diff --git a/man/BRCA1.Rd b/man/BRCA1.Rd index 3101be9a..b38174ef 100644 --- a/man/BRCA1.Rd +++ b/man/BRCA1.Rd @@ -26,9 +26,9 @@ as a function of their age (in years). Other datasets: \code{\link{BRCA1_mam}}, \code{\link{BRCA1_ova}}, +\code{\link{BRCA2}}, \code{\link{BRCA2_mam}}, \code{\link{BRCA2_ova}}, -\code{\link{BRCA2}}, \code{\link{df_scenarios}}, \code{\link{t_A}}, \code{\link{t_B}}, diff --git a/man/BRCA1_mam.Rd b/man/BRCA1_mam.Rd index 4b165de4..183f8e05 100644 --- a/man/BRCA1_mam.Rd +++ b/man/BRCA1_mam.Rd @@ -30,11 +30,11 @@ as a function of their age (in years). \code{\link{plot_crisk}} plots cumulative risk curves. Other datasets: -\code{\link{BRCA1_ova}}, \code{\link{BRCA1}}, +\code{\link{BRCA1_ova}}, +\code{\link{BRCA2}}, \code{\link{BRCA2_mam}}, \code{\link{BRCA2_ova}}, -\code{\link{BRCA2}}, \code{\link{df_scenarios}}, \code{\link{t_A}}, \code{\link{t_B}}, diff --git a/man/BRCA1_ova.Rd b/man/BRCA1_ova.Rd index dff4799b..522107fd 100644 --- a/man/BRCA1_ova.Rd +++ b/man/BRCA1_ova.Rd @@ -30,11 +30,11 @@ as a function of their age (in years). \code{\link{plot_crisk}} plots cumulative risk curves. Other datasets: -\code{\link{BRCA1_mam}}, \code{\link{BRCA1}}, +\code{\link{BRCA1_mam}}, +\code{\link{BRCA2}}, \code{\link{BRCA2_mam}}, \code{\link{BRCA2_ova}}, -\code{\link{BRCA2}}, \code{\link{df_scenarios}}, \code{\link{t_A}}, \code{\link{t_B}}, diff --git a/man/BRCA2.Rd b/man/BRCA2.Rd index dbed68b6..6d53663b 100644 --- a/man/BRCA2.Rd +++ b/man/BRCA2.Rd @@ -24,9 +24,9 @@ as a function of their age (in years). \code{\link{plot_crisk}} plots cumulative risk curves. Other datasets: +\code{\link{BRCA1}}, \code{\link{BRCA1_mam}}, \code{\link{BRCA1_ova}}, -\code{\link{BRCA1}}, \code{\link{BRCA2_mam}}, \code{\link{BRCA2_ova}}, \code{\link{df_scenarios}}, diff --git a/man/BRCA2_mam.Rd b/man/BRCA2_mam.Rd index 76e2bd39..fdfc05c0 100644 --- a/man/BRCA2_mam.Rd +++ b/man/BRCA2_mam.Rd @@ -30,11 +30,11 @@ as a function of their age (in years). \code{\link{plot_crisk}} plots cumulative risk curves. Other datasets: +\code{\link{BRCA1}}, \code{\link{BRCA1_mam}}, \code{\link{BRCA1_ova}}, -\code{\link{BRCA1}}, -\code{\link{BRCA2_ova}}, \code{\link{BRCA2}}, +\code{\link{BRCA2_ova}}, \code{\link{df_scenarios}}, \code{\link{t_A}}, \code{\link{t_B}}, diff --git a/man/BRCA2_ova.Rd b/man/BRCA2_ova.Rd index dc80a34c..df93c8b5 100644 --- a/man/BRCA2_ova.Rd +++ b/man/BRCA2_ova.Rd @@ -30,11 +30,11 @@ as a function of their age (in years). \code{\link{plot_crisk}} plots cumulative risk curves. Other datasets: +\code{\link{BRCA1}}, \code{\link{BRCA1_mam}}, \code{\link{BRCA1_ova}}, -\code{\link{BRCA1}}, -\code{\link{BRCA2_mam}}, \code{\link{BRCA2}}, +\code{\link{BRCA2_mam}}, \code{\link{df_scenarios}}, \code{\link{t_A}}, \code{\link{t_B}}, diff --git a/man/acc.Rd b/man/acc.Rd index 25e70237..da4622de 100644 --- a/man/acc.Rd +++ b/man/acc.Rd @@ -115,9 +115,9 @@ Other probabilities: Other metrics: \code{\link{accu}}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_err}()}, \code{\link{err}} } diff --git a/man/accu.Rd b/man/accu.Rd index a074574c..4a8e3df5 100644 --- a/man/accu.Rd +++ b/man/accu.Rd @@ -125,8 +125,9 @@ The corresponding generating function \code{\link{comp_accu_prob}} computes exac Other lists containing current scenario information: \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, @@ -134,17 +135,16 @@ Other lists containing current scenario information: \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} Other metrics: \code{\link{acc}}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_err}()}, \code{\link{err}} } diff --git a/man/comp_FDR.Rd b/man/comp_FDR.Rd index c37812de..92f36fcd 100644 --- a/man/comp_FDR.Rd +++ b/man/comp_FDR.Rd @@ -51,9 +51,9 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, @@ -61,8 +61,8 @@ Other functions computing probabilities: \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_FOR.Rd b/man/comp_FOR.Rd index 5f8e470d..ced5e409 100644 --- a/man/comp_FOR.Rd +++ b/man/comp_FOR.Rd @@ -50,9 +50,9 @@ Other functions computing probabilities: \code{\link{comp_FDR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, @@ -60,8 +60,8 @@ Other functions computing probabilities: \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_NPV.Rd b/man/comp_NPV.Rd index 2026e893..4b5d51b4 100644 --- a/man/comp_NPV.Rd +++ b/man/comp_NPV.Rd @@ -61,9 +61,9 @@ Other functions computing probabilities: \code{\link{comp_FDR}()}, \code{\link{comp_FOR}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, @@ -71,8 +71,8 @@ Other functions computing probabilities: \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_PPV.Rd b/man/comp_PPV.Rd index b117e154..d8ead08b 100644 --- a/man/comp_PPV.Rd +++ b/man/comp_PPV.Rd @@ -65,9 +65,9 @@ Other functions computing probabilities: \code{\link{comp_FDR}()}, \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, @@ -75,8 +75,8 @@ Other functions computing probabilities: \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_acc.Rd b/man/comp_acc.Rd index 1e5535d5..c756c3e9 100644 --- a/man/comp_acc.Rd +++ b/man/comp_acc.Rd @@ -141,14 +141,14 @@ Other functions computing probabilities: \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} Other metrics: -\code{\link{accu}}, \code{\link{acc}}, +\code{\link{accu}}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, \code{\link{comp_err}()}, diff --git a/man/comp_accu_freq.Rd b/man/comp_accu_freq.Rd index 740ea205..308eb0fb 100644 --- a/man/comp_accu_freq.Rd +++ b/man/comp_accu_freq.Rd @@ -152,10 +152,10 @@ for additional information. \code{\link{popu}} for a table of the current population. Other metrics: -\code{\link{accu}}, \code{\link{acc}}, -\code{\link{comp_accu_prob}()}, +\code{\link{accu}}, \code{\link{comp_acc}()}, +\code{\link{comp_accu_prob}()}, \code{\link{comp_err}()}, \code{\link{err}} @@ -164,8 +164,8 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, -\code{\link{comp_accu_prob}()}, \code{\link{comp_acc}()}, +\code{\link{comp_accu_prob}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, @@ -173,8 +173,8 @@ Other functions computing probabilities: \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_accu_prob.Rd b/man/comp_accu_prob.Rd index fe9c685a..2f684c6f 100644 --- a/man/comp_accu_prob.Rd +++ b/man/comp_accu_prob.Rd @@ -196,10 +196,10 @@ for additional information. \code{\link{popu}} for a table of the current population. Other metrics: -\code{\link{accu}}, \code{\link{acc}}, -\code{\link{comp_accu_freq}()}, +\code{\link{accu}}, \code{\link{comp_acc}()}, +\code{\link{comp_accu_freq}()}, \code{\link{comp_err}()}, \code{\link{err}} @@ -208,8 +208,8 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, -\code{\link{comp_accu_freq}()}, \code{\link{comp_acc}()}, +\code{\link{comp_accu_freq}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, @@ -217,8 +217,8 @@ Other functions computing probabilities: \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_comp_pair.Rd b/man/comp_comp_pair.Rd index bec34e29..d7e8c3c8 100644 --- a/man/comp_comp_pair.Rd +++ b/man/comp_comp_pair.Rd @@ -63,17 +63,17 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, \code{\link{comp_err}()}, \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_complement.Rd b/man/comp_complement.Rd index 588dac89..8f2d3e7b 100644 --- a/man/comp_complement.Rd +++ b/man/comp_complement.Rd @@ -41,17 +41,17 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complete_prob_set}()}, \code{\link{comp_err}()}, \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_complete_prob_set.Rd b/man/comp_complete_prob_set.Rd index 02d46179..1838df16 100644 --- a/man/comp_complete_prob_set.Rd +++ b/man/comp_complete_prob_set.Rd @@ -76,17 +76,17 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_err}()}, \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_err.Rd b/man/comp_err.Rd index 17ec8c62..eb67b0ba 100644 --- a/man/comp_err.Rd +++ b/man/comp_err.Rd @@ -81,26 +81,26 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} Other metrics: -\code{\link{accu}}, \code{\link{acc}}, +\code{\link{accu}}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{err}} } \concept{functions computing probabilities} diff --git a/man/comp_fart.Rd b/man/comp_fart.Rd index d1ba95f1..28eaf80d 100644 --- a/man/comp_fart.Rd +++ b/man/comp_fart.Rd @@ -45,17 +45,17 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, \code{\link{comp_err}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_freq_freq.Rd b/man/comp_freq_freq.Rd index dbf71d8d..2df66b46 100644 --- a/man/comp_freq_freq.Rd +++ b/man/comp_freq_freq.Rd @@ -83,8 +83,8 @@ all.equal(freq, freq_freq) # => should be TRUE! \code{\link{is_freq}} verifies frequency inputs. Other functions computing frequencies: -\code{\link{comp_freq_prob}()}, \code{\link{comp_freq}()}, +\code{\link{comp_freq_prob}()}, \code{\link{comp_min_N}()}, \code{\link{comp_prob_prob}()} diff --git a/man/comp_freq_prob.Rd b/man/comp_freq_prob.Rd index 7686e74c..e6232efc 100644 --- a/man/comp_freq_prob.Rd +++ b/man/comp_freq_prob.Rd @@ -206,8 +206,8 @@ comp_freq_prob(prev = 1, sens = 8, spec = 1, 100) # NAs + warning (sens & spec \code{\link{comp_min_N}} computes a suitable population size \code{\link{N}} (if missing). Other functions computing frequencies: -\code{\link{comp_freq_freq}()}, \code{\link{comp_freq}()}, +\code{\link{comp_freq_freq}()}, \code{\link{comp_min_N}()}, \code{\link{comp_prob_prob}()} diff --git a/man/comp_min_N.Rd b/man/comp_min_N.Rd index eb2f343e..c3420ff0 100644 --- a/man/comp_min_N.Rd +++ b/man/comp_min_N.Rd @@ -71,9 +71,9 @@ population size \code{\link{N}}; \code{\link{comp_prob_prob}} computes current probability information from (3 essential) probabilities. Other functions computing frequencies: +\code{\link{comp_freq}()}, \code{\link{comp_freq_freq}()}, \code{\link{comp_freq_prob}()}, -\code{\link{comp_freq}()}, \code{\link{comp_prob_prob}()} } \concept{functions computing frequencies} diff --git a/man/comp_mirt.Rd b/man/comp_mirt.Rd index af90ba96..f479d2ee 100644 --- a/man/comp_mirt.Rd +++ b/man/comp_mirt.Rd @@ -45,17 +45,17 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, \code{\link{comp_err}()}, \code{\link{comp_fart}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_ppod.Rd b/man/comp_ppod.Rd index 86ce0fd7..3c5346a7 100644 --- a/man/comp_ppod.Rd +++ b/man/comp_ppod.Rd @@ -81,17 +81,17 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, \code{\link{comp_err}()}, \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()}, \code{\link{comp_spec}()} } diff --git a/man/comp_prob.Rd b/man/comp_prob.Rd index a0d253f3..82316414 100644 --- a/man/comp_prob.Rd +++ b/man/comp_prob.Rd @@ -257,9 +257,9 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, diff --git a/man/comp_prob_freq.Rd b/man/comp_prob_freq.Rd index d13c73df..a373cd50 100644 --- a/man/comp_prob_freq.Rd +++ b/man/comp_prob_freq.Rd @@ -92,9 +92,9 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, diff --git a/man/comp_prob_prob.Rd b/man/comp_prob_prob.Rd index 26b4ce5f..76dea006 100644 --- a/man/comp_prob_prob.Rd +++ b/man/comp_prob_prob.Rd @@ -147,9 +147,9 @@ comp_prob_prob(1, 1, 1, 1) # only warning: is_complement not in tolerated ran \code{\link{comp_min_N}} computes a suitable population size \code{\link{N}} (if missing). Other functions computing frequencies: +\code{\link{comp_freq}()}, \code{\link{comp_freq_freq}()}, \code{\link{comp_freq_prob}()}, -\code{\link{comp_freq}()}, \code{\link{comp_min_N}()} Other format conversion functions: diff --git a/man/comp_sens.Rd b/man/comp_sens.Rd index 5fdeb878..94dafc96 100644 --- a/man/comp_sens.Rd +++ b/man/comp_sens.Rd @@ -45,9 +45,9 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, @@ -55,8 +55,8 @@ Other functions computing probabilities: \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_spec}()} } \concept{functions computing probabilities} diff --git a/man/comp_spec.Rd b/man/comp_spec.Rd index 4c5fe977..4a847d1b 100644 --- a/man/comp_spec.Rd +++ b/man/comp_spec.Rd @@ -45,9 +45,9 @@ Other functions computing probabilities: \code{\link{comp_FOR}()}, \code{\link{comp_NPV}()}, \code{\link{comp_PPV}()}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_comp_pair}()}, \code{\link{comp_complement}()}, \code{\link{comp_complete_prob_set}()}, @@ -55,8 +55,8 @@ Other functions computing probabilities: \code{\link{comp_fart}()}, \code{\link{comp_mirt}()}, \code{\link{comp_ppod}()}, -\code{\link{comp_prob_freq}()}, \code{\link{comp_prob}()}, +\code{\link{comp_prob_freq}()}, \code{\link{comp_sens}()} } \concept{functions computing probabilities} diff --git a/man/df_scenarios.Rd b/man/df_scenarios.Rd index 365b7d91..6024fe59 100644 --- a/man/df_scenarios.Rd +++ b/man/df_scenarios.Rd @@ -42,12 +42,12 @@ When loading \code{riskyr}, all scenarios contained in \code{\link{init_pal}} initializes color information. Other datasets: +\code{\link{BRCA1}}, \code{\link{BRCA1_mam}}, \code{\link{BRCA1_ova}}, -\code{\link{BRCA1}}, +\code{\link{BRCA2}}, \code{\link{BRCA2_mam}}, \code{\link{BRCA2_ova}}, -\code{\link{BRCA2}}, \code{\link{t_A}}, \code{\link{t_B}}, \code{\link{t_I}} diff --git a/man/err.Rd b/man/err.Rd index 9673bc22..bd0c6d06 100644 --- a/man/err.Rd +++ b/man/err.Rd @@ -66,11 +66,11 @@ Other probabilities: \code{\link{spec}} Other metrics: -\code{\link{accu}}, \code{\link{acc}}, +\code{\link{accu}}, +\code{\link{comp_acc}()}, \code{\link{comp_accu_freq}()}, \code{\link{comp_accu_prob}()}, -\code{\link{comp_acc}()}, \code{\link{comp_err}()} } \concept{metrics} diff --git a/man/freq.Rd b/man/freq.Rd index edd878be..9bc37af0 100644 --- a/man/freq.Rd +++ b/man/freq.Rd @@ -92,8 +92,9 @@ names(freq) # show names of known frequencies Other lists containing current scenario information: \code{\link{accu}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, @@ -101,11 +102,10 @@ Other lists containing current scenario information: \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{lists containing current scenario information} \keyword{datasets} diff --git a/man/num.Rd b/man/num.Rd index 789725a3..33609948 100644 --- a/man/num.Rd +++ b/man/num.Rd @@ -36,8 +36,9 @@ length(num) # => 5 Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, @@ -45,11 +46,10 @@ Other lists containing current scenario information: \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{lists containing current scenario information} \keyword{datasets} diff --git a/man/pal.Rd b/man/pal.Rd index 9ac22fdf..7e73e5de 100644 --- a/man/pal.Rd +++ b/man/pal.Rd @@ -89,8 +89,8 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, @@ -99,9 +99,9 @@ Other lists containing current scenario information: \code{\link{pal_unikn}}, \code{\link{pal_vir}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{lists containing current scenario information} \keyword{datasets} diff --git a/man/pal_bw.Rd b/man/pal_bw.Rd index f9beb217..3296507c 100644 --- a/man/pal_bw.Rd +++ b/man/pal_bw.Rd @@ -52,6 +52,7 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, +\code{\link{pal}}, \code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, @@ -60,11 +61,10 @@ Other lists containing current scenario information: \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{color palettes} \concept{lists containing current scenario information} diff --git a/man/pal_bwp.Rd b/man/pal_bwp.Rd index 72b2fe8b..00f066ab 100644 --- a/man/pal_bwp.Rd +++ b/man/pal_bwp.Rd @@ -64,6 +64,7 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, +\code{\link{pal}}, \code{\link{pal_bw}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, @@ -72,11 +73,10 @@ Other lists containing current scenario information: \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{color palettes} \concept{lists containing current scenario information} diff --git a/man/pal_crisk.Rd b/man/pal_crisk.Rd index cb8c40df..d121266e 100644 --- a/man/pal_crisk.Rd +++ b/man/pal_crisk.Rd @@ -45,8 +45,8 @@ pal_crisk # show color palette (and names) \code{\link{init_pal}} initializes color information. Other color palettes: -\code{\link{pal_bwp}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, diff --git a/man/pal_kn.Rd b/man/pal_kn.Rd index c762ac97..f3aa2c43 100644 --- a/man/pal_kn.Rd +++ b/man/pal_kn.Rd @@ -32,8 +32,8 @@ pal_kn["hi"] <- "grey" # defines a new color for hits (true positives, TP) \code{\link{init_pal}} initializes color information. Other color palettes: -\code{\link{pal_bwp}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_crisk}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, @@ -46,19 +46,19 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, \code{\link{pal_org}}, \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{color palettes} \concept{lists containing current scenario information} diff --git a/man/pal_mbw.Rd b/man/pal_mbw.Rd index d38b897a..039c2f4b 100644 --- a/man/pal_mbw.Rd +++ b/man/pal_mbw.Rd @@ -36,8 +36,8 @@ pal_mbw["hi"] <- "gold" # defines a new color for hits (true positives, TP) \code{\link{pal_bw}} for a more reduced black-and-white color palette. Other color palettes: -\code{\link{pal_bwp}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_crisk}}, \code{\link{pal_kn}}, \code{\link{pal_mod}}, @@ -50,19 +50,19 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mod}}, \code{\link{pal_org}}, \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{color palettes} \concept{lists containing current scenario information} diff --git a/man/pal_mod.Rd b/man/pal_mod.Rd index fe7606c5..8d541856 100644 --- a/man/pal_mod.Rd +++ b/man/pal_mod.Rd @@ -31,8 +31,8 @@ pal_mod["hi"] <- "gold" # defines a new color for hits (true positives, TP) \code{\link{init_pal}} initializes color information. Other color palettes: -\code{\link{pal_bwp}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_crisk}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, @@ -45,19 +45,19 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_org}}, \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{color palettes} \concept{lists containing current scenario information} diff --git a/man/pal_org.Rd b/man/pal_org.Rd index 358813b1..d9790da5 100644 --- a/man/pal_org.Rd +++ b/man/pal_org.Rd @@ -32,8 +32,8 @@ pal_org["hi"] <- "gold" # defines a new color for hits (true positives, TP) \code{\link{init_pal}} initializes color information. Other color palettes: -\code{\link{pal_bwp}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_crisk}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, @@ -46,19 +46,19 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{color palettes} \concept{lists containing current scenario information} diff --git a/man/pal_rgb.Rd b/man/pal_rgb.Rd index ab5bc712..d65df529 100644 --- a/man/pal_rgb.Rd +++ b/man/pal_rgb.Rd @@ -32,8 +32,8 @@ pal_rgb["hi"] <- "gold" # defines a new color for hits (true positives, TP) \code{\link{init_pal}} initializes color information. Other color palettes: -\code{\link{pal_bwp}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_crisk}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, @@ -46,19 +46,19 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, \code{\link{pal_org}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{color palettes} \concept{lists containing current scenario information} diff --git a/man/pal_unikn.Rd b/man/pal_unikn.Rd index 40537180..38905665 100644 --- a/man/pal_unikn.Rd +++ b/man/pal_unikn.Rd @@ -32,8 +32,8 @@ pal_unikn["hi"] <- "grey" # defines a new color for hits (true positives, TP) \code{\link{init_pal}} initializes color information. Other color palettes: -\code{\link{pal_bwp}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_crisk}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, @@ -46,19 +46,19 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, \code{\link{pal_org}}, \code{\link{pal_rgb}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{color palettes} \concept{lists containing current scenario information} diff --git a/man/pal_vir.Rd b/man/pal_vir.Rd index 1d9fab5e..2e1093c1 100644 --- a/man/pal_vir.Rd +++ b/man/pal_vir.Rd @@ -34,8 +34,8 @@ pal_vir["hi"] <- "green3" # defines a new color for hits (true positives, TP) \code{\link{init_pal}} initializes color information. Other color palettes: -\code{\link{pal_bwp}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_crisk}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, @@ -48,19 +48,19 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, \code{\link{pal_org}}, \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, -\code{\link{pal}}, \code{\link{prob}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{color palettes} \concept{lists containing current scenario information} diff --git a/man/prob.Rd b/man/prob.Rd index 52a36248..afd48a3f 100644 --- a/man/prob.Rd +++ b/man/prob.Rd @@ -136,8 +136,9 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, @@ -145,10 +146,9 @@ Other lists containing current scenario information: \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, +\code{\link{txt}}, \code{\link{txt_TF}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt_org}} } \concept{lists containing current scenario information} \keyword{datasets} diff --git a/man/t_A.Rd b/man/t_A.Rd index 21b011a6..273e12aa 100644 --- a/man/t_A.Rd +++ b/man/t_A.Rd @@ -24,12 +24,12 @@ in some target population as a function of age. \code{\link{plot_crisk}} plots cumulative risk curves. Other datasets: +\code{\link{BRCA1}}, \code{\link{BRCA1_mam}}, \code{\link{BRCA1_ova}}, -\code{\link{BRCA1}}, +\code{\link{BRCA2}}, \code{\link{BRCA2_mam}}, \code{\link{BRCA2_ova}}, -\code{\link{BRCA2}}, \code{\link{df_scenarios}}, \code{\link{t_B}}, \code{\link{t_I}} diff --git a/man/t_B.Rd b/man/t_B.Rd index 43833f59..55d28409 100644 --- a/man/t_B.Rd +++ b/man/t_B.Rd @@ -24,12 +24,12 @@ in some target population as a function of age. \code{\link{plot_crisk}} plots cumulative risk curves. Other datasets: +\code{\link{BRCA1}}, \code{\link{BRCA1_mam}}, \code{\link{BRCA1_ova}}, -\code{\link{BRCA1}}, +\code{\link{BRCA2}}, \code{\link{BRCA2_mam}}, \code{\link{BRCA2_ova}}, -\code{\link{BRCA2}}, \code{\link{df_scenarios}}, \code{\link{t_A}}, \code{\link{t_I}} diff --git a/man/t_I.Rd b/man/t_I.Rd index d0d86d3d..2971a214 100644 --- a/man/t_I.Rd +++ b/man/t_I.Rd @@ -24,12 +24,12 @@ in some target population as a function of age. \code{\link{plot_crisk}} plots cumulative risk curves. Other datasets: +\code{\link{BRCA1}}, \code{\link{BRCA1_mam}}, \code{\link{BRCA1_ova}}, -\code{\link{BRCA1}}, +\code{\link{BRCA2}}, \code{\link{BRCA2_mam}}, \code{\link{BRCA2_ova}}, -\code{\link{BRCA2}}, \code{\link{df_scenarios}}, \code{\link{t_A}}, \code{\link{t_B}} diff --git a/man/txt.Rd b/man/txt.Rd index a7f22b04..d836d15c 100644 --- a/man/txt.Rd +++ b/man/txt.Rd @@ -133,8 +133,9 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, @@ -142,7 +143,6 @@ Other lists containing current scenario information: \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, \code{\link{txt_TF}}, \code{\link{txt_org}} diff --git a/man/txt_TF.Rd b/man/txt_TF.Rd index a2feb4f2..ded65372 100644 --- a/man/txt_TF.Rd +++ b/man/txt_TF.Rd @@ -36,8 +36,9 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, @@ -45,10 +46,9 @@ Other lists containing current scenario information: \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, -\code{\link{txt_org}}, -\code{\link{txt}} +\code{\link{txt}}, +\code{\link{txt_org}} } \concept{lists containing current scenario information} \keyword{datasets} diff --git a/man/txt_org.Rd b/man/txt_org.Rd index e27941f3..cb43e15d 100644 --- a/man/txt_org.Rd +++ b/man/txt_org.Rd @@ -35,8 +35,9 @@ Other lists containing current scenario information: \code{\link{accu}}, \code{\link{freq}}, \code{\link{num}}, -\code{\link{pal_bwp}}, +\code{\link{pal}}, \code{\link{pal_bw}}, +\code{\link{pal_bwp}}, \code{\link{pal_kn}}, \code{\link{pal_mbw}}, \code{\link{pal_mod}}, @@ -44,10 +45,9 @@ Other lists containing current scenario information: \code{\link{pal_rgb}}, \code{\link{pal_unikn}}, \code{\link{pal_vir}}, -\code{\link{pal}}, \code{\link{prob}}, -\code{\link{txt_TF}}, -\code{\link{txt}} +\code{\link{txt}}, +\code{\link{txt_TF}} } \concept{lists containing current scenario information} \keyword{datasets}