improved defaults

scripts/common-functions.R

@@ -1,20 +1,28 @@
-# Functions loaded by EVERY script in the project
+# Functions and settings loaded by EVERY script in the project
 
 library(ggplot2)
+baseSize <- 10
+
+print_all <- function(d){ print(d,n=nrow(d) )}
+
 ggplot2::theme_set(
   ggplot2::theme_bw(
   )+
     theme(
       strip.background = element_rect(fill="grey95", color = NA)
+      ,panel.grid = element_line(color = "grey95")
+      ,panel.border = element_rect(color = "grey80")
       ,axis.ticks = element_blank()
+      ,text=element_text(size=baseSize)
     )
 )
+
 quick_save <- function(g,name,...){
   ggplot2::ggsave(
     filename = paste0(name,".jpg"),
     plot     = g,
     device   = "jpg",
-    path     = prints_folder,
+    path     = prints_folder, # expects this definition in `define-globals` chunk
     # width    = width,
     # height   = height,
     # units = "cm",
@@ -62,9 +70,9 @@ neat_DT <- function(x, filter_="top",...){
   return(xt)
 }
 
-dt <- neat_DT
+dt <- neat_DT # an alternative alias
 
-# print names and associated lables of variables (if attr(.,"label)) is present
+# print names and associated labels of variables (if attr(.,"label)) is present
 names_labels <- function(ds){
   dd <- as.data.frame(ds)
 
@@ -81,4 +89,4 @@ names_labels <- function(ds){
   return(nl)
 }
 # names_labels(ds=oneFile)
-print_all <- function(x){print(x,n=nrow(x))}
+

scripts/templates/report-combined.Rmd

@@ -55,17 +55,18 @@ ggplot2::theme_set(ggplot2::theme_bw()) # common theme for all graphs
 # -- 1.Attach these packages so their functions don't need to be qualified: http://r-pkgs.had.co.nz/namespace.html#search-path
 library(ggplot2)   # graphs
 library(forcats)   # factors
-library(stringr)   # strings
+library(stringr)   # strings, but consider `stringi` as more general
 library(lubridate) # dates
+library(labelled)  # labels
 # -- 2.Import only certain functions of a package into the search path.
 import::from("magrittr", "%>%")
 # -- 3. Verify these packages are available on the machine, but their functions need to be qualified: http://r-pkgs.had.co.nz/namespace.html#search-path
 requireNamespace("readr"    )# data import/export
 requireNamespace("readxl"   )# data import/export
 requireNamespace("tidyr"    )# tidy data
 requireNamespace("janitor"  )# tidy data
-requireNamespace("dplyr"    )# Avoid attaching dplyr, b/c its function names conflict with a lot of packages (esp base, stats, and plyr).
-requireNamespace("testit"   )# For asserting conditions meet expected patterns.
+requireNamespace("testit"   )# for asserting conditions meet expected patterns.
+requireNamespace("scales"   )# formatting
 ```
 
 <!-- Load the sources.  Suppress the output when loading sources. --> 

scripts/templates/report-isolated.R

@@ -10,7 +10,7 @@ cat("Working directory: ", getwd()) # Must be set to Project Directory
 # -- 1.Attach these packages so their functions don't need to be qualified: http://r-pkgs.had.co.nz/namespace.html#search-path
 library(ggplot2)   # graphs
 library(forcats)   # factors
-library(stringr)   # strings
+library(stringr)   # strings, but consider `stringi` as more general
 library(lubridate) # dates
 library(labelled)  # labels
 # -- 2.Import only certain functions of a package into the search path.
@@ -20,22 +20,19 @@ requireNamespace("readr"    )# data import/export
 requireNamespace("readxl"   )# data import/export
 requireNamespace("tidyr"    )# tidy data
 requireNamespace("janitor"  )# tidy data
-requireNamespace("dplyr"    )# Avoid attaching dplyr, b/c its function names conflict with a lot of packages (esp base, stats, and plyr).
-requireNamespace("testit"   )# For asserting conditions meet expected patterns.
+requireNamespace("testit"   )# for asserting conditions meet expected patterns.
+requireNamespace("scales"   )# formatting
 
 # ---- load-sources ------------------------------------------------------------
 base::source("./scripts/common-functions.R") # project-level
 
 # ---- declare-globals ---------------------------------------------------------
-# printed figures will go here:
-# prints_folder <- paste0("./analysis/.../prints/")
-# if(!file.exists(prints_folder)){dir.create(file.path(prints_folder))}
+# printed figures will go here when `quick_save("name",w=8,h=6)` is used:
+prints_folder <- paste0("./analysis/.../prints/")
+if (!fs::dir_exists(prints_folder)) { fs::dir_create(prints_folder) }
 
 path_data_input <- "./data-private/derived/..."
 # ---- declare-functions -------------------------------------------------------
-# printed figures will go here:
-prints_folder <- paste0("./analysis/.../prints/")
-if(!file.exists(prints_folder)){dir.create(file.path(prints_folder))}
 
 # ---- load-data ---------------------------------------------------------------
 ds0 <- readr::read_rds(path_data_input)
@@ -57,7 +54,7 @@ ds0 <- readr::read_rds(path_data_input)
 # ---- save-to-disk ------------------------------------------------------------
 
 # ---- publish ------------------------------------------------------------
-path <- "./analysis/.../report-isolated.Rmd"
+path <- "./analysis/.../report-isolated.Rmd" # connect with Rmd for publishing
 rmarkdown::render(
   input = path ,
   output_format=c(