diff --git a/design/examples/PRIMEstudy/00- Load.R b/design/examples/mCRCpub/00- Load.R similarity index 100% rename from design/examples/PRIMEstudy/00- Load.R rename to design/examples/mCRCpub/00- Load.R diff --git a/design/examples/PRIMEstudy/01- ImportPRIME.R b/design/examples/mCRCpub/01- ImportPRIME.R similarity index 78% rename from design/examples/PRIMEstudy/01- ImportPRIME.R rename to design/examples/mCRCpub/01- ImportPRIME.R index 44455c0c..fd2e179d 100644 --- a/design/examples/PRIMEstudy/01- ImportPRIME.R +++ b/design/examples/mCRCpub/01- ImportPRIME.R @@ -18,10 +18,10 @@ #' UID values #' --------------------------------- -kras<-haven::read_sas("./design/examples/PRIMEstudy/data/biomark_pds2019.sas7bdat") +kras<-haven::read_sas("./design/examples/mCRCpub/data/biomark_pds2019.sas7bdat") kras0<-kras |> select("SUBJID", "BMMTR1") -adsl<-haven::read_sas("./design/examples/PRIMEstudy/data/adsl_pds2019.sas7bdat") +adsl<-haven::read_sas("./design/examples/mCRCpub/data/adsl_pds2019.sas7bdat") adsl0<-adsl |> select("SUBJID", "ATRT", "DTHDY", "DTH") |> mutate(STUDY="1", DTHYR=DTHDY/365.25) |> @@ -31,7 +31,7 @@ UIDlist<-unique(adsl0$SUBJID) #' length(UIDlist) #' 514 -adtr<-haven::read_sas("./design/examples/PRIMEstudy/data/adls_pds2019.sas7bdat") +adtr<-haven::read_sas("./design/examples/mCRCpub/data/adls_pds2019.sas7bdat") keepinadtr0<-c("SUBJID", "VISITDY", "VISIT", "LSSLD") adtr0<-adtr |> @@ -46,7 +46,7 @@ adtr0<-adtr |> #' length(unique(adtr0$SUBJID)) #' 263 -saveRDS(adtr0, file="./design/examples/PRIMEstudy/data/PRIMEads.rds") +saveRDS(adtr0, file="./design/examples/mCRCpub/data/PRIMEads.rds") diff --git a/design/examples/PRIMEstudy/02- DescPRIME.R b/design/examples/mCRCpub/02- DescPRIME.R similarity index 95% rename from design/examples/PRIMEstudy/02- DescPRIME.R rename to design/examples/mCRCpub/02- DescPRIME.R index 390b7541..885777b0 100644 --- a/design/examples/PRIMEstudy/02- DescPRIME.R +++ b/design/examples/mCRCpub/02- DescPRIME.R @@ -11,7 +11,7 @@ #' sessionInfo() -ads<-readRDS("./design/examples/PRIMEstudy/data/PRIMEads.rds") +ads<-readRDS("./design/examples/mCRCpub/data/PRIMEads.rds") #' =============================================== #' Visualize SLD diff --git a/design/examples/PRIMEstudy/03- jmPRIME.R b/design/examples/mCRCpub/03- jmPRIME.R similarity index 96% rename from design/examples/PRIMEstudy/03- jmPRIME.R rename to design/examples/mCRCpub/03- jmPRIME.R index 8e2cad20..242daf3c 100644 --- a/design/examples/PRIMEstudy/03- jmPRIME.R +++ b/design/examples/mCRCpub/03- jmPRIME.R @@ -11,7 +11,7 @@ #' sessionInfo() -ads<-readRDS("./design/examples/PRIMEstudy/data/PRIMEads.rds") +ads<-readRDS("./design/examples/mCRCpub/data/PRIMEads.rds") #' =============================================== #' Model SLD @@ -41,7 +41,7 @@ tgi.samples<-sampleStanModel(tgi.in, data=tgi.dat, tgi.out<-as.CmdStanMCMC(tgi.samples) print(tgi.out) -#' saveRDS(tgi.out, file="./design/examples/PRIMEstudy/PRIMEtgiout.rds") +#' saveRDS(tgi.out, file="./design/examples/mCRCpub/PRIMEtgiout.rds") #' Problems here: #' iPred vs. Obs diff --git a/design/examples/PRIMEstudy/data/PRIMEads.rds b/design/examples/mCRCpub/data/PRIMEads.rds similarity index 100% rename from design/examples/PRIMEstudy/data/PRIMEads.rds rename to design/examples/mCRCpub/data/PRIMEads.rds diff --git a/design/examples/PRIMEstudy/data/adls_pds2019.sas7bdat b/design/examples/mCRCpub/data/adls_pds2019.sas7bdat similarity index 100% rename from design/examples/PRIMEstudy/data/adls_pds2019.sas7bdat rename to design/examples/mCRCpub/data/adls_pds2019.sas7bdat diff --git a/design/examples/PRIMEstudy/data/adsl_pds2019.sas7bdat b/design/examples/mCRCpub/data/adsl_pds2019.sas7bdat similarity index 100% rename from design/examples/PRIMEstudy/data/adsl_pds2019.sas7bdat rename to design/examples/mCRCpub/data/adsl_pds2019.sas7bdat diff --git a/design/examples/PRIMEstudy/data/biomark_pds2019.sas7bdat b/design/examples/mCRCpub/data/biomark_pds2019.sas7bdat similarity index 100% rename from design/examples/PRIMEstudy/data/biomark_pds2019.sas7bdat rename to design/examples/mCRCpub/data/biomark_pds2019.sas7bdat diff --git a/design/examples/PRIMEstudy/trash/expon-ph-benchmark.R b/design/examples/mCRCpub/trash/expon-ph-benchmark.R similarity index 100% rename from design/examples/PRIMEstudy/trash/expon-ph-benchmark.R rename to design/examples/mCRCpub/trash/expon-ph-benchmark.R diff --git a/design/examples/PRIMEstudy/trash/expon-ph-outputs.R b/design/examples/mCRCpub/trash/expon-ph-outputs.R similarity index 100% rename from design/examples/PRIMEstudy/trash/expon-ph-outputs.R rename to design/examples/mCRCpub/trash/expon-ph-outputs.R diff --git a/design/examples/PRIMEstudy/trash/trash.R b/design/examples/mCRCpub/trash/trash.R similarity index 100% rename from design/examples/PRIMEstudy/trash/trash.R rename to design/examples/mCRCpub/trash/trash.R