## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # Get sample data directory # pkg <- system.file("extdata", package = "fetch") # # # Create catalog # ct <- catalog(pkg, engines$csv) # # # View catalog # ct # # data catalog: 6 items # # - Source: C:/packages/fetch/inst/extdata # # - Engine: csv # # - Items: # # data item 'ADAE': 56 cols 150 rows # # data item 'ADEX': 17 cols 348 rows # # data item 'ADPR': 37 cols 552 rows # # data item 'ADPSGA': 42 cols 695 rows # # data item 'ADSL': 56 cols 87 rows # # data item 'ADVS': 37 cols 3617 rows ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # View info for catalog item # ct$ADEX # # data item 'ADEX': 17 cols 348 rows # # - Engine: csv # # - Size: 70.7 Kb # # - Last Modified: 2020-09-18 14:30:22 # # Name Column Class Label Format NAs MaxChar # # 1 ADEX STUDYID character NA 0 3 # # 2 ADEX USUBJID character NA 0 10 # # 3 ADEX SUBJID character NA 0 3 # # 4 ADEX SITEID character NA 0 2 # # 5 ADEX TRTP character NA 8 5 # # 6 ADEX TRTPN numeric NA 8 1 # # 7 ADEX TRTA character NA 8 5 # # 8 ADEX TRTAN numeric NA 8 1 # # 9 ADEX RANDFL character NA 0 1 # # 10 ADEX SAFFL character NA 0 1 # # 11 ADEX MITTFL character NA 0 1 # # 12 ADEX PPROTFL character NA 0 1 # # 13 ADEX PARAM character NA 0 45 # # 14 ADEX PARAMCD character NA 0 8 # # 15 ADEX PARAMN numeric NA 0 1 # # 16 ADEX AVAL numeric NA 16 4 # # 17 ADEX AVALCAT1 character NA 87 10 # ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # # Fetch data from a catalog # dt <- fetch(ct$ADEX) # # # View data # dt # # A tibble: 348 × 17 # # STUDYID USUBJID SUBJID SITEID TRTP TRTPN TRTA TRTAN RANDFL SAFFL MITTFL PPROTFL # # # # 1 ABC ABC-01-049 049 01 ARM D 4 ARM D 4 Y Y Y Y # # 2 ABC ABC-01-049 049 01 ARM D 4 ARM D 4 Y Y Y Y # # 3 ABC ABC-01-049 049 01 ARM D 4 ARM D 4 Y Y Y Y # # 4 ABC ABC-01-049 049 01 ARM D 4 ARM D 4 Y Y Y Y # # 5 ABC ABC-01-050 050 01 ARM B 2 ARM B 2 Y Y Y Y # # 6 ABC ABC-01-050 050 01 ARM B 2 ARM B 2 Y Y Y Y # # 7 ABC ABC-01-050 050 01 ARM B 2 ARM B 2 Y Y Y Y # # 8 ABC ABC-01-050 050 01 ARM B 2 ARM B 2 Y Y Y Y # # 9 ABC ABC-01-051 051 01 ARM A 1 ARM A 1 Y Y Y Y # # 10 ABC ABC-01-051 051 01 ARM A 1 ARM A 1 Y Y Y Y # # 338 more rows # # 5 more variables: PARAM , PARAMCD , PARAMN , AVAL , # # AVALCAT1 # # Use `print(n = ...)` to see more rows # ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # Get sample data directory # pkg <- system.file("extdata", package = "fetch") # # # Create catalog # ct <- catalog(pkg, engines$csv) # # # Subset data for a specific subject # dt <- fetch(ct$ADVS, where = expression(SUBJID == '049')) # # # View data subset # dt # # A tibble: 44 × 37 # # STUDYID USUBJID SUBJID SITEID SRCDOM SRCVAR SRCSEQ TRTP TRTPN TRTA TRTAN RANDFL # # # # 1 ABC ABC-01-049 049 01 VS VSSTRESN 9 ARM D 4 ARM D 4 Y # # 2 ABC ABC-01-049 049 01 VS VSSTRESN 41 ARM D 4 ARM D 4 Y # # 3 ABC ABC-01-049 049 01 NA NA NA ARM D 4 ARM D 4 Y # # 4 ABC ABC-01-049 049 01 VS VSSTRESN 34 ARM D 4 ARM D 4 Y # # 5 ABC ABC-01-049 049 01 VS VSSTRESN 35 ARM D 4 ARM D 4 Y # # 6 ABC ABC-01-049 049 01 VS VSSTRESN 36 ARM D 4 ARM D 4 Y # # 7 ABC ABC-01-049 049 01 VS VSSTRESN 37 ARM D 4 ARM D 4 Y # # 8 ABC ABC-01-049 049 01 VS VSSTRESN 38 ARM D 4 ARM D 4 Y # # 9 ABC ABC-01-049 049 01 VS VSSTRESN 39 ARM D 4 ARM D 4 Y # # 10 ABC ABC-01-049 049 01 VS VSSTRESN 40 ARM D 4 ARM D 4 Y # # 34 more rows # # 25 more variables: SAFFL , MITTFL , PPROTFL , TRTSDT , # # TRTEDT , ADT , ADY , ADTF , AVISIT , AVISITN , # # PARAM , PARAMCD , PARAMN , PARAMTYP , AVAL , BASE , # # CHG , AWRANGE , AWTARGET , AWTDIFF , AWLO , AWHI , # # AWU , ABLFL , ANL01FL # # Use `print(n = ...)` to see more rows # # ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # Get sample data directory # pkg <- system.file("extdata", package = "fetch") # # # Create catalog # ct <- catalog(pkg, engines$csv) # # # Subset data for a specific subject # dt <- fetch(ct$ADVS, top = 5, where = expression(SUBJID == '049')) # # # View results # dt # # A tibble: 5 × 37 # # STUDYID USUBJID SUBJID SITEID SRCDOM SRCVAR SRCSEQ TRTP TRTPN TRTA TRTAN RANDFL SAFFL # # # # 1 ABC ABC-01-… 049 01 VS VSSTR… 9 ARM D 4 ARM D 4 Y Y # # 2 ABC ABC-01-… 049 01 VS VSSTR… 41 ARM D 4 ARM D 4 Y Y # # 3 ABC ABC-01-… 049 01 NA NA NA ARM D 4 ARM D 4 Y Y # # 4 ABC ABC-01-… 049 01 VS VSSTR… 34 ARM D 4 ARM D 4 Y Y # # 5 ABC ABC-01-… 049 01 VS VSSTR… 35 ARM D 4 ARM D 4 Y Y # # 24 more variables: MITTFL , PPROTFL , TRTSDT , TRTEDT , # # ADT , ADY , ADTF , AVISIT , AVISITN , PARAM , # # PARAMCD , PARAMN , PARAMTYP , AVAL , BASE , CHG , # # AWRANGE , AWTARGET , AWTDIFF , AWLO , AWHI , AWU , # # ABLFL , ANL01FL # # ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # Get sample data directory # pkg <- system.file("extdata", package = "fetch") # # # Create catalog, applying pattern to dataset names # ct <- catalog(pkg, engines$csv, pattern = "*S*") # # # View catalog # ct # # data catalog: 3 items # # - Source: C:/packages/fetch/inst/extdata # # - Engine: csv # # - Pattern: *S* # # - Items: # # data item 'ADPSGA': 42 cols 695 rows # # data item 'ADSL': 56 cols 87 rows # # data item 'ADVS': 37 cols 3617 rows # ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # Get sample data directory # pkg <- system.file("extdata", package = "fetch") # # # Create catalog without where expression # ct1 <- catalog(pkg, engines$csv) # # # View catalog # ct1 # # data catalog: 6 items # # - Source: C:/packages/fetch/inst/extdata # # - Engine: csv # # - Items: # # data item 'ADAE': 56 cols 150 rows # # data item 'ADEX': 17 cols 348 rows # # data item 'ADPR': 37 cols 552 rows # # data item 'ADPSGA': 42 cols 695 rows # # data item 'ADSL': 56 cols 87 rows # # data item 'ADVS': 37 cols 3617 rows # # # Create catalog with where expression # ct2 <- catalog(pkg, engines$csv, where = expression(SUBJID == '049')) # # # View catalog # ct2 # # data catalog: 6 items # # - Source: C:/packages/fetch/inst/extdata # # - Engine: csv # # - Where: SUBJID == "049" # # - Items: # # # data item 'ADAE': 56 cols 5 rows # # - Where: SUBJID == "049" # # # data item 'ADEX': 17 cols 4 rows # # - Where: SUBJID == "049" # # # data item 'ADPR': 37 cols 7 rows # # - Where: SUBJID == "049" # # # data item 'ADPSGA': 42 cols 10 rows # # - Where: SUBJID == "049" # # # data item 'ADSL': 56 cols 1 rows # # - Where: SUBJID == "049" # # # data item 'ADVS': 37 cols 44 rows # # - Where: SUBJID == "049" ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # Subset data for a specific subject # dt1 <- fetch(ct2$ADVS) # # # View results of ADVS fetch # dt1 # # A tibble: 44 × 37 # # STUDYID USUBJID SUBJID SITEID SRCDOM SRCVAR SRCSEQ TRTP TRTPN TRTA TRTAN RANDFL SAFFL # # # # 1 ABC ABC-01-049 049 01 VS VSSTRESN 9 ARM D 4 ARM D 4 Y Y # # 2 ABC ABC-01-049 049 01 VS VSSTRESN 41 ARM D 4 ARM D 4 Y Y # # 3 ABC ABC-01-049 049 01 NA NA NA ARM D 4 ARM D 4 Y Y # # 4 ABC ABC-01-049 049 01 VS VSSTRESN 34 ARM D 4 ARM D 4 Y Y # # 5 ABC ABC-01-049 049 01 VS VSSTRESN 35 ARM D 4 ARM D 4 Y Y # # 6 ABC ABC-01-049 049 01 VS VSSTRESN 36 ARM D 4 ARM D 4 Y Y # # 7 ABC ABC-01-049 049 01 VS VSSTRESN 37 ARM D 4 ARM D 4 Y Y # # 8 ABC ABC-01-049 049 01 VS VSSTRESN 38 ARM D 4 ARM D 4 Y Y # # 9 ABC ABC-01-049 049 01 VS VSSTRESN 39 ARM D 4 ARM D 4 Y Y # # 10 ABC ABC-01-049 049 01 VS VSSTRESN 40 ARM D 4 ARM D 4 Y Y # # 34 more rows # # 24 more variables: MITTFL , PPROTFL , TRTSDT , TRTEDT , ADT , # # ADY , ADTF , AVISIT , AVISITN , PARAM , PARAMCD , # # PARAMN , PARAMTYP , AVAL , BASE , CHG , AWRANGE , # # AWTARGET , AWTDIFF , AWLO , AWHI , AWU , ABLFL , # # ANL01FL # # Use `print(n = ...)` to see more rows # # # # View results of ADSL fetch # dt2 <- fetch(ct2$ADSL) # # A tibble: 1 × 56 # # STUDYID USUBJID SUBJID SITEID AGE AGEU AGEGR1 SEX RACE RACEN ETHNIC ETHNICN COUNTRY # # # # 1 ABC ABC-01-049 049 01 39 YEARS 30-39 y… M WHITE 5 NOT H… 2 NA # # 43 more variables: ARM , ACTARM , TRT01P , TRT01PN , TRT01A , # # TRT01AN , TRTSDT , TRTEDT , TRTDURN , TRTDURU , TR01SDT , # # TR01EDT , INCNFL , RANDFL , RANDEXC1 , RANDEXC2 , RANDEXC3 , # # RANDEXC4 , SAFFL , SAFEXC1 , SAFEXC2 , MITTFL , MITTEXC1 , # # MITTEXC2 , PPROTFL , PPROTEX1 , PPROTEX2 , PPROTEX3 , # # PPROTEX4 , COMPLFL , STDYDISP , STDYREAS , INCNDT , RANDDT , # # DTHDT , DTHFL , MISSDOSE , TP1TRTR , TP2TRTR , TP3TRTR ,... # ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # Get sample data directory # pkg <- system.file("extdata", package = "fetch") # # # Create catalog without import spec # ct <- catalog(pkg, engines$csv) # # # View dictionary for ADVS # ct$ADVS # # data item 'ADVS': 37 cols 3617 rows # # - Engine: csv # # - Size: 1.1 Mb # # - Last Modified: 2020-09-18 14:30:22 # # Name Column Class Label Format NAs MaxChar # # 1 ADVS STUDYID character NA 0 3 # # 2 ADVS USUBJID character NA 0 10 # # 3 ADVS SUBJID character NA 0 3 # # 4 ADVS SITEID character NA 0 2 # # 5 ADVS SRCDOM character NA 85 2 # # 6 ADVS SRCVAR character NA 85 8 # # 7 ADVS SRCSEQ numeric NA 85 2 # # 8 ADVS TRTP character NA 85 5 # # 9 ADVS TRTPN numeric NA 85 1 # # 10 ADVS TRTA character NA 85 5 # # 11 ADVS TRTAN numeric NA 85 1 # # 12 ADVS RANDFL character NA 0 1 # # 13 ADVS SAFFL character NA 0 1 # # 14 ADVS MITTFL character NA 0 1 # # 15 ADVS PPROTFL character NA 0 1 # # 16 ADVS TRTSDT character NA 54 9 # Character by default # # 17 ADVS TRTEDT character NA 119 9 # Character by default # # 18 ADVS ADT character NA 0 9 # # 19 ADVS ADY numeric NA 54 4 # # 20 ADVS ADTF logical NA 3617 0 # # 21 ADVS AVISIT character NA 50 14 # # 22 ADVS AVISITN numeric NA 50 2 # # 23 ADVS PARAM character NA 0 35 # # 24 ADVS PARAMCD character NA 0 6 # # 25 ADVS PARAMN numeric NA 0 1 # # 26 ADVS PARAMTYP character NA 3532 7 # # 27 ADVS AVAL numeric NA 0 5 # # 28 ADVS BASE numeric NA 70 5 # # 29 ADVS CHG numeric NA 1312 4 # # 30 ADVS AWRANGE character NA 1331 25 # # 31 ADVS AWTARGET numeric NA 1331 3 # # 32 ADVS AWTDIFF numeric NA 1331 2 # # 33 ADVS AWLO numeric NA 1331 3 # # 34 ADVS AWHI numeric NA 1331 3 # # 35 ADVS AWU character NA 1331 4 # # 36 ADVS ABLFL character NA 2869 1 # # 37 ADVS ANL01FL character NA 448 1 # ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # Get sample data directory # pkg <- system.file("extdata", package = "fetch") # # # Create import spec # spc <- import_spec(TRTSDT = "date=%d%b%Y", # TRTEDT = "date=%d%b%Y") # # # Create catalog with import spec # ct <- catalog(pkg, engines$csv, import_specs = spc) # # # View dictionary for ADVS with Import Spec # ct$ADVS # # data item 'ADVS': 37 cols 3617 rows # # - Engine: csv # # - Size: 1.1 Mb # # - Last Modified: 2020-09-18 14:30:22 # # Name Column Class Label Format NAs MaxChar # # 1 ADVS STUDYID character NA 0 3 # # 2 ADVS USUBJID character NA 0 10 # # 3 ADVS SUBJID character NA 0 3 # # 4 ADVS SITEID character NA 0 2 # # 5 ADVS SRCDOM character NA 85 2 # # 6 ADVS SRCVAR character NA 85 8 # # 7 ADVS SRCSEQ numeric NA 85 2 # # 8 ADVS TRTP character NA 85 5 # # 9 ADVS TRTPN numeric NA 85 1 # # 10 ADVS TRTA character NA 85 5 # # 11 ADVS TRTAN numeric NA 85 1 # # 12 ADVS RANDFL character NA 0 1 # # 13 ADVS SAFFL character NA 0 1 # # 14 ADVS MITTFL character NA 0 1 # # 15 ADVS PPROTFL character NA 0 1 # # 16 ADVS TRTSDT Date NA 54 10 # Converted to Date # # 17 ADVS TRTEDT Date NA 119 10 # Converted to Date # # 18 ADVS ADT character NA 0 9 # # 19 ADVS ADY numeric NA 54 4 # # 20 ADVS ADTF logical NA 3617 0 # # 21 ADVS AVISIT character NA 50 14 # # 22 ADVS AVISITN numeric NA 50 2 # # 23 ADVS PARAM character NA 0 35 # # 24 ADVS PARAMCD character NA 0 6 # # 25 ADVS PARAMN numeric NA 0 1 # # 26 ADVS PARAMTYP character NA 3532 7 # # 27 ADVS AVAL numeric NA 0 5 # # 28 ADVS BASE numeric NA 70 5 # # 29 ADVS CHG numeric NA 1312 4 # # 30 ADVS AWRANGE character NA 1331 25 # # 31 ADVS AWTARGET numeric NA 1331 3 # # 32 ADVS AWTDIFF numeric NA 1331 2 # # 33 ADVS AWLO numeric NA 1331 3 # # 34 ADVS AWHI numeric NA 1331 3 # # 35 ADVS AWU character NA 1331 4 # # 36 ADVS ABLFL character NA 2869 1 # # 37 ADVS ANL01FL character NA 448 1 # ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # Get sample data directory # pkg <- system.file("extdata", package = "fetch") # # # Create import spec # spc <- import_spec(TRTSDT = "date=%d%b%Y", # TRTEDT = "date=%d%b%Y") # # # Create catalog with import spec # ct <- catalog(pkg, engines$csv, import_specs = spc) # # # View dictionary for ADVS with Import Spec # ct$ADVS # # data item 'ADVS': 37 cols 3617 rows # # - Engine: csv # # - Size: 1.1 Mb # # - Last Modified: 2020-09-18 14:30:22 # # Name Column Class Label Format NAs MaxChar # # 1 ADVS STUDYID character NA 0 3 # # 2 ADVS USUBJID character NA 0 10 # # 3 ADVS SUBJID character NA 0 3 # # 4 ADVS SITEID character NA 0 2 # # 5 ADVS SRCDOM character NA 85 2 # # 6 ADVS SRCVAR character NA 85 8 # # 7 ADVS SRCSEQ numeric NA 85 2 # # 8 ADVS TRTP character NA 85 5 # # 9 ADVS TRTPN numeric NA 85 1 # # 10 ADVS TRTA character NA 85 5 # # 11 ADVS TRTAN numeric NA 85 1 # # 12 ADVS RANDFL character NA 0 1 # # 13 ADVS SAFFL character NA 0 1 # # 14 ADVS MITTFL character NA 0 1 # # 15 ADVS PPROTFL character NA 0 1 # # 16 ADVS TRTSDT Date NA 54 10 # # 17 ADVS TRTEDT Date NA 119 10 # # 18 ADVS ADT character NA 0 9 # # 19 ADVS ADY numeric NA 54 4 # # 20 ADVS ADTF logical NA 3617 0 # # 21 ADVS AVISIT character NA 50 14 # # 22 ADVS AVISITN numeric NA 50 2 # # 23 ADVS PARAM character NA 0 35 # # 24 ADVS PARAMCD character NA 0 6 # # 25 ADVS PARAMN numeric NA 0 1 # # 26 ADVS PARAMTYP character NA 3532 7 # # 27 ADVS AVAL numeric NA 0 5 # # 28 ADVS BASE numeric NA 70 5 # # 29 ADVS CHG numeric NA 1312 4 # # 30 ADVS AWRANGE character NA 1331 25 # # 31 ADVS AWTARGET numeric NA 1331 3 # # 32 ADVS AWTDIFF numeric NA 1331 2 # # 33 ADVS AWLO numeric NA 1331 3 # # 34 ADVS AWHI numeric NA 1331 3 # # 35 ADVS AWU character NA 1331 4 # # 36 ADVS ABLFL character NA 2869 1 # # 37 ADVS ANL01FL character NA 448 1