Update documentation

R/match_similarity.R

@@ -139,6 +139,7 @@ match_similarity <- function(bloodmeal_profiles, human_profiles,
 #' - hu1: human ID 1
 #' - hu2: human ID 2
 #' - similarity: similarity value (# exact locus matches / # loci)
+#' @keywords internal
 get_human_similarity <- function(human_profiles) {
   human_profiles <- human_profiles |>
     tidyr::drop_na()
@@ -193,6 +194,7 @@ get_human_similarity <- function(human_profiles) {
 #' @return dataframe with two columns:
 #' - bloodmeal_id: bloodmeal ID
 #' - human_id: human ID of match, or "No match" if no match
+#' @keywords internal
 get_bloodmeal_human_similarity <- function(bloodmeal_profiles,
                                            human_profiles) {
   bloodmeal_profiles <- bloodmeal_profiles |>

vignettes/bistro.Rmd

@@ -217,9 +217,23 @@ Used by `bistro`:
 
 Used by `euroformix::contLikSearch()` when calculating log-likelihoods:
 
+- `rm_markers`: markers to not use for calculating LRs. By default, AMEL is removed because it is not standard to use for calculating LRs as it is a sex-specific marker 
 - `model_degrad`: whether or not to model peak degradation (default: TRUE)
 - `model_bw_stutt` and `model_fw_stutt`: whether or not to model peak backward and forward stutter (default: FALSE)
 - `difftol`: difference tolerance in log-likelihood across 2 iterations  (default: 1)
 - `threads`: number of threads to use when computing log-likelihoods (default: 4)
 - `seed`: seed for reproducible results (default: 1)
+- `return_lr`: whether or not to return all bloodmeal-human log10LRs. This is useful if you want to investigate the matches or perform static threshold matching (see below) (default: FALSE)
+
+## Other matching algorithms
+
+We have also implemented a few other matching algorithms including:
+
+- `match_exact()`: Exact matching of all markers and alleles
+- `match_similarity()`: Similarity matching based on the highest similarity value between humans in a reference database
+- `match_static_threshold()`: Matching based on static log10LR threshold. 
+
+These algorithms take similar inputs to `bistro()`, or in the case of `match_static_threshold()`, a `bistro()` output.
+
+Look out for our upcoming manuscript for a comparison of these methods.