot_old <- d[[paste0(name, "_rate_tot")]]
+    fvps_new <- d$fvps_new
+    ret <- fvps_new * rate_tot_old
+  }
   ret[!is.finite(ret)] <- NA
   j <- !is.na(d$coverage_new) & d$coverage_new == 0
   ret[j] <- 0
@@ -494,19 +508,19 @@ mu_fix_coverage <- function(d) {
     }
     v
   }
-
+  
   code <- make_code(args = d[c("coverage_set", "country", "year")])
   n <- table(code)
   fix <- code %in% as.integer(names(n[n > 1]))
-
+  
   d_fix <- d[fix, ]
   i <- code[fix]
-
+  
   tmp <- d_fix[tapply(seq_along(i), i, utils::head, 1), ]
   tmp$target <- unname(tapply(d_fix$target, i, sum, na.rm = TRUE))
   reached <- tapply(d_fix$coverage * d_fix$target, i, sum, na.rm = TRUE)
   tmp$coverage <- unname(reached / tmp$target)
-
+  
   ret <- rbind(d[!fix, ], tmp)
   ret[order(ret$coverage_set, ret$country, ret$year), ]
 }
@@ -518,19 +532,19 @@ mu_calculate_rate <- function(name, dat, window, n_years) {
   v_tot <- sprintf("%s_averted_rate_tot", name)
   v_use <- sprintf("%s_averted_rate", name)
   v_type <- sprintf("%s_averted_rate_type", name)
-
+  
   dat[[v_inst]] <- dat[[v_averted]] / dat$fvps
   dat[[v_inst]][
     is_blank(dat$fvps) & !is_blank(dat[[v_averted]])] <- NA
-
+  
   dat[[v_avg]] <-
     roll_sum_by(dat[[v_averted]], window, n_years) /
     roll_sum_by(dat$fvps, window, n_years)
-
+  
   dat[[v_tot]] <-
     roll_sum_by(dat[[v_averted]], Inf, n_years) /
     roll_sum_by(dat$fvps, Inf, n_years)
-
+  
   ## Some cases don't have any non-NA rates
   type <- rep(NA, nrow(dat))
   use <- rep(NA_real_, nrow(dat))
@@ -538,10 +552,10 @@ mu_calculate_rate <- function(name, dat, window, n_years) {
   i <- !is.na(dat[[v_tot]])
   type[i] <- "tot"
   use[i] <- dat[[v_tot]][i]
-
+  
   dat[[v_use]] <- use
   dat[[v_type]] <- type
-
+  
   dat
 }
 
@@ -562,15 +576,15 @@ mu_year_introduction <- function(con, dat, dat_summary){
   meta.group <- unique(group[meta.group])
   x <- merge(meta.group, dat_summary, by = c("touchstone", "modelling_group", "vaccine"), all.y=TRUE)
   stopifnot( nrow(x) == nrow(dat_summary) )
-
+  
   x$touchstone_src[ is.na(x$touchstone_src) ] <- dat$touchstone_mod$id
-
+  
   coverage.touchstone <- as.list(c(unique(x$touchstone_src)))
-
+  
   y <- do.call(rbind, lapply(coverage.touchstone, function(i) find_year_introduction(con, i)))
-
+  
   z <- merge(x, y, by=c("touchstone_src", "activity_type", "vaccine", "country"), all.x = TRUE)
-
+  
   z
 }
 

From 4defb4b829a0e01edba9ef61756d5c09367411d5 Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Wed, 16 May 2018 17:07:51 +0100
Subject: [PATCH 02/13] add gavi_support to v_coverage, so that we can do
 method2_version2

---
 R/modified_update.R                   | 13 ++++++++++---
 inst/sql/modified_update/coverage.sql |  1 +
 man/modified_update_calculate.Rd      |  3 ++-
 man/mu_scale.Rd                       |  2 +-
 4 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/R/modified_update.R b/R/modified_update.R
index 22841e8..63061e5 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -10,7 +10,7 @@
 ##'   this off of
 ##'
 ##' @export
-modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = "method1") {
+modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = "method2") {
   year_min <- 2001
   year_max <- 2030
   
@@ -23,6 +23,12 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
   touchstone_mod <- touchstone_mod[which.max(touchstone_mod$version[i]), ]
   modup_by_itself <- any(touchstone_name_mod == touchstone_use)
   meta <- mu_prepare(con, touchstone_mod$id, modup_by_itself = modup_by_itself)
+  
+  ## we are going to do mothod2 version 2
+  ## this method do original modup2 for total support, and then derive gavi_support by filtering per-year gavi_support
+  if(method == "method2_v2") {
+    meta <- meta[meta$support_type == "total", ]
+  }
   meta <- mu_impact_metadata(meta, touchstone_use)
   
   meta$touchstone_mod <-
@@ -326,7 +332,8 @@ mu_build_data <- function(con, index, meta, pop) {
   }
   dat <- merge_in(dat, mu_fix_coverage(d_cov_new),
                   c(coverage_new = "coverage",
-                    coverage_target_new = "target"))
+                    coverage_target_new = "target",
+                    gavi_support_new = "gavi_support"))
   
   
   
@@ -469,7 +476,7 @@ mu_impact_metadata <- function(meta, touchstone_use) {
 mu_scale <- function(name, d, method = "method2") {
   ## This chunck becomes simpler, since only method 2 is used throughout. - Not any more, we need method 1 now.
   ## This is method 1.
-  if (method != "method2") {
+  if (method == "method1") {
     # by default use impact_new = impact_old / coverage_old * coverage_new
     ret <- d[[name]] / d$coverage_old * d$coverage_new
     
diff --git a/inst/sql/modified_update/coverage.sql b/inst/sql/modified_update/coverage.sql
index 9a83f4e..84a4c17 100644
--- a/inst/sql/modified_update/coverage.sql
+++ b/inst/sql/modified_update/coverage.sql
@@ -2,6 +2,7 @@ SELECT coverage_set,
        coverage.country,
        coverage.year,
        coverage,
+       gavi_support,
        target
   FROM coverage
  ORDER BY coverage_set, country, year
diff --git a/man/modified_update_calculate.Rd b/man/modified_update_calculate.Rd
index fea71ea..fce7af3 100644
--- a/man/modified_update_calculate.Rd
+++ b/man/modified_update_calculate.Rd
@@ -4,7 +4,8 @@
 \alias{modified_update_calculate}
 \title{Do a modified update}
 \usage{
-modified_update_calculate(con, touchstone_name_mod, touchstone_use)
+modified_update_calculate(con, touchstone_name_mod, touchstone_use,
+  method = "method2")
 }
 \arguments{
 \item{con}{Database connection}
diff --git a/man/mu_scale.Rd b/man/mu_scale.Rd
index e8a3c5a..0dbdd01 100644
--- a/man/mu_scale.Rd
+++ b/man/mu_scale.Rd
@@ -4,7 +4,7 @@
 \alias{mu_scale}
 \title{Calculate updated impact}
 \usage{
-mu_scale(name, d)
+mu_scale(name, d, method = "method2")
 }
 \arguments{
 \item{name}{Impact type: deaths_averted or cases_averted}

From cdb2c954b20286b10780495b4ad7db5c12b53a1c Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Wed, 16 May 2018 17:18:10 +0100
Subject: [PATCH 03/13] remove MCV1 from modup if coverage touchstone is sdf9

---
 R/modified_update.R | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/R/modified_update.R b/R/modified_update.R
index 63061e5..300bfa5 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -23,7 +23,10 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
   touchstone_mod <- touchstone_mod[which.max(touchstone_mod$version[i]), ]
   modup_by_itself <- any(touchstone_name_mod == touchstone_use)
   meta <- mu_prepare(con, touchstone_mod$id, modup_by_itself = modup_by_itself)
-  
+  ## 201403gavi - SDF9 - does not have MCV1 coverage, we need to get rid of it here to avoid error
+  if (touchstone_name_mod == "201403gavi") {
+    meta <- meta[meta$vaccine != "MCV1", ]
+  }
   ## we are going to do mothod2 version 2
   ## this method do original modup2 for total support, and then derive gavi_support by filtering per-year gavi_support
   if(method == "method2_v2") {
@@ -321,8 +324,7 @@ mu_build_data <- function(con, index, meta, pop) {
   
   ## 4. new coverage
   if (is.na(x$coverage_set_new)) {
-    #stop("Import error: no new coverage found")
-    d_cov_new <- d_cov_old
+    stop("Import error: no new coverage found")
   } else {
     if(meta$touchstone_mod$touchstone_name == meta$group$touchstone_name[meta$group$index == index])  {
       d_cov_new <- d_cov_old

From 8dcf93ea06618bb7b855a6dd13a96bf8c1f6cc0c Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Tue, 22 May 2018 12:11:31 +0100
Subject: [PATCH 04/13] add codes for method2 version2

---
 R/modified_update.R              | 38 +++++++++++++++++++++++++++++---
 man/modified_update_calculate.Rd |  7 +++++-
 man/mu_scale.Rd                  |  2 ++
 3 files changed, 43 insertions(+), 4 deletions(-)

diff --git a/R/modified_update.R b/R/modified_update.R
index 300bfa5..03d5ada 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -9,8 +9,13 @@
 ##' @param touchstone_use Name of the touchstone that we are basing
 ##'   this off of
 ##'
+##' @param method two options: method1, method2
+##' method2_v2 is different from method2 in that, it takes per-year-gavi-level as an imput for gavi impact  
+##' 
+##' @param version two options: v1 and v2
+##' 
 ##' @export
-modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = "method2") {
+modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = "method2", version = "v2") {
   year_min <- 2001
   year_max <- 2030
   
@@ -23,13 +28,13 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
   touchstone_mod <- touchstone_mod[which.max(touchstone_mod$version[i]), ]
   modup_by_itself <- any(touchstone_name_mod == touchstone_use)
   meta <- mu_prepare(con, touchstone_mod$id, modup_by_itself = modup_by_itself)
-  ## 201403gavi - SDF9 - does not have MCV1 coverage, we need to get rid of it here to avoid error
+  ## 201403gavi - SDF9 - does not have MCV1 coverage, we need to get rid of it to avoid triggering error message
   if (touchstone_name_mod == "201403gavi") {
     meta <- meta[meta$vaccine != "MCV1", ]
   }
   ## we are going to do mothod2 version 2
   ## this method do original modup2 for total support, and then derive gavi_support by filtering per-year gavi_support
-  if(method == "method2_v2") {
+  if(method == "method2" & version == "v2") {
     meta <- meta[meta$support_type == "total", ]
   }
   meta <- mu_impact_metadata(meta, touchstone_use)
@@ -63,6 +68,32 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
   data$cases_averted_new <- mu_scale("cases_averted", data, method)
   
   meta$data <- data
+  
+  if(version == "v2") {
+    ## with version 2, gavi impact is filtered from total impact by per-year-gavi-level
+    group <- meta$group
+    impacts <- meta$impacts
+    
+    v <- group
+    v$support_type <- "gavi"
+    v$index <- max(v$index) + v$index
+    meta$group  <- rbind(group, v)
+    
+    v <- impacts
+    v$index <- max(v$index) + v$index
+    meta$impacts <- rbind(impacts, v)
+    
+    v <- data
+    i <- !is.na(v$gavi_support_new) & !v$gavi_support_new
+    v$coverage_new[i] <- 0.
+    v$coverage_target_new[i] <- 0.
+    v$target_pop_given_new[i] <- 0.
+    v$fvps_new[i] <- 0.
+    v$deaths_averted_new[i] <- 0.
+    v$cases_averted_new[i] <- 0.
+    meta$data <- rbind(data, v)
+  }
+  
   meta
 }
 
@@ -474,6 +505,7 @@ mu_impact_metadata <- function(meta, touchstone_use) {
 ##'
 ##' @param d Data: use impact_rate_tot (method 2)
 ##'
+##' @param method two options: method1 and method2
 ##' @export
 mu_scale <- function(name, d, method = "method2") {
   ## This chunck becomes simpler, since only method 2 is used throughout. - Not any more, we need method 1 now.
diff --git a/man/modified_update_calculate.Rd b/man/modified_update_calculate.Rd
index fce7af3..4e900f9 100644
--- a/man/modified_update_calculate.Rd
+++ b/man/modified_update_calculate.Rd
@@ -5,7 +5,7 @@
 \title{Do a modified update}
 \usage{
 modified_update_calculate(con, touchstone_name_mod, touchstone_use,
-  method = "method2")
+  method = "method2", version = "v2")
 }
 \arguments{
 \item{con}{Database connection}
@@ -15,6 +15,11 @@ that we are creating}
 
 \item{touchstone_use}{Name of the touchstone that we are basing
 this off of}
+
+\item{method}{two options: method1, method2
+method2_v2 is different from method2 in that, it takes per-year-gavi-level as an imput for gavi impact}
+
+\item{version}{two options: v1 and v2}
 }
 \description{
 Do a modified update
diff --git a/man/mu_scale.Rd b/man/mu_scale.Rd
index 0dbdd01..985cb9a 100644
--- a/man/mu_scale.Rd
+++ b/man/mu_scale.Rd
@@ -10,6 +10,8 @@ mu_scale(name, d, method = "method2")
 \item{name}{Impact type: deaths_averted or cases_averted}
 
 \item{d}{Data: use impact_rate_tot (method 2)}
+
+\item{method}{two options: method1 and method2}
 }
 \description{
 Calculate updated impact

From 182dfd1b6092cd77e9b3183294f04fcc56735088 Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Tue, 22 May 2018 12:34:19 +0100
Subject: [PATCH 05/13] undo set pop_new = 0

---
 R/modified_update.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/modified_update.R b/R/modified_update.R
index 03d5ada..36d0019 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -84,10 +84,10 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
     meta$impacts <- rbind(impacts, v)
     
     v <- data
+    v$index <- max(v$index) + v$index
     i <- !is.na(v$gavi_support_new) & !v$gavi_support_new
     v$coverage_new[i] <- 0.
     v$coverage_target_new[i] <- 0.
-    v$target_pop_given_new[i] <- 0.
     v$fvps_new[i] <- 0.
     v$deaths_averted_new[i] <- 0.
     v$cases_averted_new[i] <- 0.

From 1d660044a51409a63b49c47aed3e8559d56b3ef4 Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Tue, 22 May 2018 12:56:08 +0100
Subject: [PATCH 06/13] use per-year-gavi-level for native touchstone as well

---
 R/modified_update.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/R/modified_update.R b/R/modified_update.R
index 36d0019..2004dac 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -85,9 +85,14 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
     
     v <- data
     v$index <- max(v$index) + v$index
+    i <- !is.na(v$gavi_support) & !v$gavi_support
+    v$coverage_old[i] <- 0.
+    v$fvps[i] <- 0.
+    v$deaths_averted[i] <- 0.
+    v$cases_averted[i] <- 0.
+    
     i <- !is.na(v$gavi_support_new) & !v$gavi_support_new
     v$coverage_new[i] <- 0.
-    v$coverage_target_new[i] <- 0.
     v$fvps_new[i] <- 0.
     v$deaths_averted_new[i] <- 0.
     v$cases_averted_new[i] <- 0.
@@ -351,7 +356,7 @@ mu_build_data <- function(con, index, meta, pop) {
   d_cov_old <- DBI::dbGetQuery(con, sql, list(x$coverage_set, year_max2))
   dat <-
     merge_in(dat, mu_fix_coverage(d_cov_old),
-             c(coverage_old = "coverage", coverage_target = "target"))
+             c(coverage_old = "coverage", coverage_target = "target", gavi_support = "gavi_support"))
   
   ## 4. new coverage
   if (is.na(x$coverage_set_new)) {

From 9b6229ba860433163363d336e682515bfba33393 Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Tue, 22 May 2018 13:07:34 +0100
Subject: [PATCH 07/13] stop if method/version combination is not correct

---
 R/modified_update.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/modified_update.R b/R/modified_update.R
index 2004dac..24be37e 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -16,6 +16,9 @@
 ##' 
 ##' @export
 modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = "method2", version = "v2") {
+  if(method != "method2" & version == "v2") {
+    stop("version 2 can only be applied to method 2.")
+  }
   year_min <- 2001
   year_max <- 2030
   

From 2f4afbd92b7711740acc3297f87874926696bb01 Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Fri, 1 Jun 2018 13:49:20 +0100
Subject: [PATCH 08/13] enable to add per-year-gavi-level in the output

---
 R/modified_update.R                           | 2 ++
 inst/sql/modified_update/migrate_coverage.sql | 5 ++++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/modified_update.R b/R/modified_update.R
index 24be37e..d7ff201 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -182,6 +182,7 @@ modified_update_summary_output <- function(con, res, path_meta) {
   cols <- c(country = "country",
             year = "year",
             coverage = "coverage_old",
+            gavi_support = "gavi_support",
             population = "target_pop_given",
             population_estimated = "target_pop_estimated",
             deaths_averted_rate = "deaths_averted_rate",
@@ -191,6 +192,7 @@ modified_update_summary_output <- function(con, res, path_meta) {
             cases_averted = "cases_averted",
             cases_averted_rate = "cases_averted_rate")
   cols_update <- c(coverage = "coverage_new",
+                   gavi_support = "gavi_support_new",
                    deaths_averted = "deaths_averted_new",
                    cases_averted = "cases_averted_new",
                    fvps = "fvps_new",
diff --git a/inst/sql/modified_update/migrate_coverage.sql b/inst/sql/modified_update/migrate_coverage.sql
index 09d4088..97c3bf8 100644
--- a/inst/sql/modified_update/migrate_coverage.sql
+++ b/inst/sql/modified_update/migrate_coverage.sql
@@ -9,6 +9,9 @@ LEFT JOIN (SELECT coverage_set.* FROM coverage_set
 JOIN touchstone ON touchstone.id = coverage_set.touchstone
            WHERE touchstone = '{{{touchstone_new}}}'
            AND (coverage_set.gavi_support_level = 'with'
-             OR coverage_set.gavi_support_level = 'bestminus') )AS coverage_new
+             OR coverage_set.gavi_support_level = 'bestminus') 
+           AND name NOT IN ('Rota: MCV1, with, routine',
+                            'Hib: MCV1, with, routine',
+                            'PCV: MCV1, with, routine'))AS coverage_new
 ON coverage_old.vaccine = coverage_new.vaccine AND
 coverage_old.activity_type = coverage_new.activity_type

From f2eb16f7e638066d9fb5955a2ccf41b168b37059 Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Mon, 4 Jun 2018 11:02:16 +0100
Subject: [PATCH 09/13] add to NEWS

---
 NEWS.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 4f04375..2523c55 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,5 @@
+### jenner 0.0.16
+ * VIMC-1738 modup method 1, method 2 verison 2 (gavi impact filtered from total impact by per-year-gavi-level)
 
 ### jenner 0.0.15
  * VIMC-14628 impact_method2 sql modification post Wes' touchstone fast forward

From 8395ad987f67a06ae2cc0901e27102177d2993e3 Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Mon, 4 Jun 2018 11:02:50 +0100
Subject: [PATCH 10/13] increase version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9cd5179..4477460 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: jenner
 Title: Internal Montagu Helpers
-Version: 0.0.15
+Version: 0.0.16
 Description: Helpers for Montagu.
 License: MIT + file LICENSE
 Author: Rich FitzJohn

From ac42d3e426026c95dbabf89f14443215ce6605d6 Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Mon, 4 Jun 2018 11:56:37 +0100
Subject: [PATCH 11/13] add comments + a little bit styling

---
 R/modified_update.R | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/R/modified_update.R b/R/modified_update.R
index d7ff201..dc58463 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -16,7 +16,12 @@
 ##' 
 ##' @export
 modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = "method2", version = "v2") {
-  if(method != "method2" & version == "v2") {
+  ### current method and version we have
+  ### method 1 version 1 - impact new = impact old / coverage old * coverage new
+  ### method 2 version 1 - Rich develpped this in July 2017
+  ### method 2 version 2 - in version 2, total impact is the same as version 1, 
+  ###                     gavi impact is a subset of total impact by filtering per-year-gavi-level 
+  if (method != "method2" & version == "v2") {
     stop("version 2 can only be applied to method 2.")
   }
   year_min <- 2001
@@ -27,6 +32,8 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
                " WHERE touchstone_name = $1",
                sep = "\n")
   touchstone_mod <- DBI::dbGetQuery(con, sql, touchstone_name_mod)
+  ### touchstone 201510gavi-42 is imported from Rshiny, it contains Rubella only
+  ### It is not a target touchstone we are interested in.
   i <- touchstone_mod$id != '201510gavi-42'
   touchstone_mod <- touchstone_mod[which.max(touchstone_mod$version[i]), ]
   modup_by_itself <- any(touchstone_name_mod == touchstone_use)
@@ -37,7 +44,7 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
   }
   ## we are going to do mothod2 version 2
   ## this method do original modup2 for total support, and then derive gavi_support by filtering per-year gavi_support
-  if(method == "method2" & version == "v2") {
+  if (method == "method2" & version == "v2") {
     meta <- meta[meta$support_type == "total", ]
   }
   meta <- mu_impact_metadata(meta, touchstone_use)
@@ -72,7 +79,7 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
   
   meta$data <- data
   
-  if(version == "v2") {
+  if (version == "v2") {
     ## with version 2, gavi impact is filtered from total impact by per-year-gavi-level
     group <- meta$group
     impacts <- meta$impacts
@@ -249,7 +256,7 @@ mu_prepare <- function(con, touchstone_new, modup_by_itself = FALSE) {
   ## this duplication later.
   ## sometimes we do modup for touchstone_old = touchstone_new
   ## the if-else clause is important to deal with this
-  if(modup_by_itself) {
+  if (modup_by_itself) {
     touchstone_new2 <- NULL
   } else {
     touchstone_new2 <- touchstone_new
@@ -367,7 +374,7 @@ mu_build_data <- function(con, index, meta, pop) {
   if (is.na(x$coverage_set_new)) {
     stop("Import error: no new coverage found")
   } else {
-    if(meta$touchstone_mod$touchstone_name == meta$group$touchstone_name[meta$group$index == index])  {
+    if (meta$touchstone_mod$touchstone_name == meta$group$touchstone_name[meta$group$index == index])  {
       d_cov_new <- d_cov_old
     } else {
       d_cov_new <- DBI::dbGetQuery(con, sql, list(x$coverage_set_new, year_max2))
@@ -424,9 +431,9 @@ mu_build_data <- function(con, index, meta, pop) {
   i <- is_blank(dat$fvps) & !is_blank(dat$coverage_old)
   if (any(i)) {
     message("Creating synthetic fvps for ", x$model)
-    if((x$activity_type == "campaign")){
+    if ((x$activity_type == "campaign")){
       dat$fvps[i] <- dat$coverage_old[i] * dat$coverage_target[i]
-    }else{
+    } else {
       dat$fvps[i] <- dat$coverage_old[i] * dat$pop_routine[i]
     }
   }
@@ -469,7 +476,7 @@ mu_build_data <- function(con, index, meta, pop) {
       stop("modified update error")
   }
   #For analysis purpose, a touchstone can be 'updated' by itself - assumes equal fvps
-  if(meta$touchstone_mod$touchstone_name == meta$group$touchstone_name[meta$group$index == index])
+  if (meta$touchstone_mod$touchstone_name == meta$group$touchstone_name[meta$group$index == index])
     dat$fvps_new <- dat$fvps
   ## drop excess temporary things
   dat$.code <- NULL
@@ -518,7 +525,7 @@ mu_impact_metadata <- function(meta, touchstone_use) {
 ##' @param method two options: method1 and method2
 ##' @export
 mu_scale <- function(name, d, method = "method2") {
-  ## This chunck becomes simpler, since only method 2 is used throughout. - Not any more, we need method 1 now.
+  ## AS we need method 1 now. mu_scale includes both method 1 and method 2 now
   ## This is method 1.
   if (method == "method1") {
     # by default use impact_new = impact_old / coverage_old * coverage_new

From 5d4cdd45e583e0121479fefeb195ef77e47a90ef Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Tue, 5 Jun 2018 09:19:08 +0100
Subject: [PATCH 12/13] use integer method and version

---
 R/modified_update.R              | 27 +++++++++++++++------------
 man/modified_update_calculate.Rd |  6 +++---
 man/mu_scale.Rd                  |  2 +-
 3 files changed, 19 insertions(+), 16 deletions(-)

diff --git a/R/modified_update.R b/R/modified_update.R
index dc58463..2bdd5d8 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -9,19 +9,22 @@
 ##' @param touchstone_use Name of the touchstone that we are basing
 ##'   this off of
 ##'
-##' @param method two options: method1, method2
+##' @param method two options: 1 = method1, 2 = method2
 ##' method2_v2 is different from method2 in that, it takes per-year-gavi-level as an imput for gavi impact  
 ##' 
-##' @param version two options: v1 and v2
+##' @param version two options: 1 = v1 and 2 = v2
 ##' 
 ##' @export
-modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = "method2", version = "v2") {
+modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = 2, version = 1) {
   ### current method and version we have
-  ### method 1 version 1 - impact new = impact old / coverage old * coverage new
-  ### method 2 version 1 - Rich develpped this in July 2017
-  ### method 2 version 2 - in version 2, total impact is the same as version 1, 
-  ###                     gavi impact is a subset of total impact by filtering per-year-gavi-level 
-  if (method != "method2" & version == "v2") {
+  ### method = 1 version = 1: impact new = impact old / coverage old * coverage new (or impact rate * fvps when coverage old in (NA/0))
+  ### method = 2 version = 1: Rich develpped this in July 2017
+  ### method = 2 version = 2: in version 2, total impact is the same as version 1, 
+  ###                         gavi impact is a subset of total impact by filtering per-year-gavi-level 
+  if (!(method %in% 1:2)) {
+    stop("currently, only method 1 and 2 have been developed.")
+  }
+  if (method != 2 & version == 2) {
     stop("version 2 can only be applied to method 2.")
   }
   year_min <- 2001
@@ -44,7 +47,7 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
   }
   ## we are going to do mothod2 version 2
   ## this method do original modup2 for total support, and then derive gavi_support by filtering per-year gavi_support
-  if (method == "method2" & version == "v2") {
+  if (method == 2 & version == 2) {
     meta <- meta[meta$support_type == "total", ]
   }
   meta <- mu_impact_metadata(meta, touchstone_use)
@@ -79,7 +82,7 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
   
   meta$data <- data
   
-  if (version == "v2") {
+  if (version == 2) {
     ## with version 2, gavi impact is filtered from total impact by per-year-gavi-level
     group <- meta$group
     impacts <- meta$impacts
@@ -524,10 +527,10 @@ mu_impact_metadata <- function(meta, touchstone_use) {
 ##'
 ##' @param method two options: method1 and method2
 ##' @export
-mu_scale <- function(name, d, method = "method2") {
+mu_scale <- function(name, d, method = 2) {
   ## AS we need method 1 now. mu_scale includes both method 1 and method 2 now
   ## This is method 1.
-  if (method == "method1") {
+  if (method == 1) {
     # by default use impact_new = impact_old / coverage_old * coverage_new
     ret <- d[[name]] / d$coverage_old * d$coverage_new
     
diff --git a/man/modified_update_calculate.Rd b/man/modified_update_calculate.Rd
index 4e900f9..26b50bf 100644
--- a/man/modified_update_calculate.Rd
+++ b/man/modified_update_calculate.Rd
@@ -5,7 +5,7 @@
 \title{Do a modified update}
 \usage{
 modified_update_calculate(con, touchstone_name_mod, touchstone_use,
-  method = "method2", version = "v2")
+  method = 2, version = 1)
 }
 \arguments{
 \item{con}{Database connection}
@@ -16,10 +16,10 @@ that we are creating}
 \item{touchstone_use}{Name of the touchstone that we are basing
 this off of}
 
-\item{method}{two options: method1, method2
+\item{method}{two options: 1 = method1, 2 = method2
 method2_v2 is different from method2 in that, it takes per-year-gavi-level as an imput for gavi impact}
 
-\item{version}{two options: v1 and v2}
+\item{version}{two options: 1 = v1 and 2 = v2}
 }
 \description{
 Do a modified update
diff --git a/man/mu_scale.Rd b/man/mu_scale.Rd
index 985cb9a..9b850d4 100644
--- a/man/mu_scale.Rd
+++ b/man/mu_scale.Rd
@@ -4,7 +4,7 @@
 \alias{mu_scale}
 \title{Calculate updated impact}
 \usage{
-mu_scale(name, d, method = "method2")
+mu_scale(name, d, method = 2)
 }
 \arguments{
 \item{name}{Impact type: deaths_averted or cases_averted}

From 4054c70d2764ce57c9af83cf8b04070ecfc11cce Mon Sep 17 00:00:00 2001
From: Xiang Li <x.li@imperial.ac.uk>
Date: Wed, 6 Jun 2018 12:48:11 +0100
Subject: [PATCH 13/13] remove version 2 scripts, it cannot be resolved here

---
 R/modified_update.R                   | 54 ++-------------------------
 inst/sql/modified_update/coverage.sql |  1 -
 man/modified_update_calculate.Rd      |  4 +-
 3 files changed, 4 insertions(+), 55 deletions(-)

diff --git a/R/modified_update.R b/R/modified_update.R
index 2bdd5d8..b2b88b2 100644
--- a/R/modified_update.R
+++ b/R/modified_update.R
@@ -12,21 +12,11 @@
 ##' @param method two options: 1 = method1, 2 = method2
 ##' method2_v2 is different from method2 in that, it takes per-year-gavi-level as an imput for gavi impact  
 ##' 
-##' @param version two options: 1 = v1 and 2 = v2
-##' 
 ##' @export
-modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = 2, version = 1) {
-  ### current method and version we have
-  ### method = 1 version = 1: impact new = impact old / coverage old * coverage new (or impact rate * fvps when coverage old in (NA/0))
-  ### method = 2 version = 1: Rich develpped this in July 2017
-  ### method = 2 version = 2: in version 2, total impact is the same as version 1, 
-  ###                         gavi impact is a subset of total impact by filtering per-year-gavi-level 
+modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use, method = 2) {
   if (!(method %in% 1:2)) {
     stop("currently, only method 1 and 2 have been developed.")
   }
-  if (method != 2 & version == 2) {
-    stop("version 2 can only be applied to method 2.")
-  }
   year_min <- 2001
   year_max <- 2030
   
@@ -45,11 +35,6 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
   if (touchstone_name_mod == "201403gavi") {
     meta <- meta[meta$vaccine != "MCV1", ]
   }
-  ## we are going to do mothod2 version 2
-  ## this method do original modup2 for total support, and then derive gavi_support by filtering per-year gavi_support
-  if (method == 2 & version == 2) {
-    meta <- meta[meta$support_type == "total", ]
-  }
   meta <- mu_impact_metadata(meta, touchstone_use)
   
   meta$touchstone_mod <-
@@ -82,36 +67,6 @@ modified_update_calculate <- function(con, touchstone_name_mod, touchstone_use,
   
   meta$data <- data
   
-  if (version == 2) {
-    ## with version 2, gavi impact is filtered from total impact by per-year-gavi-level
-    group <- meta$group
-    impacts <- meta$impacts
-    
-    v <- group
-    v$support_type <- "gavi"
-    v$index <- max(v$index) + v$index
-    meta$group  <- rbind(group, v)
-    
-    v <- impacts
-    v$index <- max(v$index) + v$index
-    meta$impacts <- rbind(impacts, v)
-    
-    v <- data
-    v$index <- max(v$index) + v$index
-    i <- !is.na(v$gavi_support) & !v$gavi_support
-    v$coverage_old[i] <- 0.
-    v$fvps[i] <- 0.
-    v$deaths_averted[i] <- 0.
-    v$cases_averted[i] <- 0.
-    
-    i <- !is.na(v$gavi_support_new) & !v$gavi_support_new
-    v$coverage_new[i] <- 0.
-    v$fvps_new[i] <- 0.
-    v$deaths_averted_new[i] <- 0.
-    v$cases_averted_new[i] <- 0.
-    meta$data <- rbind(data, v)
-  }
-  
   meta
 }
 
@@ -192,7 +147,6 @@ modified_update_summary_output <- function(con, res, path_meta) {
   cols <- c(country = "country",
             year = "year",
             coverage = "coverage_old",
-            gavi_support = "gavi_support",
             population = "target_pop_given",
             population_estimated = "target_pop_estimated",
             deaths_averted_rate = "deaths_averted_rate",
@@ -202,7 +156,6 @@ modified_update_summary_output <- function(con, res, path_meta) {
             cases_averted = "cases_averted",
             cases_averted_rate = "cases_averted_rate")
   cols_update <- c(coverage = "coverage_new",
-                   gavi_support = "gavi_support_new",
                    deaths_averted = "deaths_averted_new",
                    cases_averted = "cases_averted_new",
                    fvps = "fvps_new",
@@ -371,7 +324,7 @@ mu_build_data <- function(con, index, meta, pop) {
   d_cov_old <- DBI::dbGetQuery(con, sql, list(x$coverage_set, year_max2))
   dat <-
     merge_in(dat, mu_fix_coverage(d_cov_old),
-             c(coverage_old = "coverage", coverage_target = "target", gavi_support = "gavi_support"))
+             c(coverage_old = "coverage", coverage_target = "target"))
   
   ## 4. new coverage
   if (is.na(x$coverage_set_new)) {
@@ -385,8 +338,7 @@ mu_build_data <- function(con, index, meta, pop) {
   }
   dat <- merge_in(dat, mu_fix_coverage(d_cov_new),
                   c(coverage_new = "coverage",
-                    coverage_target_new = "target",
-                    gavi_support_new = "gavi_support"))
+                    coverage_target_new = "target"))
   
   
   
diff --git a/inst/sql/modified_update/coverage.sql b/inst/sql/modified_update/coverage.sql
index 84a4c17..9a83f4e 100644
--- a/inst/sql/modified_update/coverage.sql
+++ b/inst/sql/modified_update/coverage.sql
@@ -2,7 +2,6 @@ SELECT coverage_set,
        coverage.country,
        coverage.year,
        coverage,
-       gavi_support,
        target
   FROM coverage
  ORDER BY coverage_set, country, year
diff --git a/man/modified_update_calculate.Rd b/man/modified_update_calculate.Rd
index 26b50bf..4b131c8 100644
--- a/man/modified_update_calculate.Rd
+++ b/man/modified_update_calculate.Rd
@@ -5,7 +5,7 @@
 \title{Do a modified update}
 \usage{
 modified_update_calculate(con, touchstone_name_mod, touchstone_use,
-  method = 2, version = 1)
+  method = 2)
 }
 \arguments{
 \item{con}{Database connection}
@@ -18,8 +18,6 @@ this off of}
 
 \item{method}{two options: 1 = method1, 2 = method2
 method2_v2 is different from method2 in that, it takes per-year-gavi-level as an imput for gavi impact}
-
-\item{version}{two options: 1 = v1 and 2 = v2}
 }
 \description{
 Do a modified update