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updt web
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‎docs/pkgdown.yml‎

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pandoc: '3.4'
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pandoc: 3.6.3
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pkgdown: 2.1.3
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pkgdown_sha: ~
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articles:
@@ -9,7 +9,7 @@ articles:
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tarpuy: tarpuy.html
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extra/yupana-coding: extra/yupana-coding.html
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yupana: yupana.html
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last_built: 2025-06-23T02:30Z
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last_built: 2025-07-31T22:09Z
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urls:
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reference: https://inkaverse.com/reference
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article: https://inkaverse.com/articles

‎docs/setup.r‎

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# -------------------------------------------------------------------------
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# R packages dependencies and configuration -------------------------------
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# 📄 R packages dependencies and configuration ----------------------------
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# -------------------------------------------------------------------------
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#> author .: Flavio Lozano-Isla (linkedin.com/in/flozanoisla/)
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#> date .: 2025-05-16
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#> Author .: Flavio Lozano-Isla (linkedin.com/in/flozanoisla/)
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#> Date .: 2025-07-23
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# -------------------------------------------------------------------------
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#> source("https://inkaverse.com/setup.r")
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# Optional: external setup script
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# source("https://inkaverse.com/setup.r")
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# -------------------------------------------------------------------------
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# Packages ----------------------------------------------------------------
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# 📦 Package loading and installation -------------------------------------
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# -------------------------------------------------------------------------
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14-
cran <- c(
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"devtools" # Developer tools
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, "inti" # Tools and Statistical Procedures in Plant Science
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, "FactoMineR" # Multivariate data analysis
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, "psych" # Correlation plot
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, "lme4"
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, "car"
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, "emmeans"
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, "multcomp"
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, "huito" # label design
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, "grid" # Import images as R object
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, "googlesheets4" # Read/write google sheets docs
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, "googledrive" # Download/Upload files from googledrive
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, "knitr" # Write docs using R
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, "tidyverse" # Data manipulation
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)
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# git <- c("crsh/citr") # Use zotero for docs citations
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suppressPackageStartupMessages({
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for (pkg in cran) {
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if( !require(pkg, character.only = TRUE) ) {
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cran_packages <- c(
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"devtools", "tidyverse"
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, "lme4", "car", "emmeans", "multcomp"
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, "FactoMineR", "psych"
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, "inti", "huito"
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, "googlesheets4", "googledrive"
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, "knitr", "grid", "magick"
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, "RhpcBLASctl"
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, "sessioninfo"
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)
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load_or_install <- function(pkgs) {
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for (pkg in pkgs) {
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if (!requireNamespace(pkg, quietly = TRUE)) {
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install.packages(pkg)
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library(pkg, character.only = TRUE)
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}
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}
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suppressPackageStartupMessages(library(pkg, character.only = TRUE))
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}
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# for (pkg in git) {
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# if( !require(sub(".*/", "", pkg), character.only = T) ) {
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# devtools::install_github(pkg, upgrade = T)
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# library(sub(".*/", "", pkg), character.only = T)
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# }
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# }
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})
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remove(cran
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# , git
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, pkg)
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}
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load_or_install(cran_packages)
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# -------------------------------------------------------------------------
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# Knitr options -----------------------------------------------------------
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# ⚙️ System and computation configuration ----------------------------------
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# -------------------------------------------------------------------------
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knitr::opts_chunk$set(
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fig.align = "center" # Center images in the export file
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, out.width = "98%" # Figure width in html
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# , echo = FALSE # Avoid print code in the export file
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, message = FALSE # Avoid print messages in the export file
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, warning = FALSE # Avoid print warnings in the export file
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, collapse = TRUE # Collapse text output into source blocks
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fig.align = "center",
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out.width = "98%",
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message = FALSE,
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warning = FALSE,
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collapse = TRUE
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)
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# -------------------------------------------------------------------------
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# Compile options ---------------------------------------------------------
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# -------------------------------------------------------------------------
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options(
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OutDec= "." # Use "." instead of "," in the decimal values
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, scipen = 99 # Avoid use "6e-04"
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, knitr.kable.NA = "" # NA values will appear as empty cell
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, knitr.table.format = "pipe" # Format for export tables
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, citr.use_betterbiblatex = FALSE # For zotero addin
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)
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OutDec = ".", scipen = 99,
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knitr.kable.NA = "",
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knitr.table.format = "pipe",
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citr.use_betterbiblatex = FALSE
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)
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# CPU configuration
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total_cores <- parallel::detectCores(logical = TRUE)
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usable_cores <- max(1, floor(total_cores * 0.8))
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RhpcBLASctl::blas_set_num_threads(usable_cores)
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# -------------------------------------------------------------------------
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# Authorize googledrive & googlesheets ------------------------------------
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# 🔐 Google authentication ------------------------------------------------
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# -------------------------------------------------------------------------
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googlesheets4::gs4_auth(TRUE)
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googledrive::drive_auth(TRUE)
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# -------------------------------------------------------------------------
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# 📋 Environment info -----------------------------------------------------
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# -------------------------------------------------------------------------
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# Mostrar ruta del proyecto y número de núcleos
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cat("Project directory: ", getwd(), "\n")
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cat("CPU cores detected: ", total_cores, "\n")
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cat("CPU cores in use: ", usable_cores, "\n")
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77+
# Información de sesión
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sessioninfo::session_info() %>% print()
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80+
# -------------------------------------------------------------------------
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# 🧹 Clean up -------------------------------------------------------------
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# -------------------------------------------------------------------------
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rm(cran_packages, load_or_install, total_cores, usable_cores)

‎pkgdown/favicon/setup.r‎

Lines changed: 23 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -1,20 +1,26 @@
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# -------------------------------------------------------------------------
2-
# R packages dependencies and configuration -------------------------------
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# 📄 R packages dependencies and configuration ----------------------------
33
# -------------------------------------------------------------------------
4-
#> author .: Flavio Lozano-Isla (linkedin.com/in/flozanoisla/)
5-
#> date .: 2025-07-23
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#> Author .: Flavio Lozano-Isla (linkedin.com/in/flozanoisla/)
5+
#> Date .: 2025-07-23
66
# -------------------------------------------------------------------------
77

8-
#> source("https://inkaverse.com/setup.r")
8+
# Optional: external setup script
9+
# source("https://inkaverse.com/setup.r")
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1011
# -------------------------------------------------------------------------
1112
# 📦 Package loading and installation -------------------------------------
1213
# -------------------------------------------------------------------------
1314

1415
cran_packages <- c(
15-
"devtools", "inti", "FactoMineR", "psych", "lme4", "car", "emmeans",
16-
"multcomp", "huito", "grid", "googlesheets4", "googledrive",
17-
"knitr", "tidyverse", "RhpcBLASctl", "sessioninfo", "cli"
16+
"devtools", "tidyverse"
17+
, "lme4", "car", "emmeans", "multcomp"
18+
, "FactoMineR", "psych"
19+
, "inti", "huito"
20+
, "googlesheets4", "googledrive"
21+
, "knitr", "grid", "magick"
22+
, "RhpcBLASctl"
23+
, "sessioninfo"
1824
)
1925

2026
load_or_install <- function(pkgs) {
@@ -28,16 +34,6 @@ load_or_install <- function(pkgs) {
2834

2935
load_or_install(cran_packages)
3036

31-
# Optional GitHub packages
32-
# git_packages <- c("crsh/citr")
33-
# for (repo in git_packages) {
34-
# pkg <- sub(".*/", "", repo)
35-
# if (!requireNamespace(pkg, quietly = TRUE)) {
36-
# devtools::install_github(repo, upgrade = TRUE)
37-
# }
38-
# suppressPackageStartupMessages(library(pkg, character.only = TRUE))
39-
# }
40-
4137
# -------------------------------------------------------------------------
4238
# ⚙️ System and computation configuration ----------------------------------
4339
# -------------------------------------------------------------------------
@@ -57,30 +53,32 @@ options(
5753
citr.use_betterbiblatex = FALSE
5854
)
5955

56+
# CPU configuration
6057
total_cores <- parallel::detectCores(logical = TRUE)
6158
usable_cores <- max(1, floor(total_cores * 0.8))
6259
RhpcBLASctl::blas_set_num_threads(usable_cores)
6360

64-
cli::cli_alert_info("📁 Project directory: {getwd()}")
65-
cli::cli_alert_info("🧠 Total CPU cores detected: {total_cores}")
66-
cli::cli_alert_info("🚀 BLAS threads configured to: {RhpcBLASctl::blas_get_num_threads()}")
67-
6861
# -------------------------------------------------------------------------
6962
# 🔐 Google authentication ------------------------------------------------
7063
# -------------------------------------------------------------------------
7164

72-
googlesheets4::gs4_auth(cache = ".secrets", use_oob = TRUE)
73-
googledrive::drive_auth(cache = ".secrets", use_oob = TRUE)
65+
googlesheets4::gs4_auth(TRUE)
66+
googledrive::drive_auth(TRUE)
7467

7568
# -------------------------------------------------------------------------
7669
# 📋 Environment info -----------------------------------------------------
7770
# -------------------------------------------------------------------------
7871

79-
sessioninfo::session_info()
72+
# Mostrar ruta del proyecto y número de núcleos
73+
cat("Project directory: ", getwd(), "\n")
74+
cat("CPU cores detected: ", total_cores, "\n")
75+
cat("CPU cores in use: ", usable_cores, "\n")
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77+
# Información de sesión
78+
sessioninfo::session_info() %>% print()
8079

8180
# -------------------------------------------------------------------------
8281
# 🧹 Clean up -------------------------------------------------------------
8382
# -------------------------------------------------------------------------
8483

8584
rm(cran_packages, load_or_install, total_cores, usable_cores)
86-
# rm(git_packages) # if defined

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