version 3.2.0

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: arsenal
 Title: An Arsenal of 'R' Functions for Large-Scale Statistical
         Summaries
-Version: 3.1.0
-Date: 2019-05-03
+Version: 3.2.0
+Date: 2019-06-13
 Authors@R: c(
     person("Ethan", "Heinzen", email = "heinzen.ethan@mayo.edu", role = c("aut", "cre")),
     person("Jason", "Sinnwell", role="aut"),
@@ -41,7 +41,7 @@ RoxygenNote: 6.1.1
 LazyData: true
 Encoding: UTF-8
 NeedsCompilation: no
-Packaged: 2019-05-03 13:59:18 UTC; m144326
+Packaged: 2019-06-13 20:05:07 UTC; m144326
 Author: Ethan Heinzen [aut, cre],
   Jason Sinnwell [aut],
   Elizabeth Atkinson [aut],
@@ -56,4 +56,4 @@ Author: Ethan Heinzen [aut, cre],
   Maddie McCullough [art]
 Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
 Repository: CRAN
-Date/Publication: 2019-05-03 14:20:06 UTC
+Date/Publication: 2019-06-13 20:30:18 UTC

MD5

@@ -1,14 +1,14 @@
-b9c5e4126a4ad6e7fffa3063b22fab0e *DESCRIPTION
+b4dcfe9b4f2371361d7d4e9e01e42c7d *DESCRIPTION
 07c8d8057816eac6ff49061346142fd7 *NAMESPACE
-03f2ee293cef0553da3c3e42926f485b *NEWS.md
+78c494e5f79737c26f2058024d6670ea *NEWS.md
 5b33cdf09e4978d1a2579d9592c4b1cc *R/arsenal.R
-abb1a9664cc88888a6e2f5b157c01c9b *R/arsenal_table.R
+ae4cc563cec6903508dd14f27bdb6198 *R/arsenal_table.R
 59d0400128715ca191a6f4ef69eb7fc4 *R/as.data.frame.freqlist.R
 ae9df496897ab4de26a64a2ffad239ad *R/as.data.frame.modelsum.R
 ec9777d58f7c3ed96fd74fafa087b2fb *R/as.data.frame.tableby.R
-7bdf19ee28eaada5910c825ef65555da *R/comparedf.R
+cf64d94a1c4cd1104df8884bdc11a9e5 *R/comparedf.R
 e504af4f850d271d3377bb09ec7d552d *R/comparedf.control.R
-8a1313fb84b9c624fad42e56ad428721 *R/comparedf.internal.R
+9ef1d13a6661ff41b66b73b26fa717be *R/comparedf.internal.R
 f9f65a3c5586c48d03d87b10e13979e6 *R/comparedf.tolerances.R
 d2f83d6128a6e5008822e8b71f657923 *R/defunct.R
 03fb09ede835462d843db3e527cc4355 *R/deprecated.R
@@ -22,28 +22,28 @@ f0a1429f4166c383330c680dc3f9362b *R/formulize.R
 310d0f18b36486d507146ac617eb00c1 *R/magic8.R
 f3bc182ae0dcd827a0d3d3e191db4828 *R/mdy.Date.R
 551c162106f2f1b9a25b8ccc697d13cc *R/mockstudy.R
-fefbe0db8d2c55b288a97b5cdcca8b67 *R/modelsum.R
-ac1e9e45139a00caad05c1a1369d84f3 *R/modelsum.control.R
+6cdda29d232c29b0ef7a8426cdf36f59 *R/modelsum.R
+0b1790878b9e3dc503aea8b74be9a727 *R/modelsum.control.R
 f185db7745b08bf5fede8713b58c8f2f *R/modelsum.families.R
 0e48b04e537a5666a40d0a92c9ca20c4 *R/modelsum.internal.R
 d280d3f55b975402d897e7d03047b59d *R/na.operations.R
 15be85a18a2039cd41e3bf7bb81645e5 *R/not.in.R
 e2458db48a5f1c367d36bf8cd890c549 *R/padjust.R
-bef5a31f0313bbc80b94c630ec3cd4ac *R/paired.R
+58daa2898d3eaa108413bbcf8f91fe2c *R/paired.R
 2f599abb94e552e242d5024992e6dde8 *R/paired.control.R
 20ece227c49dc16e0dadcbbca96500cf *R/paired.internal.R
 478c34566a5036fa736f0b97cf40f58e *R/paired.stat.tests.R
 e1427edd79dc20bae932449d90fb5161 *R/release_questions.R
-dee452a9211b126fd3ce4ae349cb60fe *R/summary.comparedf.R
+61d3d00697e72fe4067cb2b3eb8683af *R/summary.comparedf.R
 a9b398c9003e293c1e8f6c308c8f8fed *R/summary.freqlist.R
 fef6172e4c68c6ec93a794d7854951d2 *R/summary.modelsum.R
-9eeb16b706ecf923d80d53f050ea3573 *R/summary.tableby.R
-548264ee6d2548a2815f82ddf1e59c30 *R/tableby.R
+89c9caf443ac45b4c7c12ff2b1fdf2a9 *R/summary.tableby.R
+1336a4ebd60a44353698599eb1c2b85d *R/tableby.R
 c9fb8b29f224d3de3bdecf8ecd6940d6 *R/tableby.control.R
-ee6e5f95993724b74104205ab2070498 *R/tableby.internal.R
+5c8294f30960768d2c4f501c7a80c148 *R/tableby.internal.R
 bd1d097f9cd5925e287a66a8ba092acc *R/tableby.stat.tests.R
 21f9a2d8f24f8d2e1d14451fadc44e40 *R/tableby.stats.R
-bb3dd49aeca6fa9fbb42b1de58115e07 *R/write2.R
+a8199d9cbc7b5cc81a504f7450a2a65b *R/write2.R
 fa24ed85ce920343eb89c0f1ccb71553 *R/write2.default.R
 9a853a569d232f1d0150ba7135a7c46e *R/write2.internal.R
 c758b698e0c957f3004fd3113a10852e *R/write2specific.R
@@ -53,25 +53,25 @@ efa9906133e987f9abd69af472e09104 *README.md
 30cd2d9369ee4d94dd76dcbf5a215559 *data/mockstudy.RData
 a9b0eb3dac08dcda212cfd67abf6a5ba *inst/doc/comparedf.R
 ca30a0326f2242eeaca8977684c31da0 *inst/doc/comparedf.Rmd
-33a254a41c9c99a8c4a36918b1b3bcbc *inst/doc/comparedf.html
+2c1a49e561650d78c89ce3a91ff6eba7 *inst/doc/comparedf.html
 8a6b20817c3475bea6e85c61b4df62aa *inst/doc/freqlist.R
 2ee669dcd5bbfff01fe56a5efa887770 *inst/doc/freqlist.Rmd
-cc8cae2f4f968239ceb75b8d0954ade4 *inst/doc/freqlist.html
+46ae86cf21d9e7d7243bba6c5a19dd8e *inst/doc/freqlist.html
 959bef168b2edd04f6ef65f7ae52c649 *inst/doc/labels.R
 61e81a2662d1117e1e2edd3c7b4e873f *inst/doc/labels.Rmd
-b4ea37bcea9b1ed0f67ac3cc098c8d87 *inst/doc/labels.html
+bb29e538ef346b165ace8f2346fc0685 *inst/doc/labels.html
 5126203a30608388138304208e21c88c *inst/doc/modelsum.R
-56a13a8963c20b55ec70fffb786c4b03 *inst/doc/modelsum.Rmd
-dc1d9fb5df5c3f0f334bbfa6c0d5a039 *inst/doc/modelsum.html
+5e814739399f30f7842173d2182196fa *inst/doc/modelsum.Rmd
+b0f0aa1b73af2c1412f5ed75ba49ddf6 *inst/doc/modelsum.html
 5952422462e488184a0279fc950ce329 *inst/doc/paired.R
 c5648935a8f77b50b4e0dac60e9c8edf *inst/doc/paired.Rmd
-009d52b4885cdd82f56ec8f3e45fb7ca *inst/doc/paired.html
+d0fd004ee3435c439f81be9a48ffe91b *inst/doc/paired.html
 3403766f99d562f36710b21486bdca45 *inst/doc/tableby.R
 03284bc47fc9d4b2855bee84804929c5 *inst/doc/tableby.Rmd
-521dc162c92ba64d99d880fdd02476d9 *inst/doc/tableby.html
+139d970b261afe31311b4f282917f5eb *inst/doc/tableby.html
 ac0f06cd6853cad72041d42887b0dd7c *inst/doc/write2.R
 070dcaff0d24e34fc2ee83350c592edb *inst/doc/write2.Rmd
-01a98ac9412014e61196a6ffb131fbcc *inst/doc/write2.html
+612f51b70cd8205fbe248ccb16b568f2 *inst/doc/write2.html
 24de5e45bd9a676927300962673534fd *man/NA.operations.Rd
 fddd35de21bd3139cfd8df7526681165 *man/arsenal-defunct.Rd
 1df478ecf265a7b0ea7f8701e1e793ff *man/arsenal-deprecated.Rd
@@ -113,41 +113,41 @@ be95212fdcc541dfa85913d60442d41b *man/tableby.control.Rd
 60ce70b48e1530b5a1419e9f9aaed771 *man/tableby.internal.Rd
 c270363525a365445eefe6a19b0bbcf6 *man/tableby.stats.Rd
 63d0ada03a137dfb7c9042d36b2978af *man/tableby.stats.internal.Rd
-d97e865e49ae9815d34cec8303d0f5bc *man/write2.Rd
+3734d8a04519e86b83b22bc8d6dcea7b *man/write2.Rd
 bd37dd5f49360a5a5d2a676bec1a8dd5 *man/write2.internal.Rd
 c7fc15db72ee5bc262c6b816ae565f48 *man/write2specific.Rd
 a0caade19c743fa6c1dfb2cbdb537a01 *man/yaml.Rd
 b86d96d2b720f7aeeb3b9412b87d67ef *tests/testthat.R
 48bee3e500877f2e38183bac2f96c09e *tests/testthat/helper-data.R
 0e1b2cd238f9c449a27ba0cb5abd358b *tests/testthat/helper-script.R
 422b5e4f05f56ef1f659e4c98d318ef5 *tests/testthat/mdat.rds
-85c2ca41ad03d0024299f71a861b5ba9 *tests/testthat/test_comparedf.R
+cccc5048fbbe33d25398dba3c4be4f55 *tests/testthat/test_comparedf.R
 f12f36814298535220fe0c326cebbe05 *tests/testthat/test_formulize.R
 3bb24311a37e7c16473a6ef2e3686494 *tests/testthat/test_freqlist.R
 c04c29dbdce4f382d34b30c0bbe57684 *tests/testthat/test_keep.labels.R
 de47e8a77a6ad7ac83d6c414ef092ab9 *tests/testthat/test_lhs_freqlist.R
 6b2b35b56aaac54280fd855b42d39770 *tests/testthat/test_lhs_modelsum.R
-0594e850a6ba34b3790a5d71448a4e60 *tests/testthat/test_lhs_tableby.R
+1d457ad15dd3dba305f2ca7227e5ab39 *tests/testthat/test_lhs_tableby.R
 d1f8bfd04242feecbb078b3b1b6a8b54 *tests/testthat/test_modelsum.R
-24c7c0a28e636eb7939780e768954039 *tests/testthat/test_paired.R
-3a9f5f951b4a22c5e33f873042d6d1ef *tests/testthat/test_tableby.R
-7bdcbe4161dbc385515d4287bcfbd08b *tests/testthat/test_write2.R
+55b2813ac0ea150bae2332b91721c87b *tests/testthat/test_paired.R
+144ae2b443142733c884265f95ef15b8 *tests/testthat/test_tableby.R
+4ee82f2c3d172bd162ad62c80783f998 *tests/testthat/test_write2.R
 a3cb5fc2c67b666bd620946a87f19db7 *tests/testthat/write2.char.html.Rmd
 ba6f1bee225bd630589a71a317b22127 *tests/testthat/write2.freqlist.doc.Rmd
 e8c763ecc2290ce29980a96ca5a06703 *tests/testthat/write2.freqlist.html.Rmd
-8322b7c9c82ef447c1a996729986859a *tests/testthat/write2.lm.pdf.Rmd
+f36e89c7b1e05f8cbecb243947236092 *tests/testthat/write2.lm.pdf.Rmd
 5b7b0951780ce2a0173e211c94008b60 *tests/testthat/write2.modelsum.html.Rmd
 f5607094f5254cb9f4f52858bf937378 *tests/testthat/write2.multititles.pdf.Rmd
 313cfea9983de10e4f9b66706f4cc317 *tests/testthat/write2.mylist.pdf.Rmd
 5eaf850ce8e0c8d50583a44104915d63 *tests/testthat/write2.mylist2.doc.Rmd
 fc47e093d3d5bd5ddfb72a3a057786c9 *tests/testthat/write2.mylists.pdf.Rmd
 30b1725d421f80f460816a1cf453cda3 *tests/testthat/write2.render.html.Rmd
 91341e80ce604a3f513b99d4f93116ec *tests/testthat/write2.tableby.html.Rmd
-af61cd8368e9c8a04c22c0a1045a57a5 *tests/testthat/write2.yaml.pdf.Rmd
+2664f1e86af3bc19f4364e0eb1d1ab88 *tests/testthat/write2.yaml.pdf.Rmd
 ca30a0326f2242eeaca8977684c31da0 *vignettes/comparedf.Rmd
 2ee669dcd5bbfff01fe56a5efa887770 *vignettes/freqlist.Rmd
 61e81a2662d1117e1e2edd3c7b4e873f *vignettes/labels.Rmd
-56a13a8963c20b55ec70fffb786c4b03 *vignettes/modelsum.Rmd
+5e814739399f30f7842173d2182196fa *vignettes/modelsum.Rmd
 c5648935a8f77b50b4e0dac60e9c8edf *vignettes/paired.Rmd
 03284bc47fc9d4b2855bee84804929c5 *vignettes/tableby.Rmd
 070dcaff0d24e34fc2ee83350c592edb *vignettes/write2.Rmd

NEWS.md

@@ -1,3 +1,33 @@
+# arsenal v3.2.0
+
+* `comparedf()`:
+
+    - Fixed a bug when "row.names" was used in combination with other by-variables. (#212)
+
+    - Allowed for comparison of variables which have any class in common. (#216)
+
+    - `summary.comparedf()`:
+
+        * Removed the "comparedf.frame.summary" class from the first element to allow it to print. (#211)
+
+        * Fixed a bug with reporting blank by-variables. (#213)
+
+        * Fixed a bug with reporting by-variables as variables in common. (#214)
+
+* `modelsum()`: added Wald confidence intervals to `binom.stats=`. (#219)
+
+* `tableby()` / `paired()`:
+
+    - Fixed a bug with `merge.arsenal_table()` losing control parameters for `tableby()` objects. (#221)
+
+    - Allowed for variable-name-only `labelTranslations=` assignment for terms with inline statistical test specification.
+      Backward compatibility should be maintained here. (#220)
+
+    - Fixed a bug with assigning `NULL` labels with inline statistical test specifications. (#222)
+
+    - `summary.tableby()`: fixed a bug with formatting when strata aren't in alphabetical order and have different number of elements
+      (e.g., if only one includes missing values). (#215)
+
 # arsenal v3.1.0
 
 * `tableby()` / `paired()`: 

R/arsenal_table.R

@@ -156,7 +156,14 @@ make_ms_labs <- function(x)
         val <- unname(value[L])
         for(j in seq_along(x$tables[[i]]$x))
         {
-          if(nm %in% x$tables[[i]]$x[[j]]$term) x$tables[[i]]$x[[j]]$label[x$tables[[i]]$x[[j]]$term == nm] <- val
+          if(nm %in% x$tables[[i]]$x[[j]]$term)
+          {
+            x$tables[[i]]$x[[j]]$label[x$tables[[i]]$x[[j]]$term == nm] <- val
+          } else if(nm %in% x$tables[[i]]$x[[j]]$term.orig)
+          {
+            # for backwards-compatibility
+            x$tables[[i]]$x[[j]]$label[x$tables[[i]]$x[[j]]$term.orig == nm] <- val
+          }
         }
         for(j in seq_along(x$tables[[i]]$adjust))
         {
@@ -215,10 +222,13 @@ merge.arsenal_table <- function(x, y, all = FALSE, all.x = all, all.y = all, ...
     if(!identical(x$tables[[ytrm]]$strata, y$tables[[ytrm]]$strata)) stop("Strata not identical for term ", ytrm)
     if(!identical(x$tables[[ytrm]]$adjust, y$tables[[ytrm]]$adjust)) stop("Adjust not identical for term ", ytrm)
     if(x$tables[[ytrm]]$hasWeights != y$tables[[ytrm]]$hasWeights) stop("Weights not present in both objects for term ", ytrm)
-    if(!identical(x$tables[[ytrm]]$family, y$tables[[ytrm]]$family)) stop("Weights not present in both objects for term ", ytrm)
+    if(!identical(x$tables[[ytrm]]$family, y$tables[[ytrm]]$family)) stop("'family' not the same in both objects for term ", ytrm)
 
     xtrms <- names(y$tables[[ytrm]]$x)
     x$tables[[ytrm]]$x[xtrms] <- y$tables[[ytrm]]$x
+    if(!is.null(x$tables[[ytrm]]$control.list) && !is.null(y$tables[[ytrm]]$control.list))
+      x$tables[[ytrm]]$control.list[xtrms] <- y$tables[[ytrm]]$control.list
+
     for(j in seq_along(x$tables[[ytrm]]$tables))
     {
       x$tables[[ytrm]]$tables[[j]][xtrms] <- y$tables[[ytrm]]$tables[[j]]

R/comparedf.R

@@ -78,14 +78,14 @@ comparedf <- function(x, y, by = NULL, by.x = by, by.y = by, control = NULL, ...
   if("row.names" %in% by.x)
   {
     x[["..row.names.."]] <- if(byrow) seq_len(nrow(x)) else row.names(x)
-    by.x <- "..row.names.."
+    by.x[by.x == "row.names"] <- "..row.names.."
   }
   if("row.names" %in% by.y)
   {
     y[["..row.names.."]] <- if(byrow) seq_len(nrow(y)) else row.names(y)
-    by.y <- "..row.names.."
+    by.y[by.y == "row.names"] <- "..row.names.."
   }
-  frame.summary$by <- list(by.x, by.y)
+  frame.summary$by <- set_attr(list(by.x, by.y), "byrow", byrow)
   frame.summary$attrs <- tmp.attrs
 
   #### tweak the column names ####
@@ -147,7 +147,7 @@ print.comparedf <- function(x, ...)
   cat("Function Call: \n")
   print(x$Call)
   cat("\n")
-  cat("Shared: ", sum(!idx_var_sum(x, "vars.not.shared")), " variables and ", x$frame.summary$n.shared[1], " observations.\n", sep = "")
+  cat("Shared: ", sum(idx_var_sum(x, "nonby.vars.shared")), " non-by variables and ", x$frame.summary$n.shared[1], " observations.\n", sep = "")
   cat("Not shared: ", sum(idx_var_sum(x, "vars.not.shared")), " variables and ",
       n.diff.obs(x), " observations.\n", sep = "")
   cat("\n")

R/comparedf.internal.R

@@ -80,7 +80,7 @@ compare_values <- function(i, v, df, byvars, contr)
   int.num <- function(vr) is.integer(vr) || is.numeric(vr)
   fac.chr <- function(vr) is.factor(vr)  || is.character(vr)
 
-  if(!identical(v$class.x[i], v$class.y[i]) &&
+  if(length(intersect(v$class.x[[i]], v$class.y[[i]])) == 0 &&
      !(contr$int.as.num && int.num(var.x) && int.num(var.y)) &&
      !(contr$factor.as.char && fac.chr(var.x) && fac.chr(var.y))) return("Not compared")
 
@@ -154,13 +154,16 @@ compare_attrs <- function(i, v, x_, y_)
 ####################################################################################################
 ####################################################################################################
 
-idx_var_sum <- function(object, which = c("vars.not.shared", "vars.compared", "vars.not.compared",
+idx_var_sum <- function(object, which = c("vars.not.shared", "nonby.vars.shared", "vars.compared", "vars.not.compared",
                                           "differences.found", "non.identical.attributes", "by.variables"))
 {
   which <- match.arg(which, several.ok = FALSE)
   if(which == "vars.not.shared")
   {
     vapply(object$vars.summary$values, is.null, logical(1))
+  } else if(which == "nonby.vars.shared")
+  {
+    vapply(object$vars.summary$values, function(elt) !is.null(elt) && !identical(elt, "by-variable"), logical(1))
   } else if(which == "vars.not.compared")
   {
     vapply(object$vars.summary$values, identical, logical(1), y = "Not compared")

R/modelsum.R

@@ -252,7 +252,12 @@ modelsum <- function(formula,  family="gaussian", data, adjust=NULL, na.action =
           coeffORTidy <- broom::tidy(fit, exponentiate=TRUE, conf.int=TRUE, conf.level=control$conf.level)
           coeffORTidy[coeffORTidy$term == "Intercept", -1] <- NA
           coeffTidy <- broom::tidy(fit, exponentiate=FALSE, conf.int=TRUE, conf.level=control$conf.level)
-          coeffTidy <- cbind(coeffTidy, OR=coeffORTidy$estimate, CI.lower.OR=coeffORTidy$conf.low, CI.upper.OR=coeffORTidy$conf.high)
+
+          waldTidy <- broom::confint_tidy(fit, conf.level=control$conf.level, func = stats::confint.default)
+
+          coeffTidy <- cbind(coeffTidy, OR=coeffORTidy$estimate, CI.lower.OR=coeffORTidy$conf.low, CI.upper.OR=coeffORTidy$conf.high,
+                             CI.lower.wald=waldTidy$conf.low, CI.upper.wald=waldTidy$conf.high,
+                             CI.lower.OR.wald=exp(waldTidy$conf.low), CI.upper.OR.wald=exp(waldTidy$conf.high))
           modelGlance <- c(broom::glance(fit), concordance = pROC::auc(rocOut))
 
         } else if (family == "quasipoisson" || family == "poisson") {

R/modelsum.control.R

@@ -93,7 +93,9 @@ modelsum.control <- function(
   ##Other  model fits:  logLik,AIC,BIC
   binomial.stats.valid <- c(
     "Nmiss", "OR", "CI.lower.OR", "CI.upper.OR", "p.value", "concordance",  # default
-    "estimate", "CI.OR", "CI.estimate", "CI.lower.estimate", "CI.upper.estimate", "N", "Nmiss2", "endpoint", "std.error", "statistic",
+    "estimate", "CI.OR", "CI.estimate", "CI.lower.estimate", "CI.upper.estimate",
+    "CI.wald", "CI.lower.wald", "CI.upper.wald", "CI.OR.wald", "CI.lower.OR.wald", "CI.upper.OR.wald",
+    "N", "Nmiss2", "endpoint", "std.error", "statistic",
     "logLik", "AIC", "BIC", "null.deviance", "deviance", "df.residual", "df.null"
   )
 
@@ -108,6 +110,12 @@ modelsum.control <- function(
   if(any(binomial.stats == "CI.estimate")) {
     binomial.stats <- unique(c(binomial.stats[binomial.stats != "CI.estimate"], "CI.lower.estimate", "CI.upper.estimate"))
   }
+  if(any(binomial.stats == "CI.wald")) {
+    binomial.stats <- unique(c(binomial.stats[binomial.stats != "CI.wald"], "CI.lower.wald", "CI.upper.wald"))
+  }
+  if(any(binomial.stats == "CI.OR.wald")) {
+    binomial.stats <- unique(c(binomial.stats[binomial.stats != "CI.OR.wald"], "CI.lower.OR.wald", "CI.upper.OR.wald"))
+  }
 
   ##########################
   ## Gaussian stats:
@@ -155,7 +163,7 @@ modelsum.control <- function(
   }
 
   ##########################
-  ## Poisson stats:
+  ## Negbin stats:
   ##########################
 
   negbin.stats.valid <- c(

R/paired.R

@@ -182,7 +182,8 @@ paired <- function(formula, data, id, na.action, subset=NULL, strata, control =
     xTerms <- Map(modeldf, names(modeldf), f = function(col, nm) {
       if(is.null(nameEff <- attr(col, "name"))) nameEff <- nm
       if(is.null(labelEff <- attr(col, "label"))) labelEff <- nameEff
-      list(variable=nameEff, label=labelEff, term=nm)
+      if(is.null(termEff <- attr(col, "term"))) termEff <- nm
+      list(variable=nameEff, label=labelEff, term=termEff, term.orig = nm)
     })
     names(xTerms) <- vapply(xTerms, "[[", NA_character_, "variable")
 

R/summary.comparedf.R

@@ -25,7 +25,7 @@ summary.comparedf <- function(object, ..., show.attrs = FALSE)
 
   #### start with summaries of the data.frames ####
 
-  frame.summary <- object$frame.summary[c("version", "arg", "ncol", "nrow")]
+  frame.summary <- as.data.frame(object$frame.summary[c("version", "arg", "ncol", "nrow")])
 
   #### after we've done all that, summaries of the overall comparison ####
   diffs.byvar <- diffs(object, by.var = TRUE)
@@ -34,15 +34,17 @@ summary.comparedf <- function(object, ..., show.attrs = FALSE)
   nobs.uneq <- length(unique(diffs.tab$row.x))
   comparison.summary <- data.frame(
     statistic = c(
-      "Number of by-variables", "Number of variables in common", "Number of variables compared",
+      "Number of by-variables",
+      "Number of non-by variables in common", "Number of variables compared",
       "Number of variables in x but not y", "Number of variables in y but not x",
       "Number of variables compared with some values unequal", "Number of variables compared with all values equal",
       "Number of observations in common", "Number of observations in x but not y", "Number of observations in y but not x",
       "Number of observations with some compared variables unequal", "Number of observations with all compared variables equal",
       "Number of values unequal"
     ),
     value = c(
-      sum(idx_var_sum(object, "by.variables")), sum(!idx_var_sum(object, "vars.not.shared")), sum(idx_var_sum(object, "vars.compared")),
+      (!attr(object$frame.summary$by, "byrow"))*sum(idx_var_sum(object, "by.variables")),
+      sum(idx_var_sum(object, "nonby.vars.shared")), sum(idx_var_sum(object, "vars.compared")),
       sum(is.na(object$vars.summary$var.y)), sum(is.na(object$vars.summary$var.x)),
       sum(diffs.byvar$n > 0), sum(diffs.byvar$n == 0),
       nobs.shared, nrow(object$frame.summary$unique[[1]]), nrow(object$frame.summary$unique[[2]]),