# Layout for Baseline Prevalence of NAbslyt_bl <-basic_table(show_colcounts =TRUE) %>%split_cols_by("ACTARM",split_fun =add_combo_levels(combodf) ) %>%count_patients_with_flags("USUBJID",flag_variables =c("ADABLPFL", "PADABLPFL"),table_names ="t1",.stats ="count",var_labels ="Baseline Prevalence of NAbs",show_labels ="visible" ) %>%count_patients_with_flags("USUBJID",flag_variables ="PNABBLFL",table_names ="t2",.indent_mods =1L ) %>%count_patients_with_flags("USUBJID",flag_variables ="NNABBLFL",.stats ="count",table_names ="t3",.indent_mods =1L,show_labels ="hidden" )# Layout for incidence of NAbslyt_pb <-basic_table(show_colcounts =TRUE) %>%split_cols_by("ACTARM",split_fun =add_combo_levels(combodf) ) %>%count_patients_with_flags("USUBJID",flag_variables =c("ADPBLPFL", "ADAPFL"),.stats ="count",var_labels ="Incidence of Treatment Emergent NAbs",show_labels ="visible",table_names ="tb1" ) %>%count_patients_with_flags("USUBJID",flag_variables ="TENABPFL",table_names ="tb2",.indent_mods =1L,show_labels ="hidden" ) %>%count_patients_with_flags("USUBJID",flag_variables =c("TINPBFL", "TENPBFL"),.stats ="count",table_names ="tb3",.indent_mods =1L,show_labels ="hidden" ) %>%count_patients_with_flags("USUBJID",flag_variables ="NABNFL",table_names ="tb4",.indent_mods =1L,show_labels ="hidden" ) %>%count_patients_with_flags("USUBJID",flag_variables ="TUNPBFL",.stats ="count",table_names ="tb5",.indent_mods =1L,show_labels ="hidden" )result_1 <-build_table(lyt_bl, df = adab_b, alt_counts_df = adsl)result_2 <-build_table(lyt_pb, df = adab_pb, alt_counts_df = adsl)# Combine tablesresult <-rbind(result_1, result_2)# Change the column orderresult <-cbind_rtables(result[, 1], result[, 3]) %>%cbind_rtables(result[, 4]) %>%cbind_rtables(result[, 2]) %>%cbind_rtables(result[, 5])main_title(result) <-paste("Baseline Prevalence and Incidence of Treatment Emergent NAbs")subtitles(result) <-paste("Protocol:", unique(adab$PARCAT1)[1])main_footer(result) <-"NAb = Neutralizing Antibodies ADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies) Baseline evaluable patient for ADA = a patient with an ADA assay result from a baseline sample(s) Baseline evaluable patient for NAb = a patient with a NAb assay result from a baseline sample(s) Post-baseline evaluable patient for ADA = a patient with an ADA assay result from at least one post-baseline sample Post-baseline evaluable patient for NAb = a patient with a NAb assay result from at least one post-baseline sample Number of patients positive for ADA = the number of post-baseline evaluable patients for ADA determined to have Treatment Emergent ADA during the study period.Number of patients positive for Treatment Emergent NAb = the number (and percentage) of post-baseline evaluable patients for ADA determined to have treatment-induced NAb or treatment-enhanced NAb during the study period.Treatment-induced = a patient with negative or missing baseline result(s) and at least one positive post-baseline result. Treatment-enhanced = a patient with positive result at baseline who has one or more post-baseline titer results that are at least 0.60 t.u. greater than the baseline titer result.Number of patients negative for Treatment Emergent NAb = number of post-baseline evaluable patients with negative or missing baseline NAb result(s) and all negative post-baseline NAb results, or a patient who is NAb treatment unaffected.Treatment unaffected = A post-baseline evaluable patient with a positive result at baseline and (a) where all post-baseline titer results are less than 0.60 t.u. greater than the baseline titer result, OR (b) where all post-baseline results are negative or missing. For any positive sample with titer result less than the minimum reportable titer or any positive sample where a titer cannot be obtained, titer value is imputed as equal to the minimum reportable titer."result
Baseline Prevalence and Incidence of Treatment Emergent NAbs
Protocol: A: Drug X Antibody
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A: Drug X C: Combination <Missing> B: Placebo All Drug X
(N=134) (N=132) (N=0) (N=134) (N=266)
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Baseline Prevalence of NAbs
Baseline evaluable patients for ADA 134 132 0 0 266
Patients with a positive ADA sample at baseline 63 64 0 0 127
Patients with a positive NAb sample at baseline 0 0 0 0 0
Patient with no positive NAb samples at baseline 0 0 0 0 0
Incidence of Treatment Emergent NAbs
Post-baseline evaluable patients for ADA 134 132 0 0 266
Patients positive for ADA 66 59 0 0 125
Patients positive for Treatment Emergent NAb 0 0 0 0 0
Treatment-induced NAb 0 0 0 0 0
Treatment-enhanced NAb 0 0 0 0 0
Patients negative for NAb 0 0 0 0 0
Treatment unaffected 0 0 0 0 0
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NAb = Neutralizing Antibodies ADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies) Baseline evaluable patient for ADA = a patient with an ADA assay result from a baseline sample(s)
Baseline evaluable patient for NAb = a patient with a NAb assay result from a baseline sample(s)
Post-baseline evaluable patient for ADA = a patient with an ADA assay result from at least one post-baseline sample
Post-baseline evaluable patient for NAb = a patient with a NAb assay result from at least one post-baseline sample
Number of patients positive for ADA = the number of post-baseline evaluable patients for ADA determined to have Treatment Emergent ADA during the study period.
Number of patients positive for Treatment Emergent NAb = the number (and percentage) of post-baseline evaluable patients for ADA determined to have treatment-induced NAb or treatment-enhanced NAb during the study period.
Treatment-induced = a patient with negative or missing baseline result(s) and at least one positive post-baseline result. Treatment-enhanced = a patient with positive result at baseline who has one or more post-baseline titer results that are at least 0.60 t.u. greater than the baseline titer result.
Number of patients negative for Treatment Emergent NAb = number of post-baseline evaluable patients with negative or missing baseline NAb result(s) and all negative post-baseline NAb results, or a patient who is NAb treatment unaffected.
Treatment unaffected = A post-baseline evaluable patient with a positive result at baseline and (a) where all post-baseline titer results are less than 0.60 t.u. greater than the baseline titer result, OR (b) where all post-baseline results are negative or missing. For any positive sample with titer result less than the minimum reportable titer or any positive sample where a titer cannot be obtained, titer value is imputed as equal to the minimum reportable titer.
Experimental use!
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