diff --git a/dev/articles/adrs.html b/dev/articles/adrs.html index 4a04d7e3..86655cdb 100644 --- a/dev/articles/adrs.html +++ b/dev/articles/adrs.html @@ -209,8 +209,8 @@

Read in Data= adsl_vars, by_vars = exprs(STUDYID, USUBJID) ) -
- +
+

Pre-processing of Input Records @@ -258,8 +258,8 @@

Select Overal PARCAT2 = "Investigator", PARCAT3 = "RECIST 1.1" )

-
- +
+

Partial Date Imputation and Deriving ADT, @@ -278,8 +278,8 @@

Partial Date I date_imputation = "last" ) %>% mutate(AVISIT = VISIT)

-
- +
+

Derive AVALC and AVAL @@ -295,8 +295,8 @@

Derive AVALC and AVAL AVALC = RSSTRESC, AVAL = aval_resp(AVALC) )

-
- +
+

Flag Worst Assessment at Each Date (ANL01FL) @@ -330,8 +330,8 @@

Flag Worst Assessment at Each Date (ANL01FL) ), filter = !is.na(AVAL) & ADT >= RANDDT )

-
-

Here is an alternative example where those records occurring after +

+

Here is an alternative example where those records occurring after new anti-cancer therapy are additionally excluded (where NACTDT would be pre-derived as first date of new anti-cancer therapy. See admiralonco Creating and Using New Anti-Cancer Start Date for @@ -363,8 +363,8 @@

Flag Assessments up to First PD (ANL02FL) selection = "before", inclusive = TRUE ) -
- +
+

Select Source Assessments for Parameter derivations @@ -373,8 +373,8 @@

Select Source Asses assessments up to and including first PD are considered.

 ovr <- filter(adrs, PARAMCD == "OVR" & ANL01FL == "Y" & ANL02FL == "Y")
-
- +
+

@@ -528,8 +528,8 @@

Derive Progressive Disease Parameter= "Y" ) )

-
-

For progressive disease, response and death parameters shown in steps +

+

For progressive disease, response and death parameters shown in steps here and below, in our examples we show these as ADRS parameters, but they could equally be achieved via ADSL dates or ADEVENT parameters. If you prefer to store as an @@ -577,8 +577,8 @@

Derive Response Parameter ANL01FL = "Y" ) ) -
- +
+

Derive Clinical Benefit Parameter @@ -627,8 +627,8 @@

Derive Clinical Benefit Parameter= "Y" ) )

-
- +
+

Derive Best Overall Response Parameter @@ -667,8 +667,8 @@

Derive Best Overall Response Parameter ANL01FL = "Y" ) )

-
-

Note that the above gives pre-defined AVAL values +

+

Note that the above gives pre-defined AVAL values (defined by aval_resp()) of: "CR" ~ 1, "PR" ~ 2, "SD" ~ 3, "NON-CR/NON-PD" ~ 4, "PD" ~ 5, @@ -719,8 +719,8 @@

Derive Best Overall Response of CR/PR Parameter ANL01FL = "Y" ) ) -
- +
+

Derive Response Parameters requiring Confirmation @@ -897,8 +897,8 @@

Derive Response Parameters requiring Confirmation= "Y" ) )

-
- +
+

Derive Non-standard Parameters @@ -1017,8 +1017,8 @@

Derive Parameters using Independent Review Facility (IRF)/Blinded PARCAT2 = "Blinded Independent Central Review", PARCAT3 = "RECIST 1.1" )

-
-

Then in all the calls to the parameter derivation functions you would +

+

Then in all the calls to the parameter derivation functions you would replace ovr = ovr with ovr == ovrb in the value of the source_datasets argument.

@@ -1052,8 +1052,8 @@

Derive Death Parameter ) ) %>% select(-DTHDT) -
- +
+

Derive Last Disease Assessment Parameters @@ -1078,8 +1078,8 @@

Derive Last Disease Assessment Parameters ANL01FL = "Y" ) )

-
- +
+

Derive Measurable Disease at Baseline Parameter @@ -1110,8 +1110,8 @@

Derive Measurable Disease at Baseline Parameter ANL01FL = "Y" ) )

-
- +
+

Assign ASEQ @@ -1125,8 +1125,8 @@

Assign ASEQ order = exprs(PARAMCD, ADT, VISITNUM, RSSEQ), check_type = "error" )

-
- +
+

Add ADSL variables @@ -1140,8 +1140,8 @@

Add ADSL variables dataset_add = select(adsl, !!!negate_vars(adsl_vars)), by_vars = exprs(STUDYID, USUBJID) )

-
- +
+
diff --git a/dev/articles/adrs_basic.html b/dev/articles/adrs_basic.html index d50e6489..7164629e 100644 --- a/dev/articles/adrs_basic.html +++ b/dev/articles/adrs_basic.html @@ -209,8 +209,8 @@

Read in Data= adsl_vars, by_vars = exprs(STUDYID, USUBJID) )

-
- +
+

Pre-processing of Input Records @@ -258,8 +258,8 @@

Select Overal PARCAT2 = "Investigator", PARCAT3 = "RECIST 1.1" )

-
- +
+

Partial Date Imputation and Deriving ADT, @@ -278,8 +278,8 @@

Partial Date I date_imputation = "last" ) %>% mutate(AVISIT = VISIT)

-
- +
+

Derive AVALC and AVAL @@ -295,8 +295,8 @@

Derive AVALC and AVAL AVALC = RSSTRESC, AVAL = aval_resp(AVALC) )

-
- +
+

Flag Worst Assessment at Each Date (ANL01FL) @@ -330,8 +330,8 @@

Flag Worst Assessment at Each Date (ANL01FL) ), filter = !is.na(AVAL) & ADT >= RANDDT )

-
-

Here is an alternative example where those records occurring after +

+

Here is an alternative example where those records occurring after new anti-cancer therapy are additionally excluded (where NACTDT would be pre-derived as first date of new anti-cancer therapy. See admiralonco Creating and Using New Anti-Cancer Start Date for @@ -409,8 +409,8 @@

Derive Progressive Disease Parameter= "Y" ) ) -
-

For progressive disease, response and death parameters shown in steps +

+

For progressive disease, response and death parameters shown in steps here and below, in our examples we show these as ADRS parameters, but they could equally be achieved via ADSL dates or ADEVENT parameters. If you prefer to store as an @@ -463,8 +463,8 @@

Derive Response Parameter ANL01FL = "Y" ) ) -
- +
+

Derive Clinical Benefit Parameter @@ -504,8 +504,8 @@

Derive Clinical Benefit Parameter= "Y" ) )

-
- +
+

Derive Best Overall Response Parameter @@ -535,8 +535,8 @@

Derive Best Overall Response Parameter ANL01FL = "Y" ) )

-
-

Note that the above gives pre-defined AVAL values +

+

Note that the above gives pre-defined AVAL values (defined by aval_resp()) of: "CR" ~ 1, "PR" ~ 2, "SD" ~ 3, "NON-CR/NON-PD" ~ 4, "PD" ~ 5, @@ -589,8 +589,8 @@

Derive Best Overall Response of CR/PR Parameter ANL01FL = "Y" ) ) -
- +
+

Derive Response Parameters requiring Confirmation @@ -686,8 +686,8 @@

Derive Response Parameters requiring Confirmation= "Y" ) )

-
- +
+

Derive Parameters using Independent Review Facility (IRF)/Blinded @@ -713,8 +713,8 @@

Derive Parameters using Independent Review Facility (IRF)/Blinded PARCAT2 = "Blinded Independent Central Review", PARCAT3 = "RECIST 1.1" )

-
-

Then in all the calls to the parameter derivation functions you would +

+

Then in all the calls to the parameter derivation functions you would replace the PARAMCD == "OVR" source with PARAMCD == "OVRR1".

@@ -748,8 +748,8 @@

Derive Death Parameter ) ) %>% select(-DTHDT) -
- +
+

Derive Last Disease Assessment Parameters @@ -774,8 +774,8 @@

Derive Last Disease Assessment Parameters ANL01FL = "Y" ) )

-
- +
+

Derive Measurable Disease at Baseline Parameter @@ -806,8 +806,8 @@

Derive Measurable Disease at Baseline Parameter ANL01FL = "Y" ) )

-
- +
+

Assign ASEQ @@ -821,8 +821,8 @@

Assign ASEQ order = exprs(PARAMCD, ADT, VISITNUM, RSSEQ), check_type = "error" )

-
- +
+

Add ADSL variables @@ -836,8 +836,8 @@

Add ADSL variables dataset_add = select(adsl, !!!negate_vars(adsl_vars)), by_vars = exprs(STUDYID, USUBJID) )

-
- +
+
diff --git a/dev/articles/adtr.html b/dev/articles/adtr.html index d3d1d92f..6cf6aff5 100644 --- a/dev/articles/adtr.html +++ b/dev/articles/adtr.html @@ -269,8 +269,8 @@

Merge TR with TU and Derive New "NON-NODAL" ) )

-
-

Furthermore, you could create additional new variables that are +

+

Furthermore, you could create additional new variables that are required downstream when deriving the required parameters. For example, here we include lesion ID expected (LSEXP) and lesion ID assessed (LSASS).

@@ -280,8 +280,8 @@

Merge TR with TU and Derive New LSEXP = TRLNKID, LSASS = if_else(!is.na(TRSTRESN), TRLNKID, NA_character_) ) -
- +
+

Pre-processing of Input Records @@ -320,8 +320,8 @@

Partial Date I reference_date = RANDDT, source_vars = exprs(ADT) )

-
- +
+

Unscheduled visits @@ -382,8 +382,8 @@

Derive Parameters for Lesion Diameters (LDIAMn ANL01FL = if_else(!is.na(AVAL), "Y", NA_character_) ) %>% select(-tmp_lesion_nr)

-
- +
+

Derive Parameter for Sum of Diameter and Analysis Flag @@ -423,8 +423,8 @@

Derive Parameter for Sum of Diameter and Analysis Flag PARCAT3 = "RECIST 1.1" ) )

-
-

The analysis flag ANL01FL flags the sum of diameters +

+

The analysis flag ANL01FL flags the sum of diameters where the number of lesions assessed at baseline and at post-baseline match. To assess whether the number of lesions expected and assessed match, you could compare lesion identifiers (TR.TRLNKID) or @@ -518,8 +518,8 @@

Derive NADIR mode = "first", check_type = "none" ) -
- +
+

Derive Change from Baseline (CHG, @@ -539,8 +539,8 @@

Derive Change from Baseline (CHG, CHGNAD = AVAL - NADIR, PCHGNAD = if_else(NADIR == 0, NA_real_, 100 * CHGNAD / NADIR) )

-
- +
+

Derive Additional Flag Variables @@ -565,8 +565,8 @@

1. Take the date of PD from new_var = PDFL, condition = AVALC == "Y" )
-
- +
+
2. Take the first date when the overall response is PD @@ -587,8 +587,8 @@
2. Take the new_var = PDFL, condition = RSSTRESC == "PD" )
-
- +
+
3. Target lesion response of no CR at the current @@ -601,8 +601,8 @@
= if_else(NADIR == 0, "Y", NA_character_), PDFL = if_else(is.na(CRFL) & CRNFL == "Y", "Y", NA_character_) )
-
- +
+
4. Calculate from source data @@ -628,8 +628,8 @@
4. Calculate from source dataNA_character_ ) )
-
- +
+ @@ -669,8 +669,8 @@

Derive Analysis Flags ANLzzFL filter = ANL01FL == "Y" & POSTRNDFL == "Y" ) %>% select(-POSTRNDFL) -
-

Analysis 03 flag (ANL03FL) includes all sum of diameters +

+

Analysis 03 flag (ANL03FL) includes all sum of diameters where all lesions were assessed (where ANL01FL == "Y") until the patient has PD, indicated by using the PDFL variable.

@@ -689,8 +689,8 @@

Derive Analysis Flags ANLzzFL ), filter = ANL01FL == "Y" | PDFL == "Y" ) -
-

Analysis 04 flag (ANL04FL) includes all sum of diameters +

+

Analysis 04 flag (ANL04FL) includes all sum of diameters where all lesions were assessed (where ANL01FL == "Y") and additionally those indicating PD using the PDFL variable.

@@ -699,8 +699,8 @@

Derive Analysis Flags ANLzzFL mutate( ANL04FL = if_else(ANL01FL == "Y" | PDFL == "Y", "Y", NA_character_) ) -
-
+

+
 adtr <- bind_rows(adtr, adtr_sum)
@@ -716,8 +716,8 @@

Derive Analysis Sequence Number (ASEQ)= exprs(PARAMCD, AVISITN, TRSEQ), check_type = "error" )

-
- +
+

Add ADSL Variables @@ -731,8 +731,8 @@

Add ADSL Variables= select(adsl, !!!negate_vars(adsl_vars)), by_vars = exprs(STUDYID, USUBJID) )

-
- +
+
diff --git a/dev/articles/adtte.html b/dev/articles/adtte.html index 06a1dedd..7e2e8879 100644 --- a/dev/articles/adtte.html +++ b/dev/articles/adtte.html @@ -374,8 +374,8 @@

Pre-Defined Time-to-Event Sour source_datasets = list(adsl = adsl, adrs = adrs), set_values_to = exprs(PARAMCD = "RSD", PARAM = "Duration of Response") )

-
- +
+

Creating Your Own Time-to-Event Source Objects @@ -469,8 +469,8 @@

Derive Analysis Value (AVAL) start_date = STARTDT, end_date = ADT )

-
-

Other time units, such as months that we commonly see in oncology +

+

Other time units, such as months that we commonly see in oncology analyses, can be requested by specifying the out_unit parameter. See the example below. Note that because of the underlying lubridate::time_length() function that is used here this @@ -507,8 +507,8 @@

Derive Analysis Sequence Number (ASEQ)= exprs(PARAMCD), check_type = "error" ) -
- +
+

Add ADSL Variables @@ -523,8 +523,8 @@

Add ADSL Variables= exprs(ARMCD, ARM, ACTARMCD, ACTARM, AGE, SEX), by_vars = exprs(STUDYID, USUBJID) )

-
- +
+
diff --git a/dev/articles/irecist.html b/dev/articles/irecist.html index df0e90f7..d8908287 100644 --- a/dev/articles/irecist.html +++ b/dev/articles/irecist.html @@ -203,8 +203,8 @@

Read in Data= adsl_vars, by_vars = exprs(STUDYID, USUBJID) )

-
- +
+

Pre-processing of Input Records @@ -251,8 +251,8 @@

Select Overal PARCAT2 = "Investigator", PARCAT3 = "iRECIST" )

-
- +
+

Partial Date Imputation and Deriving ADT, @@ -271,8 +271,8 @@

Partial Date I date_imputation = "last" ) %>% mutate(AVISIT = VISIT)

-
- +
+

Derive AVALC and AVAL @@ -308,8 +308,8 @@

Derive AVALC and AVAL AVALC = RSSTRESC, AVAL = aval_resp_new(AVALC) )

-
- +
+

Flag Worst Assessment at Each Date (ANL01FL) @@ -331,8 +331,8 @@

Flag Worst Assessment at Each Date (ANL01FL) ), filter = !is.na(AVAL) & AVALC != "MISSING" & ADT >= RANDDT )

-
-

Here is an alternative example where those records occurring after +

+

Here is an alternative example where those records occurring after new anti-cancer therapy are additionally excluded (where NACTDT would be pre-derived as first date of new anti-cancer therapy. See admiralonco Creating and Using New Anti-Cancer Start Date for @@ -364,8 +364,8 @@

Flag Assessments up to First iCPD (ANL02FL) selection = "before", inclusive = TRUE ) -
- +
+

Select Source Assessments for Parameter derivations @@ -374,8 +374,8 @@

Select Source Asses assessments up to and including first iCPD are considered.

 ovr <- filter(adrs, PARAMCD == "OVR" & ANL01FL == "Y" & ANL02FL == "Y")
-
- +
+

@@ -523,8 +523,8 @@

Derive Confirmed and Unconfirmed Progressive Disease Parameter ) ) ovr <- ovr_orig

-
-

For progressive disease and response shown in steps here and below, +

+

For progressive disease and response shown in steps here and below, in our examples we show these as ADRS parameters, but they could equally be achieved via ADSL dates or ADEVENT parameters.If you prefer to store as an ADSL date, @@ -568,8 +568,8 @@

Derive Response Parameter ANL01FL = "Y" ) ) -
- +
+

Derive Clinical Benefit Parameter @@ -619,8 +619,8 @@

Derive Clinical Benefit Parameter), check_type = "none" )

-
- +
+

Derive Best Overall Response Parameter @@ -698,11 +698,11 @@

Derive Best Overall Response Parameter ibor_ne <- event( description = paste( - "Define not evaluable (NE) for best overall response (iBOR) as iSD, NON-iCR/NON-iUPD,", - "or NE (should be specified after ibor_isd and ibor_non_icriupd)" + "Define not evaluable (NE) for best overall response (iBOR) as iCR, iPR, iSD,", + "NON-iCR/NON-iUPD, or NE (should be specified after ibor_isd and ibor_non_icriupd)" ), dataset_name = "ovr", - condition = AVALC %in% c("iSD", "NON-iCR/NON-iUPD", "NE"), + condition = AVALC %in% c("iCR", "iPR", "iSD", "NON-iCR/NON-iUPD", "NE"), set_values_to = exprs(AVALC = "NE") ) @@ -727,8 +727,8 @@

Derive Best Overall Response Parameter ANL01FL = "Y" ) )

-
- +
+

Derive Response Parameters requiring Confirmation @@ -907,8 +907,8 @@

Derive Response Parameters requiring Confirmation= "Y" ) )

-
- +
+

Other Endpoints diff --git a/dev/articles/nactdt.html b/dev/articles/nactdt.html index 68f5b3ea..1a5cbe26 100644 --- a/dev/articles/nactdt.html +++ b/dev/articles/nactdt.html @@ -214,8 +214,8 @@

Single Source new_vars = exprs(NACTDT = convert_dtc_to_dt(CMSTDTC)), filter_add = CMSCAT == "CHEMOTHERAPY" & CMCAT == "ON TREATMENT" )

-
- +
+

Multiple Sources - Prerequisite Steps @@ -267,8 +267,8 @@

Multiple Sources - Derive New Anti-Cancer Start Date and Merge w ), mode = "first" )

-
- +
+

Using the New Anti-Cancer Therapy Date @@ -322,8 +322,8 @@

Derive Date Parameter= "New Anti-Cancer Therapy Start Date" ) )

-
- +
+