NEWS.md

In Flavjack/inti: Tools and Statistical Procedures in Plant Science

inti4improve

• Improve PCA supplementary variables
• Select the dimension in PCA
• Sub module for PCA with variable contribution and dimension correlation
• Include lattice
• Include LCD
• Dashboard for Tarpuy experiment progress

inti 0.6.8 (In progress)

• Avoid label overlapping in the significance
• Update pkgdown web page

inti 0.6.7

• Rticles
• Fix table conversion when only is present one table
• Yupana
• Avoid different bar widths
• New project template info
• Increase y limits for better error visualization
• Re arrange statistic information
• Repare agricolae table summary anova
• Tarpuy
• Update budget template
• Update experimental plan information

inti 0.6.6

• Package
• New function related outliers_remove() => "remove_outliers" to work with formula

• New function related plot_diag() => "plot_diagnostic" to work with formula

• Rticles

• Fix Tables and Figures order in final document

• Tarpuy

• Change name of the trait tab from abbreviation to trait
• Update traits tab for include two formats: date and mcategorical
• Fix sort of the traits in field book app
• New option for generate the qr-code for each plot

inti 0.6.5

• Package

• Include Addins for Google authentication and renew process

• Rticles

• Fix title position in article
• Fix figure caption and cross reference

inti 0.6.4

• Update bootstrap in apps
• Tarpuy:
• Alows to exclude or delete {when} or {sample} colums
• Allow defaultValue for traits
• Rticles
• Include images using markdown syntax ![]()

=> Fix if "defaultvalue" is in the trait table

inti 0.6.3

• gdocs2qmd()
• change params: template ==> theme
• reference-doc: style_rticle.docx
• Tarpuy
• Field book design allows different number of rows
• Design without replication (observation plots) ==> design_noreps()
• Fix traits name order

inti 0.6.2

• gdocs2qmd()
• Bug with: "Unknown element type at this position: UNSUPPORTED"
• The function works for articles and thesis
• Include the cover page using a table
• Include R markdown templates from RStudio
• Rticles vignettes updated

inti 0.6.1

• Tarpuy:
• Include google sheet and docs in PLEX
• Allow empty rows and without filling
• Drop values in sheet traits with "X"
• Only generate traits sheets

• Seed is set by default

• Deprecated:

• include_figure()

• New function

• include_pdf()

• gdocs2qmd()

• Word document with different output structure

inti 0.6.0

• Fix for dev dplyr (Thanks @hadley)
• tarpuy_plotdesign()
• Autoconvert as factor for plot design
• Default names in plot to "row" and "columns"
• New function: design_repblock for "rcbd", "crd" for any factor number
• Yupana create by default the sheet locale = "en_US" to use the decimal point
• yupana_mvr allow to select specific numeric variables
• tarpuy_varlist adapted to field book app
• Tarpuy: new module for use the information in Field Book app https://play.google.com/store/apps/details?id=com.fieldbook.tracker
• Rename function: tarpuy_varlist ==> tarpuy_traits

inti 0.5.8

• gdocs2qmd(format) allow transform to quarto or Rmarkdown format

• Update RStudio download link to posit

• Yupana - fieldbook module:

• [X] Use "_" or "." to separate the traits factors: yupana_reshape()
• [X] Load and Save in a specific sheet

inti 0.5.7

• Update functions bookdown to quarto:
• figure2rmd() ==> figure2qmd()
• table2rmd() ==> table2qmd()
• gdocs2rmd() ==> gdocs2qmd()
• Fix plot_raw(): "length(x) = 2 > 1' in coercion to 'logical(1)"
• Update jc_tombola()
• outliers_remove(drop.na = FALSE) avoid drop NA values by default
• H2cal() outliers are changed to NA in the data.frame
• yupana_mvr(): update function for correlation and PCA
• Yupana: update multivariate analysis

inti 0.5.6

• Package: web_table()
• autoWidth = TRUE
• columnwidth argument
• width argument
• Fix plot_smr(): "length(x) = 2 > 1' in coercion to 'logical(1)"
• New function: split_folder()
• Yupana: add scale and method in correlation plot

inti 0.5.5

• Yupana: update yupana_import() using if_any() instead across()
• Tarpuy: in dsg the column qr ==> barcode
• Tarpuy: update sheets names in intro section
• Tarypu: export field-book in specific sheet
• Tarpuy: select sheet for field-book sketch
• Tarpuy: create field-book only with the factor list
• Tarpuy: column with [] in design are omitted in the field-book generation
• CRAN comments: if (class(model) == "lmerMod") => if ( is(model, "lmerMod")

inti 0.5.4

• outliers_remove(): change cbind() by cbind.data.frame().
• Fix apps auth.
• Thanks to Uwe Ligges to allow consecutive CRAN updates.

inti 0.5.3

• Complete location name in experimental information.
• Avoid labels in axis and legend using "".
• Update vignettes using bookdown.
• Fix table summary in H2cal().
• Update diagnostic plot in plot_diag() to lm and lmerMod.
• Update code for logIn modules in apps.
• Update correlation graph in yupana.

inti 0.5.2

• Package
• Fix CRAN comments
• Fix path to install Tarpuy dependencies
• Include huito logo in apps
• Fix factors in Tarpuy field-book export
• Update code from tarpuy_design()
• Update barcode column for split using "_"
• Update function tarpuy_plex()

inti 0.5.1

• Package
• H2cal(): BLUEs from H2cal may be wrong if other fixed effects in the model (#10).
  • Thanks Jim Holland (@ncsumaize) for the suggestion to improve the function.
• New functions: gdoc2rmd(), table2rmd(), figure2rmd()
  • Use Articul8 Add-ons from Google docs to build Rticles
• Update pkgdown

inti 0.5.0

Changes are incompatible with the old versions.

• Package
• yupana_export_smr ==> yupana_export()
  • Extract all the information from yupana_analysis
• yupana_import_smr ==> yupana_import()
  • Import information from the web and yupana_analysis

• Update function H2cal()

• Yupana

• Include statistics and anova table in export results
• Clean headers in export data, exclude "{}"

• Update load/save interface

• Tarpuy

• Variable list only include arguments with {}
  • You can exclude: {evaluation} or {sampling}

inti 0.4.4

• Package
• jc_tombola()
  • Update function and selection paper by meeting
• yupana_analysis()
  • Include last_factor selection
• yupana_mvr()
  • Function not need last_factor
• Include package version in the apps

• Fixed navigation bar in the apps

• Yupana

• PCA for individual in the bottom
• Include version in the output table
• Dimension for plots in multivariate analysis

inti 0.4.3

• Yupana
• Show equation with adjusted R in scatter plot graph
• sig include all the variables from the summary table
• In plots if the number of reps is 1 the sig and error is "none"

inti 0.4.2

• Package
• Include info plot_smr() and plot_raw
• plot_smr()
  • Delete legend border
• Transparent logos background
• New vignette for coding with yupana
• Update Rticles and Books template
• Fix web_table() to export in xlsx
• plot_raw() with scientific notation in labels

• Include new data set potato

• Yupana

• Legend position load correct
• Headers with [] are excluded in the analysis

Agradecimiento a Pedro Barriga por sus sugerencias para mejorar yupana()

inti 0.4.1

• Package
• plot_smr()
  • Add significance font size
• plot_raw()
  • Allows vector with colors for plots
  • Include "scatter plot"
• H2cal() include trial option for MET

• New video for the version > 0.4.1

• Yupana

• Add equations in regressions plot
• Include scatter plot in "Exploratory" module

inti 0.4.0

Changes incompatible with the old versions.

Major changes

• Rticles
• Deprecated: create_rticles() & rticles()
• Deprecated shiny app: rticles
• Now you can create your docs using Rmarkdown templates
  • Rticles
  • Books

• Vignette for explain the dependencies to use rticles

• Yupana

• Styled messages
• New module: Exploratory
• Update in the modules
  • No need fbsm
  • Reactivity in the analysis
• Export model information
• Overwrite graph info
• Design with 3 factor use facet_grid()
• Allow import/export information for plots

• Reduce font size in the significance

• Tarpuy

• Styled messages
• Vignette for explain the modules in the app

• Overwrite fieldbook info

• Package

• New function: plot_raw()
  • Box plot graph
• Update function: fieldbook_mvr --> yupana_mvr()
  • Can be used independently
• symbols to internal data
  • Table to create footnotes
• rename functions
• Include new logo
• Vignettes: comparison between H2cal() and asreml
• Add data base for MET
• Logo for the package and apps

Agradecimiento a Khaterine por la idea en el diseño de los logos

inti 0.3.0

• Yupana
• Fix {arguments} from xlimits to ylimits

• Update tables style

• Rticles

• Update template files

• Package

• Vignette for describe the arguments and options in Yupana
• Delete redundant functions info_figure() & info_grahics()
• Update functions: include_figure() & include_figure()
• Update function plot_smr() include:
  • xtext: labels for the x level
  • gtext: labels for the group levels

inti 0.2.0

Changes incompatible with the old versions.

Major changes

• Package

• Arguments changed in the syntax for fbsm and graphics.

• Yupana

• Delete error messages in console when run the app
• Change dependency: ggpubr --> cowplot
• Multivariate analysis need factor levels n>2

• Allows copy the Statistics table

• Yupana

• Delete error messages in console when run the app

• fix dates in experiments

• Rticles

• update code for unzip Articul8 files

• Package

• ´mean_comparison´ update
  • No remove the treatments column
  • Allows plot 3 factors comparison facet_grid()
  • New arguments for plot: xlimits, xrotation, dimension, opt
  • Delete redundant arguments; limits, brakes
  • Suggest use "*" instead of ":"
  • Include additional layers to the plot. e.g. coord_flip()
  • Save plot dimensions in the exported sheet
• web_table fix resize table in web

Bug fixes

• Yupana & Tarpuy

• add pkgs.R file to load dependencies in apps

• Tarpuy

• fix auto-install packages in inti::tarpuy(T)

inti 0.1.3

Major changes

• Rticles
• update bootstrap

• include code section

• Yupana & Tarpuy

• google auth verification

• Tarpuy

• Include QR code in fieldbook

• Apps

• bslib dependence install from CRAN
• Include video for local installation
• Suppress messages when load apps

inti 0.1.2

Major changes

• Package
• Exclude package multtest from the depends
• CRAN error: include_table
• Search engine in the web page

inti 0.1.1

Major changes

• Yupana & Tarpuy
• now apps work locally
• update bootstrap

• update packages dependencies for apps

• Yupana

• Graphs: button for generate and refresh graphs
• Fieldbook: plot_label in fieldbook summary for label axis in plots
• Analysis: export analysis with sheet name

• Analysis: round digits in export table

• Package

• new functions: info_figure() & info_table()
• update pkgdown documentation

Bug fixes

• Yupana & Tarpuy

• fix problem with 'cloud.json'

• Yupana

• Multivariate: exclude variables without variation in PCA
• Multivariate: exclude columns with all NA values
• Graphs: app not stop if graph arguments are wrong

• update from observeEvent() --> reactive()

• rticles

• update app with the new bookdown release

inti 0.1.0

• First package release

Flavjack/inti documentation built on April 12, 2025, 5:56 p.m.