v1.0.4 release

.Rbuildignore

@@ -5,3 +5,5 @@
 ^data-raw$
 ^archive$
 ^\.git$
+^config$
+^scripts$

.gitignore

@@ -8,8 +8,5 @@ README.Rmd
 # Ignore data files
 /archive
 /data-raw
-<<<<<<< HEAD
 inst/doc
 inst/rmarkdown/templates/docx_letter
-=======
->>>>>>> 5f675318c758311140ae387150324351c1da0776

DESCRIPTION

@@ -1,44 +1,43 @@
 Package: biometrics
 Title: Report Templates for the Telethon Kids Institute
-Version: 1.0.3.999
+Version: 1.0.4
 Authors@R: c(person("Paul", "Stevenson",
     email = "Paul.Stevenson@telethonkids.org.au", role = c("aut", "cre")),
     person("Matthew", "Cooper",
     email = "Matt.Cooper@telethonkids.org.au", role = c("aut")))
-Date: 2019-02-08
+Date: 2019-05-21
 Description: A pair of templates have been created that incorporate styling
     themes present throughout the Telethon Kids Institute style guide, web page
-    and template documents. Currently, templates are available to produce
-    stand-alone HTML reports and ioslides presentations. These templates also
-    include colour palates that will automatically reproduce Telethon Kids style
-    in R graphics. A number of helper functions and data-sets are also available.
+    and template documents. Templates are available to produce stand-alone HTML
+    reports and ioslides presentations. These templates also include colour
+    palates that will automatically reproduce Telethon Kids style in R graphics.
+    A number of helper functions and data-sets are also available.
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Depends:
     R (>= 3.5.0)
 Imports:
-    data.table (>= 1.11.4),
-    ggplot2 (>= 3.0.0),
-    dplyr (>= 0.7.6),
-    tidyr (>= 0.8.1),
-    readr (>= 1.1.1),
+    ggplot2 (>= 3.1.0),
+    dplyr (>= 0.8.0.1),
+    tidyr (>= 0.8.2),
+    readr (>= 1.3.1),
     purrr (>= 0.2.5),
-    tibble (>= 1.4.2),
+    tibble (>= 2.0.1),
     stringr (>= 1.3.1),
     forcats (>= 0.3.0),
     lubridate (>= 1.7.4),
-    yaml (>= 2.1.18),
-    XML (>= 3.98-1.11),
-    knitr (>= 1.20),
-    kableExtra (>= 0.9.0),
+    yaml (>= 2.2.0),
+    XML (>= 3.98-1.16),
+    knitr (>= 1.21),
+    kableExtra (>= 1.0.0),
     GGally (>= 1.4.0),
-    broom (>= 0.5.0),
-    lme4 (>= 1.1-18-1),
+    broom (>= 0.5.1),
     repmis (>= 0.5),
     ProjectTemplate (>= 0.8.2),
-    igraph (>= 1.2.2)
+    igraph (>= 1.2.2),
+    jtools (>= 2.0.1)
 Suggests:
-    rmarkdown (>= 1.10)
+    rmarkdown (>= 1.11)
 VignetteBuilder: knitr
 RoxygenNote: 6.1.1

NAMESPACE

@@ -1,32 +1,36 @@
 # Generated by roxygen2: do not edit by hand
+
+export(abbreviator)
 export(format_model)
 export(group_interval)
 export(meansd)
 export(nPer)
+export(recoder)
 export(roll_up)
 export(round_df)
 export(scale_color_telethonkids)
 export(scale_fill_telethonkids)
-export(telethonkids_colours)
 export(telethonkids_cols)
 export(telethonkids_pal)
-export(telethonkids_palettes)
 export(variable_rollup)
 export(variables)
-import(data.table)
 import(dplyr)
 import(ggplot2)
 import(tibble)
-import(tidyr)
 importFrom(broom,tidy)
-importFrom(data.table,shift)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_at)
 importFrom(dplyr,select)
 importFrom(grDevices,colorRampPalette)
+importFrom(graphics,plot)
 importFrom(igraph,components)
 importFrom(igraph,graph_from_data_frame)
+importFrom(igraph,layout_with_fr)
+importFrom(lubridate,int_overlaps)
 importFrom(lubridate,interval)
-importFrom(magrittr,"%>%")
+importFrom(stats,sd)
 importFrom(tidyr,spread)
+importFrom(utils,View)
+importFrom(utils,read.delim)
+importFrom(utils,write.table)

NEWS.md

@@ -1,8 +1,19 @@
+# biometrics v1.0.4
+* Updated HTML report template to better align with current workflow
+  - created analysis plan
+  - added markdown hooks to template
+  - plotly works 'out of the box'
+  - added 'recoder' to the templates
+* Added format_model function
+* Added excel_ref package data
+* Moved telethonkids_colours and telethonkids_palletes in to package data
+* Documentation updates
+
 # biometrics v1.0.3
 * Changed the logic behind group_interval, which should now be more robust
 * Added abbreviator function that creates Bootstrap 4 tooltip with an abbreviation and its definition
 * Added recoder function that reads a text files and saves with UTF-8 encoding
-* Added round_df function that rounds dataframes to a specified number of decimal points
+* Added round_df function that rounds data frames to a specified number of decimal points
 * Some minor updates to html_report
 
 # biometrics v1.0.2

R/abbreviator.R

@@ -7,14 +7,13 @@
 #'
 #' @return a html anchor (i.e. <a ...>KEY</a>) defining a tooltip with the abbreviation's definition (defined in data.table column "def").
 #'
-#' @import data.table
-#'
 #' @examples
 #' \dontrun{
+#' library(data.table)
+#'
 #' abbrv <- data.table(abbrv = c("PGS"), def = c("Paul G Stevenson"), key = "abbrv")
 #'
 #' abbreviator("PGS", abbrv)
-#'
 #' }
 #'
 #' @export

R/data.R

@@ -1,19 +1,33 @@
-#' @title Excel column reference map
-#' @description A data table of alpha/numeric key/value pairs, where key is the
+#' Excel column reference map
+#'
+#' A data table of alpha/numeric key/value pairs, where key is the
 #' letter sequence of the excel column. Range of letter sequence is A - ZZZ.
-#' Usage: excel_ref["ABC"]$numbers that return the column number of that letter
-#' sequence.
+#'
+#' @docType data
+#'
+#' @usage data(excel_ref)
+#'
 #' @format A data table with 18278 rows and 2 columns:
 #' \describe{
 #'   \item{\code{letters}}{character Excel column reference letters}
 #'   \item{\code{numbers}}{integer corresponding column number}
 #' }
+#'
+#' @examples
+#' \donttest{
+#'   excel_ref["ABC"]$numbers
+#' }
 "excel_ref"
 
-#' @title ICD-10 hash table
-#' @description A data.table that maps ICD-10 classification code to the disease
-#'   name, disease category, parent category and disease group. Codes were
-#'   sourced from GNU Health (downloaded June-2018).
+#' ICD-10 hash table
+#'
+#' A data.table that maps ICD-10 classification code to the disease
+#' name, disease category, parent category and disease group. Codes were
+#' sourced from GNU Health (downloaded June-2018).
+#'
+#' @docType data
+#'
+#' @usage data(ICD10)
 #'
 #' @format A data frame with 6820 rows and 5 variables:
 #' \describe{
@@ -23,15 +37,21 @@
 #'   \item{\code{parent_category}}{character parent disease category}
 #'   \item{\code{disease_group}}{character Infections/notifiable}
 #'}
+#'
 #' @source \url{http://health.gnu.org/}
 "ICD10"
 
-#' @title ICD-10-AM hash table
-#' @description A data.table that maps ICD-10-AM classification code to the
-#'   disease name, disease category, parent category and disease group. ICD-10
-#'   codes were sourced from GNU Health (downloaded June 2018) and mappings to
-#'   ICD-10-AM were sourced from the Australian Consortium for Classification
-#'   Development (downloaded 8-June-2018).
+#' ICD-10-AM hash table
+#'
+#' A data.table that maps ICD-10-AM classification code to the
+#' disease name, disease category, parent category and disease group. ICD-10
+#' codes were sourced from GNU Health (downloaded June 2018) and mappings to
+#' ICD-10-AM were sourced from the Australian Consortium for Classification
+#' Development (downloaded 8-June-2018).
+#'
+#' @docType data
+#'
+#' @usage data(ICD10AM)
 #'
 #' @format A data frame with 10680 rows and 7 variables:
 #' \describe{
@@ -45,3 +65,31 @@
 #'}
 #' @source \url{https://www.accd.net.au/Downloads.aspx}
 "ICD10AM"
+
+#' Telethon Kids Institute colours
+#'
+#' Hex codes for the Telethon Kids colours per the 2014 Brand Style Guide.
+#'
+#' @docType data
+#'
+#' @usage data(telethonkids_colours)
+#'
+#' @format A named vector key = pantone matching system color, value = hex colour
+#'   code
+"telethonkids_colours"
+
+#' Telethon Kids Institute Palettes
+#'
+#' Telethon Kids colour palettes per the 2014 Brand Style Guide.
+#'
+#' @docType data
+#'
+#' @usage data(telethonkids_palettes)
+#'
+#' @format
+#' \describe{
+#'   \item{\code{light}}{Light Colour Tone Palette}
+#'   \item{\code{dark}}{Dark Colour Tone Palette}
+#'   \item{\code{grey}}{Typography Palette}
+#' }
+"telethonkids_palettes"

R/format_model.R

@@ -28,8 +28,8 @@ format_model <- function(x, effects = NULL, conf.level = 0.95, dp = 2) {
   a <- broom::tidy(x, effects = effects, conf.int = T, conf.level = conf.level)
   b <- a %>%
     round_df(dp) %>%
-    dplyr::mutate(text1 = paste0(estimate, " (", 100 * conf.level, "% CI: ", conf.low, " to ", conf.high, ")"),
-                  text2 = paste0("(", estimate, "; , ", 100 * conf.level, "% CI: ", conf.low, " to ", conf.high, ")")) %>%
-    dplyr::select(term, text1, text2)
+    dplyr::mutate(text1 = paste0(.data$estimate, " (", 100 * .data$conf.level, "% CI: ", .data$conf.low, " to ", .data$conf.high, ")"),
+                  text2 = paste0("(", .data$estimate, "; , ", 100 * .data$conf.level, "% CI: ", .data$conf.low, " to ", .data$conf.high, ")")) %>%
+    dplyr::select(.data$term, .data$text1, .data$text2)
   dplyr::left_join(a, b, by = "term")
 }

R/group_interval.R

@@ -13,9 +13,11 @@
 #' @return an integer vector of group numbers
 #'
 #' @import dplyr
-#' @importFrom igraph components graph_from_data_frame
-#' @importFrom lubridate interval
+#' @importFrom igraph components graph_from_data_frame layout_with_fr
+#' @importFrom lubridate interval int_overlaps
 #' @importFrom tidyr spread
+#' @importFrom utils View
+#' @importFrom graphics plot
 #'
 #' @examples
 #'
@@ -45,12 +47,12 @@ group_interval <- function(dat, buffer, start, end, .view_mat = F, .view_graph =
 
   dat <- dat %>%
     mutate(rid = 1:nrow(dat),# add in row id
-           intervals = interval(interval_lower, interval_upper)) # define admissions as intervals incorporating buffer
+           intervals = interval(.data$interval_lower, .data$interval_upper)) # define admissions as intervals incorporating buffer
 
   df_overlap <- bind_cols(
     expand.grid(dat$rid, dat$rid), # make a 2 col table with every combination of id numbers
     expand.grid(dat$intervals, dat$intervals)) %>% # make a combination of every interval
-    mutate(overlap = int_overlaps(Var11, Var21)) %>% # determine if intervals overlap
+    mutate(overlap = int_overlaps(.data$Var11, .data$Var21)) %>% # determine if intervals overlap
     rename("row" = "Var1", "col" = "Var2")
 
   # Find groups via graph theory See igraph package
@@ -59,15 +61,15 @@ group_interval <- function(dat, buffer, start, end, .view_mat = F, .view_graph =
 
   # create a 2 column df with row (index) and group number, arrange on row number and return distinct values
   df_groups <- data_frame(row = as.integer(names(groups)), group = groups) %>%
-    arrange(row) %>%
+    arrange(.data$row) %>%
     distinct()
 
   # View df
   if (.view_mat) {
     df_view <- df_overlap %>%
-      select(row, col, overlap) %>%
-      spread(key = col, value = overlap) %>% # turn into a n x n data_frame
-      select(-row)
+      select(.data$row, .data$col, .data$overlap) %>%
+      spread(key = .data$col, value = .data$overlap) %>% # turn into a n x n data_frame
+      select(-.data$row)
     df_view[lower.tri(df_view, diag = F)] <- F # set lower triangle to FALSE (keep diagonals as TRUE)
     apply(df_view, 2, function(x) ifelse(!x, NA, x)) %>% # change FALSE to NA
       View()

R/meansd.R

@@ -1,7 +1,25 @@
+#' meansd
+#'
+#' Return the mean and sd of a vector
+#'
+#' @param x a numeric vector
+#' @param dpp (default 2) the number of decimal points to return the mean
+#' @param dps (default 2) the number of decimal points to return the standard deviation
+#'
+#' @return A string the form of "mean (sd)" at the specified precision
+#'
+#' @importFrom stats sd
+#'
+#' @examples
+#' \dontrun{
+#'   data(mtcars)
+#'
+#'   meansd(mtcars$cyl)
+#' }
+#'
 #' @export
-
 meansd <- function(x, dpp=2, dps=2){
-  if(any(class(x)!="numeric" | class(x)!="interger")) {} else{print("Check you format")}
+  if(any(class(x)!="numeric" | class(x)!="interger")) {} else{print("Check your format")}
   x <- as.numeric(x)
   paste0(sprintf(paste0("%.",dpp,"f"), mean(x, na.rm=T)),
          " (",

R/nPer.R

@@ -1,4 +1,17 @@
-#' @title printing N and percentage
+#' nPer
+#'
+#' Printing N and percentage
+#'
+#' @param vec numeric vector
+#' @param intGroup xxxx
+#' @param dp (default 1)
+#'
+#' @return xxxx
+#'
+#' @examples
+#' \dontrun{
+#'   nPer(xxx)
+#' }
 #'
 #' @export
 

R/recoder.R

@@ -2,12 +2,11 @@
 #'
 #' @param x path to the file
 #'
-#' @examples
+#' @importFrom utils read.delim write.table
 #'
+#' @examples
 #' \dontrun{
-#'
 #' recoder("packages.bib")
-#'
 #' }
 #'
 #' @export

R/roll_up.R

@@ -10,7 +10,6 @@
 #'
 #' @return A data frame is returned with a id variable (matching the first column of the input data frame) and columns for values.
 #'
-#' @importFrom magrittr %>%
 #' @import dplyr
 #'
 #' @examples