System dependency specification file

rfacts has strict system dependencies.

FACTS Linux engines (>= 6.2.4)
FLFLL (>= 6.2.4)
Mono (>= 5.20.1.19)

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,2

Required columns

executable_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.

Connecting `rfacts` to the system dependencies

To 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_type

Use 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 rows

If you change RFACTS_PATHS, you need to call reset_rfacts_paths() or restart R in order for the changes to take effect.

System configuration

System dependency specification file

Required columns

Connecting rfacts to the system dependencies

Connecting `rfacts` to the system dependencies