materials

shannonpileggi · Oct 26, 2022 · 80d796f · 80d796f
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diff --git a/.gitignore b/.gitignore
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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
diff --git a/LICENSE.md b/LICENSE.md
diff --git a/README.html b/README.html
diff --git a/README.md b/README.md
@@ -1 +1,30 @@
-# debugging-nhsr
+# Debugging in R for NHS-R
+
+# When
+
+Thursday 3rd November 2022
+
+ * GMT +1 02:00 pm – 5:00 pm
+
+ * EDT    10:00 am – 1:00 pm
+
+# Where
+
+This workshop will take place online.
+
+# Pre-requisites
+
+Knowledge of how to write a function in R.
+
+# Learning objectives:
+
+* Review code troubleshooting tips.
+
+* Discuss debugging functions (traceback(), browser(), debug(), trace(), and recover()) and the additional benefits of employing some of these strategies within RStudio.
+
+* Distinguish between strategies for debugging your own code versus someone else’s code
+
+# Note
+
+This workshop is limited to NHS employees and those who work in UK public
+sector organisations such as PHE, local councils and DHSC.
diff --git a/debugging-nhsr.Rproj b/debugging-nhsr.Rproj
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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
diff --git a/demo/error-inspector-strsplit.R b/demo/error-inspector-strsplit.R
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+f <- function(x) { strsplit(x, ",") }
+g <- function(x) { f(x) }
+
+g(factor("a,b"))
+
+
diff --git a/demo/error_inspector.R b/demo/error_inspector.R
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+# IDE Error Inspector not triggered
+f <- function(x) x + 1
+g <- function(x) f(x)
+g("a")
+
+# IDE Error Inspector not triggered
+strsplit(factor("a,b"), ",")
+
+# IDE Error Inspector not triggered
+f <- function(x) strsplit(x, ",")
+f(factor("a,b"))
+
+# IDE Error Inspector yes triggered
+g <- function(x) f(x)
+g(factor("a,b"))
+
+
+
+options(error = recover)
diff --git a/demo/error_recover.R b/demo/error_recover.R
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+source("demo/my_functions.R")
+options(error = recover)
+g("a")
+options(error = NULL)
+
+
diff --git a/demo/my_functions.R b/demo/my_functions.R
@@ -0,0 +1,7 @@
+f <- function(x) {
+   x + 1
+}
+
+g <- function(x) f(x)
+
+
diff --git a/demo/trace-colSums.R b/demo/trace-colSums.R
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+
+colSums(1:3)
+
+
+
+trace(colSums, browser)
+colSums(1:3)
+# ls.str() in browser
+untrace(colSums)
+
+
+
+x <- as.list(body(colSums))
+View(x)
+
+# identify spot to insert code
+as.list(x[[3]][[1]])
+# equivalent notation
+as.list(x[[c(3, 1)]])
+
+# insert browser at step 3.1
+trace(colSums, browser, at = list(c(3, 1)))
+# execute function
+colSums(1:3)
+# ls.str() handy in browser
+# cancel tracing
+untrace(colSums)
+
+
diff --git a/demo/warning.R b/demo/warning.R
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+options(warn = 0) # default, warnings deferred to end
+options(warn = 1) # print warning when it happens
+options(warn = 2) # converts all warnings to errors, allows you to use regular debugging tools
diff --git a/img/IDE_break-in-code.PNG b/img/IDE_break-in-code.PNG
diff --git a/img/IDE_debug_menu.png b/img/IDE_debug_menu.png
diff --git a/img/IDE_debug_menu_crop.png b/img/IDE_debug_menu_crop.png
diff --git a/img/IDE_debug_on-error.png b/img/IDE_debug_on-error.png
diff --git a/img/IDE_error-inspector.PNG b/img/IDE_error-inspector.PNG
diff --git a/img/IDE_message-only.PNG b/img/IDE_message-only.PNG
diff --git a/img/break-in-code.png b/img/break-in-code.png
diff --git a/img/breakpoint.PNG b/img/breakpoint.PNG
diff --git a/img/butterflies.gif b/img/butterflies.gif
diff --git a/img/cheatsheet-debug-console.PNG b/img/cheatsheet-debug-console.PNG
diff --git a/img/cheatsheet-interactive-debugger.PNG b/img/cheatsheet-interactive-debugger.PNG
diff --git a/img/colSums-body.png b/img/colSums-body.png
diff --git a/img/colSums-list-investigate.PNG b/img/colSums-list-investigate.PNG
diff --git a/img/colSums-list.PNG b/img/colSums-list.PNG
diff --git a/img/console_break-in-code.PNG b/img/console_break-in-code.PNG
diff --git a/img/console_error-inspector.PNG b/img/console_error-inspector.PNG
diff --git a/img/console_message-only.PNG b/img/console_message-only.PNG
diff --git a/img/debug_on-error.PNG b/img/debug_on-error.PNG
diff --git a/img/debugging-overview.gif b/img/debugging-overview.gif
diff --git a/img/debugging.jpg b/img/debugging.jpg
diff --git a/img/debugging_ide.svg b/img/debugging_ide.svg
diff --git a/img/debugging_pick.svg b/img/debugging_pick.svg
diff --git a/img/debugging_special.svg b/img/debugging_special.svg
diff --git a/img/debugging_theirs.svg b/img/debugging_theirs.svg
diff --git a/img/debugging_tools.svg b/img/debugging_tools.svg
diff --git a/img/debugging_yours.svg b/img/debugging_yours.svg
diff --git a/img/df_patient_characteristics_str_hl.png b/img/df_patient_characteristics_str_hl.png
diff --git a/img/haystack.PNG b/img/haystack.PNG
diff --git a/img/interactive-debugger.PNG b/img/interactive-debugger.PNG
diff --git a/img/options-error-recover.PNG b/img/options-error-recover.PNG
diff --git a/img/package-structure.PNG b/img/package-structure.PNG
diff --git a/img/process-naked.jpg b/img/process-naked.jpg
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diff --git a/img/reprex-logo.png b/img/reprex-logo.png
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diff --git a/img/rlang_last-trace.PNG b/img/rlang_last-trace.PNG
diff --git a/img/rstudio-ide.pdf b/img/rstudio-ide.pdf
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diff --git a/img/swat-bugs.gif b/img/swat-bugs.gif
diff --git a/img/traceback-ordering.PNG b/img/traceback-ordering.PNG
diff --git a/img/traceback.PNG b/img/traceback.PNG
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