example for paper

[Yousuf28]

workflow 01

Include uncertain in all appropriate case

we are good for this workflow

designStudies_T <- getStudiesSDESIGN(dbToken = myDbToken, studyDesignFilter = 'PARALLEL', inclUncertain = TRUE)

dateStudies_T <- getStudiesSTSTDTC(dbToken = myDbToken, studyList = designStudies_T, inclUncertain = TRUE)

controlAnimals_T <- getControlSubj(dbToken = myDbToken, studyList = dateStudies_T, inclUncertain = TRUE)

animals_sex_T <- getSubjSex(myDbToken, controlAnimals_T, inclUncertain = TRUE, sexFilter = "M")

animals_species_T <- getSubjSpeciesStrain(myDbToken, animals_sex_T, inclUncertain = TRUE, speciesFilter = "RAT")

animals_route_T <- getSubjRoute(myDbToken, animals_species_T, inclUncertain = TRUE, routeFilter = c('ORAL GAVAGE', 'INTRAVENOUS'))

DSdata_T <- getSubjData(dbToken = myDbToken, animalList = animals_route_T, 'ds')

MIdata_T <- getSubjData(dbToken = myDbToken, animalList = animals_route_T, 'mi')

DSanimals_T <- merge(DSdata_T[,c('USUBJID', 'DSSTDY')], animals_route_T, by = 'USUBJID', allow.cartesian = T)

[Yousuf28]

Workflow 02

Modified at each step while uncertain TRUE

I need some help about what we want to include at each step

study design

designStudies_M <- getStudiesSDESIGN(dbToken = myDbToken, studyDesignFilter = 'PARALLEL', inclUncertain = TRUE)

this is all the available study design
all_design <- c( "PARALLEL", "PARTIALLY BLOCKED UNBALANCED", "PARTIALLY BLOCKED BALANCED", "SINGLE ARM", "NA", "BLOCKED", "PARALELL", "PARALLEL\r\n", "PARALLEL,PARALLEL", "NOT AVAILABLE", "Blocked", "Parallel", "Not Available", "SINGLE GROUP", "Partially Blocked Unbalanced", "PARTIALLY BLOCKED BALANCED", "PARRALLEL", "PPARALLEL", "ONE TYPE TREATMENT" )

so I hand picked only that are parallel.

modified_design <- c( "PARALLEL", "PARALELL", "PARALLEL\r\n", "PARALLEL,PARALLEL", "Parallel", "PARRALLEL", "PPARALLEL" )

filter selected study design:
designStudies_MD <- designStudies_M[SDESIGN %in% modified_design, ]

date

dateStudies_MD <- getStudiesSTSTDTC(dbToken = myDbToken, studyList = designStudies_MD, inclUncertain = TRUE)

this is the STSTDTC column where there is NOT_VALID_MSG
valid_msg_ststdtc <- c("43006", "43349", NA, NA, "2019-005-21", "NOT AVAILABLE", NA, "2013-14-05", "6/6/2018")

So I looked into all the related studies. EXPENDTC is available for all those STSTDC except "NOT AVAILABLE" one.
So I only removed study where STSTDTC is "NOT AVAILABLE" one.

dateStudies_M <- dateStudies_MD[STUDYID != "FY10-087"]

Questions: should I remove all the STSTDTC where there is a valid message?

control animals

controlAnimals_M <- getControlSubj(dbToken = myDbToken, studyList = dateStudies_M, inclUncertain = TRUE)

sex

animals_sex_M <- getSubjSex(myDbToken, controlAnimals_M, inclUncertain = TRUE, sexFilter = "M")

species

animals_species_M <- getSubjSpeciesStrain(myDbToken, animals_sex_M, inclUncertain = TRUE, speciesFilter = "RAT")

we get lot of different strain for RAT.

all_strain <- c( "SPRAGUE-DAWLEY", "WISTAR HAN", "WISTAR", "CD1(ICR)", "FISCHER 344", "SPRAGUE DAWLEY", "RNU", "CRL:CD(SD) SPRAGUE DAWLEY RAT", "OFA(SD)", "LONG EVANS", "CD(SD)", "WISTAR WU", "CR SPRAGUE DAWLEY" )

question: which strain we want to hand pick?

Route

animals_route_M <- getSubjRoute(myDbToken, animals_species_M, inclUncertain = TRUE, routeFilter = c('ORAL GAVAGE', 'INTRAVENOUS'))

these are the different route,
c("ORAL GAVAGE", "INTRAVENOUS", "ORAL", NA, "INTRAVENOUS BOLUS")

I will only include "ORAL GAVAGE" and "INTRAVENOUS"