minor changes

covid19AgeModel/inst/scripts/post-processing-etas.R

@@ -140,16 +140,16 @@ if(!file.exists(file) | args_dir[['overwrite']])
  cat("\nWrite ",file," ... ")
  saveRDS(mcnts, file=file)
  file2 <- gsub('_by_age','',file)
- cat("\nWrite ",file," ... ")
+ cat("\nWrite ",file2," ... ")
  saveRDS(ocnts, file=file2)
  })
  cat(" \n -------------------------------- \n summarise marginal contact intensities by age: end \n -------------------------------- \n")
 }
 if(file.exists(file))
 {
  mcnts <- readRDS(file)
- file <- gsub('_by_age','',file)
- ocnts <- readRDS(file)
+ file2 <- gsub('_by_age','',file)
+ ocnts <- readRDS(file2)
 }
 
 # handle if forecast period is to be included in plots
@@ -189,7 +189,17 @@ file <- paste0(outfile.base,'-marginal_contact_intensities_across_states_weighte
 if(!file.exists(file) | args_dir[['overwrite']])
 {
  cat(" \n -------------------------------- \n summarise marginal contact intensities across states: start \n -------------------------------- \n")
- tryCatch({ 
+ tryCatch({ 
+ round.choose <- function(x, roundTo, dir = 1) {
+ if(dir == 1) { ##ROUND UP
+ x + (roundTo - x %% roundTo)
+ } else {
+ if(dir == 0) { ##ROUND DOWN
+ x - (x %% roundTo)
+ }
+ }
+ }
+
  weighted_contacts <- make_contact_intensities_across_states_summaries(plot.pars.basic$regions, 
  plot.pars.basic$mobility_data,
  plot.pars.basic$dates,
@@ -220,7 +230,7 @@ if(!file.exists(file) | args_dir[['overwrite']])
  file2 <- paste0(outfile.base,'-marginal_contact_intensities_across_states_weighted_age.rds')
  saveRDS(age_specific, file=file2, version = 2)
 
- p <- make_age_contact_boxplot(age_specific, outfile.base)
+ #p <- make_age_contact_boxplot(age_specific, outfile.base)
 
 
  })

covid19AgeModel/inst/scripts/post-processing-make-daily-weekly-deaths-expected-observed-plot.R

@@ -1,8 +1,8 @@
-# post-processing-make-deaths-panel-plot.R
+# post-processing-make-daily-weekly-deaths-expected-observed-plot.R
 # 
 ###############################################################################
 
-cat(" \n -------------------------------- \n \n post-processing-make-deaths-panel-plot.R \n \n -------------------------------- \n")
+cat(" \n -------------------------------- \n \n post-processing-make-daily-weekly-deaths-expected-observed-plot.R \n \n -------------------------------- \n")
 
 suppressMessages(library(data.table, quietly = TRUE))
 suppressMessages(library(bayesplot, quietly = TRUE))
@@ -130,3 +130,5 @@ df.weekly = find_observed_death_fourageband(e_adeaths_weekly, "weekly")
 
 plot_expected_observed_death(df.daily, "daily")
 plot_expected_observed_death(df.weekly, "weekly")
+
+cat(" \n -------------------------------- \n \n Completed post-processing-make-daily-weekly-deaths-expected-observed-plot.R \n \n -------------------------------- \n")

covid19AgeModel/inst/scripts/post-processing-plot-age-newcases.R

@@ -1,8 +1,8 @@
-# post-processing-plot-mean-age-newcases.R
+# post-processing-plot-age-newcases.R
 # 
 ###############################################################################
 
-cat(" \n -------------------------------- \n \n Running post-processing-plot-mean-age-newcases.R \n \n -------------------------------- \n")
+cat(" \n -------------------------------- \n \n Running post-processing-plot-age-newcases.R \n \n -------------------------------- \n")
 
 suppressMessages(library(data.table, quietly = TRUE))
 suppressMessages(library(bayesplot, quietly = TRUE))
@@ -82,6 +82,10 @@ if(!file.exists(file) | args_dir[['overwrite']])
  cat("\nWrite ",file," ... ")
  saveRDS(e_newcases_byage_c, file=file)
 }
+if(file.exists(file))
+{
+ e_newcases_byage_c <- readRDS(file)
+}
 cat("\n ----------- plot_proportion_newcases_byage_c ----------- \n")
 
 #
@@ -134,7 +138,10 @@ if(!file.exists(file) | args_dir[['overwrite']])
  cat("\nWrite ",file," ... ")
  saveRDS(e_age_newcases, file=file)
 }
-
+if(file.exists(file))
+{
+ e_age_newcases <- readRDS(file)
+}
 cat("\n ----------- plot_mean_age_new_cases ----------- \n")
 
 #
@@ -168,4 +175,4 @@ ggplot(e_age_newcases, aes(x = date)) +
  scale_colour_viridis(begin=0,end=1,direction=-1) +
  ggsave(paste0(outfile.base,'-mean_ageofinfection.png'), w = 210, h = 310, units = "mm")
 
-cat(" \n -------------------------------- \n \n Completed post-processing-plot-mean-age-newcases.R \n \n -------------------------------- \n")
+cat(" \n -------------------------------- \n \n Completed post-processing-plot-age-newcases.R \n \n -------------------------------- \n")

covid19AgeModel/inst/scripts/post-processing-summarise-antibody.R

@@ -1,8 +1,8 @@
-# post-processing-validate-prop_antibodys.R
+# post-processing-summarise-antibody.R
 # 
 ###############################################################################
 
-cat(" \n -------------------------------- \n \n post-processing-validate-prop_antibodys.R \n \n -------------------------------- \n")
+cat(" \n -------------------------------- \n \n post-processing-summarise-antibody.R \n \n -------------------------------- \n")
 
 suppressMessages(library(data.table, quietly = TRUE))
 suppressMessages(library(bayesplot, quietly = TRUE))
@@ -349,7 +349,7 @@ cat("\n ----------- plot estimated/observed attack rates ----------- \n")
 da <- copy( artable[[1]] )
 
 da <- subset(da, select=-c(L_est,L_obs))
-da <- reshape2::melt(da, measure.vars=c('M_est','CL_est','CU_est','M_obs','CL_obs','CU_obs'))
+da <- as.data.table( reshape2::melt(da, measure.vars=c('M_est','CL_est','CU_est','M_obs','CL_obs','CU_obs')) )
 set(da, NULL, 'value', da[, as.numeric(value)/100]) 
 da[, mtype:= gsub('est','Estimated',gsub('obs','Survey',gsub('^([A-Za-z]+)_([A-Za-z]+)$','\\2',variable)))]
 da[, stat:= gsub('^([A-Za-z]+)_([A-Za-z]+)$','\\1',variable)]
@@ -379,4 +379,4 @@ for (i in 1:length(lags)) {
  ggsave(file=paste0(outfile.base, "-prop_antibody_validation_lag",lags[i],".png"),g,w=7, h=10)
 }
 
-cat(" \n -------------------------------- \n \n completed post-processing-validate-prop_antibodys.R \n \n -------------------------------- \n")
+cat(" \n -------------------------------- \n \n completed post-processing-summarise-antibody.R \n \n -------------------------------- \n")