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rfacts has strict system dependencies.
Before you can use rfacts to simulate trials in R, you must specify the paths to all these executable files in a CSV file. You can see an example CSV file at inst/example_paths.csv in the rfacts package source.
path <- system.file("example_paths.csv", package = "rfacts")
writeLines(readLines(path))
#> executable_type,facts_version,path,engine_name,param_set,param_type
#> mono,6.2.4,/PATH/TO/mono/mono-5.20.1.19/bin/mono,NA,NA,NA
#> mono,6.2.5,/PATH/TO/mono/mono-5.20.1.19/bin/mono,NA,NA,NA
#> flfll,6.2.4,/PATH/TO/flfll/prd/prior_versions/version_6.2.5/FLFLL.exe,NA,NA,NA
#> flfll,6.2.5,/PATH/TO/flfll/prd/prior_versions/version_6.2.5/FLFLL.exe,NA,NA,NA
#> engine,6.0.0.1,/PATH/TO/facts/engines/contin/6.0.0.1/contin.x,contin,NucleusParameterSet,1
#> engine,6.0.0.1,/PATH/TO/facts/engines/dichot/6.0.0.1/dichot.x,dichot,NucleusParameterSet,2
#> engine,6.0.0.1,/PATH/TO/facts/engines/multep/6.0.0.1/multep.x,multep,MultipleEndpointParameterSet,1
#> engine,6.0.0.1,/PATH/TO/facts/engines/tte/6.0.0.1/tte.x,tte,TTEDesignParameterSet,3
#> engine,6.0.0.1,/PATH/TO/facts/engines/aipf_contin/5.0.0.7/aipf_contin.x,aipf_contin,AIPFParameterSet,1
#> engine,6.0.0.1,/PATH/TO/facts/engines/aipf_dichot/5.0.0.7/aipf_dichot.x,aipf_dichot,AIPFParameterSet,2
#> engine,6.0.0.1,/PATH/TO/facts/engines/aipf_tte/5.0.0.9/aipf_tte.x,aipf_tte,AIPFParameterSet,3
#> engine,6.0.0.1,/PATH/TO/facts/engines/CRM/0.3.8.2/CRM.x,crm,CRMDesignParamSet,0
#> engine,6.2.5,/PATH/TO/facts/engines/contin/6.0.0.4/contin.x,contin,NucleusParameterSet,1
#> engine,6.2.5,/PATH/TO/facts/engines/dichot/6.0.0.4/dichot.x,dichot,NucleusParameterSet,2
#> engine,6.2.5,/PATH/TO/facts/engines/multep/6.0.0.4/multep.x,multep,MultipleEndpointParameterSet,1
#> engine,6.2.5,/PATH/TO/facts/engines/tte/6.0.0.4/tte.x,tte,TTEDesignParameterSet,3
#> engine,6.2.5,/PATH/TO/facts/engines/aipf_contin/6.0.0.4/aipf_contin.x,aipf_contin,AIPFParameterSet,1
#> engine,6.2.5,/PATH/TO/facts/engines/aipf_dichot/6.0.0.4/aipf_dichot.x,aipf_dichot,AIPFParameterSet,2
#> engine,6.2.5,/PATH/TO/facts/engines/aipf_tte/6.0.0.4/aipf_tte.x,aipf_tte,AIPFParameterSet,3
#> engine,6.2.5,/PATH/TO/facts/engines/CRM/6.0.0.4/CRM.x,crm,CRMDesignParamSet,0
#> engine,6.2.5,/PATH/TO/facts/engines/contin/6.0.0.4/contin.x,contin,SDBaseParameterSet,1
#> engine,6.2.5,/PATH/TO/facts/engines/dichot/6.0.0.4/dichot.x,dichot,SDBaseParameterSet,2executable_type: Must be "mono", "flfll", or "engine" to denote the general type of the executable.facts_version: The version of FACTS with which this executable is compatible.path: File path to the executable.engine_name: For engines only. Name of the engine. Must be one of the engine types in the example CSV file at system.file("example_paths.csv", package = "rfacts").param_set: For engines only. Parameter set designation listed in the XML code of FACTS files for that engine.param_type: For engines only. Parameter type designation listed in the XML code of FACTS files for that engine.rfacts to the system dependenciesTo allow rfacts to find the CSV file above, you must set the RFACTS_PATHS environment variable. For a single R session, you can do this with Sys.setenv(RFACTS_PATHS = "path/to/file.csv"). To set RFACTS_PATHS permanently for all future sessions, open your .Renviron file with usethis::edit_r_environ() and add a line with RFACTS_PATHS=path/to/file.csv. Then, restart R so the changes take effect. Verify that you did this correctly by checking the value of the environment variable.
Sys.getenv("RFACTS_PATHS")
#> [1] "/tmp/RtmpmVNWMt/Rinst24627673cd7a/rfacts/example_paths.csv"Check the system dependency information with rfacts_paths().
library(rfacts)
rfacts_paths()
#> # A tibble: 22 × 6
#> executable_type facts_version path engin…¹ param…² param…³
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 mono 6.2.4 /PATH/TO/mono/mono-5.2… <NA> <NA> <NA>
#> 2 mono 6.2.5 /PATH/TO/mono/mono-5.2… <NA> <NA> <NA>
#> 3 flfll 6.2.4 /PATH/TO/flfll/prd/pri… <NA> <NA> <NA>
#> 4 flfll 6.2.5 /PATH/TO/flfll/prd/pri… <NA> <NA> <NA>
#> 5 engine 6.0.0.1 /PATH/TO/facts/engines… contin Nucleu… 1
#> 6 engine 6.0.0.1 /PATH/TO/facts/engines… dichot Nucleu… 2
#> 7 engine 6.0.0.1 /PATH/TO/facts/engines… multep Multip… 1
#> 8 engine 6.0.0.1 /PATH/TO/facts/engines… tte TTEDes… 3
#> 9 engine 6.0.0.1 /PATH/TO/facts/engines… aipf_c… AIPFPa… 1
#> 10 engine 6.0.0.1 /PATH/TO/facts/engines… aipf_d… AIPFPa… 2
#> # … with 12 more rows, and abbreviated variable names ¹engine_name, ²param_set,
#> # ³param_typeUse rfacts_sitrep() to verify that all the executables exist and are indeed executable. This vignette uses toy paths that do not actually exist. In your setup, if exists and is_executable are all TRUE, then your setup is configured correctly.
rfacts_sitrep()
#> # A tibble: 22 × 5
#> executable_type facts_version exists is_executable path
#> <chr> <chr> <lgl> <lgl> <chr>
#> 1 mono 6.2.4 FALSE FALSE /PATH/TO/mono/mono-5.20.1…
#> 2 mono 6.2.5 FALSE FALSE /PATH/TO/mono/mono-5.20.1…
#> 3 flfll 6.2.4 FALSE FALSE /PATH/TO/flfll/prd/prior_…
#> 4 flfll 6.2.5 FALSE FALSE /PATH/TO/flfll/prd/prior_…
#> 5 engine 6.0.0.1 FALSE FALSE /PATH/TO/facts/engines/co…
#> 6 engine 6.0.0.1 FALSE FALSE /PATH/TO/facts/engines/di…
#> 7 engine 6.0.0.1 FALSE FALSE /PATH/TO/facts/engines/mu…
#> 8 engine 6.0.0.1 FALSE FALSE /PATH/TO/facts/engines/tt…
#> 9 engine 6.0.0.1 FALSE FALSE /PATH/TO/facts/engines/ai…
#> 10 engine 6.0.0.1 FALSE FALSE /PATH/TO/facts/engines/ai…
#> # … with 12 more rowsIf you change RFACTS_PATHS, you need to call reset_rfacts_paths() or restart R in order for the changes to take effect.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.