Generates a standard TTE summary table with median survival, confidence intervals, hazard ratios, and optional landmark estimates for efficacy endpoints like OS, PFS, EFS.
Usage
create_tte_summary_table(
data,
time_var = "AVAL",
event_var = "CNSR",
trt_var = "TRT01P",
ref_group = NULL,
conf_level = 0.95,
check_ph = TRUE,
landmarks = NULL,
time_unit = "months",
title = "Time-to-Event Summary",
footnotes = character(),
autofit = TRUE,
...
)Arguments
- data
An ADaMData object (with domain "ADTTE") or an ADTTE data frame. Required columns include: time variable (default: "AVAL"), event variable (default: "CNSR"), and the treatment variable (default: "TRT01P" for data frames, or @trt_var for ADaMData).
- time_var
Time variable name (default: "AVAL")
- event_var
Event indicator variable. If "CNSR" (ADaM censoring flag), it will be automatically inverted (0=event becomes 1=event). Otherwise expects 1=event, 0=censor. Default: "CNSR"
- trt_var
Treatment variable name (default: "TRT01P"). Ignored for ADaMData objects which use their own trt_var property.
- ref_group
Reference group for HR calculation. If NULL, uses first level of treatment variable.
- conf_level
Confidence level for intervals (default: 0.95)
- check_ph
Logical. Whether to test proportional hazards assumption and warn on violations (default: TRUE)
- landmarks
Numeric vector of timepoints for landmark survival estimates (e.g., c(12, 24) for 12 and 24 month rates). NULL for none.
- time_unit
Character string for time unit display (default: "months")
- title
Table title
- footnotes
Character vector of footnotes to append to the table.
- autofit
Logical, whether to autofit column widths (default: TRUE)
- ...
Additional arguments passed to
create_clinical_table
Examples
# Create time-to-event summary with data frame
adtte <- data.frame(
USUBJID = sprintf("SUBJ%02d", 1:40),
TRT01P = rep(c("Placebo", "Active"), each = 20),
AVAL = c(rexp(20, 0.05), rexp(20, 0.03)),
CNSR = sample(0:1, 40, replace = TRUE, prob = c(0.7, 0.3))
)
table <- create_tte_summary_table(adtte)
#> Automatically wrapping data.frame in ADaMData object
print(table)
#> <pharmhand::ClinicalTable>
#> @ type : chr "tte_summary"
#> @ title : chr "Time-to-Event Summary"
#> @ metadata :List of 7
#> .. $ theme : chr "hta"
#> .. $ km_fit :List of 18
#> .. ..$ n : int [1:2] 20 20
#> .. ..$ time : num [1:40] 11 11.2 12.5 13 21.3 ...
#> .. ..$ n.risk : num [1:40] 20 19 18 17 16 15 14 13 12 11 ...
#> .. ..$ n.event : num [1:40] 1 1 1 0 0 1 1 1 1 1 ...
#> .. ..$ n.censor : num [1:40] 0 0 0 1 1 0 0 0 0 0 ...
#> .. ..$ surv : num [1:40] 0.95 0.9 0.85 0.85 0.85 ...
#> .. ..$ std.err : num [1:40] 0.0513 0.0745 0.0939 0.0939 0.0939 ...
#> .. ..$ cumhaz : num [1:40] 0.05 0.103 0.158 0.158 0.158 ...
#> .. ..$ std.chaz : num [1:40] 0.05 0.0726 0.0914 0.0914 0.0914 ...
#> .. ..$ strata : Named int [1:2] 20 20
#> .. .. ..- attr(*, "names")= chr [1:2] "TRT01P=Active" "TRT01P=Placebo"
#> .. ..$ type : chr "right"
#> .. ..$ logse : logi TRUE
#> .. ..$ conf.int : num 0.95
#> .. ..$ conf.type: chr "log"
#> .. ..$ lower : num [1:40] 0.859 0.778 0.707 0.707 0.707 ...
#> .. ..$ upper : num [1:40] 1 1 1 1 1 ...
#> .. ..$ t0 : num 0
#> .. ..$ call : language survfit(formula = surv_formula, data = df, conf.int = conf_level)
#> .. ..- attr(*, "class")= chr "survfit"
#> .. $ cox_fit :List of 21
#> .. ..$ coefficients : Named num 1.2
#> .. .. ..- attr(*, "names")= chr "TRT01PPlacebo"
#> .. ..$ var : num [1, 1] 0.209
#> .. ..$ loglik : num [1:2] -76.4 -72.8
#> .. ..$ score : num 7.69
#> .. ..$ iter : int 4
#> .. ..$ linear.predictors: num [1:40] 1.2 1.2 1.2 1.2 1.2 ...
#> .. ..$ residuals : Named num [1:40] -0.566 -1.378 0.502 0.962 -0.995 ...
#> .. .. ..- attr(*, "names")= chr [1:40] "1" "2" "3" "4" ...
#> .. ..$ means : Named num 0
#> .. .. ..- attr(*, "names")= chr "TRT01PPlacebo"
#> .. ..$ method : chr "efron"
#> .. ..$ n : int 40
#> .. ..$ nevent : num 27
#> .. ..$ terms :Classes 'terms', 'formula' language survival::Surv(AVAL, event) ~ TRT01P
#> .. .. .. ..- attr(*, "variables")= language list(survival::Surv(AVAL, event), TRT01P)
#> .. .. .. ..- attr(*, "factors")= int [1:2, 1] 0 1
#> .. .. .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. .. .. ..$ : chr [1:2] "survival::Surv(AVAL, event)" "TRT01P"
#> .. .. .. .. .. ..$ : chr "TRT01P"
#> .. .. .. ..- attr(*, "term.labels")= chr "TRT01P"
#> .. .. .. ..- attr(*, "specials")=Dotted pair list of 5
#> .. .. .. .. ..$ strata : NULL
#> .. .. .. .. ..$ tt : NULL
#> .. .. .. .. ..$ frailty: NULL
#> .. .. .. .. ..$ ridge : NULL
#> .. .. .. .. ..$ pspline: NULL
#> .. .. .. ..- attr(*, "order")= int 1
#> .. .. .. ..- attr(*, "intercept")= num 1
#> .. .. .. ..- attr(*, "response")= int 1
#> .. .. .. ..- attr(*, ".Environment")=<environment: 0x5616105970f8>
#> .. .. .. ..- attr(*, "predvars")= language list(survival::Surv(AVAL, event), TRT01P)
#> .. .. .. ..- attr(*, "dataClasses")= Named chr [1:2] "nmatrix.2" "factor"
#> .. .. .. .. ..- attr(*, "names")= chr [1:2] "survival::Surv(AVAL, event)" "TRT01P"
#> .. ..$ assign :List of 1
#> .. .. ..$ TRT01P: int 1
#> .. ..$ wald.test : Named num 6.93
#> .. .. ..- attr(*, "names")= chr "TRT01PPlacebo"
#> .. ..$ concordance : Named num [1:7] 214 71 267 0 0 ...
#> .. .. ..- attr(*, "names")= chr [1:7] "concordant" "discordant" "tied.x" "tied.y" ...
#> .. ..$ y : 'Surv' num [1:40, 1:2] 16.084+ 28.719+ 14.372 0.551 34.411 2.774 30.790 31.039 26.846 7.320 ...
#> .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. ..$ : chr [1:40] "1" "2" "3" "4" ...
#> .. .. .. ..$ : chr [1:2] "time" "status"
#> .. .. ..- attr(*, "type")= chr "right"
#> .. ..$ timefix : logi TRUE
#> .. ..$ formula :Class 'formula' language survival::Surv(AVAL, event) ~ TRT01P
#> .. .. .. ..- attr(*, ".Environment")=<environment: 0x5616105970f8>
#> .. ..$ xlevels :List of 1
#> .. .. ..$ TRT01P: chr [1:2] "Active" "Placebo"
#> .. ..$ contrasts :List of 1
#> .. .. ..$ TRT01P: chr "contr.treatment"
#> .. ..$ call : language survival::coxph(formula = surv_formula, data = df)
#> .. ..- attr(*, "class")= chr "coxph"
#> .. $ ph_test :List of 6
#> .. ..$ results :'data.frame': 1 obs. of 5 variables:
#> .. .. ..$ variable : chr "TRT01P"
#> .. .. ..$ rho : num NA
#> .. .. ..$ chisq : num 0.733
#> .. .. ..$ p_value : num 0.392
#> .. .. ..$ violation: logi FALSE
#> .. ..$ global_test: num 0.392
#> .. ..$ violation : logi FALSE
#> .. ..$ model :List of 21
#> .. .. ..$ coefficients : Named num 1.2
#> .. .. .. ..- attr(*, "names")= chr "TRT01PPlacebo"
#> .. .. ..$ var : num [1, 1] 0.209
#> .. .. ..$ loglik : num [1:2] -76.4 -72.8
#> .. .. ..$ score : num 7.69
#> .. .. ..$ iter : int 4
#> .. .. ..$ linear.predictors: num [1:40] 1.2 1.2 1.2 1.2 1.2 ...
#> .. .. ..$ residuals : Named num [1:40] -0.566 -1.378 0.502 0.962 -0.995 ...
#> .. .. .. ..- attr(*, "names")= chr [1:40] "1" "2" "3" "4" ...
#> .. .. ..$ means : Named num 0
#> .. .. .. ..- attr(*, "names")= chr "TRT01PPlacebo"
#> .. .. ..$ method : chr "efron"
#> .. .. ..$ n : int 40
#> .. .. ..$ nevent : num 27
#> .. .. ..$ terms :Classes 'terms', 'formula' language survival::Surv(AVAL, event) ~ TRT01P
#> .. .. .. .. ..- attr(*, "variables")= language list(survival::Surv(AVAL, event), TRT01P)
#> .. .. .. .. ..- attr(*, "factors")= int [1:2, 1] 0 1
#> .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. .. .. .. ..$ : chr [1:2] "survival::Surv(AVAL, event)" "TRT01P"
#> .. .. .. .. .. .. ..$ : chr "TRT01P"
#> .. .. .. .. ..- attr(*, "term.labels")= chr "TRT01P"
#> .. .. .. .. ..- attr(*, "specials")=Dotted pair list of 5
#> .. .. .. .. .. ..$ strata : NULL
#> .. .. .. .. .. ..$ tt : NULL
#> .. .. .. .. .. ..$ frailty: NULL
#> .. .. .. .. .. ..$ ridge : NULL
#> .. .. .. .. .. ..$ pspline: NULL
#> .. .. .. .. ..- attr(*, "order")= int 1
#> .. .. .. .. ..- attr(*, "intercept")= num 1
#> .. .. .. .. ..- attr(*, "response")= int 1
#> .. .. .. .. ..- attr(*, ".Environment")=<environment: 0x5616105970f8>
#> .. .. .. .. ..- attr(*, "predvars")= language list(survival::Surv(AVAL, event), TRT01P)
#> .. .. .. .. ..- attr(*, "dataClasses")= Named chr [1:2] "nmatrix.2" "factor"
#> .. .. .. .. .. ..- attr(*, "names")= chr [1:2] "survival::Surv(AVAL, event)" "TRT01P"
#> .. .. ..$ assign :List of 1
#> .. .. .. ..$ TRT01P: int 1
#> .. .. ..$ wald.test : Named num 6.93
#> .. .. .. ..- attr(*, "names")= chr "TRT01PPlacebo"
#> .. .. ..$ concordance : Named num [1:7] 214 71 267 0 0 ...
#> .. .. .. ..- attr(*, "names")= chr [1:7] "concordant" "discordant" "tied.x" "tied.y" ...
#> .. .. ..$ y : 'Surv' num [1:40, 1:2] 16.084+ 28.719+ 14.372 0.551 34.411 2.774 30.790 31.039 26.846 7.320 ...
#> .. .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. .. ..$ : chr [1:40] "1" "2" "3" "4" ...
#> .. .. .. .. ..$ : chr [1:2] "time" "status"
#> .. .. .. ..- attr(*, "type")= chr "right"
#> .. .. ..$ timefix : logi TRUE
#> .. .. ..$ formula :Class 'formula' language survival::Surv(AVAL, event) ~ TRT01P
#> .. .. .. .. ..- attr(*, ".Environment")=<environment: 0x5616105970f8>
#> .. .. ..$ xlevels :List of 1
#> .. .. .. ..$ TRT01P: chr [1:2] "Active" "Placebo"
#> .. .. ..$ contrasts :List of 1
#> .. .. .. ..$ TRT01P: chr "contr.treatment"
#> .. .. ..$ call : language survival::coxph(formula = surv_formula, data = df)
#> .. .. ..- attr(*, "class")= chr "coxph"
#> .. ..$ zph :List of 7
#> .. .. ..$ table : num [1:2, 1:3] 0.733 0.733 1 1 0.392 ...
#> .. .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. .. ..$ : chr [1:2] "TRT01P" "GLOBAL"
#> .. .. .. .. ..$ : chr [1:3] "chisq" "df" "p"
#> .. .. ..$ x : num [1:27] 0 0.025 0.05 0.075 0.101 ...
#> .. .. ..$ time : num [1:27] 0.551 2.774 5.415 7.32 11.04 ...
#> .. .. ..$ y : num [1:27, 1] 2.51 2.56 2.62 2.75 -2.75 ...
#> .. .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. .. ..$ : chr [1:27] "0.5512" "2.774" "5.415" "7.32" ...
#> .. .. .. .. ..$ : chr "TRT01P"
#> .. .. ..$ var : num [1, 1] 5.65
#> .. .. ..$ transform: chr "km"
#> .. .. ..$ call : language survival::cox.zph(fit = model)
#> .. .. ..- attr(*, "class")= chr "cox.zph"
#> .. ..$ plot : NULL
#> .. $ ref_group: chr "Active"
#> .. $ landmarks: NULL
#> .. $ time_unit: chr "months"
#> @ data : tibble [5 × 3] (S3: tbl_df/tbl/data.frame)
#> $ Statistic: chr [1:5] "N" "Events n (%)" "Median (95% CI)" "HR (95% CI)" ...
#> $ Active : chr [1:5] "20" "13 (65.0)" "57.5 (25.9, NE)" "Reference" ...
#> $ Placebo : chr [1:5] "20" "14 (70.0)" "20.4 (13.9, NE)" "3.33 (1.36, 8.17)" ...
#> @ flextable :List of 7
#> .. $ header :List of 8
#> .. ..$ dataset :'data.frame': 2 obs. of 3 variables:
#> .. .. ..$ Statistic: chr [1:2] "Time-to-Event Summary" "Statistic"
#> .. .. ..$ Active : chr [1:2] "Time-to-Event Summary" "Active"
#> .. .. ..$ Placebo : chr [1:2] "Time-to-Event Summary" "Placebo"
#> .. ..$ content :List of 5
#> .. .. ..$ data :List of 6
#> .. .. .. ..$ :'data.frame': 1 obs. of 19 variables:
#> .. .. .. .. ..$ txt : chr "Time-to-Event Summary"
#> .. .. .. .. ..$ font.size : num NA
#> .. .. .. .. ..$ italic : logi NA
#> .. .. .. .. ..$ bold : logi NA
#> .. .. .. .. ..$ underlined : logi NA
#> .. .. .. .. ..$ color : chr NA
#> .. .. .. .. ..$ shading.color : chr NA
#> .. .. .. .. ..$ font.family : chr NA
#> .. .. .. .. ..$ hansi.family : chr NA
#> .. .. .. .. ..$ eastasia.family: chr NA
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#> .. .. .. .. ..$ eq_data : chr NA
#> .. .. .. .. ..$ word_field_data: chr NA
#> .. .. .. .. ..$ img_data :List of 1
#> .. .. .. .. .. ..$ : NULL
#> .. .. .. .. ..$ .chunk_index : int 1
#> .. .. .. ..$ :'data.frame': 1 obs. of 19 variables:
#> .. .. .. .. ..$ txt : chr "Statistic"
#> .. .. .. .. ..$ font.size : num NA
#> .. .. .. .. ..$ italic : logi NA
#> .. .. .. .. ..$ bold : logi NA
#> .. .. .. .. ..$ underlined : logi NA
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#> .. .. .. .. ..$ eq_data : chr NA
#> .. .. .. .. ..$ word_field_data: chr NA
#> .. .. .. .. ..$ img_data :List of 1
#> .. .. .. .. .. ..$ : NULL
#> .. .. .. .. ..$ .chunk_index : int 1
#> .. .. .. ..$ :'data.frame': 1 obs. of 19 variables:
#> .. .. .. .. ..$ txt : chr "Time-to-Event Summary"
#> .. .. .. .. ..$ font.size : num NA
#> .. .. .. .. ..$ italic : logi NA
#> .. .. .. .. ..$ bold : logi NA
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#> .. .. .. ..$ :'data.frame': 1 obs. of 19 variables:
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#> .. .. .. .. ..$ font.size : num NA
#> .. .. .. .. ..$ italic : logi NA
#> .. .. .. .. ..$ bold : logi NA
#> .. .. .. .. ..$ underlined : logi NA
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#> .. .. .. .. ..$ shading.color : chr NA
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#> .. .. .. .. ..$ hansi.family : chr NA
#> .. .. .. .. ..$ eastasia.family: chr NA
#> .. .. .. .. ..$ cs.family : chr NA
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#> .. .. .. .. ..$ url : chr NA
#> .. .. .. .. ..$ eq_data : chr NA
#> .. .. .. .. ..$ word_field_data: chr NA
#> .. .. .. .. ..$ img_data :List of 1
#> .. .. .. .. .. ..$ : NULL
#> .. .. .. .. ..$ .chunk_index : int 1
#> .. .. .. ..$ :'data.frame': 1 obs. of 19 variables:
#> .. .. .. .. ..$ txt : chr "Time-to-Event Summary"
#> .. .. .. .. ..$ font.size : num NA
#> .. .. .. .. ..$ italic : logi NA
#> .. .. .. .. ..$ bold : logi NA
#> .. .. .. .. ..$ underlined : logi NA
#> .. .. .. .. ..$ color : chr NA
#> .. .. .. .. ..$ shading.color : chr NA
#> .. .. .. .. ..$ font.family : chr NA
#> .. .. .. .. ..$ hansi.family : chr NA
#> .. .. .. .. ..$ eastasia.family: chr NA
#> .. .. .. .. ..$ cs.family : chr NA
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#> .. .. .. .. ..$ width : num NA
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#> .. .. .. .. ..$ url : chr NA
#> .. .. .. .. ..$ eq_data : chr NA
#> .. .. .. .. ..$ word_field_data: chr NA
#> .. .. .. .. ..$ img_data :List of 1
#> .. .. .. .. .. ..$ : NULL
#> .. .. .. .. ..$ .chunk_index : int 1
#> .. .. .. ..$ :'data.frame': 1 obs. of 19 variables:
#> .. .. .. .. ..$ txt : chr "Placebo"
#> .. .. .. .. ..$ font.size : num NA
#> .. .. .. .. ..$ italic : logi NA
#> .. .. .. .. ..$ bold : logi NA
#> .. .. .. .. ..$ underlined : logi NA
#> .. .. .. .. ..$ color : chr NA
#> .. .. .. .. ..$ shading.color : chr NA
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#> .. .. .. .. ..$ img_data :List of 1
#> .. .. .. .. .. ..$ : NULL
#> .. .. .. .. ..$ .chunk_index : int 1
#> .. .. .. ..- attr(*, "dim")= int [1:2] 2 3
#> .. .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. .. ..$ : NULL
#> .. .. .. .. ..$ : chr [1:3] "Statistic" "Active" "Placebo"
#> .. .. ..$ keys : chr [1:3] "Statistic" "Active" "Placebo"
#> .. .. ..$ nrow : int 2
#> .. .. ..$ ncol : int 3
#> .. .. ..$ default:List of 1
#> .. .. .. ..$ :'data.frame': 1 obs. of 19 variables:
#> .. .. .. .. ..$ txt : chr ""
#> .. .. .. .. ..$ font.size : num NA
#> .. .. .. .. ..$ italic : logi NA
#> .. .. .. .. ..$ bold : logi NA
#> .. .. .. .. ..$ underlined : logi NA
#> .. .. .. .. ..$ color : chr NA
#> .. .. .. .. ..$ shading.color : chr NA
#> .. .. .. .. ..$ font.family : chr NA
#> .. .. .. .. ..$ hansi.family : chr NA
#> .. .. .. .. ..$ eastasia.family: chr NA
#> .. .. .. .. ..$ cs.family : chr NA
#> .. .. .. .. ..$ vertical.align : chr NA
#> .. .. .. .. ..$ width : num NA
#> .. .. .. .. ..$ height : num NA
#> .. .. .. .. ..$ url : chr NA
#> .. .. .. .. ..$ eq_data : chr NA
#> .. .. .. .. ..$ word_field_data: chr NA
#> .. .. .. .. ..$ img_data :List of 1
#> .. .. .. .. .. ..$ : NULL
#> .. .. .. .. ..$ .chunk_index : int 1
#> .. .. .. ..- attr(*, "class")= chr "paragraph"
#> .. .. ..- attr(*, "class")= chr "chunkset_struct"
#> .. ..$ col_keys : chr [1:3] "Statistic" "Active" "Placebo"
#> .. ..$ colwidths : Named num [1:3] 1.11 1.02 1.09
#> .. .. ..- attr(*, "names")= chr [1:3] "Statistic" "Active" "Placebo"
#> .. ..$ rowheights: num [1:2] 0.276 0.276
#> .. ..$ hrule : chr [1:2] "auto" "auto"
#> .. ..$ spans :List of 2
#> .. .. ..$ rows : num [1:2, 1:3] 3 1 0 1 0 1
#> .. .. ..$ columns: num [1:2, 1:3] 1 1 1 1 1 1
#> .. ..$ styles :List of 3
#> .. .. ..$ cells:List of 22
#> .. .. .. ..$ vertical.align :List of 5
#> .. .. .. .. ..$ data : chr [1:2, 1:3] "center" "center" "center" "center" ...
#> .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. .. .. .. ..$ : NULL
#> .. .. .. .. .. .. ..$ : chr [1:3] "Statistic" "Active" "Placebo"
#> .. .. .. .. ..$ keys : chr [1:3] "Statistic" "Active" "Placebo"
#> .. .. .. .. ..$ nrow : int 2
#> .. .. .. .. ..$ ncol : int 3
#> .. .. .. .. ..$ default: chr "center"
#> .. .. .. .. ..- attr(*, "class")= chr "fpstruct"
#> .. .. .. ..$ width :List of 5
#> .. .. .. .. ..$ data : num [1:2, 1:3] NA NA NA NA NA NA
#> .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. .. .. .. ..$ : NULL
#> .. .. .. .. .. .. ..$ : chr [1:3] "Statistic" "Active" "Placebo"
#> .. .. .. .. ..$ keys : chr [1:3] "Statistic" "Active" "Placebo"
#> .. .. .. .. ..$ nrow : int 2
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#> .. .. .. .. ..$ default: num NA
#> .. .. .. .. ..- attr(*, "class")= chr "fpstruct"
#> .. .. .. ..$ height :List of 5
#> .. .. .. .. ..$ data : num [1:2, 1:3] NA NA NA NA NA NA
#> .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. .. .. .. ..$ : NULL
#> .. .. .. .. .. .. ..$ : chr [1:3] "Statistic" "Active" "Placebo"
#> .. .. .. .. ..$ keys : chr [1:3] "Statistic" "Active" "Placebo"
#> .. .. .. .. ..$ nrow : int 2
#> .. .. .. .. ..$ ncol : int 3
#> .. .. .. .. ..$ default: num NA
#> .. .. .. .. ..- attr(*, "class")= chr "fpstruct"
#> .. .. .. ..$ margin.bottom :List of 5
#> .. .. .. .. ..$ data : int [1:2, 1:3] 0 0 0 0 0 0
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