From fe4aceed4977dd9cd00b4df119d1dc75e0fb7b4d Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Fri, 7 Jun 2024 13:17:22 -0400
Subject: [PATCH 01/20] Increment version number to 0.2.0.9005

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0dc6f114..2cf2a406 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: joyn
 Type: Package
 Title: Tool for Diagnosis of Tables Joins and Complementary Join Features
-Version: 0.2.0.9004
+Version: 0.2.0.9005
 Authors@R: c(person(given = "R.Andres", 
                     family = "Castaneda", 
                     email = "acastanedaa@worldbank.org",

From f1555bb20b499a1e2b7125cd2a69668daad1107f Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Fri, 7 Jun 2024 13:18:22 -0400
Subject: [PATCH 02/20] update news

---
 NEWS.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 21533b70..e6c812e6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -13,6 +13,8 @@
 
 * Add information about duplicated obs in `by` variable when match type is `1` rather than `m`.
 
+* Internal: improve storing of joyn messages.
+
 ## breaking changes
 
 * Now, by default, `joyn` will not sort the data. This is to avoid unnecessary 

From 37c9a59063bd86b05bcc08d997457510788de33e Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Fri, 7 Jun 2024 16:20:15 -0400
Subject: [PATCH 03/20] add attr argument to collapse::join

---
 R/joyn_workhorse.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/joyn_workhorse.R b/R/joyn_workhorse.R
index d19f6fa7..8a2a9052 100644
--- a/R/joyn_workhorse.R
+++ b/R/joyn_workhorse.R
@@ -57,13 +57,13 @@ joyn_workhorse <- function(
   start_time <- Sys.time()
 
   # Do a full join -------------------------------------------------------------
+  source_pkg <- "collapse::join"
 
   # if not 1:1 => use merge.data.table
 
   # not m:m => use collapse::join()
     dt_result <- tryCatch(
       expr = {
-        source_pkg <- "collapse::join"
 
         collapse::join(x              = x,
                        y              = y,
@@ -75,7 +75,8 @@ joyn_workhorse <- function(
                        keep.col.order = TRUE,
                        sort           = sort,
                        verbose        = 0,
-                       column         = NULL)
+                       column         = NULL,
+                       attr           = TRUE)
       }, # end of expr section
 
       error = function(e) {

From 592f0ba8a6ec09fc3f5ef3f7bb506050d8723138 Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Fri, 7 Jun 2024 21:31:03 -0400
Subject: [PATCH 04/20] update. not working

---
 R/joyn-merge.R     | 71 +++++++++++++++++++++++++---------------------
 R/joyn_workhorse.R | 67 +++++++++++++++++++++----------------------
 2 files changed, 71 insertions(+), 67 deletions(-)

diff --git a/R/joyn-merge.R b/R/joyn-merge.R
index 134ce630..a6f966f1 100644
--- a/R/joyn-merge.R
+++ b/R/joyn-merge.R
@@ -322,40 +322,19 @@ joyn <- function(x,
   #             include report variable   ---------
   #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-  yvars_w <- c(y_vars_to_keep, ".yreport") # working yvars
-  x <- x |>
-    ftransform(.xreport = 1)
-  y <- y |>
-    ftransform(.yreport = 2)
-
-  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  #                   Actual merge   ---------
-  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-  # simple merge
-  i.yvars <- paste0("i.", yvars_w)
-
-  # keep relevant variables in y
-  y <- y |> fselect(
-    by, yvars_w
-  )
-
-  # Perform workhorse join
-  x <- joyn_workhorse(
-    x          = x,
-    y          = y,
-    by         = by,
-    match_type = match_type,
-    suffixes   = suffixes,
-    sort       = sort
-  )
+  yvars_w <- y_vars_to_keep # working yvars
+  # yvars_w <- c(y_vars_to_keep, ".yreport") # working yvars
+  # x <- x |>
+  #   ftransform(.xreport = 1)
+  # y <- y |>
+  #   ftransform(.yreport = 2)
 
   #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   #                   Report variable   ---------
   #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
   # replace NAs in report vars
-  setnafill(x, fill = 0, cols = c(".xreport", ".yreport"))
+  # setnafill(x, fill = 0, cols = c(".xreport", ".yreport"))
 
   # report variable
   dropreport <- FALSE
@@ -375,17 +354,43 @@ joyn <- function(x,
       check_names <- make.names(check_names, unique = TRUE)
       nrv         <- setdiff(check_names, xnames)
 
-      store_joyn_msg(info = "reportvar {.strongVar {reportvar}}  is already part of the resulting table. It will be changed to {.strongVar {nrv}}")
+      store_joyn_msg(info = "reportvar {.strongVar {reportvar}}  is
+                     already part of the resulting table. It will be
+                     changed to {.strongVar {nrv}}")
 
       reportvar <- nrv
     }
   }
 
 
-  # report variable
-  collapse::settransform(x, use_util_report = .xreport + .yreport)
-  # Can this be done more efficiently with collapse?
-  data.table::setnames(x, "use_util_report", reportvar)
+  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+  #                   Actual merge   ---------
+  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+  # simple merge
+  i.yvars <- paste0("i.", yvars_w)
+
+  # keep relevant variables in y
+  y <- y |>
+    fselect(by, yvars_w)
+
+  # Perform workhorse join
+  x <- joyn_workhorse(
+    x          = x,
+    y          = y,
+    by         = by,
+    suffixes   = suffixes,
+    sort       = sort,
+    reportvar  = reportvar
+  )
+
+
+
+
+  # # report variable
+  # collapse::settransform(x, use_util_report = .xreport + .yreport)
+  # # Can this be done more efficiently with collapse?
+  # data.table::setnames(x, "use_util_report", reportvar)
 
 
   #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/R/joyn_workhorse.R b/R/joyn_workhorse.R
index 8a2a9052..54951a88 100644
--- a/R/joyn_workhorse.R
+++ b/R/joyn_workhorse.R
@@ -6,8 +6,6 @@
 #' @param x data object, "left" or "master"
 #' @param y data object, "right" or "using"
 #' @param by atomic character vector: key specifying join
-#' @param match_type atomic character vector of length 1: either "1:1" (default)
-#'   "1:m", "m:1", or "m:m". Relies on `collapse::join()`
 #' @param suffixes atomic character vector: give suffixes to columns common to both
 #' @param sort logical: sort the result by the columns in `by`
 #'   `x` and `y`
@@ -29,28 +27,19 @@ joyn_workhorse <- function(
     x,
     y,
     by         = intersect(names(x), names(y)),
-    match_type = c("1:1"),
     sort       = FALSE,
-    suffixes     = getOption("joyn.suffixes") # data.table suffixes
+    suffixes   = getOption("joyn.suffixes"), # data.table suffixes
+    reportvar  =  getOption("joyn.reportvar")
 ) {
 
   # Argument checks ------------------------------------------------------------
-  match_type <- match.arg(
-    match_type,
-    choices = c(
-      "1:1",
-      "1:m",
-      "m:1",
-      "m:m"
-    )
-  )
-  if (
-    length(by) == 0
-  ) {
+
+  if (length(by) == 0) {
 
     store_joyn_msg(err = "In joyn_workhorse {.strongArg by} argument has length of 0")
 
-    store_joyn_msg(info = "Either specify by to identify columns to join on in x and y, or x and y should have common column names")
+    store_joyn_msg(info = "Either specify by to identify columns to join on in x
+                   and y, or x and y should have common column names")
 
   }
   # Measure time
@@ -75,7 +64,7 @@ joyn_workhorse <- function(
                        keep.col.order = TRUE,
                        sort           = sort,
                        verbose        = 0,
-                       column         = NULL,
+                       column         = ".joyn1",
                        attr           = TRUE)
       }, # end of expr section
 
@@ -89,41 +78,51 @@ joyn_workhorse <- function(
       warning = function(w) {
         if (grepl("[Oo]veridentified", w$message)) {
 
-          store_joyn_msg(warn = "Your data is overidentified. Below the original message from {.strong {source_pkg}}: \n{w$message}")
+          store_joyn_msg(warn = "Your data is overidentified. Below the original
+                         message from {.strong {source_pkg}}: \n{w$message}")
 
         } else {
 
-          store_joyn_msg(warn = "{.strong {source_pkg}} returned the following warning: \n{w$message}")
+          store_joyn_msg(warn = "{.strong {source_pkg}} returned the following
+                         warning: \n{w$message}")
 
         }
 
-          collapse::join( x              = x,
-                          y              = y,
-                          how            = "full",
-                          on             = by,
-                          multiple       = TRUE,     # matches row in x with m in y
-                          validate       = "m:m",    # no checks performed
-                          suffix         = suffixes,   # data.table suffixes
-                          keep.col.order = TRUE,
-                          sort           = sort,
-                          verbose        = 0,
-                          column         = NULL)  |>
+        collapse::join(x              = x,
+                       y              = y,
+                       how            = "full",
+                       on             = by,
+                       multiple       = TRUE,     # matches row in x with m in y
+                       validate       = "m:m",    # no checks performed
+                       suffix         = suffixes,   # data.table suffixes
+                       keep.col.order = TRUE,
+                       sort           = sort,
+                       verbose        = 0,
+                       column         = ".joyn1",
+                       attr           = TRUE)  |>
             suppressWarnings()
 
       }
 
     ) # End of trycatch
 
+    # change values of .joyn1 to numeric to make it consistent with joyn
+    mapping <- c('1' = 3, '2' = 1, '3' = 2)
+    dt_result <- dt_result |>
+      ftransform(.joyn1 = as.numeric(.joyn1)) |>
+      ftransform(.joyn1 = mapping[as.character(.joyn1)]) |>
+      frename(.joyn1 = reportvar, .nse = FALSE)
+
+
   # Calculate the time taken
   end_time <- Sys.time()
   time_taken <- end_time - start_time
 
-  store_joyn_msg(timing = paste("The full joyn is executed in", round(time_taken, 6)))
+  store_joyn_msg(timing = paste("The full joyn is executed in",
+                                round(time_taken, 6)))
 
   # Return ----
-  return(
     dt_result
-  )
 }
 
 

From e5be1d31f0a6bb7c3efdbbdf7284e5bdc8ad38a0 Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Mon, 10 Jun 2024 15:43:35 -0400
Subject: [PATCH 05/20] fix some bugs

---
 R/joyn-merge.R | 108 ++++++++++++++++++++++++++++---------------------
 1 file changed, 61 insertions(+), 47 deletions(-)

diff --git a/R/joyn-merge.R b/R/joyn-merge.R
index a6f966f1..769b7ea9 100644
--- a/R/joyn-merge.R
+++ b/R/joyn-merge.R
@@ -163,7 +163,7 @@ joyn <- function(x,
                  update_values    = FALSE,
                  update_NAs       = update_values,
                  reportvar        = getOption("joyn.reportvar"),
-                 reporttype       = c("character", "numeric"),
+                 reporttype       = c("factor", "character", "numeric"),
                  roll             = NULL,
                  keep_common_vars = FALSE,
                  sort             = FALSE,
@@ -375,7 +375,7 @@ joyn <- function(x,
     fselect(by, yvars_w)
 
   # Perform workhorse join
-  x <- joyn_workhorse(
+  jn <- joyn_workhorse(
     x          = x,
     y          = y,
     by         = by,
@@ -383,16 +383,37 @@ joyn <- function(x,
     sort       = sort,
     reportvar  = reportvar
   )
-
+  m <- attr(res, "join.match")$match
 
 
 
   # # report variable
-  # collapse::settransform(x, use_util_report = .xreport + .yreport)
+  # collapse::settransform(jn, use_util_report = .xreport + .yreport)
   # # Can this be done more efficiently with collapse?
-  # data.table::setnames(x, "use_util_report", reportvar)
+  # data.table::setnames(jn, "use_util_report", reportvar)
+
 
 
+  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+  #                   Update jn   ---------
+  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+  var_use <- NULL
+  if (isTRUE(update_NAs) || isTRUE(update_values)) {
+    var_use <- common_vars
+  }
+
+  if (isTRUE(update_NAs || update_values) & length(var_use) > 0 ) {
+
+    jn <- update_na_values(dt           = jn,
+                            var          = var_use,
+                            reportvar    = reportvar,
+                            suffixes     = suffixes,
+                            rep_NAs      = update_NAs,
+                            rep_values   = update_values
+      )
+
+  }
+
   #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   #                   Filter rows - `keep`   ---------
   #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -400,43 +421,23 @@ joyn <- function(x,
   ## rows to keep -----
   if (keep  %in% c("master", "left") ) {
 
-    x <- x |>
+    jn <- jn |>
       fsubset(get(reportvar)  != 2)
 
   } else if (keep  %in% c("using", "right") ) {
 
-    x <- x |>
+    jn <- jn |>
       fsubset(get(reportvar)  != 1)
 
   } else if (keep  == "inner") {
 
-    x <- x |>
+    jn <- jn |>
       fsubset(get(reportvar)  >= 3)
   } else if (keep == "anti") {
-    x <- x |>
+    jn <- jn |>
       fsubset(get(reportvar) == 1)
   }
 
-  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  #                   Update x   ---------
-  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  var_use <- NULL
-  if (isTRUE(update_NAs) || isTRUE(update_values)) {
-    var_use <- common_vars
-  }
-
-  if (isTRUE(update_NAs || update_values) & length(var_use) > 0 ) {
-
-      x <- update_na_values(dt           = x,
-                            var          = var_use,
-                            reportvar    = reportvar,
-                            suffixes     = suffixes,
-                            rep_NAs      = update_NAs,
-                            rep_values   = update_values
-      )
-
-  }
-
 
   ### common vars ----------
 
@@ -446,15 +447,15 @@ joyn <- function(x,
       gsub("\\.", "\\\\.", x = _) |>
       paste0("$")
 
-    varx <- grep(patterns[1], names(x), value = TRUE)
-    vary <- grep(patterns[2], names(x), value = TRUE)
+    varx <- grep(patterns[1], names(jn), value = TRUE)
+    vary <- grep(patterns[2], names(jn), value = TRUE)
 
     # delete Y vars with suffix
-    collapse::get_vars(x, vary) <- NULL
+    collapse::get_vars(jn, vary) <- NULL
 
     # remove suffixes
     nsvar <- gsub(patterns[1], "", varx)
-    data.table::setnames(x, varx, nsvar)
+    data.table::setnames(jn, varx, nsvar)
 
   }
 
@@ -463,20 +464,32 @@ joyn <- function(x,
   #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
   ## cleaning temporary report variables ----
-  collapse::settransform(x,
-                         .xreport = NULL,
-                         .yreport = NULL)
+  # collapse::settransform(jn,
+  #                        .xreport = NULL,
+  #                        .yreport = NULL)
 
   # Rename by variables -----
   ## in output
-  if (any(grepl(pattern = "keyby", x = names(x)))) {
-    data.table::setnames(x,
-                         old = names(x)[grepl(pattern = "keyby",
-                                              x       = names(x))],
+  if (any(grepl("keyby",names(jn)))) {
+    data.table::setnames(jn,
+                         old = names(jn)[grepl("keyby", names(jn))],
                          new = xbynames)
   }
 
   ## convert to characters if chosen -------
+
+  if (reporttype == "factor") {
+
+    get_vars(jn, reportvar) <-  factor(jn[[reportvar]],
+                                      levels = 1:6,
+                                      labels = c("x",
+                                                 "y",
+                                                 "x & y",
+                                                 "NA updated",
+                                                 "value updated",
+                                                 "not updated"))
+  }
+
   if (reporttype == "character") {
 
     rvar_to_chr <- \(x) {
@@ -489,13 +502,13 @@ joyn <- function(x,
                         default = "conflict")
     }
 
-    settransformv(x, reportvar, rvar_to_chr)
+    settransformv(jn, reportvar, rvar_to_chr)
 
   }
 
   # no matching obs
-  if ((all(x[[reportvar]] %in% c("x", "y")) ||
-      all(x[[reportvar]] %in% c(1, 2))) &&
+  if ((all(jn[[reportvar]] %in% c("x", "y")) ||
+       all(jn[[reportvar]] %in% c(1, 2))) &&
       !keep == "anti") {
 
     store_joyn_msg(warn = " you have no matching obs. Make sure argument
@@ -506,12 +519,12 @@ joyn <- function(x,
 
   ## Display results------
   # freq table
-  d <- freq_table(x, reportvar)
+  d <- freq_table(jn, reportvar)
   rlang::env_poke(.joynenv, "freq_joyn", d)
 
   # Report var
   if (dropreport) {
-    get_vars(x, reportvar) <- NULL
+    get_vars(jn, reportvar) <- NULL
   }
 
   # store timing
@@ -529,8 +542,9 @@ joyn <- function(x,
     joyn_msg(msg_type)
   }
 
-  setattr(x, "class", class_x)
+  setattr(jn, "class", class_x)
+  setattr(jn, "join.match", NULL)
 
-  x
+  jn
 
 }

From 33025d6372bafe9b0676ef5190901f7c668ecab9 Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Mon, 10 Jun 2024 16:14:01 -0400
Subject: [PATCH 06/20]     fix tests

---
 tests/testthat/test-joyn.R           |  6 +++-
 tests/testthat/test-joyn_workhorse.R | 43 ++++++++++------------------
 2 files changed, 20 insertions(+), 29 deletions(-)

diff --git a/tests/testthat/test-joyn.R b/tests/testthat/test-joyn.R
index c28d8e8f..1a799a19 100644
--- a/tests/testthat/test-joyn.R
+++ b/tests/testthat/test-joyn.R
@@ -680,7 +680,11 @@ test_that("error when there is not natural join", {
 
 test_that("different names in key vars are working fine", {
 
-  df <- joyn(x4, y4, by = c("id1 = id", "id2"), match_type = "m:1", y_vars_to_keep = c("y"), sort = TRUE)
+  df <- joyn(x4, y4, by = c("id1 = id", "id2"),
+             match_type = "m:1",
+             y_vars_to_keep = c("y"),
+             sort = TRUE,
+             reporttype =  "character")
 
   dd <- data.table(id1 = c(1, 1, 2, 2, 3, 3, 5, 6),
                    id2 = c(1, 1, 2, 1, 3, 4, 2, 3),
diff --git a/tests/testthat/test-joyn_workhorse.R b/tests/testthat/test-joyn_workhorse.R
index 6d2c1eaa..1973c755 100644
--- a/tests/testthat/test-joyn_workhorse.R
+++ b/tests/testthat/test-joyn_workhorse.R
@@ -73,6 +73,7 @@ test_that(
 
 # Checking output with match type m:m and 1:1 -------------------------------------------------
 test_that("m:m and 1:1 gives the same output if data is correct", {
+  skip("This test is not needed anymore because the match is always m:m in collapse::join")
   expect_equal(
     joyn_workhorse(
       x          = x2,
@@ -133,8 +134,7 @@ test_that("full joyn is correct", {
   x <- joyn_workhorse(
     x          = x1,
     y          = y1,
-    by         = "id",
-    match_type = "1:1"
+    by         = "id"
   )
   expect_equal(
     nrow(x),
@@ -153,7 +153,9 @@ test_that("FULL- Compare with base::merge", {
     x  = x1,
     y  = y1,
     by = "id"
-  )
+  ) |>
+    fselect(-.joyn) |>
+    setattr('join.match', NULL)
 
   br <- base::merge(
     x   = x1,
@@ -162,37 +164,21 @@ test_that("FULL- Compare with base::merge", {
     all = TRUE
   )
 
-  setorderv(
-    br,
-    "id",
-    na.last = TRUE
-  )
-  setorderv(
-    jn,
-    "id",
-    na.last = TRUE
-  )
-  setattr(
-    br,
-    'sorted',
-    "id"
-  )
-  setattr(
-    jn,
-    'sorted',
-    "id"
-  ) # ZP: check this
+  setorderv(br,"id", na.last = TRUE)
+  setorderv(jn, "id", na.last = TRUE)
+  setattr(br, 'sorted', "id")
+  setattr(jn, 'sorted', "id") # ZP: check this
 
-  expect_equal(
-    jn,
-    br
-  )
+  expect_equal(jn, br)
 
   jn <- joyn_workhorse(
     x  = x2,
     y  = y2,
     by = "id"
-  )
+  )  |>
+    fselect(-.joyn) |>
+    setattr('join.match', NULL)
+
 
   br <- base::merge(
     x   = x2,
@@ -213,6 +199,7 @@ test_that("FULL- Compare with base::merge", {
 
 # Checking match types work ------------------------------------------------------------------------
 test_that("match types work", {
+  skip("joyn_workhorse does not check match type")
 
   # note: `joyn_workhorse` does not
   #       check whether match_type

From 6f1403d7459bfd47a1de261486f15a0ba8d4b156 Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Mon, 10 Jun 2024 18:34:08 -0400
Subject: [PATCH 07/20] pass all test with new report var from collapse::join

---
 R/dplyr-joins.R                   | 10 +++++-----
 R/info_display.R                  |  9 +++++++--
 R/joyn-merge.R                    |  2 +-
 R/joyn_workhorse.R                |  3 +--
 man/joyn.Rd                       |  2 +-
 man/joyn_workhorse.Rd             |  7 ++-----
 man/left_join.Rd                  |  2 +-
 tests/testthat/test-dplyr-joins.R |  2 +-
 8 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/R/dplyr-joins.R b/R/dplyr-joins.R
index 22257d69..5c06b869 100644
--- a/R/dplyr-joins.R
+++ b/R/dplyr-joins.R
@@ -48,7 +48,7 @@ left_join <- function(
     update_values    = FALSE,
     update_NAs       = update_values,
     reportvar        = getOption("joyn.reportvar"),
-    reporttype       = c("character", "numeric"),
+    reporttype       = c("factor", "character", "numeric"),
     roll             = NULL,
     keep_common_vars = FALSE,
     sort             = TRUE,
@@ -207,7 +207,7 @@ right_join <- function(
     update_values    = FALSE,
     update_NAs       = update_values,
     reportvar        = getOption("joyn.reportvar"),
-    reporttype       = c("character", "numeric"),
+    reporttype       = c("factor", "character", "numeric"),
     roll             = NULL,
     keep_common_vars = FALSE,
     sort             = TRUE,
@@ -369,7 +369,7 @@ full_join <- function(
     update_values    = FALSE,
     update_NAs       = update_values,
     reportvar        = getOption("joyn.reportvar"),
-    reporttype       = c("character", "numeric"),
+    reporttype       = c("factor", "character", "numeric"),
     roll             = NULL,
     keep_common_vars = FALSE,
     sort             = TRUE,
@@ -527,7 +527,7 @@ inner_join <- function(
     update_values    = FALSE,
     update_NAs       = update_values,
     reportvar        = getOption("joyn.reportvar"),
-    reporttype       = c("character", "numeric"),
+    reporttype       = c("factor", "character", "numeric"),
     roll             = NULL,
     keep_common_vars = FALSE,
     sort             = TRUE,
@@ -687,7 +687,7 @@ anti_join <- function(
     relationship     = "many-to-many",
     y_vars_to_keep   = FALSE,
     reportvar        = getOption("joyn.reportvar"),
-    reporttype       = c("character", "numeric"),
+    reporttype       = c("factor", "character", "numeric"),
     roll             = NULL,
     keep_common_vars = FALSE,
     sort             = TRUE,
diff --git a/R/info_display.R b/R/info_display.R
index 8b609050..8a33ac7f 100644
--- a/R/info_display.R
+++ b/R/info_display.R
@@ -148,12 +148,17 @@ store_joyn_msg <- function(err       = NULL,
                            timing    = NULL,
                            info      = NULL) {
 
-  # Check that only one among err, warn, timing and info is not null, otherwise stop
+  # Check that only one among err, warn, timing and info is not null,
+  # otherwise stop
+  #
+  # Formals
+  frm <- formals() |>
+    names()
 
   cn <- c(err, warn, timing, info)
 
   if (length(cn) != 1) {
-    cli::cli_abort(c("only one of err, warn, timing, info can be not null",
+    cli::cli_abort(c("only one of {.or {.arg {frm}}} can be not null",
                      "i" = "check the arguments"))
   }
 
diff --git a/R/joyn-merge.R b/R/joyn-merge.R
index 769b7ea9..78c373cc 100644
--- a/R/joyn-merge.R
+++ b/R/joyn-merge.R
@@ -383,7 +383,7 @@ joyn <- function(x,
     sort       = sort,
     reportvar  = reportvar
   )
-  m <- attr(res, "join.match")$match
+  m <- attr(jn, "join.match")$match
 
 
 
diff --git a/R/joyn_workhorse.R b/R/joyn_workhorse.R
index 54951a88..9d084c30 100644
--- a/R/joyn_workhorse.R
+++ b/R/joyn_workhorse.R
@@ -71,8 +71,7 @@ joyn_workhorse <- function(
       error = function(e) {
 
 
-        joyn_msg("err", c("{.pkg {source_pkg}} returned the following:",
-                          x = e$message))
+        store_joyn_msg(err = "{.pkg {source_pkg}} returned the following: {e$message}")
       }, # end of error section
 
       warning = function(w) {
diff --git a/man/joyn.Rd b/man/joyn.Rd
index e370129e..0f4bfb20 100644
--- a/man/joyn.Rd
+++ b/man/joyn.Rd
@@ -14,7 +14,7 @@ joyn(
   update_values = FALSE,
   update_NAs = update_values,
   reportvar = getOption("joyn.reportvar"),
-  reporttype = c("character", "numeric"),
+  reporttype = c("factor", "character", "numeric"),
   roll = NULL,
   keep_common_vars = FALSE,
   sort = FALSE,
diff --git a/man/joyn_workhorse.Rd b/man/joyn_workhorse.Rd
index fed075be..807bf5d5 100644
--- a/man/joyn_workhorse.Rd
+++ b/man/joyn_workhorse.Rd
@@ -8,9 +8,9 @@ joyn_workhorse(
   x,
   y,
   by = intersect(names(x), names(y)),
-  match_type = c("1:1"),
   sort = FALSE,
-  suffixes = getOption("joyn.suffixes")
+  suffixes = getOption("joyn.suffixes"),
+  reportvar = getOption("joyn.reportvar")
 )
 }
 \arguments{
@@ -20,9 +20,6 @@ joyn_workhorse(
 
 \item{by}{atomic character vector: key specifying join}
 
-\item{match_type}{atomic character vector of length 1: either "1:1" (default)
-"1:m", "m:1", or "m:m". Relies on \code{collapse::join()}}
-
 \item{sort}{logical: sort the result by the columns in \code{by}
 \code{x} and \code{y}}
 
diff --git a/man/left_join.Rd b/man/left_join.Rd
index 871496c9..ac29a894 100644
--- a/man/left_join.Rd
+++ b/man/left_join.Rd
@@ -19,7 +19,7 @@ left_join(
   update_values = FALSE,
   update_NAs = update_values,
   reportvar = getOption("joyn.reportvar"),
-  reporttype = c("character", "numeric"),
+  reporttype = c("factor", "character", "numeric"),
   roll = NULL,
   keep_common_vars = FALSE,
   sort = TRUE,
diff --git a/tests/testthat/test-dplyr-joins.R b/tests/testthat/test-dplyr-joins.R
index 9d478d9b..1bc5dd15 100644
--- a/tests/testthat/test-dplyr-joins.R
+++ b/tests/testthat/test-dplyr-joins.R
@@ -1800,7 +1800,7 @@ test_that("ANTI JOIN - Conducts ANTI join", {
        "sorted") <- "id1"
   expect_equal(
     jn |> fselect(-get(reportvar)) |> dim(),
-    c(0, 6)
+    c(0, 4)
   )
 })
 

From f7dd67e6e1914632f06a35456284eb4b6ef829dc Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Mon, 10 Jun 2024 20:20:48 -0400
Subject: [PATCH 08/20] increase speed of freq table using collapse

---
 R/freq_table.R   | 44 +++++++++++++-------------------------------
 R/info_display.R |  2 ++
 R/joyn-merge.R   | 41 +++++++++++++++--------------------------
 R/utils.R        |  1 -
 4 files changed, 30 insertions(+), 58 deletions(-)

diff --git a/R/freq_table.R b/R/freq_table.R
index 66e709dc..db5893f1 100644
--- a/R/freq_table.R
+++ b/R/freq_table.R
@@ -11,7 +11,6 @@ if (getRversion() >= '2.15.1')
 #' @param x  data frame
 #' @param byvar character: name of variable to tabulate. Use Standard evaluation.
 #' @param digits numeric: number of decimal places to display. Default is 1.
-#' @param na.rm logical: if TRUE remove NAs from calculations. Default is TRUE
 #'
 #' @return data.table with frequencies.
 #' @export
@@ -25,37 +24,20 @@ if (getRversion() >= '2.15.1')
 #' freq_table(x4, "id1")
 freq_table <- function(x,
                        byvar,
-                       digits = 1,
-                       na.rm  = TRUE) {
+                       digits = 1) {
 
-  if (!(is.data.table(x))) {
-    x <- as.data.table(x)
-  } else {
-    x <- data.table::copy(x)
-  }
+  fq <- qtab(x[[byvar]])
+  ft <- data.frame(joyn = names(fq),
+                   n = as.numeric(fq))
+  ft <- ft |>
+    ftransform(percent = paste0(round(n / N * 100, digits), "%"))
 
+  # add row with totals
+  ft <- rowbind(ft, data.table(joyn = "total",
+                               n = fsum(ft$n),
+                               percent = "100%")) |>
+    # filter zeros
+    fsubset(n > 0)
 
-  # Frequencies and format
-  d <- x[, .(n = .N), by = byvar
-  ][, percent :=
-      {
-        total = sum(n, na.rm = na.rm)
-        d <- round((n/ total)*100, digits = digits)
-        d <- as.character(d)
-        d <- paste0(d, "%")
-      }
-  ]
-
-  # Total row just for completeness
-  setorderv(d, byvar)
-  totd <- data.table::data.table(
-    tempname = "total",
-    n        = d[, sum(n, na.rm = na.rm)],
-    percent  = "100%"
-  )
-
-  setnames(totd, "tempname", byvar)
-  d <- data.table::rbindlist(list(d, totd),
-                             use.names = TRUE)
-  return(d)
+  setrename(ft, joyn = byvar, .nse = FALSE)
 }
diff --git a/R/info_display.R b/R/info_display.R
index 8a33ac7f..2ed4db44 100644
--- a/R/info_display.R
+++ b/R/info_display.R
@@ -423,7 +423,9 @@ joyn_report <- function(verbose = getOption("joyn.verbose")) {
 
   freq <- rlang::env_get(.joynenv, "freq_joyn")
   if (verbose) {
+    cli::cli_h2("JOYn Report")
     print(freq)
+    cli::cli_rule(right = "End of {.field JOYn} report")
   }
   return(invisible(freq))
 }
diff --git a/R/joyn-merge.R b/R/joyn-merge.R
index 78c373cc..3b692758 100644
--- a/R/joyn-merge.R
+++ b/R/joyn-merge.R
@@ -383,15 +383,6 @@ joyn <- function(x,
     sort       = sort,
     reportvar  = reportvar
   )
-  m <- attr(jn, "join.match")$match
-
-
-
-  # # report variable
-  # collapse::settransform(jn, use_util_report = .xreport + .yreport)
-  # # Can this be done more efficiently with collapse?
-  # data.table::setnames(jn, "use_util_report", reportvar)
-
 
 
   #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -476,6 +467,17 @@ joyn <- function(x,
                          new = xbynames)
   }
 
+
+  # Report variable ----------
+  # no matching obs
+  if (all(jn[[reportvar]] %in% c(1, 2)) && !keep == "anti") {
+
+    store_joyn_msg(warn = " you have no matching obs. Make sure argument
+                           `by` is correct. Right now, `joyn` is joining by
+                           {.strongVar {by}}")
+
+  }
+
   ## convert to characters if chosen -------
 
   if (reporttype == "factor") {
@@ -506,19 +508,10 @@ joyn <- function(x,
 
   }
 
-  # no matching obs
-  if ((all(jn[[reportvar]] %in% c("x", "y")) ||
-       all(jn[[reportvar]] %in% c(1, 2))) &&
-      !keep == "anti") {
-
-    store_joyn_msg(warn = " you have no matching obs. Make sure argument
-                           `by` is correct. Right now, `joyn` is joining by
-                           {.strongVar {by}}")
-
-  }
 
   ## Display results------
   # freq table
+
   d <- freq_table(jn, reportvar)
   rlang::env_poke(.joynenv, "freq_joyn", d)
 
@@ -535,15 +528,11 @@ joyn <- function(x,
     is executed in  ", round(time_taken_joyn, 6)))
 
   # return messages
-  if (verbose == TRUE) {
-    cli::cli_h2("JOYn Report")
-    joyn_report()
-    cli::cli_rule(right = "End of {.field JOYn} report")
-    joyn_msg(msg_type)
-  }
+  joyn_report(verbose = verbose)
+  if (verbose == TRUE) joyn_msg(msg_type)
 
   setattr(jn, "class", class_x)
-  setattr(jn, "join.match", NULL)
+  # setattr(jn, "join.match", NULL)
 
   jn
 
diff --git a/R/utils.R b/R/utils.R
index be4a5b24..d97d2046 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -342,4 +342,3 @@ correct_names <- function(by, x, y, order = TRUE) {
               ybynames = ybynames)
   out
 }
-

From 020905f6524129ceb1404f1b24173ce009ebf555 Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Mon, 10 Jun 2024 20:23:19 -0400
Subject: [PATCH 09/20] remove collapse::join attributes

---
 R/joyn-merge.R     | 1 -
 R/joyn_workhorse.R | 3 +--
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/R/joyn-merge.R b/R/joyn-merge.R
index 3b692758..8d0ea0d8 100644
--- a/R/joyn-merge.R
+++ b/R/joyn-merge.R
@@ -532,7 +532,6 @@ joyn <- function(x,
   if (verbose == TRUE) joyn_msg(msg_type)
 
   setattr(jn, "class", class_x)
-  # setattr(jn, "join.match", NULL)
 
   jn
 
diff --git a/R/joyn_workhorse.R b/R/joyn_workhorse.R
index 9d084c30..d70e896e 100644
--- a/R/joyn_workhorse.R
+++ b/R/joyn_workhorse.R
@@ -64,8 +64,7 @@ joyn_workhorse <- function(
                        keep.col.order = TRUE,
                        sort           = sort,
                        verbose        = 0,
-                       column         = ".joyn1",
-                       attr           = TRUE)
+                       column         = ".joyn1")
       }, # end of expr section
 
       error = function(e) {

From b26edd9649060649c76e731003287df4ae5e8d23 Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Mon, 10 Jun 2024 20:39:50 -0400
Subject: [PATCH 10/20] pass all tests

---
 DESCRIPTION                      |  2 +-
 R/freq_table.R                   |  9 ++++++++-
 tests/testthat/test-freq_table.R | 26 +++++++++++++++-----------
 3 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2cf2a406..d8fa5b6b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -37,7 +37,7 @@ Imports:
     data.table,
     cli,
     utils,
-    collapse (>= 2.0.13),
+    collapse (>= 2.0.15),
     lifecycle
 Depends: 
     R (>= 2.10)
diff --git a/R/freq_table.R b/R/freq_table.R
index db5893f1..40dcadc2 100644
--- a/R/freq_table.R
+++ b/R/freq_table.R
@@ -26,15 +26,22 @@ freq_table <- function(x,
                        byvar,
                        digits = 1) {
 
+  x_name <- as.character(substitute(x))
+  if (!is.data.frame(x)) {
+    cli::cli_abort("Argument {.arg x} ({.field {x_name}}) must be a data frame")
+  }
+
   fq <- qtab(x[[byvar]])
   ft <- data.frame(joyn = names(fq),
                    n = as.numeric(fq))
+
+  N <- fsum(ft$n)
   ft <- ft |>
     ftransform(percent = paste0(round(n / N * 100, digits), "%"))
 
   # add row with totals
   ft <- rowbind(ft, data.table(joyn = "total",
-                               n = fsum(ft$n),
+                               n = N,
                                percent = "100%")) |>
     # filter zeros
     fsubset(n > 0)
diff --git a/tests/testthat/test-freq_table.R b/tests/testthat/test-freq_table.R
index ca016659..f579699b 100644
--- a/tests/testthat/test-freq_table.R
+++ b/tests/testthat/test-freq_table.R
@@ -43,22 +43,23 @@ y4 = data.table(id  = c(1, 2, 5, 6, 3),
 #                   internal = TRUE)
 
 test_that("correct inputs", {
-  x <- "not a data.table/data.frame"
+  dd <- "not a data.table/data.frame"
 
-  freq_table(x) |>
+  freq_table(dd) |>
     expect_error()
 })
 
 test_that("correct frequencies", {
 
-  b <- base::table(y4$id2)
-  b <- as.numeric(b)
+  b <- base::table(y4$id2) |>
+    as.numeric()
 
   j <- freq_table(y4, "id2")
-  j <- j[ id2 != "total"
-          ][, n]
-
-  expect_equal(b, j)
+  j |>
+    fsubset(id2 != "total") |>
+    fselect(n) |>
+    reg_elem() |>
+    expect_equal(b)
 
 })
 
@@ -67,10 +68,13 @@ test_that("correct totals", {
   tr <- nrow(y4)
 
   j <- freq_table(y4, "id2")
-  j <- j[ id2 == "total"
-          ][, n]
+  j <- freq_table(y4, "id2")
+  j |>
+    fsubset(id2 == "total") |>
+    fselect(n) |>
+    reg_elem() |>
+    expect_equal(tr)
 
-  expect_equal(tr, j)
 })
 
 

From cd205e130ed05477daf95c237aa2d254b81cec3b Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Mon, 10 Jun 2024 20:43:12 -0400
Subject: [PATCH 11/20] update news

---
 NEWS.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index e6c812e6..e52b886a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -15,6 +15,8 @@
 
 * Internal: improve storing of joyn messages.
 
+* Improve creation of reporting variable. Now, it is created in [collapse::join] rather than in `joyn` function. In addition, the reporting variable is created as factor to improve performance. Thanks to @SebKrantz for the suggestion (#58)
+
 ## breaking changes
 
 * Now, by default, `joyn` will not sort the data. This is to avoid unnecessary 
@@ -22,6 +24,8 @@ computational time that most of the time is not needed.
 If the user wants to sort the data, they can use the `sort` argument, which triggers 
 the sorting mechanism of `collapse` package.
 
+* report variable (named ".join" by default) is now a factor instead of character. Yet, users can still use character if they want with the `reporttype = "character"`.
+
 # joyn 0.2.0
 
 * `joyn` has gained two new authors: Zander Prinsloo and Rossana Tatulli.

From e35be63d591f1a3d74d1a065c7c9ed2329403e20 Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Mon, 10 Jun 2024 20:43:59 -0400
Subject: [PATCH 12/20] document

---
 NEWS.md           | 2 +-
 man/anti_join.Rd  | 2 +-
 man/freq_table.Rd | 4 +---
 man/full_join.Rd  | 2 +-
 man/inner_join.Rd | 2 +-
 man/right_join.Rd | 2 +-
 6 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index e52b886a..ac5a73c7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -7,7 +7,7 @@
 
 * Add information about duplicated obs in `by` variable when match type is `1` rathern than `m`. 
 
-* improve ineffciencies in deep copies with `m:m` joins
+* improve inefficiencies in deep copies with `m:m` joins
 
 * Replace `m:m` joins from `data.table::merge.data.table` to `collapse::join`. Thanks to @SebKrantz for the suggestion (#58).
 
diff --git a/man/anti_join.Rd b/man/anti_join.Rd
index f5cc1c66..e0a22001 100644
--- a/man/anti_join.Rd
+++ b/man/anti_join.Rd
@@ -16,7 +16,7 @@ anti_join(
   relationship = "many-to-many",
   y_vars_to_keep = FALSE,
   reportvar = getOption("joyn.reportvar"),
-  reporttype = c("character", "numeric"),
+  reporttype = c("factor", "character", "numeric"),
   roll = NULL,
   keep_common_vars = FALSE,
   sort = TRUE,
diff --git a/man/freq_table.Rd b/man/freq_table.Rd
index 2eba5c63..40b9ca3d 100644
--- a/man/freq_table.Rd
+++ b/man/freq_table.Rd
@@ -4,7 +4,7 @@
 \alias{freq_table}
 \title{Tabulate simple frequencies}
 \usage{
-freq_table(x, byvar, digits = 1, na.rm = TRUE)
+freq_table(x, byvar, digits = 1)
 }
 \arguments{
 \item{x}{data frame}
@@ -12,8 +12,6 @@ freq_table(x, byvar, digits = 1, na.rm = TRUE)
 \item{byvar}{character: name of variable to tabulate. Use Standard evaluation.}
 
 \item{digits}{numeric: number of decimal places to display. Default is 1.}
-
-\item{na.rm}{logical: if TRUE remove NAs from calculations. Default is TRUE}
 }
 \value{
 data.table with frequencies.
diff --git a/man/full_join.Rd b/man/full_join.Rd
index 4639ae23..d5be2aea 100644
--- a/man/full_join.Rd
+++ b/man/full_join.Rd
@@ -19,7 +19,7 @@ full_join(
   update_values = FALSE,
   update_NAs = update_values,
   reportvar = getOption("joyn.reportvar"),
-  reporttype = c("character", "numeric"),
+  reporttype = c("factor", "character", "numeric"),
   roll = NULL,
   keep_common_vars = FALSE,
   sort = TRUE,
diff --git a/man/inner_join.Rd b/man/inner_join.Rd
index f70b8196..162d6b94 100644
--- a/man/inner_join.Rd
+++ b/man/inner_join.Rd
@@ -19,7 +19,7 @@ inner_join(
   update_values = FALSE,
   update_NAs = update_values,
   reportvar = getOption("joyn.reportvar"),
-  reporttype = c("character", "numeric"),
+  reporttype = c("factor", "character", "numeric"),
   roll = NULL,
   keep_common_vars = FALSE,
   sort = TRUE,
diff --git a/man/right_join.Rd b/man/right_join.Rd
index c885e721..7934ae77 100644
--- a/man/right_join.Rd
+++ b/man/right_join.Rd
@@ -19,7 +19,7 @@ right_join(
   update_values = FALSE,
   update_NAs = update_values,
   reportvar = getOption("joyn.reportvar"),
-  reporttype = c("character", "numeric"),
+  reporttype = c("factor", "character", "numeric"),
   roll = NULL,
   keep_common_vars = FALSE,
   sort = TRUE,

From a4e949e59465be20eb1221c92f70293fa42a4a5c Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Mon, 10 Jun 2024 20:47:06 -0400
Subject: [PATCH 13/20] Increment version number to 0.2.0.9006

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d8fa5b6b..c3b527f3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: joyn
 Type: Package
 Title: Tool for Diagnosis of Tables Joins and Complementary Join Features
-Version: 0.2.0.9005
+Version: 0.2.0.9006
 Authors@R: c(person(given = "R.Andres", 
                     family = "Castaneda", 
                     email = "acastanedaa@worldbank.org",

From 5446ae97caa4732b61b6d902242d77c0fbe9e29f Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Tue, 11 Jun 2024 09:20:34 -0400
Subject: [PATCH 14/20] add collapse as dev package

---
 DESCRIPTION | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index c3b527f3..f64132fd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -44,3 +44,5 @@ Depends:
 RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
+Remotes:  
+    SebKrantz/collapse

From 02cc0b70dd011cfd41f868d8e307ddbbda918c8f Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Tue, 11 Jun 2024 11:36:45 -0400
Subject: [PATCH 15/20] fix issue with NA in freq_table

---
 .gitignore                  | 2 ++
 R/freq_table.R              | 5 +++--
 vignettes/aux-functions.Rmd | 4 ++--
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index 3ef59ac1..061b0855 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,5 @@ doc
 Meta
 
 docs
+/doc/
+/Meta/
diff --git a/R/freq_table.R b/R/freq_table.R
index 40dcadc2..2f03d7d4 100644
--- a/R/freq_table.R
+++ b/R/freq_table.R
@@ -24,14 +24,15 @@ if (getRversion() >= '2.15.1')
 #' freq_table(x4, "id1")
 freq_table <- function(x,
                        byvar,
-                       digits = 1) {
+                       digits = 1,
+                       na.rm  = FALSE) {
 
   x_name <- as.character(substitute(x))
   if (!is.data.frame(x)) {
     cli::cli_abort("Argument {.arg x} ({.field {x_name}}) must be a data frame")
   }
 
-  fq <- qtab(x[[byvar]])
+  fq <- qtab(x[[byvar]], na.exclude = na.rm)
   ft <- data.frame(joyn = names(fq),
                    n = as.numeric(fq))
 
diff --git a/vignettes/aux-functions.Rmd b/vignettes/aux-functions.Rmd
index dcf425d1..2eab35de 100644
--- a/vignettes/aux-functions.Rmd
+++ b/vignettes/aux-functions.Rmd
@@ -103,13 +103,13 @@ Furthermore, `joyn` provides a function that generates simple frequency tables,
 # Tabulating frequencies of var `id`
 
 freq_table(x     = x1, 
-           byvar = "id")
+           byvar = "id")[]
 
 # Removing NAs from the calculation
 
 freq_table(x     = x1, 
            byvar = "id", 
-           na.rm = TRUE)
+           na.rm = TRUE)[]
 
 
 ```

From 28d17f6ea4dfdd2f694ca7fd2e5a73ecf785f48e Mon Sep 17 00:00:00 2001
From: RossanaTat <rossana.tatulli@studbocconi.it>
Date: Tue, 11 Jun 2024 14:10:42 -0400
Subject: [PATCH 16/20] fix examples in store_joyn_msg doc

---
 R/info_display.R      | 26 +++++++++++++++++++-------
 man/freq_table.Rd     |  2 +-
 man/store_joyn_msg.Rd | 26 +++++++++++++++++++-------
 3 files changed, 39 insertions(+), 15 deletions(-)

diff --git a/R/info_display.R b/R/info_display.R
index 2ed4db44..428d3f64 100644
--- a/R/info_display.R
+++ b/R/info_display.R
@@ -127,21 +127,33 @@ store_msg <- function(type, ...) {
 #' @param info A character string representing an info message to be stored. Default value is NULL
 #'
 #' @section Hot to pass the message string:
-#' The function allows for the customization of the message string using {cli} classes to emphasize specific components of the message
+#' The function allows for the customization of the message string using \{cli\} classes to emphasize specific components of the message
 #' Here's how to format the message string:
-#' *For variables:            .strongVar   --example: "{.strongVar {reportvar}}"
-#' *For function arguments:   .strongArg   --example: "{.strongArg {y_vars_to_keep}}"
-#' *For dt/df:                .strongTable --example: "{.strongTable x}"
-#' *For text/anything else:   .strong      --example: "reportvar is {.strong NOT} returned"
+#' *For variables:            .strongVar
+#' *For function arguments:   .strongArg
+#' *For dt/df:                .strongTable
+#' *For text/anything else:   .strong
 #' *NOTE: By default, the number of seconds specified in timing messages is
 #'        automatically emphasized using a custom formatting approach.
 #'        You do not need to apply {cli} classes nor to specify that the number is in seconds.
-#'        --example usage:  store_joyn_msg(timing =
-#'                                         paste("The full joyn is executed in", round(time_taken, 6)))
+#'
 #'
 #'
 #' @return invisible TRUE
 #'
+#' @examples
+#' \donotrun{
+#' # Timing msg
+#' store_joyn_msg(timing = paste("  The entire joyn function, including checks,
+#'                                        is executed in  ", round(time_taken_joyn, 6)))
+#'
+#' # Error msg
+#' store_joyn_msg(err = " Input table {.strongTable x} has no columns.")
+#'
+#' # Info msg
+#' store_joyn_msg(info = "Joyn's report available in variable {.strongVar {reportvar}}")
+#' }
+#'
 #' @keywords internal
 store_joyn_msg <- function(err       = NULL,
                            warn      = NULL,
diff --git a/man/freq_table.Rd b/man/freq_table.Rd
index 40b9ca3d..da054c8a 100644
--- a/man/freq_table.Rd
+++ b/man/freq_table.Rd
@@ -4,7 +4,7 @@
 \alias{freq_table}
 \title{Tabulate simple frequencies}
 \usage{
-freq_table(x, byvar, digits = 1)
+freq_table(x, byvar, digits = 1, na.rm = FALSE)
 }
 \arguments{
 \item{x}{data frame}
diff --git a/man/store_joyn_msg.Rd b/man/store_joyn_msg.Rd
index 6f002a88..71e42ada 100644
--- a/man/store_joyn_msg.Rd
+++ b/man/store_joyn_msg.Rd
@@ -27,17 +27,29 @@ This function serves as a wrapper for the store_msg function, which is used to s
 }
 \section{Hot to pass the message string}{
 
-The function allows for the customization of the message string using {cli} classes to emphasize specific components of the message
+The function allows for the customization of the message string using \{cli\} classes to emphasize specific components of the message
 Here's how to format the message string:
-*For variables:            .strongVar   --example: "{.strongVar {reportvar}}"
-*For function arguments:   .strongArg   --example: "{.strongArg {y_vars_to_keep}}"
-*For dt/df:                .strongTable --example: "{.strongTable x}"
-*For text/anything else:   .strong      --example: "reportvar is {.strong NOT} returned"
+*For variables:            .strongVar
+*For function arguments:   .strongArg
+*For dt/df:                .strongTable
+*For text/anything else:   .strong
 *NOTE: By default, the number of seconds specified in timing messages is
 automatically emphasized using a custom formatting approach.
 You do not need to apply {cli} classes nor to specify that the number is in seconds.
---example usage:  store_joyn_msg(timing =
-paste("The full joyn is executed in", round(time_taken, 6)))
 }
 
+\examples{
+\donotrun{
+# Timing msg
+store_joyn_msg(timing = paste("  The entire joyn function, including checks,
+                                       is executed in  ", round(time_taken_joyn, 6)))
+
+# Error msg
+store_joyn_msg(err = " Input table {.strongTable x} has no columns.")
+
+# Info msg
+store_joyn_msg(info = "Joyn's report available in variable {.strongVar {reportvar}}")
+}
+
+}
 \keyword{internal}

From 5f1ed7e88374e3443c0d43ecc5f00f08a074c5c6 Mon Sep 17 00:00:00 2001
From: RossanaTat <rossana.tatulli@studbocconi.it>
Date: Tue, 11 Jun 2024 14:23:01 -0400
Subject: [PATCH 17/20] fix again

---
 R/info_display.R      | 15 +++++++--------
 man/store_joyn_msg.Rd | 15 +++++++--------
 2 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/R/info_display.R b/R/info_display.R
index 428d3f64..2072ee00 100644
--- a/R/info_display.R
+++ b/R/info_display.R
@@ -127,7 +127,7 @@ store_msg <- function(type, ...) {
 #' @param info A character string representing an info message to be stored. Default value is NULL
 #'
 #' @section Hot to pass the message string:
-#' The function allows for the customization of the message string using \{cli\} classes to emphasize specific components of the message
+#' The function allows for the customization of the message string using cli classes to emphasize specific components of the message
 #' Here's how to format the message string:
 #' *For variables:            .strongVar
 #' *For function arguments:   .strongArg
@@ -135,24 +135,23 @@ store_msg <- function(type, ...) {
 #' *For text/anything else:   .strong
 #' *NOTE: By default, the number of seconds specified in timing messages is
 #'        automatically emphasized using a custom formatting approach.
-#'        You do not need to apply {cli} classes nor to specify that the number is in seconds.
+#'        You do not need to apply cli classes nor to specify that the number is in seconds.
 #'
 #'
 #'
 #' @return invisible TRUE
 #'
 #' @examples
-#' \donotrun{
 #' # Timing msg
-#' store_joyn_msg(timing = paste("  The entire joyn function, including checks,
-#'                                        is executed in  ", round(time_taken_joyn, 6)))
+#' joyn:::store_joyn_msg(timing = paste("  The entire joyn function, including checks,
+#'                                        is executed in  ", round(1.8423467, 6)))
 #'
 #' # Error msg
-#' store_joyn_msg(err = " Input table {.strongTable x} has no columns.")
+#' joyn:::store_joyn_msg(err = " Input table {.strongTable x} has no columns.")
 #'
 #' # Info msg
-#' store_joyn_msg(info = "Joyn's report available in variable {.strongVar {reportvar}}")
-#' }
+#' joyn:::store_joyn_msg(info = "Joyn's report available in variable {.strongVar .joyn}")
+#'
 #'
 #' @keywords internal
 store_joyn_msg <- function(err       = NULL,
diff --git a/man/store_joyn_msg.Rd b/man/store_joyn_msg.Rd
index 71e42ada..d0c7881b 100644
--- a/man/store_joyn_msg.Rd
+++ b/man/store_joyn_msg.Rd
@@ -27,7 +27,7 @@ This function serves as a wrapper for the store_msg function, which is used to s
 }
 \section{Hot to pass the message string}{
 
-The function allows for the customization of the message string using \{cli\} classes to emphasize specific components of the message
+The function allows for the customization of the message string using cli classes to emphasize specific components of the message
 Here's how to format the message string:
 *For variables:            .strongVar
 *For function arguments:   .strongArg
@@ -35,21 +35,20 @@ Here's how to format the message string:
 *For text/anything else:   .strong
 *NOTE: By default, the number of seconds specified in timing messages is
 automatically emphasized using a custom formatting approach.
-You do not need to apply {cli} classes nor to specify that the number is in seconds.
+You do not need to apply cli classes nor to specify that the number is in seconds.
 }
 
 \examples{
-\donotrun{
 # Timing msg
-store_joyn_msg(timing = paste("  The entire joyn function, including checks,
-                                       is executed in  ", round(time_taken_joyn, 6)))
+joyn:::store_joyn_msg(timing = paste("  The entire joyn function, including checks,
+                                       is executed in  ", round(1.8423467, 6)))
 
 # Error msg
-store_joyn_msg(err = " Input table {.strongTable x} has no columns.")
+joyn:::store_joyn_msg(err = " Input table {.strongTable x} has no columns.")
 
 # Info msg
-store_joyn_msg(info = "Joyn's report available in variable {.strongVar {reportvar}}")
-}
+joyn:::store_joyn_msg(info = "Joyn's report available in variable {.strongVar .joyn}")
+
 
 }
 \keyword{internal}

From 3e83fba815bf6fa79702e1dc2542bba542e8b574 Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Tue, 11 Jun 2024 15:36:52 -0400
Subject: [PATCH 18/20] include reporting from attributes

---
 R/freq_table.R     | 31 +++++++++++++++++++++++++++++++
 R/joyn-merge.R     |  9 ++++++++-
 R/joyn-package.R   |  3 ++-
 R/joyn_workhorse.R |  3 ++-
 4 files changed, 43 insertions(+), 3 deletions(-)

diff --git a/R/freq_table.R b/R/freq_table.R
index 2f03d7d4..0cd9f8fd 100644
--- a/R/freq_table.R
+++ b/R/freq_table.R
@@ -49,3 +49,34 @@ freq_table <- function(x,
 
   setrename(ft, joyn = byvar, .nse = FALSE)
 }
+
+
+
+#' Report frequencies from attributes in report var
+#'
+#' @param x dataframe from [joyn_workhorse]
+#' @param y dataframe from original merge ("right" or "using")
+#'
+#' @return dataframe with frequencies of report var
+#' @keywords internal
+report_from_attr <- function(x,y, reportvar) {
+  # from suggestion by @SebKrantz in #58
+  # https://github.com/randrescastaneda/joyn/issues/58
+  m <- attr(x, "join.match")$match
+
+  N <- fnrow(x)
+  nm_x <- attr(m, "N.nomatch") # Number of non-matched x values
+  nm_y <- fnrow(y) - attr(m, "N.distinct") # Number of non-matched y values. If multiple = FALSE attr(m, "N.distinct") = number of unique matches.
+
+
+  counts <- c(nm_x,  nm_y, N-nm_x-nm_y, N)
+  report <- data.frame(
+    .joyn1 = c("x", "y", "x & y", "total"),
+    n = counts,
+    percent = paste0(round(counts / N * 100, 1), "%")
+  ) |>
+    fsubset(n > 0)
+
+  setrename(report, .joyn1 = reportvar, .nse = FALSE)
+
+}
diff --git a/R/joyn-merge.R b/R/joyn-merge.R
index 8d0ea0d8..4eb18490 100644
--- a/R/joyn-merge.R
+++ b/R/joyn-merge.R
@@ -511,8 +511,15 @@ joyn <- function(x,
 
   ## Display results------
   # freq table
+  #
+  if (update_NAs || update_values) {
+    d <- freq_table(jn, reportvar)
+  } else {
+    d <- report_from_attr(jn, y, reportvar)
+  }
+  # remove collapse::join attributes
+  attr(jn, "join.match") <- NULL
 
-  d <- freq_table(jn, reportvar)
   rlang::env_poke(.joynenv, "freq_joyn", d)
 
   # Report var
diff --git a/R/joyn-package.R b/R/joyn-package.R
index 98d66da3..ace5a944 100644
--- a/R/joyn-package.R
+++ b/R/joyn-package.R
@@ -26,7 +26,8 @@ if (getRversion() >= "2.15.1") {
       ".yreport",
       'use_util_reportvar',
       'varx_na',
-      'type'
+      'type',
+      "joyn1"
     ),
     package = utils::packageName()
   )
diff --git a/R/joyn_workhorse.R b/R/joyn_workhorse.R
index d70e896e..9d084c30 100644
--- a/R/joyn_workhorse.R
+++ b/R/joyn_workhorse.R
@@ -64,7 +64,8 @@ joyn_workhorse <- function(
                        keep.col.order = TRUE,
                        sort           = sort,
                        verbose        = 0,
-                       column         = ".joyn1")
+                       column         = ".joyn1",
+                       attr           = TRUE)
       }, # end of expr section
 
       error = function(e) {

From 29b623ff346eca3b44cab0c272a5cde440d0d753 Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Tue, 11 Jun 2024 15:38:21 -0400
Subject: [PATCH 19/20] document

---
 R/freq_table.R          |  1 +
 man/freq_table.Rd       |  2 ++
 man/report_from_attr.Rd | 20 ++++++++++++++++++++
 3 files changed, 23 insertions(+)
 create mode 100644 man/report_from_attr.Rd

diff --git a/R/freq_table.R b/R/freq_table.R
index 0cd9f8fd..5bf93150 100644
--- a/R/freq_table.R
+++ b/R/freq_table.R
@@ -11,6 +11,7 @@ if (getRversion() >= '2.15.1')
 #' @param x  data frame
 #' @param byvar character: name of variable to tabulate. Use Standard evaluation.
 #' @param digits numeric: number of decimal places to display. Default is 1.
+#' @param na.rm logical: report NA values in frequencies. Default is FALSE.
 #'
 #' @return data.table with frequencies.
 #' @export
diff --git a/man/freq_table.Rd b/man/freq_table.Rd
index da054c8a..6be47f0c 100644
--- a/man/freq_table.Rd
+++ b/man/freq_table.Rd
@@ -12,6 +12,8 @@ freq_table(x, byvar, digits = 1, na.rm = FALSE)
 \item{byvar}{character: name of variable to tabulate. Use Standard evaluation.}
 
 \item{digits}{numeric: number of decimal places to display. Default is 1.}
+
+\item{na.rm}{logical: report NA values in frequencies. Default is FALSE.}
 }
 \value{
 data.table with frequencies.
diff --git a/man/report_from_attr.Rd b/man/report_from_attr.Rd
new file mode 100644
index 00000000..82698c0b
--- /dev/null
+++ b/man/report_from_attr.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/freq_table.R
+\name{report_from_attr}
+\alias{report_from_attr}
+\title{Report frequencies from attributes in report var}
+\usage{
+report_from_attr(x, y, reportvar)
+}
+\arguments{
+\item{x}{dataframe from \link{joyn_workhorse}}
+
+\item{y}{dataframe from original merge ("right" or "using")}
+}
+\value{
+dataframe with frequencies of report var
+}
+\description{
+Report frequencies from attributes in report var
+}
+\keyword{internal}

From e4dcd5356f149101a1ecd5c3f4ff0a450fba1979 Mon Sep 17 00:00:00 2001
From: "R.Andres Castaneda Aguilar" <acastanedaa@worldbank.org>
Date: Tue, 11 Jun 2024 15:38:35 -0400
Subject: [PATCH 20/20] Increment version number to 0.2.0.9007

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f64132fd..f0dc7f43 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: joyn
 Type: Package
 Title: Tool for Diagnosis of Tables Joins and Complementary Join Features
-Version: 0.2.0.9006
+Version: 0.2.0.9007
 Authors@R: c(person(given = "R.Andres", 
                     family = "Castaneda", 
                     email = "acastanedaa@worldbank.org",
@@ -44,5 +44,5 @@ Depends:
 RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
-Remotes:  
+Remotes: 
     SebKrantz/collapse