inst/dataprep/Summ_Stat_Calc.R

In MiguelRodo/VaccCompData: Data package for novel TBV vaccine comparison paper

# Set-up ------------------------------------------------------------------

# names of current objects
currObjVec = ls()

# tmax --------------------------------------------------------------------

### Sub

tmaxSub17IncTbl = sub17IncTbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

tmaxSub17IncITbl = sub17IncITbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

tmaxSub17ExcTbl = sub17ExcTbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

tmaxSub17ExcITbl = sub17ExcITbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

tmaxSubSingle17Tbl = subSingle17Tbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) )

tmaxSubSingle17ITbl = subSingle17ITbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) )

tmax17IncTbl = join17IncTbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

tmax17IncITbl = join17IncITbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

tmax17ExcTbl = join17ExcTbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

tmax17ExcITbl = join17ExcITbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

tmaxSingle17Tbl = single17Tbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) )

tmaxSingle17ITbl = single17ITbl %>%
  filter( timePoint %in% c( 182, 292, 210, 168, 364, 224, 294, 365, -1 ) )

### Baseline---------------------------------------------------------

bl17IncTbl = join17IncTbl %>%
  filter( timePoint == 0 ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

bl17IncITbl = join17IncITbl %>%
  filter( timePoint == 0 ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

bl17ExcTbl = join17ExcTbl %>%
  filter( timePoint == 0 | vaccine == 8 ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

bl17ExcITbl = join17ExcITbl %>%
  filter( timePoint == 0 | vaccine == 8 ) %>%
  mutate( cd = str_sub( cytCombo, start = 3, end = 3 ) )

blSingle17Tbl = single17Tbl %>% filter( timePoint == 0 )

blSingle17ITbl = single17ITbl %>% filter( timePoint == 0 )

# Clear Workspace ---------------------------------------------------------

# remove all objects but initial objects (currObjVec) and processed data tibble (l8Tbl)
rm( list = setdiff( ls(), c( currObjVec, "tmaxSub17IncTbl", "tmaxSub17ExcTbl", "tmaxSubSingle17Tbl", "tmax17IncTbl", "tmax17ExcTbl", "tmaxSingle17Tbl", "bl17IncTbl", "bl17ExcTbl", "blSingle17Tbl",
                             "tmaxSub17IncITbl", "tmaxSub17ExcITbl", "tmaxSubSingle17ITbl", "tmax17IncITbl", "tmax17ExcITbl", "tmaxSingle17ITbl", "bl17IncITbl", "bl17ExcITbl", "blSingle17ITbl") ) )