Merge pull request #43 from rcalinjageman/development

markdown for plot axis titles, updated DR CI note, better handling of…

R/00jmv.R

@@ -0,0 +1,76 @@
+
+# This file is automatically generated, you probably don't want to edit this
+
+.jmvrefs <- list(
+    `lc_median_bs`=list(
+        `type`="article", 
+        `author`="Bonett, D.G. & Price, R. M.", 
+        `year`=2002, 
+        `title`="Statistical inference for a linear function of medians: Confidence intervals, hypothesis testing, and sample size requirements", 
+        `publisher`="Psychological Methods", 
+        `volume`=7, 
+        `pages`="370-383", 
+        `url`="https://psycnet.apa.org/doiLanding?doi=10.1037%2F1082-989X.7.3.370"), 
+    `lc_stdmean_bs`=list(
+        `type`="article", 
+        `author`="Bonett, D.G.", 
+        `year`=2008, 
+        `title`="Confidence intervals for standardized linear contrasts of means", 
+        `publisher`="Psychological Methods", 
+        `volume`=13, 
+        `pages`="99-109", 
+        `url`="https://psycnet.apa.org/doiLanding?doi=10.1037%2F1082-989X.13.2.99"), 
+    `median_ps`=list(
+        `type`="article", 
+        `author`="Bonett, D.G. & Price, R. M.", 
+        `year`=2020, 
+        `title`="Interval estimation for linear functions of medians in within-subjects and mixed designs", 
+        `publisher`="British Journal of Mathematical and Statistical Psychology", 
+        `volume`=73, 
+        `pages`="333-346", 
+        `url`="https://bpspsychub.onlinelibrary.wiley.com/doi/10.1111/bmsp.12171"), 
+    `ratio_ps`=list(
+        `type`="article", 
+        `author`="Bonett, D.G. & Price, R. M.", 
+        `year`=2020, 
+        `title`="Confidence intervals for ratios of means and medians", 
+        `publisher`="Journal of Educational and Behavioral Statistics", 
+        `volume`=45, 
+        `pages`="750-770", 
+        `url`="https://journals.sagepub.com/doi/10.3102/1076998620934125"), 
+    `metafor`=list(
+        `type`="article", 
+        `author`="Viechtbauer, W.", 
+        `year`=2010, 
+        `title`="Conducting Meta-Analyses in R with the metafor Package", 
+        `publisher`="Journal of Statistical Software", 
+        `volume`=36, 
+        `pages`="1-48", 
+        `url`="https://doi.org/10.18637/jss.v036.i03"), 
+    `ggdist`=list(
+        `type`="article", 
+        `author`="Kay, M.", 
+        `year`=2002, 
+        `title`="ggdist: Visualizations of Distributions and Uncertainty in the Grammar of Graphics", 
+        `publisher`="IEEE Transactions on Visualization and Computer Graphics", 
+        `volume`=30, 
+        `pages`="414-424", 
+        `url`="https://zenodo.org/records/7933524"), 
+    `prop1`=list(
+        `type`="article", 
+        `author`="Agresti, A. & Coull, B. A.", 
+        `year`=1998, 
+        `title`="Approximate is better than exact for interval estimation of binomial proportions", 
+        `publisher`="The American Statistician", 
+        `volume`=52, 
+        `pages`="119-126", 
+        `url`="https://www.tandfonline.com/doi/abs/10.1080/00031305.1998.10480550"), 
+    `prop_paired`=list(
+        `type`="article", 
+        `author`="Bonett, D.G. & Price, R. M.", 
+        `year`=2012, 
+        `title`="Adjusted wald confidence interval for a difference of binomial proportions based on paired data", 
+        `publisher`="Journal of Educational and Behavioral Statistics", 
+        `volume`=37, 
+        `pages`="479-488", 
+        `url`="https://journals.sagepub.com/doi/10.3102/1076998611411915"))

R/estimate_mdiff_ind_contrast.R

@@ -889,17 +889,16 @@ Invalid groups are those with n < 2.
 
         estimate$es_mean_ratio_properties <- list(
           message_html = paste(
-            if (no_negs) "" else "WARNING!  Your data has negative values.  ",
-            "This effect-size measure is appropriate only for true ratio scales where values < 0 are impossible.
-            For more information on this effect size, see Bonett & Price (2020) doi: 10.3102/1076998620934125.",
+            if (no_negs) "" else "WARNING!  Your dataset includes negative values.  ",
+            "This effect-size measure is appropriate only for true ratio scales.",
             sep = ""
           )
         )
 
         if (!no_negs) {
           estimate$warnings <- c(
             estimate$warnings,
-            "neg_values" = "The ratio between group effect size is appropriate only for true ratio scales where values < 0 are impossible.  Your data has negative values and therefore any ratio between groups is invalid and should not be interpreted."
+            "neg_values" = "The ratio between group effect size is appropriate only for true ratio scales where values < 0 are impossible.  Your data include at least one negative value, so the requested ratio effect size is not reported."
           )
         }
 

R/estimate_mdiff_paired.R

@@ -639,17 +639,16 @@ estimate_mdiff_paired.data.frame <- function(
 
   estimate$es_mean_ratio_properties <- list(
     message_html = paste(
-      if (no_negs) "" else "WARNING!  Your data has negative values.  ",
-      "This effect-size measure is appropriate only for true ratio scales where values < 0 are impossible.
-      For more information on this effect size, see Bonett & Price (2020) doi: 10.3102/1076998620934125.",
+      if (no_negs) "" else "WARNING!  Your dataset includes negative values.  ",
+      "This effect-size measure is appropriate only for true ratio scales.",
       sep = ""
     )
   )
 
   if (!no_negs) {
     estimate$warnings <- c(
       estimate$warnings,
-      "neg_values" = "The ratio between measures effect size is appropriate only for true ratio scales where values < 0 are impossible.  Your data has negative values and therefore the any ratio between measures is invalid and should not be interpreted."
+      "neg_values" = "The ratio between group effect size is appropriate only for true ratio scales where values < 0 are impossible.  Your data include at least one negative value, so the requested ratio effect size is not reported."
     )
   }
 

R/estimate_mdiff_two.R

@@ -147,8 +147,8 @@
 #' )
 #'
 #' \dontrun{
-#' # To visualize the estimated median difference (raw data only)
-#' plot_mdiff(estimate, effect_size = "median")
+#' # To visualize the estimated mean difference
+#' plot_mdiff(estimate, effect_size = "mean")
 #' }
 
 #'
@@ -164,8 +164,8 @@
 #'   )
 #'
 #' \dontrun{
-#' # To visualize the estimated mean difference
-#' plot_mdiff(estimate, effect_size = "mean")
+#' # To visualize the estimated median difference (raw data only)
+#' plot_mdiff(estimate, effect_size = "median")
 #' }
 #'
 #'

R/jamovidescribe.b.R

@@ -279,10 +279,10 @@ jamovidescribeClass <- if (requireNamespace('jmvcore', quietly=TRUE)) R6::R6Clas
 
 
           myplot <- myplot + ggplot2::theme(
-            axis.text.y = element_text(size = axis.text.y),
-            axis.title.y = element_text(size = axis.title.y),
-            axis.text.x = element_text(size = axis.text.x),
-            axis.title.x = element_text(size = axis.title.x)
+            axis.text.y = ggtext::element_markdown(size = axis.text.y),
+            axis.title.y = ggtext::element_markdown(size = axis.title.y),
+            axis.text.x = ggtext::element_markdown(size = axis.text.x),
+            axis.title.x = ggtext::element_markdown(size = axis.title.x)
           )
 
 

R/jamovimagnitude.b.R

@@ -276,10 +276,10 @@ jamovimagnitudeClass <- if (requireNamespace('jmvcore', quietly=TRUE)) R6::R6Cla
 
 
             myplot <- myplot + ggplot2::theme(
-                axis.text.y = element_text(size = axis.text.y),
-                axis.title.y = element_text(size = axis.title.y),
-                axis.text.x = element_text(size = axis.text.x),
-                axis.title.x = element_text(size = axis.title.x)
+              axis.text.y = ggtext::element_markdown(size = axis.text.y),
+              axis.title.y = ggtext::element_markdown(size = axis.title.y),
+              axis.text.x = ggtext::element_markdown(size = axis.text.x),
+              axis.title.x = ggtext::element_markdown(size = axis.title.x)
             )
 
 

R/jamovimagnitude.h.R

@@ -1098,7 +1098,8 @@ jamovimagnitudeResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6C
                 requiresData=TRUE,
                 width=400,
                 height=300,
-                renderFun=".magnitude_plot"))}))
+                renderFun=".magnitude_plot",
+                refs="ggdist"))}))
 
 jamovimagnitudeBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
     "jamovimagnitudeBase",

R/jamovimdiff2x2.h.R

@@ -2389,6 +2389,7 @@ jamovimdiff2x2Results <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                 name="es_median_difference",
                 title="Median Difference",
                 visible="(effect_size == 'median_difference' & design == 'fully_between')",
+                refs="lc_median_bs",
                 rows="15 - switch - outcome_variable - grouping_variable_A - grouping_variable_B - outcome_variable_level1 - outcome_variable_level2 - outcome_variable_name_bs - grouping_variable - repeated_measures_name - outcome_variable_name - conf_level - effect_size - assume_equal_variance - show_details",
                 columns=list(
                     list(
@@ -2540,6 +2541,7 @@ jamovimdiff2x2Results <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                 name="es_smd",
                 title="Standardized Mean Difference",
                 rows=5,
+                refs="lc_stdmean_bs",
                 visible="(effect_size == 'mean_difference' & design == 'fully_between')",
                 clearWith=list(
                     "switch",
@@ -2810,6 +2812,7 @@ jamovimdiff2x2Results <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                 requiresData=TRUE,
                 width=700,
                 height=400,
+                refs="ggdist",
                 renderFun=".estimation_plot"))
             self$add(jmvcore::Image$new(
                 options=options,

R/jamovimdiffindcontrast.h.R

@@ -2191,6 +2191,7 @@ jamovimdiffindcontrastResults <- if (requireNamespace("jmvcore", quietly=TRUE))
                     "effect_size",
                     "assume_equal_variance",
                     "show_details"),
+                refs="lc_median_bs",
                 columns=list(
                     list(
                         `name`="outcome_variable_name", 
@@ -2300,6 +2301,7 @@ jamovimdiffindcontrastResults <- if (requireNamespace("jmvcore", quietly=TRUE))
                 title="Standardized Mean Difference",
                 rows=1,
                 visible="(effect_size == 'mean_difference')",
+                refs="lc_stdmean_bs",
                 clearWith=list(
                     "switch",
                     "outcome_variable",
@@ -2521,6 +2523,7 @@ jamovimdiffindcontrastResults <- if (requireNamespace("jmvcore", quietly=TRUE))
                 options=options,
                 name="estimation_plots",
                 title="Estimation Figure",
+                refs="ggdist",
                 template=jmvcore::Image$new(
                     options=options,
                     title="$key",

R/jamovimdiffpaired.b.R

@@ -315,6 +315,10 @@ jamovi_mdiff_paired <- function(self, save_raw_data = FALSE) {
         if (!is.na(estimate$warnings["neg_values"])) {
           estimate$warnings <- estimate$warnings[names(estimate$warnings) != "neg_values"]
         }
+      } else {
+        to_show <- is.na(estimate$warnings["neg_values"])
+        self$results$es_mean_ratio$setVisible(to_show & self$options$effect_size == "mean_difference")
+        self$results$es_median_ratio$setVisible(to_show & self$options$effect_size == "median_difference")
       }
 
       notes <- c(notes, estimate$warnings)

R/jamovimdiffpaired.h.R

@@ -2037,6 +2037,7 @@ jamovimdiffpairedResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R
                 name="es_smd",
                 title="Standardized Mean Difference",
                 rows=1,
+                refs="lc_stdmean_bs",
                 visible="(effect_size == 'mean_difference')",
                 clearWith=list(
                     "switch",
@@ -2115,6 +2116,7 @@ jamovimdiffpairedResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R
                 title="Ratio of Means",
                 visible="(show_ratio & effect_size == 'mean_difference')",
                 rows=1,
+                refs="ratio_ps",
                 clearWith=list(
                     "switch",
                     "reference_measure",
@@ -2175,6 +2177,7 @@ jamovimdiffpairedResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R
                 name="es_median_difference",
                 title="Median Difference",
                 visible="(effect_size == 'median_difference')",
+                refs="median_ps",
                 rows=3,
                 clearWith=list(
                     "switch",
@@ -2234,6 +2237,7 @@ jamovimdiffpairedResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R
                 title="Ratio of Medians",
                 visible="(show_ratio & effect_size == 'median_difference')",
                 rows=1,
+                refs="ratio_ps",
                 clearWith=list(
                     "switch",
                     "reference_measure",
@@ -2439,6 +2443,7 @@ jamovimdiffpairedResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R
                 width=300,
                 height=450,
                 requiresData=TRUE,
+                refs="ggdist",
                 renderFun=".estimation_plots"))}))
 
 jamovimdiffpairedBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(

R/jamovimdifftwo.b.R

@@ -294,6 +294,10 @@ jamovi_mdiff_two <- function(
         if (!is.na(estimate$warnings["neg_values"])) {
           estimate$warnings <- estimate$warnings[names(estimate$warnings) != "neg_values"]
         }
+      } else {
+        to_show <- is.na(estimate$warnings["neg_values"])
+        self$results$es_mean_ratio$setVisible(to_show & self$options$effect_size == "mean_difference")
+        self$results$es_median_ratio$setVisible(to_show & self$options$effect_size == "median_difference")
       }
 
       notes <- c(notes, estimate$warnings)

R/jamovimdifftwo.h.R

@@ -1869,6 +1869,7 @@ jamovimdifftwoResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                 name="es_smd",
                 title="Standardized Mean Difference",
                 rows=1,
+                refs="lc_stdmean_bs",
                 visible="(effect_size == 'mean_difference')",
                 clearWith=list(
                     "switch",
@@ -1953,6 +1954,7 @@ jamovimdifftwoResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                 title="Ratio of Means",
                 visible="(show_ratio & effect_size == 'mean_difference')",
                 rows="(outcome_variable)",
+                refs="ratio_ps",
                 clearWith=list(
                     "switch",
                     "outcome_variable",
@@ -2015,6 +2017,7 @@ jamovimdifftwoResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                 title="Median Difference",
                 visible="(effect_size == 'median_difference')",
                 rows=3,
+                refs="lc_median_bs",
                 clearWith=list(
                     "switch",
                     "outcome_variable",
@@ -2074,6 +2077,7 @@ jamovimdifftwoResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                 title="Ratio of Medians",
                 visible="(show_ratio & effect_size == 'median_difference')",
                 rows="(outcome_variable)",
+                refs="ratio_ps",
                 clearWith=list(
                     "switch",
                     "outcome_variable",
@@ -2286,6 +2290,7 @@ jamovimdifftwoResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                 options=options,
                 name="estimation_plots",
                 title="Estimation Figure",
+                refs="ggdist",
                 template=jmvcore::Image$new(
                     options=options,
                     title="$key",

R/jamovimetamdiff.h.R

@@ -1909,6 +1909,7 @@ jamovimetamdiffResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6C
                 name="es_meta",
                 title="Meta-Analytic Effect Sizes",
                 rows=1,
+                refs="metafor",
                 clearWith=list(
                     "switch",
                     "comparison_means",

R/jamovimetamean.h.R

@@ -1806,6 +1806,7 @@ jamovimetameanResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                 name="es_meta",
                 title="Meta-Analytic Effect Sizes",
                 rows=1,
+                refs="metafor",
                 clearWith=list(
                     "means",
                     "sds",

R/jamovimetapdiff.h.R

@@ -1750,6 +1750,7 @@ jamovimetapdiffResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6C
                 options=options,
                 name="es_meta",
                 title="Meta-Analytic Effect Sizes",
+                refs="metafor",
                 rows=1,
                 clearWith=list(
                     "reference_cases",

R/jamovimetaproportion.h.R

@@ -1699,6 +1699,7 @@ jamovimetaproportionResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6
                 name="es_meta",
                 title="Meta-Analytic Effect Sizes",
                 rows=1,
+                refs="metafor",
                 clearWith=list(
                     "cases",
                     "ns",

R/jamovimetar.h.R

@@ -1714,6 +1714,7 @@ jamovimetarResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class
                 name="es_meta",
                 title="Meta-Analytic Effect Sizes",
                 rows=1,
+                refs="metafor",
                 clearWith=list(
                     "rs",
                     "ns",

R/jamovipdiffpaired.h.R

@@ -873,6 +873,7 @@ jamovipdiffpairedResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R
                 name="es_proportion_difference",
                 title="Proportion Difference",
                 rows=3,
+                refs="prop_paired",
                 clearWith=list(
                     "reference_measure",
                     "comparison_measure",
@@ -1027,6 +1028,7 @@ jamovipdiffpairedResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R
                 width=300,
                 height=450,
                 requiresData=TRUE,
+                refs="ggdist",
                 renderFun=".estimation_plots"))}))
 
 jamovipdiffpairedBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(