default to dataframe as output argument

IndrajeetPatil · Oct 14, 2020 · 2ba6b75 · 2ba6b75 · lintr-bot · Oct 14, 2020
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Showing 27 changed files with 66 additions and 78 deletions.
diff --git a/API b/API
@@ -2,13 +2,13 @@
 
 ## Exported functions
 
-bf_contingency_tab(data, x, y = NULL, counts = NULL, ratio = NULL, sampling.plan = "indepMulti", fixed.margin = "rows", prior.concentration = 1, caption = NULL, output = "results", k = 2L, ...)
-bf_corr_test(data, x, y, bf.prior = 0.707, caption = NULL, output = "results", k = 2L, ...)
+bf_contingency_tab(data, x, y = NULL, counts = NULL, ratio = NULL, sampling.plan = "indepMulti", fixed.margin = "rows", prior.concentration = 1, caption = NULL, output = "dataframe", k = 2L, ...)
+bf_corr_test(data, x, y, bf.prior = 0.707, caption = NULL, output = "dataframe", k = 2L, ...)
 bf_expr(bf.object, k = 2L, conf.level = 0.95, conf.method = "hdi", centrality = "median", output = "null", caption = NULL, anova.design = FALSE, ...)
 bf_extractor(bf.object, ...)
-bf_meta(data, d = prior("norm", c(mean = 0, sd = 0.3)), tau = prior("invgamma", c(shape = 1, scale = 0.15)), k = 2L, output = "results", caption = NULL, messages = TRUE, ...)
-bf_oneway_anova(data, x, y, bf.prior = 0.707, caption = NULL, output = "results", paired = FALSE, k = 2L, ...)
-bf_ttest(data, x, y = NULL, test.value = 0, paired = FALSE, bf.prior = 0.707, caption = NULL, output = "results", k = 2L, ...)
+bf_meta(data, d = prior("norm", c(mean = 0, sd = 0.3)), tau = prior("invgamma", c(shape = 1, scale = 0.15)), k = 2L, output = "dataframe", caption = NULL, ...)
+bf_oneway_anova(data, x, y, bf.prior = 0.707, caption = NULL, output = "dataframe", paired = FALSE, k = 2L, ...)
+bf_ttest(data, x, y = NULL, test.value = 0, paired = FALSE, bf.prior = 0.707, caption = NULL, output = "dataframe", k = 2L, ...)
 meta_data_check(data)
 
 ## Reexported objects

diff --git a/NEWS.md b/NEWS.md
@@ -9,6 +9,9 @@ BREAKING CHANGES
     hypothesis (`BF10`) and its `log` value to avoid cluttered dataframe since
     all the other columns were essentially mathematical transformations of it
     and not really relevant.
+
+  - The `output` argument's default value has been changed from too generic
+    `"results"` to `"dataframe"`.
 
 MAJOR CHANGES
 

diff --git a/R/bf_contingency_tab.R b/R/bf_contingency_tab.R
@@ -82,7 +82,7 @@ bf_contingency_tab <- function(data,
                                fixed.margin = "rows",
                                prior.concentration = 1,
                                caption = NULL,
-                               output = "results",
+                               output = "dataframe",
                                k = 2L,
                                ...) {
 
@@ -230,7 +230,7 @@ bf_contingency_tab <- function(data,
   # return the text results or the dataframe with results
   return(switch(
     EXPR = output,
-    "results" = dplyr::select(df, -dplyr::matches("error|time|code")),
+    "dataframe" = dplyr::select(df, -dplyr::matches("error|time|code")),
     bf_message
   ))
 }
diff --git a/R/bf_corr_test.R b/R/bf_corr_test.R
@@ -47,7 +47,7 @@ bf_corr_test <- function(data,
                          y,
                          bf.prior = 0.707,
                          caption = NULL,
-                         output = "results",
+                         output = "dataframe",
                          k = 2L,
                          ...) {
 
@@ -62,7 +62,7 @@ bf_corr_test <- function(data,
   # return the text results or the dataframe with results
   switch(
     EXPR = output,
-    "results" = bf_extractor(bf_object),
+    "dataframe" = bf_extractor(bf_object),
     bf_expr(bf_object, k = k, output = output, caption = caption, ...)
   )
 }
diff --git a/R/bf_meta.R b/R/bf_meta.R
@@ -7,7 +7,6 @@
 #'   sizes or outcomes)  and `std.error` (corresponding standard errors). These
 #'   two columns will be used for `yi`  and `sei` arguments in `metafor::rma`
 #'   (for parametric analysis) or `metaplus::metaplus` (for robust analysis).
-#' @param messages Deprecated. Retained only for backward compatibility.
 #' @inheritParams bf_expr
 #' @inheritParams metaBMA::meta_random
 #' @inheritDotParams metaBMA::meta_random -y -SE
@@ -48,7 +47,6 @@
 #'   data = df,
 #'   k = 3,
 #'   iter = 1500,
-#'   messages = TRUE,
 #'   # customizing analysis with additional arguments
 #'   control = list(max_treedepth = 15)
 #' )
@@ -61,9 +59,8 @@ bf_meta <- function(data,
                     d = prior("norm", c(mean = 0, sd = 0.3)),
                     tau = prior("invgamma", c(shape = 1, scale = 0.15)),
                     k = 2L,
-                    output = "results",
+                    output = "dataframe",
                     caption = NULL,
-                    messages = TRUE,
                     ...) {
 
   # check the data contains needed column
@@ -72,7 +69,7 @@ bf_meta <- function(data,
   #----------------------- meta-analysis -------------------------------
 
   # extracting results from random-effects meta-analysis
-  meta_res <-
+  mod <-
     metaBMA::meta_random(
       y = data$estimate,
       SE = data$std.error,
@@ -84,12 +81,9 @@ bf_meta <- function(data,
   #----------------------- preparing caption -------------------------------
 
   # creating a dataframe with posterior estimates
-  df_estimates <-
-    as_tibble(meta_res$estimates, rownames = "term") %>%
-    dplyr::filter(.data = ., term == "d")
-
-  # dataframe with bayes factors
-  df <- tibble(bf10 = meta_res$BF["random_H1", "random_H0"])
+  df <-
+    as_tibble(mod$estimates, rownames = "term") %>%
+    dplyr::mutate(.data = ., bf10 = mod$BF["random_H1", "random_H0"])
 
   # changing aspects of the caption based on what output is needed
   if (output %in% c("null", "caption", "H0", "h0")) {
@@ -127,16 +121,16 @@ bf_meta <- function(data,
         top.text = caption,
         bf.sub = bf.sub,
         bf = specify_decimal_p(x = bf.value, k = k),
-        d.pmean = specify_decimal_p(x = df_estimates$mean[[1]], k = k),
-        d.pmean.LB = specify_decimal_p(x = df_estimates$hpd95_lower[[1]], k = k),
-        d.pmean.UB = specify_decimal_p(x = df_estimates$hpd95_upper[[1]], k = k)
+        d.pmean = specify_decimal_p(x = df$mean[[1]], k = k),
+        d.pmean.LB = specify_decimal_p(x = df$hpd95_lower[[1]], k = k),
+        d.pmean.UB = specify_decimal_p(x = df$hpd95_upper[[1]], k = k)
       )
     )
 
   # return the text results or the dataframe with results
   return(switch(
     EXPR = output,
-    "results" = df,
+    "dataframe" = df,
     bf_message
   ))
 }
diff --git a/R/bf_oneway_anova.R b/R/bf_oneway_anova.R
@@ -55,7 +55,7 @@ bf_oneway_anova <- function(data,
                             y,
                             bf.prior = 0.707,
                             caption = NULL,
-                            output = "results",
+                            output = "dataframe",
                             paired = FALSE,
                             k = 2L,
                             ...) {
@@ -112,7 +112,7 @@ bf_oneway_anova <- function(data,
   # return the text results or the dataframe with results
   switch(
     EXPR = output,
-    "results" = bf_extractor(bf_object),
+    "dataframe" = bf_extractor(bf_object),
     bf_expr(bf_object, k = k, output = output, caption = caption, anova.design = TRUE, ...)
   )
 }
diff --git a/R/bf_ttest.R b/R/bf_ttest.R
@@ -54,7 +54,7 @@ bf_ttest <- function(data,
                      paired = FALSE,
                      bf.prior = 0.707,
                      caption = NULL,
-                     output = "results",
+                     output = "dataframe",
                      k = 2L,
                      ...) {
 
@@ -118,7 +118,7 @@ bf_ttest <- function(data,
   # return the text results or the dataframe with results
   switch(
     EXPR = output,
-    "results" = bf_extractor(bf_object),
+    "dataframe" = bf_extractor(bf_object),
     bf_expr(bf_object, k = k, output = output, caption = caption, ...)
   )
 }
diff --git a/R/helpers_bf_tests.R b/R/helpers_bf_tests.R
@@ -66,7 +66,7 @@ bf_extractor <- function(bf.object, ...) {
 #'   which will return expression with evidence in favor of the null hypothesis,
 #'   or `"alternative"` (or `"title"` or `"H1"` or `"h1"`), which will return
 #'   expression with evidence in favor of the alternative hypothesis, or
-#'   `"results"`, which will return a dataframe with results all the details).
+#'   `"dataframe"`, which will return a dataframe with results all the details).
 #' @param anova.design Whether the object is from `BayesFactor::anovaBF`
 #'   (default: `FALSE`). The expression is different for anova designs because
 #'   not all details are available.

diff --git a/codemeta.json b/codemeta.json
@@ -229,5 +229,5 @@
     "name": "Comprehensive R Archive Network (CRAN)",
     "url": "https://cran.r-project.org"
   },
-  "fileSize": "1655.411KB"
+  "fileSize": "1659.995KB"
 }
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: '2.11'
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2020-10-14T08:30Z
+last_built: 2020-10-14T21:22Z
 urls:
   reference: https://indrajeetpatil.github.io/tidyBF//reference
   article: https://indrajeetpatil.github.io/tidyBF//articles

diff --git a/docs/reference/bf_contingency_tab.html b/docs/reference/bf_contingency_tab.html
diff --git a/docs/reference/bf_corr_test.html b/docs/reference/bf_corr_test.html
diff --git a/docs/reference/bf_expr.html b/docs/reference/bf_expr.html
diff --git a/docs/reference/bf_meta.html b/docs/reference/bf_meta.html
diff --git a/docs/reference/bf_oneway_anova.html b/docs/reference/bf_oneway_anova.html