Merge pull request #30 from ankemt/summary-20

Create a summary of statistics from the treatment ratio object

DESCRIPTION

@@ -12,13 +12,14 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.1
 Imports:
- brio,
- dplyr,
- magrittr,
- robustbase (>= 0.93-6),
- stringr,
- tidyr,
- tidyselect
+    brio,
+    dplyr,
+    magrittr,
+    robustbase (>= 0.93-6),
+    stats,
+    stringr,
+    tidyr,
+    tidyselect
 Suggests: 
     testthat (>= 3.1.5)
 Config/testthat/edition: 3

NAMESPACE

@@ -4,4 +4,5 @@ export(find_outliers)
 export(parse_MEA_file)
 export(parse_designfile)
 export(treatment_ratio)
+export(treatment_stats)
 import(magrittr)

R/treatment_stats.R

@@ -0,0 +1,16 @@
+#' Generate statistics for a treatment dataframe
+#'
+#' @param ratio_df resulting dataframe of the `treatment_ratio` function
+#'
+#' @return dataframe with summary statistics
+#' @export
+treatment_stats <- function(ratio_df){
+
+  df <- ratio_df |>
+    dplyr::group_by(Metric_type, Parameter, Group) |>
+    dplyr::summarize(n_wells = dplyr::n(),
+                     Ratio_avg = mean(Treatment_ratio, na.rm=T),
+                     Ratio_stdv = stats::sd(Treatment_ratio),
+                     Ratio_SEM = stats::sd(Treatment_ratio)/sqrt(n_wells))
+  return(df)
+}

tests/testthat/test-treatment_stats.R

@@ -0,0 +1,34 @@
+test_that("Summary is calculated correctly",{
+  load("output_treatment_ratio.Rda")
+
+  statsum <- treatment_stats(output_treatment_ratio)
+  expect_true("tbl_df" %in% class(statsum))
+  expect_equal(nrow(statsum), 288)
+
+  expected_cols <- c("Ratio_avg",
+                     "Ratio_stdv",
+                     "Ratio_SEM",
+                     "n_wells",
+                     "Group",
+                     "Metric_type",
+                     "Parameter")
+  for(cname in expected_cols){
+    expect_true(cname %in% names(statsum),
+                info=paste("Variable:",cname))
+  }
+
+  # there are 8 wells per group in the example data
+  expect_true(mean(statsum$n_wells) == 8)
+
+  # check some values
+  vals <- statsum[statsum$Parameter == "Mean Firing Rate (Hz)",]$Ratio_SEM
+  vals <- round(vals, digits = 8)
+  known_vals <- c(0.15674431,
+                  0.04957502,
+                  0.09320916,
+                  0.12364473,
+                  0.28510038,
+                  0.12974997)
+  expect_true(all(known_vals %in% vals))
+
+})