inst/dataprep/Sub_Baseline.R

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

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

# names of current objects
currObjVec = ls()


# Calculation -------------------------------------------------------------

sub17IncTbl = join17IncTbl %>%
  group_by( vaccine, infxn, cytCombo ) %>%
  mutate( med = median( resp[timePoint==0] ) ) %>% # calculate median day zero response for each vaccine, infection status and cytCombo combination
  ungroup() %>%
  arrange( timePoint ) %>%
  group_by( vaccine, infxn, cytCombo, ptid ) %>% # subtract either an individual's on baseline, or the median baseline for its vaccine, infection status and cytokine combination if day zero is missing
  do( calcSub( . ) ) %>%
  select( - med ) %>%
  ungroup()

sub17IncITbl = join17IncITbl %>%
  group_by( vaccine, infxn, stim, cytCombo ) %>%
  mutate( med = median( resp[timePoint==0] ) ) %>% # calculate median day zero response for each vaccine, infection status and cytCombo combination
  ungroup() %>%
  arrange( timePoint ) %>%
  group_by( vaccine, infxn, cytCombo, stim, ptid ) %>% # subtract either an individual's on baseline, or the median baseline for its vaccine, infection status and cytokine combination if day zero is missing
  do( calcSub( . ) ) %>%
  select( - med ) %>%
  ungroup()

sub17ExcTbl = join17ExcTbl %>%
  filter( vaccine != 8 ) %>%
  group_by( vaccine, infxn, cytCombo ) %>%
  mutate( med = median( resp[timePoint==0] ) ) %>% # calculate median day zero response for each vaccine, infection status and cytCombo combination
  ungroup() %>%
  arrange( timePoint ) %>%
  group_by( vaccine, infxn, cytCombo, ptid ) %>% # subtract either an individual's on baseline, or the median baseline for its vaccine, infection status and cytokine combination if day zero is missing
  do( calcSub( . ) ) %>%
  select( - med ) %>%
  ungroup() %>%
  bind_rows( joinMegTbl1 )

sub17ExcITbl = join17ExcITbl %>%
  filter( vaccine != 8 ) %>%
  group_by( vaccine, infxn, stim, cytCombo ) %>%
  mutate( med = median( resp[timePoint==0] ) ) %>% # calculate median day zero response for each vaccine, infection status and cytCombo combination
  ungroup() %>%
  arrange( timePoint ) %>%
  group_by( vaccine, infxn, cytCombo, stim, ptid ) %>% # subtract either an individual's on baseline, or the median baseline for its vaccine, infection status and cytokine combination if day zero is missing
  do( calcSub( . ) ) %>%
  select( - med ) %>%
  ungroup() %>%
  bind_rows( joinMegITbl1 )

subSingle17Tbl = single17Tbl %>%
  group_by( vaccine, infxn, cd ) %>%
  mutate( med = median( resp[timePoint==0] ) ) %>% # calculate median day zero response for each vaccine, infection status and cytCombo combination
  ungroup() %>%
  arrange( timePoint ) %>%
  group_by( vaccine, infxn, cd, ptid ) %>% # subtract either an individual's on baseline, or the median baseline for its vaccine, infection status and cytokine combination if day zero is missing
  do( calcSub( . ) ) %>%
  select( - med ) %>%
  ungroup()

subSingle17ITbl = single17ITbl %>%
  group_by( vaccine, infxn, cd ) %>%
  mutate( med = median( resp[timePoint==0] ) ) %>% # calculate median day zero response for each vaccine, infection status and cytCombo combination
  ungroup() %>%
  arrange( timePoint ) %>%
  group_by( vaccine, infxn, cd, ptid ) %>% # subtract either an individual's on baseline, or the median baseline for its vaccine, infection status and cytokine combination if day zero is missing
  do( calcSub( . ) ) %>%
  select( - med ) %>%
  ungroup()

# Testing -----------------------------------------------------------------

calcVec = sub17IncTbl %>% filter( ptid == 116 & cytCombo == "CD4Gp2pTp17p") %>% extract2( "resp")
testVec = join17IncTbl %>%
  filter( ptid == 116 & cytCombo == "CD4Gp2pTp17p" ) %>%
  mutate( resp = resp - resp[1] ) %>%
  extract2( "resp")
if( !identical( testVec, calcVec ) ) print( "sub17IncTbl error" )

calcVec = sub17ExcTbl %>% filter( ptid == 165 & cytCombo == "CD4Gp2pTp") %>% extract2( "resp")
testMed = join17ExcTbl %>%
  filter( vaccine == 5 & infxn == 0 & timePoint == 0 & cytCombo == "CD4Gp2pTp" )  %>%
  summarise( med = median( resp ) ) %>%
  extract2( "med" )
testVec = join17ExcTbl %>%
  filter( ptid == 165 & cytCombo == "CD4Gp2pTp" ) %>%
  mutate( resp = resp - testMed ) %>%
  extract2( "resp")
if( !identical( testVec, calcVec ) ) print( "sub17IncTbl error" )

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

# remove all objects but initial objects (currObjVec) and processed data tibble (l8Tbl)
rm( list = setdiff( ls(), c( currObjVec, "sub17IncTbl", "sub17ExcTbl", "subSingle17Tbl", "sub17IncITbl", "sub17ExcITbl", "subSingle17ITbl" ) ) )