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High-Performance Open-Source Archive

NEWS

inti4improve (In progress)

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 0.7.0

Include new function rticle() to render native .md from google docs to article
Update Tarpuy
- Include matrix for experiments
- CRediT – Contributor Role Taxonomy

inti 0.6.92

Improve scihub() project
- Include link for manuscript template
- Update ReadMe.qmd

inti 0.6.91

Improve templates for scihub() for works from bash
Update color pallet to Brewer

inti 0.6.9

Improve templates for scihub()
H2cal() was updated to include factors as formula
Fix error in gdocs2qmd

inti 0.6.8

Avoid label overlapping in the significance
Update pkgdown web page
Fix table export in gdocs2qmd()
Update ANOVA table for kable()
Exclude rmarkdown template ==> update to scihub research repository
- Include Addins: SciHub

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:
- Use “_” or “.” to separate the traits factors: yupana_reshape()
- 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

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