Type:	Package
Title:	Generate Machine- And Human-Readable Plot Labels for Experiments
Version:	0.2.0
Maintainer:	Alexander Wireko Kena <alex.kena24@gmail.com>
Description:	A no-frills open-source solution for designing plot labels affixed with QR codes. It features 'EasyQrlabelr', a 'BrAPI-compliant' 'shiny' app that simplifies the process of plot label design for non-R users. It builds on the methods described by Wu 'et al.' (2020) <doi:10.1111/2041-210X.13405>.
License:	GPL (≥ 3)
BugReports:	https://github.com/awkena/qrlabelr/issues
Encoding:	UTF-8
LazyData:	true
RoxygenNote:	7.2.3
Imports:	argonDash (≥ 0.2.0), argonR (≥ 0.2.0), assertthat (≥ 0.2.1), bslib (≥ 0.4.2), desplot (≥ 1.10), dplyr (≥ 1.0.10), ggplot2 (≥ 3.4.2), grid, purrr (≥ 1.0.1), QBMS (≥ 0.9.1), qrencoder (≥ 0.1.0), raster (≥ 3.6.23), reactable (≥ 0.4.3), readxl (≥ 1.4.1), shiny, shinycssloaders (≥ 1.0.0), shinyjs (≥ 2.1.0), shinyWidgets (≥ 0.7.6), tools, utils, uuid
Suggests:	covr, knitr, rlang (≥ 1.1.1), rmarkdown, shinytest2 (≥ 0.2.1), testthat (≥ 3.0.0), vdiffr (≥ 1.0.5)
VignetteBuilder:	knitr
Depends:	R (≥ 4.1.0), shinyBS (≥ 0.61.1)
Config/testthat/edition:	3
Language:	en-US
NeedsCompilation:	no
Packaged:	2023-12-20 18:28:13 UTC; awkena
Author:	Alexander Wireko Kena [aut, cre], Ebenezer Ogoe [aut], Clara Cruet Burgos [aut], Geoffrey Preston Morris [aut], Rubi Raymundo-Carhuapoma [aut], Yihan Wu [ctb], Robert Colautti [ctb], Colorado State University [cph], Kwame Nkrumah University of Science and Technology [cph], Feed The Future Innovation Lab for Crop Improvement [fnd], Project Artemis [fnd]
Repository:	CRAN
Date/Publication:	2023-12-20 18:40:02 UTC

Make an enhanced field layout plot with border rows.

Description

A helper function that adds border rows to the entire perimeter of a field laid out in a rectangular or square grid. Each experimental plot must have a coordinate that is specified by row and column numbers in the grid layout.

Usage

add_border(
  x,
  row_id = "ROW",
  col_id = "COLUMN",
  rep_id = "REP",
  trt_id = "TREATMENT",
  title = "Field layout",
  text_sz = 3,
  axis_title_sz = 12,
  xlab = "Column",
  ylab = "Row",
  border_bg = "grey80",
  text_col = "grey10"
)

Arguments

Value

A 'ggplot2' graphical object of field layout with border rows around the entire perimeter.

Note

This function works best with input field books generated with the 'FielDHub' package

Examples

# Plot a field layout with border rows
library(qrlabelr)

set.seed(123)

add_border(x = data.frame(LOCATION = rep("BAMBEY", 12), 
                         PLOT = c(1001:1012),
                         ROW = c(rep(1, 6), rep(2, 6)),
                         COLUMN = c(1:6, 1:6),
                         REP = rep(1, 12),
                         TREATMENT = sample(paste0("G-", 1:12))),
text_sz = 3)

Create custom machine- and human-readable rectangular plot labels

Description

Create print-ready customized plot labels affixed with QR codes given the page setup, label dimensions, the number of rows and columns of labels to print per page.

Usage

create_label(
  wdt = 2,
  hgt = 1,
  page_wdt = 8.5,
  page_hgt = 11,
  top_mar = 0.625,
  bot_mar = 0.625,
  left_mar = 0.625,
  right_mar = 0.625,
  numrow = 8L,
  numcol = 3L,
  filename = "PlotLabel",
  font_sz = 8,
  Treetag = FALSE,
  family = "sans",
  rounded = TRUE,
  print_across = TRUE,
  rect = TRUE,
  top_left_1 = NULL,
  top_left_2 = NULL,
  top_right_1 = NULL,
  top_right_2 = NULL,
  center_right_1 = NULL,
  center_right_2 = NULL,
  center_right_3 = NULL,
  bottom_left_1 = NULL,
  bottom_left_2 = NULL,
  unique_id = NULL,
  ec_level = 3,
  ...
)

Arguments

Value

A PDF file containing experimental plot labels affixed with QR codes, saved to the default or working directory.

See Also

field_label and gp_label

Examples

library(qrlabelr)
file <- tempfile()

if(file.exists(file)) 
# Create rectangular plot labels based on the Avery 94220 template-- the default template
create_label(
font_sz = 10,
filename = file, 
print_across = TRUE,
rect = TRUE,
top_left_1 = paste("Plot:", 101:105), 
top_left_2 = paste("Row:", c(rep(1, 3), rep(2, 2))), 
top_right_1 = paste("Rep:", rep(1, 5)), 
top_right_2 = paste("Col:", c(1:3, 1:2)), 
center_right_1 = paste("iBLOCK:", c(rep(1, 3), rep(2, 2))), 
center_right_2 = paste("Seed:", rep("OFF_NUR", 5)), 
center_right_3 = rep("AWk", 5), 
bottom_left_1 = paste("Loc:", rep("BAMBEY", 5)), 
bottom_left_2 = paste0("G-", 1:5),
unique_id = paste("KUMASI2023_PYT", c(101:105), 
                  c(rep(1, 3), rep(2, 2)), c(1:3, 1:2),
                  sep = "_"), 
ec_level = 1)

Create field plot labels embossed with QR codes

Description

Create machine- and human-readable plot labels that are well-suited for field experiments.

Usage

field_label(
  dat,
  get_unique_id = c("ruid", "uuid", "custom"),
  unique_id = NULL,
  filename = "PlotLabel",
  Year = NULL,
  rname = NULL,
  Trial = "PYT",
  seed_source = FALSE,
  IBlock = FALSE,
  rep_id = "REP",
  plot_id = "PLOT",
  row_id = "ROW",
  col_id = "COLUMN",
  loc_id = "LOCATION",
  entry_id = "TREATMENT",
  IBlock_id = "IBLOCK",
  seed_source_id = NULL,
  ...
)

Arguments

Details

The default column identifiers for LOCATION, PLOT, ROW, COLUMN/RANGE, REP, TREATMENT are based on the column IDs of a field book generated using the 'FielDHub' package. If user imports any field book generated with other programs, the user must specify the equivalent column identifiers used for LOCATION, PLOT, REP, ROW, COLUMN, and TREATMENT/ENTRY in the imported field book.

if get_unique_id = 'ruid' (i.e. Reproducible Unique IDs), the function concatenates location, year, trial name, plot, row and column IDs. if get_unique_id = 'uuid' (i.e. Universal Unique IDs), the function generates UUIDs by time randomly. Note that UUIDs are uninformative and not reproducible.

If input field book already has unique IDs for each plot, the get_unique_id argument should be set to 'custom'; and the unique_id argument must be specified as a string using the column name in the input field book that denotes plot unique IDs.

if Year is NULL, the function uses the current year as defined in the 'sys.time()'.

If the user is printing labels for any incomplete block design, the imported field book must include an IBLOCK column if the users wishes to display intra-blocking information for experimental plots on the label.

Set the IBlock argument to TRUE if the field layout has incomplete blocks within replications. The imported field book must include an IBLOCK column if the IBlock argument is set to TRUE.

Value

A PDF file containing field plot labels affixed with QR codes, and a data frame of an updated field book; all saved to the default or working directory.

See Also

create_label and gp_label

Examples

library(qrlabelr)
df <- data.frame(LOCATION = rep("BAMBEY", 5),
                PLOT = 1001:1005,
                ROW = c(rep(1, 3), rep(2, 2)),
                COLUMN = c(1:3, 1:2),
                REP = rep(1, 5),
                IBLOCK = c(rep(1, 3), rep(2, 2)),
                TREATMENT = paste0("G-", 1:5),
                SEED_SOURCE = rep("OFF_NUR", 5))
df$ids <- paste0(df$LOCATION,'2023', '_PYT', '_', df$PLOT, '_', df$ROW, '_',
                 df$COLUMN)
file <- tempfile()

if(file.exists(file)) 
field_label(
  dat = df,
  wdt = 5, 
  hgt = 2,
  page_wdt = 8.5, 
  page_hgt = 11,
  top_mar = 0.75, 
  bot_mar = 0.75, 
  left_mar = 1.75, 
  right_mar = 1.75, 
  numrow = 4L, 
  numcol = 1L, 
  filename = file, 
  font_sz = 20, 
  Trial = "PYT", 
  Year = 2023, 
  family = "sans", 
  rounded = TRUE, 
  IBlock = TRUE,
  get_unique_id = "ruid", 
  rname = "AW Kena", 
  seed_source = TRUE, 
  seed_source_id = "SEED_SOURCE",
  ec_level = 1)
 

Create a general-purpose (gp) label with text aligned in a landscape orientation.

Description

This is a wrapper that gives more flexibility to the user to design any general-purpose label affixed with QR codes. It gives nine(9) text positions in landscape orientation that can be filled with human-readable text items as specified by the user. Arguments are passed to the 'create_label()' function.

Usage

gp_label(
  dat,
  get_unique_id = c("uuid", "custom"),
  unique_id = NULL,
  filename = "PlotLabel",
  top_left_txt1 = NULL,
  top_left_txt2 = NULL,
  top_right_txt1 = NULL,
  top_right_txt2 = NULL,
  center_right_txt1 = NULL,
  center_right_txt2 = NULL,
  center_right_txt3 = NULL,
  bottom_left_txt1 = NULL,
  bottom_left_txt2 = NULL,
  top_left_id1 = NULL,
  top_left_id2 = NULL,
  top_right_id1 = NULL,
  top_right_id2 = NULL,
  center_right_id1 = NULL,
  center_right_id2 = NULL,
  center_right_id3 = NULL,
  bottom_left_id1 = NULL,
  bottom_left_id2 = NULL,
  ...
)

Arguments

Value

A PDF file containing plot labels affixed with QR codes, and a data frame of an updated field book; all saved to the default or working directory.

See Also

create_label and field_label

Examples

library(qrlabelr)
df <- data.frame(LOCATION = rep("BAMBEY", 5),
                 PLOT = 1001:1005,
                 ROW = c(rep(1, 3), rep(2, 2)),
                 COLUMN = c(1:3, 1:2),
                 REP = rep(1, 5),
                 IBLOCK = c(rep(1, 3), rep(2, 2)),
                 TREATMENT = paste0("G-", 1:5),
                 SEED_SOURCE = rep("OFF_NUR", 5))

df$ids <- paste0(df$LOCATION,'2023', '_PYT', '_', df$PLOT, '_', df$ROW, '_',
                 df$COLUMN)
file <- tempfile()

if(file.exists(file)) 
gp_label(dat = df,
         wdt = 5,
         hgt = 2,
         page_wdt = 8.5,
         page_hgt = 11,
         top_mar = 0.75,
         bot_mar = 0.75,
         left_mar = 1.75,
         right_mar = 1.75,
         numrow = 4L,
         numcol = 1L,
         filename = file,
         font_sz = 20,
         rname = "Adoma",
         get_unique_id = "custom",
         unique_id = 'ids',
         family = "sans",
         top_left_txt1 = 'Plot:',
         top_left_txt2 = 'Row:',
         top_right_txt1 = 'Rep:',
         top_right_txt2 = 'Col:',
         center_right_txt1 = 'iBlock:',
         center_right_txt2 = 'Seed:',
         center_right_txt3 = 'Adoma',
         top_left_id1 = 'PLOT',
         top_left_id2 = 'ROW',
         top_right_id1 = 'REP',
         top_right_id2 = 'COLUMN',
         center_right_id1 = 'IBLOCK',
         center_right_id2 = 'SEED_SOURCE',
         bottom_left_id1 = 'ids',
         bottom_left_id2 = 'TREATMENT',
         ec_level = 1)

Create a general-purpose (gp) label with text aligned in a portrait orientation.

Description

This is a standalone function that gives more flexibility to the user to design any general-purpose label affixed with QR codes. It gives 10 text positions in portrait orientation that can be filled with human-readable text items as specified by the user.

This function creates print-ready customized plot labels affixed with QR codes given the page setup, label dimensions, the number of rows and columns of labels to print per page.

Usage

gp_label_portrait(
  dat,
  wdt = 2,
  hgt = 1,
  page_wdt = 8.5,
  page_hgt = 11,
  top_mar = 0.625,
  bot_mar = 0.625,
  left_mar = 0.625,
  right_mar = 0.625,
  numrow = 8L,
  numcol = 3L,
  filename = "PlotLabel",
  font_sz = 8,
  family = "sans",
  rounded = TRUE,
  print_across = TRUE,
  rect = TRUE,
  bot_txt1 = NULL,
  bot_txt2 = NULL,
  bot_txt3 = NULL,
  cent_txt1 = NULL,
  cent_txt2 = NULL,
  cent_txt3 = NULL,
  cent_txt4 = NULL,
  top_txt1 = NULL,
  top_txt2 = NULL,
  top_txt3 = NULL,
  bot_txt1_id = NULL,
  bot_txt2_id = NULL,
  bot_txt3_id = NULL,
  cent_txt1_id = NULL,
  cent_txt2_id = NULL,
  cent_txt3_id = NULL,
  cent_txt4_id = NULL,
  top_txt1_id = NULL,
  top_txt2_id = NULL,
  top_txt3_id = NULL,
  unique_id = NULL,
  ec_level = 3
)

Arguments

Value

A PDF file containing labels affixed with QR codes, saved to the default or working directory.

See Also

field_label and gp_label

Examples

# Create a general-purpose label in a portrait text orientation based on the 
# 2 x 1 inch Avery 94220 template for laser-jet printers
library(qrlabelr)
df <- data.frame(LOCATION = rep("BAMBEY", 5),
                 PLOT = 1001:1005,
                 ROW = c(rep(1, 3), rep(2, 2)),
                 COLUMN = c(1:3, 1:2),
                 REP = rep(1, 5),
                 IBLOCK = c(rep(1, 3), rep(2, 2)),
                 TREATMENT = paste0("G-", 1:5),
                 SEED_SOURCE = rep("OFF_NUR", 5))

df$ids <- paste0(df$LOCATION,'2023', '_PYT', '_', df$PLOT, '_', df$ROW, '_',
                 df$COLUMN)
file <- tempfile()

if(file.exists(file)) 
gp_label_portrait(
dat = df,
wdt = 2,
hgt = 1,
page_wdt = 8.5,
page_hgt = 11,
top_mar = 0.625,
bot_mar = 0.625,
left_mar = 0.625,
right_mar = 0.625,
numrow = 8L,
numcol = 3L,
filename = file,
font_sz = 10,
family = 'sans',
rounded = TRUE,
print_across = TRUE,
rect = TRUE,
bot_txt1 = 'Rubi',
cent_txt2 = 'Rep:',
cent_txt3 = 'R:',
cent_txt4 = 'r:',
top_txt1 = 'P:',
top_txt2 = 'B:',
bot_txt2_id = 'ids',
bot_txt3_id = 'LOCATION',
cent_txt1_id = 'TREATMENT',
cent_txt2_id = 'REP',
cent_txt3_id = 'COLUMN',
cent_txt4_id = 'ROW',
top_txt1_id = 'PLOT',
top_txt2_id = 'IBLOCK',
top_txt3_id = 'SEED_SOURCE',
unique_id = 'ids',
ec_level = 1)

Make QR codes

Description

A helper function for QR code generation using the 'qrencoder' library for faster QR code generation. It converts the generated QR code into a raster grob image that can be plotted using the ‘grid.draw()' function in the ’grid' package.

Usage

make_qrcode(my_id, ec_level = 3)

Arguments

Value

A QR code as a raster grob image object that can be plotted with the 'grid.draw()' function in the 'grid' package.

Examples

library(qrlabelr)
qr <- make_qrcode("KUMASI2023_PYT_101_1_1", ec_level = 1)

# Plot QR code using the grid package
grid::pushViewport(grid::viewport(x = grid::unit(0.5, "npc"),
                                  y = grid::unit(0.5, "npc"),
                                  width = grid::unit(1, "in"),
                                  height = grid::unit(1, "in")))
grid::grid.draw(qr)
# clean up any open graphical device
# grDevices::graphics.off()

Generate Machine- And Human-Readable Plot Labels for Experiments.

Description

A no-frills open-source solution for designing experimental or trial plot labels affixed with QR codes. 'qrlabelr' is an R package that features 'EasyQrlabelr', a Shiny app that simplifies the complicated process of plot label design for non-R users. It also offers easily 'customizable' functions that enable plot label generation outside the Shiny app. It generates field plot labels that are compatible with the widely used digital data collection mobile app, Field Book. Our software builds on the foundation of an existing open-source program to offer more flexibility in plot label creation steps; guarantees true string fidelity after QR encoding; and provides faster label generation to users..

Available vignettes

This package comes with one vignette to get users up to speed as soon as possible. It provides a more thorough guide on how to use qrlabelr, from the data import stage to the generation of labels and saving it for printing. To access the vignette, run the command: browseVignettes("qrlabelr")

Author(s)

Alexander Kena | Ebenezer Ogoe

rcbd

Description

A sample field book generated with the 'FielDHub' package based on a Randomized Complete Block Design layout at two locations.

Usage

data(rcbd)

Format

A data frame with 144 observations and 7 variables:

SN

double contains observation serial numbers.

LOCATION

character contains information on plot location.

PLOT

double contains the plot number.

ROW

double contains the row number.

COLUMN

double contains the column number.

REP

double contains the replication number.

TREATMENT

character contains the treatment identifier.

Launch 'EasyQrlabelr'.

Description

An interface function to launch the 'EasyQrlabelr' 'shiny' app.

Usage

run_app()

Value

No return value, called for side effects. Opens the 'EasyQrlabelr' 'shiny' app in your default browser.

Examples

library(qrlabelr)
if(interactive())
qrlabelr::run_app()

Square Lattice

Description

A sample data set to create field plot and general_purpose labels.

Usage

data(square_lattice)

Format

A data frame with 216 observations and 11 variables:

SN

double contains observation serial numbers.

LOCATION

character contains information on plot location.

PLOT

double contains the plot number.

ROW

double contains the row number.

COLUMN

double contains the column number.

REP

double contains the replication number.

IBLOCK

double contains the incomplete block number.

UNIT

double contains the unit number.

ENTRY

double contains the entry number.

TREATMENT

character contains the treatment identifier.

SEED_SOURCE

character contains the seed source identifier.