From 68dda9b8fbd73f8b31d89e436d9bf7f108c64533 Mon Sep 17 00:00:00 2001 From: Zena Lapp Date: Thu, 16 Nov 2023 19:37:42 -0700 Subject: [PATCH] Update documentation --- man/bistro.Rd | 6 +++--- man/calc_allele_freqs.Rd | 2 +- man/calc_log10_lrs.Rd | 6 +++--- man/calc_one_log10_lr.Rd | 6 +++--- man/check_bistro_inputs.Rd | 6 +++--- man/check_if_allele_freqs.Rd | 2 +- man/filter_peaks.Rd | 2 +- man/format_allele_freqs.Rd | 2 +- man/format_bloodmeal_profiles.Rd | 2 +- man/format_human_profiles.Rd | 2 +- man/get_bloodmeal_human_similarity.Rd | 4 ++-- man/get_human_similarity.Rd | 2 +- man/match_exact.Rd | 4 ++-- man/match_similarity.Rd | 4 ++-- man/prep_bloodmeal_profiles.Rd | 2 +- man/prep_human_profiles.Rd | 2 +- man/rm_twins.Rd | 2 +- 17 files changed, 28 insertions(+), 28 deletions(-) diff --git a/man/bistro.Rd b/man/bistro.Rd index 43566f2..78badc3 100644 --- a/man/bistro.Rd +++ b/man/bistro.Rd @@ -26,11 +26,11 @@ bistro( ) } \arguments{ -\item{bloodmeal_profiles}{Tibble with alleles for all bloodmeals in reference +\item{bloodmeal_profiles}{Tibble or data frame with alleles for all bloodmeals in reference database including 4 columns: SampleName, Marker, Allele, Height. Height must be numeric or coercible to numeric.} -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} \item{kit}{STR kit name from euroformix. To see a list of all kits embedded @@ -42,7 +42,7 @@ threshold will be filtered out. If prior filtering was performed, this number should be equal to or greater than that number. Also used for \code{threshT} argument in \code{\link[euroformix:contLikSearch]{euroformix::contLikSearch()}}.} -\item{pop_allele_freqs}{Data frame where the first column is the STR allele +\item{pop_allele_freqs}{Tibble or data frame where the first column is the STR allele and the following columns are the frequency of that allele for different markers. Alleles that do not exist for a given marker are coded as NA. If NULL and \code{calc_allele_freqs = TRUE}, then population allele frequencies diff --git a/man/calc_allele_freqs.Rd b/man/calc_allele_freqs.Rd index 33f0109..4d5bb6a 100644 --- a/man/calc_allele_freqs.Rd +++ b/man/calc_allele_freqs.Rd @@ -7,7 +7,7 @@ calc_allele_freqs(human_profiles, rm_markers = NULL) } \arguments{ -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} \item{rm_markers}{A vector indicating what markers should be removed prior to diff --git a/man/calc_log10_lrs.Rd b/man/calc_log10_lrs.Rd index 0c38d5d..1f70d72 100644 --- a/man/calc_log10_lrs.Rd +++ b/man/calc_log10_lrs.Rd @@ -22,14 +22,14 @@ calc_log10_lrs( ) } \arguments{ -\item{bloodmeal_profiles}{Tibble with alleles for all bloodmeals in reference +\item{bloodmeal_profiles}{Tibble or data frame with alleles for all bloodmeals in reference database including 4 columns: SampleName, Marker, Allele, Height. Height must be numeric or coercible to numeric.} -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} -\item{pop_allele_freqs}{Data frame where the first column is the STR allele +\item{pop_allele_freqs}{Tibble or data frame where the first column is the STR allele and the following columns are the frequency of that allele for different markers. Alleles that do not exist for a given marker are coded as NA. If NULL and \code{calc_allele_freqs = TRUE}, then population allele frequencies diff --git a/man/calc_one_log10_lr.Rd b/man/calc_one_log10_lr.Rd index 1a215f8..2f44bcc 100644 --- a/man/calc_one_log10_lr.Rd +++ b/man/calc_one_log10_lr.Rd @@ -22,20 +22,20 @@ calc_one_log10_lr( ) } \arguments{ -\item{bloodmeal_profiles}{Tibble with alleles for all bloodmeals in reference +\item{bloodmeal_profiles}{Tibble or data frame with alleles for all bloodmeals in reference database including 4 columns: SampleName, Marker, Allele, Height. Height must be numeric or coercible to numeric.} \item{bloodmeal_id}{Bloodmeal id from the \code{SampleName} column in \code{bloodmeal_profiles} for which to compute the log10_lr} -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} \item{human_id}{Human id from the \code{SampleName} column in \code{human_profiles} for which to compute the log10_lr} -\item{pop_allele_freqs}{Data frame where the first column is the STR allele +\item{pop_allele_freqs}{Tibble or data frame where the first column is the STR allele and the following columns are the frequency of that allele for different markers. Alleles that do not exist for a given marker are coded as NA. If NULL and \code{calc_allele_freqs = TRUE}, then population allele frequencies diff --git a/man/check_bistro_inputs.Rd b/man/check_bistro_inputs.Rd index 7a354ad..dd15d59 100644 --- a/man/check_bistro_inputs.Rd +++ b/man/check_bistro_inputs.Rd @@ -26,11 +26,11 @@ check_bistro_inputs( ) } \arguments{ -\item{bloodmeal_profiles}{Tibble with alleles for all bloodmeals in reference +\item{bloodmeal_profiles}{Tibble or data frame with alleles for all bloodmeals in reference database including 4 columns: SampleName, Marker, Allele, Height. Height must be numeric or coercible to numeric.} -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} \item{kit}{STR kit name from euroformix. To see a list of all kits embedded @@ -42,7 +42,7 @@ threshold will be filtered out. If prior filtering was performed, this number should be equal to or greater than that number. Also used for \code{threshT} argument in \code{\link[euroformix:contLikSearch]{euroformix::contLikSearch()}}.} -\item{pop_allele_freqs}{Data frame where the first column is the STR allele +\item{pop_allele_freqs}{Tibble or data frame where the first column is the STR allele and the following columns are the frequency of that allele for different markers. Alleles that do not exist for a given marker are coded as NA. If NULL and \code{calc_allele_freqs = TRUE}, then population allele frequencies diff --git a/man/check_if_allele_freqs.Rd b/man/check_if_allele_freqs.Rd index 121f8b1..68add86 100644 --- a/man/check_if_allele_freqs.Rd +++ b/man/check_if_allele_freqs.Rd @@ -7,7 +7,7 @@ check_if_allele_freqs(pop_allele_freqs, calc_allele_freqs, kit_df) } \arguments{ -\item{pop_allele_freqs}{Data frame where the first column is the STR allele +\item{pop_allele_freqs}{Tibble or data frame where the first column is the STR allele and the following columns are the frequency of that allele for different markers. Alleles that do not exist for a given marker are coded as NA. If NULL and \code{calc_allele_freqs = TRUE}, then population allele frequencies diff --git a/man/filter_peaks.Rd b/man/filter_peaks.Rd index 04281a7..27f71ec 100644 --- a/man/filter_peaks.Rd +++ b/man/filter_peaks.Rd @@ -7,7 +7,7 @@ filter_peaks(bloodmeal_profiles, peak_thresh) } \arguments{ -\item{bloodmeal_profiles}{Tibble with alleles for all bloodmeals in reference +\item{bloodmeal_profiles}{Tibble or data frame with alleles for all bloodmeals in reference database including 4 columns: SampleName, Marker, Allele, Height. Height must be numeric or coercible to numeric.} diff --git a/man/format_allele_freqs.Rd b/man/format_allele_freqs.Rd index 54e621e..8bad800 100644 --- a/man/format_allele_freqs.Rd +++ b/man/format_allele_freqs.Rd @@ -7,7 +7,7 @@ format_allele_freqs(pop_allele_freqs) } \arguments{ -\item{pop_allele_freqs}{Data frame where the first column is the STR allele +\item{pop_allele_freqs}{Tibble or data frame where the first column is the STR allele and the following columns are the frequency of that allele for different markers. Alleles that do not exist for a given marker are coded as NA. If NULL and \code{calc_allele_freqs = TRUE}, then population allele frequencies diff --git a/man/format_bloodmeal_profiles.Rd b/man/format_bloodmeal_profiles.Rd index 259d1c4..d6fe324 100644 --- a/man/format_bloodmeal_profiles.Rd +++ b/man/format_bloodmeal_profiles.Rd @@ -7,7 +7,7 @@ format_bloodmeal_profiles(bloodmeal_profiles) } \arguments{ -\item{bloodmeal_profiles}{Tibble with alleles for all bloodmeals in reference +\item{bloodmeal_profiles}{Tibble or data frame with alleles for all bloodmeals in reference database including 4 columns: SampleName, Marker, Allele, Height. Height must be numeric or coercible to numeric.} } diff --git a/man/format_human_profiles.Rd b/man/format_human_profiles.Rd index 58fa15f..08380c2 100644 --- a/man/format_human_profiles.Rd +++ b/man/format_human_profiles.Rd @@ -7,7 +7,7 @@ format_human_profiles(human_profiles) } \arguments{ -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} } \value{ diff --git a/man/get_bloodmeal_human_similarity.Rd b/man/get_bloodmeal_human_similarity.Rd index 2932542..58e5a32 100644 --- a/man/get_bloodmeal_human_similarity.Rd +++ b/man/get_bloodmeal_human_similarity.Rd @@ -8,11 +8,11 @@ based on similarity values} get_bloodmeal_human_similarity(bloodmeal_profiles, human_profiles) } \arguments{ -\item{bloodmeal_profiles}{Tibble with alleles for all bloodmeals in reference +\item{bloodmeal_profiles}{Tibble or data frame with alleles for all bloodmeals in reference database including 4 columns: SampleName, Marker, Allele, Height. Height must be numeric or coercible to numeric.} -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} } \value{ diff --git a/man/get_human_similarity.Rd b/man/get_human_similarity.Rd index 7f5107f..7964f75 100644 --- a/man/get_human_similarity.Rd +++ b/man/get_human_similarity.Rd @@ -7,7 +7,7 @@ get_human_similarity(human_profiles) } \arguments{ -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} } \value{ diff --git a/man/match_exact.Rd b/man/match_exact.Rd index 1b63834..bf0648a 100644 --- a/man/match_exact.Rd +++ b/man/match_exact.Rd @@ -15,11 +15,11 @@ match_exact( ) } \arguments{ -\item{bloodmeal_profiles}{Tibble with alleles for all bloodmeals in reference +\item{bloodmeal_profiles}{Tibble or data frame with alleles for all bloodmeals in reference database including 4 columns: SampleName, Marker, Allele, Height. Height must be numeric or coercible to numeric.} -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} \item{bloodmeal_ids}{Vector of bloodmeal ids from the SampleName column in diff --git a/man/match_similarity.Rd b/man/match_similarity.Rd index 9a7b85e..6f31b68 100644 --- a/man/match_similarity.Rd +++ b/man/match_similarity.Rd @@ -17,11 +17,11 @@ match_similarity( ) } \arguments{ -\item{bloodmeal_profiles}{Tibble with alleles for all bloodmeals in reference +\item{bloodmeal_profiles}{Tibble or data frame with alleles for all bloodmeals in reference database including 4 columns: SampleName, Marker, Allele, Height. Height must be numeric or coercible to numeric.} -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} \item{bloodmeal_ids}{Vector of bloodmeal ids from the SampleName column in diff --git a/man/prep_bloodmeal_profiles.Rd b/man/prep_bloodmeal_profiles.Rd index 7b49a8d..0d39e74 100644 --- a/man/prep_bloodmeal_profiles.Rd +++ b/man/prep_bloodmeal_profiles.Rd @@ -13,7 +13,7 @@ prep_bloodmeal_profiles( ) } \arguments{ -\item{bloodmeal_profiles}{Tibble with alleles for all bloodmeals in reference +\item{bloodmeal_profiles}{Tibble or data frame with alleles for all bloodmeals in reference database including 4 columns: SampleName, Marker, Allele, Height. Height must be numeric or coercible to numeric.} diff --git a/man/prep_human_profiles.Rd b/man/prep_human_profiles.Rd index 7dfcd03..f23d1f5 100644 --- a/man/prep_human_profiles.Rd +++ b/man/prep_human_profiles.Rd @@ -12,7 +12,7 @@ prep_human_profiles( ) } \arguments{ -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} \item{human_ids}{Vector of human ids from the SampleName column in diff --git a/man/rm_twins.Rd b/man/rm_twins.Rd index 6c34eac..e372415 100644 --- a/man/rm_twins.Rd +++ b/man/rm_twins.Rd @@ -7,7 +7,7 @@ rm_twins(human_profiles) } \arguments{ -\item{human_profiles}{Tibble with alleles for all humans in reference +\item{human_profiles}{Tibble or data frame with alleles for all humans in reference database including three columns: SampleName, Marker, Allele.} } \value{