Merge pull request #34 from rcalinjageman/development

estimate_r and estimate_rdiff_two - tests and documention, Changed all class functions to is functions, changes for statpsych 1.5

NAMESPACE

@@ -5,7 +5,6 @@ export(CI_diamond_ratio)
 export(CI_smd_ind_contrast)
 export(CI_smd_one)
 export(esci_plot_difference_axis_x)
-export(estimate_correlation)
 export(estimate_magnitude)
 export(estimate_mdiff_2x2_between)
 export(estimate_mdiff_2x2_mixed)
@@ -18,6 +17,7 @@ export(estimate_pdiff_one)
 export(estimate_pdiff_paired)
 export(estimate_pdiff_two)
 export(estimate_proportion)
+export(estimate_r)
 export(estimate_rdiff_two)
 export(geom_meta_diamond_h)
 export(jamovicorrelation)
@@ -56,6 +56,7 @@ export(plot_meta)
 export(plot_pdiff)
 export(plot_proportion)
 export(plot_rdiff)
+export(plot_scatter)
 export(test_correlation)
 export(test_mdiff)
 export(test_pdiff)
@@ -98,4 +99,5 @@ importFrom(stats,quantile)
 importFrom(stats,rnorm)
 importFrom(stats,sd)
 importFrom(utils,head)
+importFrom(utils,packageVersion)
 importFrom(utils,tail)

NEWS.md

@@ -1,7 +1,7 @@
-# esci (0.01)
+esci version 0.99 (Release data: March 2024)
+===========
 
-## Information
+Changes:
 
-- Alpha release; expect breaking changes still to come, especially with
+* Alpha release; expect breaking changes still to come, especially with
 graphing functions.
-- Released to jamovi is 1.01

R/class_estimate.R

@@ -106,7 +106,7 @@ esci_estimate_consolidate <- function(estimate_list) {
   # Cycle through the list
   for (estimate in estimate_list) {
     # Check if the current list item is an estimate
-    if (class(estimate) == "esci_estimate") {
+    if (is(estimate, "esci_estimate")) {
 
       # Handle warnings, consolidating with outcome variable name
       if(length(estimate$warnings) > 0 ) {

R/esci-package.R

@@ -42,6 +42,7 @@
 #' @importFrom stats sd
 #' @importFrom utils head
 #' @importFrom utils tail
+#' @importFrom utils packageVersion
 #' @importFrom grid grobName
 #' @import ggplot2
 #' @import ggdist
@@ -54,4 +55,5 @@ esci_solve_imports <- function() {
   Rdpack::get_usage
   mathjaxr::preview_rd
   R6::is.R6
+  utils::packageVersion
 }

R/estimate_magnitude.R

@@ -162,14 +162,14 @@ estimate_magnitude <- function(
     # We check to see if we have a tidy column name by trying to evaluate it
     is_column_name <- try(outcome_variable, silent = TRUE)
 
-    if(class(is_column_name) == "try-error") {
+    if(is(is_column_name, "try-error")) {
       # Column names have been passed, check if need to be quoted up
 
       outcome_variable_enquo <- rlang::enquo(outcome_variable)
       outcome_variable_quoname <- try(
         eval(rlang::as_name(outcome_variable_enquo)), silent = TRUE
       )
-      if (class(outcome_variable_quoname) != "try-error") {
+      if (!is(outcome_variable_quoname, "try-error")) {
         # This only succeeds if outcome_variable was passed unquoted
         # Reset outcome_variable to be fully quoted
         outcome_variable <- outcome_variable_quoname
@@ -178,12 +178,12 @@ estimate_magnitude <- function(
       # Ready to be analyzed as a list of string column names
       analysis_type <- "data.frame"
 
-    } else if (class(outcome_variable) == "numeric") {
+    } else if (is(outcome_variable, "numeric")) {
       # At this stage, we know that y was not a tidy column name,
       #  so it should be either a vector of raw data (class = numeric)
       #  or a vector of column names passed as strings
       analysis_type <- "vector"
-    } else if (class(outcome_variable) == "character") {
+    } else if (is(outcome_variable, "character")) {
       # Ok, must have been string column names
       if (length(outcome_variable) == 1) {
         analysis_type <- "data.frame"

R/estimate_mdiff_2x2_between.R

@@ -214,12 +214,12 @@ estimate_mdiff_2x2_between <- function(
     # Check grouping_variable -- if it is an unquoted column name
     #  turn it into a string and store back to grouping_variable
     is_column_name <- try(grouping_variable_A, silent = TRUE)
-    if(class(is_column_name) == "try-error") {
+    if(is(is_column_name, "try-error")) {
       grouping_variable_A_enquo <- rlang::enquo(grouping_variable_A)
       grouping_variable_A_enquo_name <- try(
         eval(rlang::as_name(grouping_variable_A_enquo)), silent = TRUE
       )
-      if (class(grouping_variable_A_enquo_name) != "try-error") {
+      if (!is(grouping_variable_A_enquo_name, "try-error")) {
         # This only succeeds if the columns were passed unquoted
         # So now replace grouping_variable with a quoted version
         grouping_variable_A <- grouping_variable_A_enquo_name
@@ -228,12 +228,12 @@ estimate_mdiff_2x2_between <- function(
 
 
     is_column_name <- try(grouping_variable_B, silent = TRUE)
-    if(class(is_column_name) == "try-error") {
+    if(is(is_column_name, "try-error")) {
       grouping_variable_B_enquo <- rlang::enquo(grouping_variable_B)
       grouping_variable_B_enquo_name <- try(
         eval(rlang::as_name(grouping_variable_B_enquo)), silent = TRUE
       )
-      if (class(grouping_variable_B_enquo_name) != "try-error") {
+      if (!is(grouping_variable_B_enquo_name, "try-error")) {
         # This only succeeds if the columns were passed unquoted
         # So now replace grouping_variable with a quoted version
         grouping_variable_B <- grouping_variable_B_enquo_name
@@ -244,13 +244,13 @@ estimate_mdiff_2x2_between <- function(
     #   could be tidy column names, string column names, or vectors
     # We check to see if we have a tidy column name by trying to evaluate it
     is_column_name <- try(outcome_variable, silent = TRUE)
-    if(class(is_column_name) == "try-error") {
+    if(is(is_column_name, "try-error")) {
       # Column names have been passed, check if need to be quoted up
       outcome_variable_enquo <- rlang::enquo(outcome_variable)
       outcome_variable_quoname <- try(
         eval(rlang::as_name(outcome_variable_enquo)), silent = TRUE
       )
-      if (class(outcome_variable_quoname) != "try-error") {
+      if (!is(outcome_variable_quoname, "try-error")) {
         # This only succeeds if outcome_variable was passed unquoted
         # Reset outcome_variable to be fully quoted
         outcome_variable <- outcome_variable_quoname
@@ -259,12 +259,12 @@ estimate_mdiff_2x2_between <- function(
       # Ready to be analyzed as a list of string column names
       analysis_type <- "data.frame"
 
-    } else if (class(outcome_variable) == "numeric") {
+    } else if (is(outcome_variable, "numeric")) {
       # At this stage, we know that y was not a tidy column name,
       #  so it should be either a vector of raw data (class = numeric)
       #  or a vector of column names passed as strings
       analysis_type <- "vector"
-    } else if (class(outcome_variable) == "character") {
+    } else if (is(outcome_variable, "character")) {
       # Ok, must have been string column names
       if (length(outcome_variable) == 1) {
         analysis_type <- "data.frame"
@@ -831,7 +831,7 @@ estimate_mdiff_2x2_between.summary <- function(
   )
 
   for (x in 1:length(estimate)) {
-    if (class(estimate[[x]]) == "esci_estimate") {
+    if (is(estimate[[x]], "esci_estimate")) {
       estimate[[x]]$overview <- overview
       estimate[[x]]$properties$data_type <- "summary"
       estimate[[x]]$properties$data_source <- NULL
@@ -1138,7 +1138,7 @@ estimate_mdiff_2x2_between.data.frame <- function(
 
 
   for (x in 1:length(estimate)) {
-    if (class(estimate[[x]]) == "esci_estimate") {
+    if (is(estimate[[x]], "esci_estimate")) {
         estimate[[x]]$overview <- overview
         estimate[[x]]$raw_data <- if (save_raw_data) raw_data else NULL
         estimate[[x]]$properties$data_type <- "data.frame"

R/estimate_mdiff_2x2_mixed.R

@@ -149,7 +149,7 @@ estimate_mdiff_2x2_mixed <- function(
   outcome_variable_level1_enquo_name <- try(
     eval(rlang::as_name(outcome_variable_level1_enquo)), silent = TRUE
   )
-  if (class(outcome_variable_level1_enquo_name) != "try-error") {
+  if (!is(outcome_variable_level1_enquo_name, "try-error")) {
     # This only succeeds if the columns were passed unquoted
     # So now replace outcome_variable_level1 with a quoted version
     outcome_variable_level1 <- outcome_variable_level1_enquo_name
@@ -160,7 +160,7 @@ estimate_mdiff_2x2_mixed <- function(
   outcome_variable_level2_enquo_name <- try(
     eval(rlang::as_name(outcome_variable_level2_enquo)), silent = TRUE
   )
-  if (class(outcome_variable_level2_enquo_name) != "try-error") {
+  if (!is(outcome_variable_level2_enquo_name, "try-error")) {
     # This only succeeds if the columns were passed unquoted
     # So now replace outcome_variable_level2 with a quoted version
     outcome_variable_level2 <- outcome_variable_level2_enquo_name
@@ -170,7 +170,7 @@ estimate_mdiff_2x2_mixed <- function(
   grouping_variable_enquo_name <- try(
     eval(rlang::as_name(grouping_variable_enquo)), silent = TRUE
   )
-  if (class(grouping_variable_enquo_name) != "try-error") {
+  if (!is(grouping_variable_enquo_name, "try-error")) {
     # This only succeeds if the columns were passed unquoted
     # So now replace grouping_variable with a quoted version
     grouping_variable <- grouping_variable_enquo_name
@@ -428,7 +428,7 @@ estimate_mdiff_2x2_mixed <- function(
   overview$outcome_variable_name <- outcome_variable_name
 
   for (x in 1:length(estimate)) {
-    if (class(estimate[[x]]) == "esci_estimate") {
+    if (is(estimate[[x]], "esci_estimate")) {
       estimate[[x]]$overview <- overview
       estimate[[x]]$raw_data <- if (save_raw_data) raw_data else NULL
       estimate[[x]]$properties$data_type <- "data.frame"

R/estimate_mdiff_ind_contrast.R

@@ -196,12 +196,12 @@ estimate_mdiff_ind_contrast <- function(
     # Check grouping_variable -- if it is an unquoted column name
     #  turn it into a string and store back to grouping_variable
     is_column_name <- try(grouping_variable, silent = TRUE)
-    if(class(is_column_name) == "try-error") {
+    if(is(is_column_name, "try-error")) {
       grouping_variable_enquo <- rlang::enquo(grouping_variable)
       grouping_variable_enquo_name <- try(
         eval(rlang::as_name(grouping_variable_enquo)), silent = TRUE
       )
-      if (class(grouping_variable_enquo_name) != "try-error") {
+      if (!is(grouping_variable_enquo_name, "try-error")) {
         # This only succeeds if the columns were passed unquoted
         # So now replace grouping_variable with a quoted version
         grouping_variable <- grouping_variable_enquo_name
@@ -213,14 +213,14 @@ estimate_mdiff_ind_contrast <- function(
     # We check to see if we have a tidy column name by trying to evaluate it
     is_column_name <- try(outcome_variable, silent = TRUE)
 
-    if(class(is_column_name) == "try-error") {
+    if(is(is_column_name, "try-error")) {
       # Column names have been passed, check if need to be quoted up
 
       outcome_variable_enquo <- rlang::enquo(outcome_variable)
       outcome_variable_quoname <- try(
         eval(rlang::as_name(outcome_variable_enquo)), silent = TRUE
       )
-      if (class(outcome_variable_quoname) != "try-error") {
+      if (!is(outcome_variable_quoname, "try-error")) {
         # This only succeeds if outcome_variable was passed unquoted
         # Reset outcome_variable to be fully quoted
         outcome_variable <- outcome_variable_quoname
@@ -229,12 +229,12 @@ estimate_mdiff_ind_contrast <- function(
       # Ready to be analyzed as a list of string column names
       analysis_type <- "data.frame"
 
-    } else if (class(outcome_variable) == "numeric") {
+    } else if (is(outcome_variable, "numeric")) {
       # At this stage, we know that y was not a tidy column name,
       #  so it should be either a vector of raw data (class = numeric)
       #  or a vector of column names passed as strings
       analysis_type <- "vector"
-    } else if (class(outcome_variable) == "character") {
+    } else if (is(outcome_variable, "character")) {
       # Ok, must have been string column names
       if (length(outcome_variable) == 1) {
         analysis_type <- "data.frame"

R/estimate_mdiff_one.R

@@ -210,14 +210,14 @@ estimate_mdiff_one <- function(
     # We check to see if we have a tidy column name by trying to evaluate it
     is_column_name <- try(outcome_variable, silent = TRUE)
 
-    if(class(is_column_name) == "try-error") {
+    if(is(is_column_name, "try-error")) {
       # Column names have been passed, check if need to be quoted up
 
       outcome_variable_enquo <- rlang::enquo(outcome_variable)
       outcome_variable_quoname <- try(
         eval(rlang::as_name(outcome_variable_enquo)), silent = TRUE
       )
-      if (class(outcome_variable_quoname) != "try-error") {
+      if (!is(outcome_variable_quoname, "try-error")) {
         # This only succeeds if outcome_variable was passed unquoted
         # Reset outcome_variable to be fully quoted
         outcome_variable <- outcome_variable_quoname
@@ -227,12 +227,12 @@ estimate_mdiff_one <- function(
       # Ready to be analyzed as a list of string column names
       analysis_type <- "data.frame"
 
-    } else if (class(outcome_variable) == "numeric") {
+    } else if (is(outcome_variable, "numeric")) {
       # At this stage, we know that y was not a tidy column name,
       #  so it should be either a vector of raw data (class = numeric)
       #  or a vector of column names passed as strings
       analysis_type <- "vector"
-    } else if (class(outcome_variable) == "character") {
+    } else if (is(outcome_variable, "character")) {
       # Ok, must have been string column names
       if (length(outcome_variable) == 1) {
         if (outcome_variable_name == "My outcome variable") {

R/estimate_mdiff_paired.R

@@ -247,12 +247,12 @@ estimate_mdiff_paired <- function(
     # Check reference_measure -- if it is an unquoted column name
     #  turn it into a string and store back to grouping_variable
     is_column_name <- try(reference_measure, silent = TRUE)
-    if(class(is_column_name) == "try-error") {
+    if(is(is_column_name, "try-error")) {
       reference_measure_enquo <- rlang::enquo(reference_measure)
       reference_measure_enquo_name <- try(
         eval(rlang::as_name(reference_measure_enquo)), silent = TRUE
       )
-      if (class(reference_measure_enquo_name) != "try-error") {
+      if (!is(reference_measure_enquo_name, "try-error")) {
         # This only succeeds if the columns were passed unquoted
         # So now replace grouping_variable with a quoted version
         reference_measure <- reference_measure_enquo_name
@@ -263,26 +263,26 @@ estimate_mdiff_paired <- function(
     #   could be tidy column names, string column names, or vectors
     # We check to see if we have a tidy column name by trying to evaluate it
     is_column_name <- try(comparison_measure, silent = TRUE)
-    if(class(is_column_name) == "try-error") {
+    if(is(is_column_name, "try-error")) {
       # Column names have been passed, check if need to be quoted up
 
       comparison_measure_enquo <- rlang::enquo(comparison_measure)
       comparison_measure_quoname <- try(
         eval(rlang::as_name(comparison_measure_enquo)), silent = TRUE
       )
-      if (class(comparison_measure_quoname) != "try-error") {
+      if (!is(comparison_measure_quoname, "try-error")) {
         # This only succeeds if outcome_variable was passed unquoted
         # Reset outcome_variable to be fully quoted
         comparison_measure <- comparison_measure_quoname
       }
       analysis_type <- "data.frame"
 
-    } else if (class(comparison_measure) == "numeric") {
+    } else if (is(comparison_measure, "numeric")) {
       # At this stage, we know that y was not a tidy column name,
       #  so it should be either a vector of raw data (class = numeric)
       #  or a vector of column names passed as strings
       analysis_type <- "vector"
-    } else if (class(comparison_measure) == "character") {
+    } else if (is(comparison_measure, "character")) {
       # Ok, must have been string column names
       if (length(comparison_measure) == 1) {
         analysis_type <- "data.frame"

R/estimate_mdiff_two.R

@@ -263,13 +263,13 @@ estimate_mdiff_two <- function(
       is_char <- try(
         is.character(grouping_variable), silent = TRUE
       )
-      if (class(is_char) == "try-error") {
+      if (is(is_char, "try-error")) {
         # If not a character, must have been quoted
         grouping_variable_enquo <- rlang::enquo(grouping_variable)
         grouping_variable_quoname <- try(
           eval(rlang::as_name(grouping_variable_enquo)), silent = TRUE
         )
-        if (class(grouping_variable_quoname) != "try-error") {
+        if (!is(grouping_variable_quoname, "try-error")) {
           # This only succeeds if outcome_variable was passed unquoted
           # Reset outcome_variable to be fully quoted
           grouping_variable <- grouping_variable_quoname
@@ -283,13 +283,13 @@ estimate_mdiff_two <- function(
       is_char <- try(
         is.character(outcome_variable), silent = TRUE
       )
-      if (class(is_char) == "try-error") {
+      if (is(is_char, "try-error")) {
         # If not a character, must have been quoted
         outcome_variable_enquo <- rlang::enquo(outcome_variable)
         outcome_variable_quoname <- try(
           eval(rlang::as_name(outcome_variable_enquo)), silent = TRUE
         )
-        if (class(outcome_variable_quoname) != "try-error") {
+        if (!is(outcome_variable_quoname, "try-error")) {
           # This only succeeds if outcome_variable was passed unquoted
           # Reset outcome_variable to be fully quoted
           outcome_variable <- outcome_variable_quoname