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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -20,3 +20,4 @@ src/rust/uncomment.sh | |
| ^CRAN-SUBMISSION$ | ||
| ^.*\.Rproj$ | ||
| ^\.Rproj\.user$ | ||
| .lintr | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| linters: linters_with_defaults( | ||
| line_length_linter = NULL, | ||
| indentation_linter = NULL, | ||
| commas_linter = NULL, | ||
| infix_spaces_linter = NULL | ||
| ) # see vignette("lintr") | ||
| encoding: "UTF-8" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,95 +1,95 @@ | ||
| multi_by_validate <- function(a,b, by) { | ||
| # first pass to handle dplyr::join_by() call | ||
| if (inherits(by, "dplyr_join_by")) { | ||
| if (any(by$condition != "==")) { | ||
| stop("Inequality joins are not supported.") | ||
| } | ||
| new_by <- by$y | ||
| names(new_by) <- by$x | ||
| by <- new_by | ||
| multi_by_validate <- function(a, b, by) { | ||
| # first pass to handle dplyr::join_by() call | ||
| if (inherits(by, "dplyr_join_by")) { | ||
| if (any(by$condition != "==")) { | ||
| stop("Inequality joins are not supported.") | ||
| } | ||
| new_by <- by$y | ||
| names(new_by) <- by$x | ||
| by <- new_by | ||
| } | ||
|
|
||
| if (is.null(by)) { | ||
| by_a <- intersect(names(a), names(b)) | ||
| by_b <- intersect(names(a), names(b)) | ||
| if (is.null(by)) { | ||
| by_a <- intersect(names(a), names(b)) | ||
| by_b <- intersect(names(a), names(b)) | ||
| } else { | ||
| if (!is.null(names(by))) { | ||
| by_a <- names(by) | ||
| by_b <- by | ||
| } else { | ||
| if (!is.null(names(by))) { | ||
| by_a <- names(by) | ||
| by_b <- by | ||
| } else { | ||
| by_a <- by | ||
| by_b <- by | ||
| } | ||
|
|
||
| stopifnot(by_a %in% names(a)) | ||
| stopifnot(by_b %in% names(b)) | ||
| by_a <- by | ||
| by_b <- by | ||
| } | ||
| return(list( | ||
| by_a, | ||
| by_b | ||
| )) | ||
| stopifnot(by_a %in% names(a)) | ||
| stopifnot(by_b %in% names(b)) | ||
| } | ||
| return(list( | ||
| by_a, | ||
| by_b | ||
| )) | ||
| } | ||
|
|
||
| #` @importFrom stats pnorm | ||
| euclidean_join_core <- function (a, b, by = NULL, n_bands = 30, band_width = 10, threshold=1.0, r=.5, progress = FALSE, mode="inner") { | ||
|
|
||
| stopifnot("'radius' must be greater than 0" = threshold > 0) | ||
|
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| by <- multi_by_validate(a,b,by) | ||
| by_a <- by[[1]] | ||
| by_b <- by[[2]] | ||
| stopifnot("There should be no NA's in by_a[1]"=!any(is.na(dplyr::pull(a,by_a[1])))) | ||
| stopifnot("There should be no NA's in by_a[2]"=!any(is.na(dplyr::pull(a,by_a[2])))) | ||
| stopifnot("There should be no NA's in by_b[1]"=!any(is.na(dplyr::pull(b,by_b[1])))) | ||
| stopifnot("There should be no NA's in by_b[2]"=!any(is.na(dplyr::pull(b,by_b[2])))) | ||
| # ` @importFrom stats pnorm | ||
| euclidean_join_core <- function(a, b, by = NULL, n_bands = 30, band_width = 10, threshold = 1.0, r = .5, progress = FALSE, mode = "inner") { | ||
| stopifnot("'radius' must be greater than 0" = threshold > 0) | ||
|
|
||
| thresh_prob <- euclidean_probability(threshold, n_bands, band_width, r) | ||
| if (thresh_prob < .95) { | ||
| str <- paste0("A pair of records at the threshold (", threshold, | ||
| ") have only a ", round(thresh_prob*100), "% chance of being compared.\n", | ||
| "Please consider changing `n_bands` and `band_width`, and `r`.") | ||
|
|
||
| warning(str) | ||
| } | ||
| by <- multi_by_validate(a, b, by) | ||
| by_a <- by[[1]] | ||
| by_b <- by[[2]] | ||
| stopifnot("There should be no NA's in by_a[1]" = !anyNA(a[[by_a[1]]])) | ||
| stopifnot("There should be no NA's in by_a[2]" = !anyNA(a[[by_a[2]]])) | ||
| stopifnot("There should be no NA's in by_b[1]" = !anyNA(b[[by_b[1]]])) | ||
| stopifnot("There should be no NA's in by_b[2]" = !anyNA(b[[by_b[2]]])) | ||
|
|
||
| match_table <- rust_p_norm_join( | ||
| a_mat = as.matrix(dplyr::select(a, dplyr::all_of(by_a))), | ||
| b_mat = as.matrix(dplyr::select(b, dplyr::all_of(by_b))), | ||
| radius = threshold, | ||
| band_width = band_width, | ||
| n_bands = n_bands, | ||
| r = r, | ||
| progress = progress, | ||
| seed = round(runif(1,0,2^32)) | ||
| thresh_prob <- euclidean_probability(threshold, n_bands, band_width, r) | ||
| if (thresh_prob < .95) { | ||
| str <- paste0( | ||
| "A pair of records at the threshold (", threshold, | ||
| ") have only a ", round(thresh_prob * 100), "% chance of being compared.\n", | ||
| "Please consider changing `n_bands` and `band_width`, and `r`." | ||
| ) | ||
|
|
||
| names_in_both <- intersect(names(a), names(b)) | ||
| warning(str) | ||
| } | ||
|
|
||
| names(a)[names(a) %in% names_in_both] <- | ||
| paste0(names(a)[names(a) %in% names_in_both], ".x") | ||
| names(b)[names(b) %in% names_in_both] <- | ||
| paste0(names(b)[names(b) %in% names_in_both], ".y") | ||
| match_table <- rust_p_norm_join( | ||
| a_mat = as.matrix(dplyr::select(a, dplyr::all_of(by_a))), | ||
| b_mat = as.matrix(dplyr::select(b, dplyr::all_of(by_b))), | ||
| radius = threshold, | ||
| band_width = band_width, | ||
| n_bands = n_bands, | ||
| r = r, | ||
| progress = progress, | ||
| seed = round(runif(1, 0, 2^32)) | ||
| ) | ||
|
|
||
| matches <- dplyr::bind_cols(a[match_table[, 1], ], b[match_table[, 2], ]) | ||
| names_in_both <- intersect(names(a), names(b)) | ||
|
|
||
| # No need to look for rows that don't match | ||
| if (mode == "inner") { | ||
| return(matches) | ||
| } | ||
| names(a)[names(a) %in% names_in_both] <- | ||
| paste0(names(a)[names(a) %in% names_in_both], ".x") | ||
| names(b)[names(b) %in% names_in_both] <- | ||
| paste0(names(b)[names(b) %in% names_in_both], ".y") | ||
|
|
||
| not_matched_a <- ! seq(nrow(a)) %in% match_table[,1] | ||
| not_matched_b <- ! seq(nrow(b)) %in% match_table[,2] | ||
| matches <- dplyr::bind_cols(a[match_table[, 1], ], b[match_table[, 2], ]) | ||
|
|
||
| if (mode == "left") { | ||
| matches <- dplyr::bind_rows(matches,a[not_matched_a,]) | ||
| } else if (mode == "right") { | ||
| matches <- dplyr::bind_rows(matches,b[not_matched_b,]) | ||
| } else if (mode == "full") { | ||
| matches <- dplyr::bind_rows(matches,a[not_matched_a,],b[not_matched_b,]) | ||
| } else if (mode == "anti") { | ||
| matches <- dplyr::bind_rows(a[not_matched_a,], b[not_matched_b,]) | ||
| } else { | ||
| stop("Invalid Mode Selected!") | ||
| } | ||
| # No need to look for rows that don't match | ||
| if (mode == "inner") { | ||
| return(matches) | ||
| } | ||
|
|
||
| not_matched_a <- !seq(nrow(a)) %in% match_table[, 1] | ||
| not_matched_b <- !seq(nrow(b)) %in% match_table[, 2] | ||
|
|
||
| if (mode == "left") { | ||
| matches <- dplyr::bind_rows(matches, a[not_matched_a, ]) | ||
| } else if (mode == "right") { | ||
| matches <- dplyr::bind_rows(matches, b[not_matched_b, ]) | ||
| } else if (mode == "full") { | ||
| matches <- dplyr::bind_rows(matches, a[not_matched_a, ], b[not_matched_b, ]) | ||
| } else if (mode == "anti") { | ||
| matches <- dplyr::bind_rows(a[not_matched_a, ], b[not_matched_b, ]) | ||
| } else { | ||
| stop("Invalid Mode Selected!") | ||
| } | ||
| return(matches) | ||
| } |
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