Last updated: 2023-11-30
Checks: 7 0
Knit directory: HenriqueDGen/
This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20211012) was run prior to running
the code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 4ade56b. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish or
wflow_git_commit). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .DS_Store
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: data/.DS_Store
Ignored: output/.DS_Store
Ignored: output/Figures/.DS_Store
Untracked files:
Untracked: analysis/IndSel.Rmd
Untracked: output/BLUPsSel.csv
Untracked: output/Correlogram.tiff
Unstaged changes:
Modified: analysis/Den_IndSH.Rmd
Modified: analysis/PCA_DAPC.Rmd
Modified: analysis/_site.yml
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were
made to the R Markdown (analysis/index.Rmd) and HTML
(docs/index.html) files. If you’ve configured a remote Git
repository (see ?wflow_git_remote), click on the hyperlinks
in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | fef5cf2 | LucianoRogerio | 2023-07-26 | Adicao Dados 2022 |
| html | fef5cf2 | LucianoRogerio | 2023-07-26 | Adicao Dados 2022 |
| Rmd | e020351 | LucianoRogerio | 2022-03-29 | Update Henrique Analysis |
| html | e020351 | LucianoRogerio | 2022-03-29 | Update Henrique Analysis |
| Rmd | 350ad46 | LucianoRogerio | 2022-03-23 | Names updates from Data files |
| html | 350ad46 | LucianoRogerio | 2022-03-23 | Names updates from Data files |
| Rmd | 3b2edda | HenriqueBernardino | 2022-03-16 | Dados Produtivos Corrigidos |
| Rmd | 90b66eb | LucianoRogerio | 2022-03-08 | Update analysis Mixed models Henrique |
| html | 90b66eb | LucianoRogerio | 2022-03-08 | Update analysis Mixed models Henrique |
| Rmd | 224eb2d | LucianoRogerio | 2022-03-01 | Atividades Henrique 1 de março |
| html | 224eb2d | LucianoRogerio | 2022-03-01 | Atividades Henrique 1 de março |
| Rmd | 89ac868 | HenriqueBernardino | 2022-01-29 | Análise de Correlações |
| Rmd | 6e4c5ee | HenriqueBernardino | 2022-01-26 | Prepação arquivos para o modelos mistos |
| html | 6e4c5ee | HenriqueBernardino | 2022-01-26 | Prepação arquivos para o modelos mistos |
| Rmd | 119cc22 | LucianoRogerio | 2022-01-18 | Atividades Henrique 18 Janeiro |
| html | 119cc22 | LucianoRogerio | 2022-01-18 | Atividades Henrique 18 Janeiro |
| Rmd | 8fec827 | LucianoRogerio | 2021-12-07 | fix the introduction section |
| html | 8fec827 | LucianoRogerio | 2021-12-07 | fix the introduction section |
| Rmd | d124c30 | LucianoRogerio | 2021-12-07 | Update of the webpage to english writting |
| html | d124c30 | LucianoRogerio | 2021-12-07 | Update of the webpage to english writting |
| Rmd | f272038 | LucianoRogerio | 2021-12-07 | Update of the analysis and website layout |
| html | f272038 | LucianoRogerio | 2021-12-07 | Update of the analysis and website layout |
| Rmd | e535227 | LucianoRogerio | 2021-11-24 | Update Layout Website |
| html | e535227 | LucianoRogerio | 2021-11-24 | Update Layout Website |
| html | 62922ff | LucianoRogerio | 2021-11-18 | Build site. |
| Rmd | f51cdc6 | LucianoRogerio | 2021-11-18 | Add the Dendrogram analysis |
| Rmd | 97d638d | LucianoRogerio | 2021-11-02 | Update of html links |
| html | 97d638d | LucianoRogerio | 2021-11-02 | Update of html links |
| html | b9ef481 | LucianoRogerio | 2021-11-02 | Build site and add new Data |
| Rmd | 7286357 | LucianoRogerio | 2021-11-02 | Insercao do caractere Area de Antracnose e PCA |
| html | 4842664 | LucianoRogerio | 2021-10-19 | Build site. |
| Rmd | 3dbea3e | LucianoRogerio | 2021-10-19 | Fix link to MixedModels page |
| html | 39d114b | LucianoRogerio | 2021-10-19 | Build site. |
| Rmd | a740a97 | LucianoRogerio | 2021-10-19 | Fix link to MixedModels page |
| Rmd | b9ece4f | LucianoRogerio | 2021-10-12 | Second Commit |
| html | b9ece4f | LucianoRogerio | 2021-10-12 | Second Commit |
| Rmd | d2d70ff | LucianoRogerio | 2021-10-12 | Second Commit |
| html | d2d70ff | LucianoRogerio | 2021-10-12 | Second Commit |
| Rmd | 9293d6c | LucianoRogerio | 2021-10-12 | Start workflowr project. |
Descriptive and deviance analysis were performed to verify the distribution and the genotypic effects for resistance to foliar diseases.
suppressMessages(library(tidyverse))
library(here)here() starts at /Users/luciano/Documents/GitHub/HenriqueDGensuppressMessages(library(reactable))
# Data read by R using here package to allow the read in any computer with different directory path
PhenoData <- readRDS(here::here("data", "DadosFenotipicos.rds"))
#write.table(PhenoData, file = "data/xx.csv", quote = F, sep = ",", row.names = F)
#PhenoData2 <- read.table("data/xx.csv", header = T, sep = ",")
#saveRDS(PhenoData2, file = here::here("data", "DadosFenotipicos.rds"))
# Add the control information for the Mixed Models analysis
control <- names(table(PhenoData$accession_name)[table(PhenoData$accession_name) > 30])
PhenoData$control <- ifelse(PhenoData$accession_name %in% control, PhenoData$accession_name, "999")
PhenoData$new <- ifelse(PhenoData$accession_name %in% control, 0, 1)
# Change the Disease names to english abbreviations
colnames(PhenoData)[10:13] <- c("Anth", "WhLS", "BrLS", "BlLS")Anthracnosis (Anth), White Leaf spot (WhLS), Brown Leaf spot (BrLS), Blight Leaf Spot (BlLS).
lnfUtl <- colnames(PhenoData)[c(1:6, 14:15)]
PhenoData$talhao_number <- NULL
PhenoData$Idade <- NULL
PhenoData$is_a_control <- NULL
traits <- colnames(PhenoData)[!colnames(PhenoData) %in% lnfUtl]
PhenoData2 <- PhenoData %>% gather(key = traits, value = Y, -all_of(lnfUtl))
saveRDS(PhenoData2, here::here("output", "DadosDoencasv2.RDS"))Anthracnosis (Anth), White Leaf spot (WhLS), Brown Leaf spot (BrLS), Blight Leaf Spot (BlLS).
library(reshape2); library(tidyverse)
Attaching package: 'reshape2'The following object is masked from 'package:tidyr':
smithsDadosProdutivos <- read.table(here::here("data", "Dados Produtivos 2011-2022.csv"), header = T, sep = ",",
na.strings = "NA")
head(DadosProdutivos) Ano Campo Local Fazenda Genotipos.BGM Genotipos Delineamento
1 2011 Agroverde1 CruzAlmas CNPMF BGM-0023 BGM-0023 DBC
2 2011 Agroverde1 CruzAlmas CNPMF BGM-0023 BGM-0023 DBC
3 2011 Agroverde1 CruzAlmas CNPMF BGM-0023 BGM-0023 DBC
4 2011 Agroverde1 CruzAlmas CNPMF BGM-0025 BGM-0025 DBC
5 2011 Agroverde1 CruzAlmas CNPMF BGM-0025 BGM-0025 DBC
6 2011 Agroverde1 CruzAlmas CNPMF BGM-0025 BGM-0025 DBC
Controle Bloco Linha Coluna Stand AP APsF DMC DRY PTR PRC PRNC
1 0 1 27 7 18 128 NA 29.91 12.08 47.81 41.56 6.25
2 0 2 25 14 17 229 NA 29.93 11.61 45.94 35.06 10.88
3 0 3 16 24 20 268 NA 31.52 19.14 71.25 59.95 11.30
4 0 1 7 2 16 174 NA 35.34 6.52 21.25 13.96 7.29
5 0 2 4 11 17 202 NA 26.68 5.51 25.00 19.91 5.09
6 0 3 3 20 17 230 NA 27.92 3.78 16.25 9.19 7.06
PPA NR Vigor Vigor45D Vigor6M Vigor12M Retencao.foliar
1 46.88 NA NA NA NA NA NA
2 49.06 NA NA NA NA NA NA
3 56.56 NA NA NA NA NA NA
4 21.25 NA NA NA NA NA NA
5 27.50 NA NA NA NA NA NA
6 29.38 NA NA NA NA NA NAcolnames(DadosProdutivos)[c(5, 13:26)] <- c("Genotipo_BGM","AP", "APsF","DMC", "DRY",
"PTR","PRC", "PRNC","PPA","NR","Vigor",
"Vigor45D","Vigor6M","Vigor12M", "RF")
DadosPhen2 <- DadosProdutivos %>% dplyr::select(-c(AP, APsF, PRC, PRNC, Vigor, Vigor45D, Vigor6M))
head(DadosPhen2) Ano Campo Local Fazenda Genotipo_BGM Genotipos Delineamento
1 2011 Agroverde1 CruzAlmas CNPMF BGM-0023 BGM-0023 DBC
2 2011 Agroverde1 CruzAlmas CNPMF BGM-0023 BGM-0023 DBC
3 2011 Agroverde1 CruzAlmas CNPMF BGM-0023 BGM-0023 DBC
4 2011 Agroverde1 CruzAlmas CNPMF BGM-0025 BGM-0025 DBC
5 2011 Agroverde1 CruzAlmas CNPMF BGM-0025 BGM-0025 DBC
6 2011 Agroverde1 CruzAlmas CNPMF BGM-0025 BGM-0025 DBC
Controle Bloco Linha Coluna Stand DMC DRY PTR PPA NR Vigor12M RF
1 0 1 27 7 18 29.91 12.08 47.81 46.88 NA NA NA
2 0 2 25 14 17 29.93 11.61 45.94 49.06 NA NA NA
3 0 3 16 24 20 31.52 19.14 71.25 56.56 NA NA NA
4 0 1 7 2 16 35.34 6.52 21.25 21.25 NA NA NA
5 0 2 4 11 17 26.68 5.51 25.00 27.50 NA NA NA
6 0 3 3 20 17 27.92 3.78 16.25 29.38 NA NA NADadosPhenfin <- reshape2::melt(data = DadosPhen2, id.vars = c("Ano", "Campo",
"Fazenda", "Local",
"Delineamento","Controle",
"Genotipo_BGM","Genotipos",
"Bloco", "Linha",
"Coluna", "Stand"),
variable.name = "Trait",
value.name = "y") %>%
dplyr::filter(!is.na(y)) %>%
dplyr::mutate(Ano = Ano,
Campo = Campo,
Local = Local,
trial = match(paste(Ano, Campo, Local, sep = "."), unique(paste(Ano, Campo, Local, sep = "."))),
studyDesign = Delineamento,
clone = Genotipo_BGM,
rep = Bloco,
check = ifelse(Controle == "1", clone, "999"),
check = ifelse(clone %in% unique(check), clone, "999"),
new = ifelse(check != "999", 0, 1),
.keep = "unused") %>% dplyr::select(-c("Genotipos")) %>%
dplyr::filter(Trait != "NR" | (Trait=="NR" & y < 30))
head(DadosPhenfin) Ano Campo Fazenda Local Linha Coluna Stand Trait y trial
1 2011 Agroverde1 CNPMF CruzAlmas 27 7 18 DMC 29.91 1
2 2011 Agroverde1 CNPMF CruzAlmas 25 14 17 DMC 29.93 1
3 2011 Agroverde1 CNPMF CruzAlmas 16 24 20 DMC 31.52 1
4 2011 Agroverde1 CNPMF CruzAlmas 7 2 16 DMC 35.34 1
5 2011 Agroverde1 CNPMF CruzAlmas 4 11 17 DMC 26.68 1
6 2011 Agroverde1 CNPMF CruzAlmas 3 20 17 DMC 27.92 1
studyDesign clone rep check new
1 DBC BGM-0023 1 999 1
2 DBC BGM-0023 2 999 1
3 DBC BGM-0023 3 999 1
4 DBC BGM-0025 1 999 1
5 DBC BGM-0025 2 999 1
6 DBC BGM-0025 3 999 1saveRDS(object = DadosPhenfin, file = here::here("output", "DadosFenotipicos.rds"))
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.0
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Sao_Paulo
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reshape2_1.4.4 reactable_0.4.4 here_1.0.1 lubridate_1.9.2
[5] forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2 purrr_1.0.2
[9] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.3
[13] tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12
[5] hms_1.1.3 digest_0.6.33 magrittr_2.0.3 timechange_0.2.0
[9] evaluate_0.21 grid_4.3.1 fastmap_1.1.1 plyr_1.8.8
[13] rprojroot_2.0.3 workflowr_1.7.0 jsonlite_1.8.7 whisker_0.4.1
[17] promises_1.2.1 fansi_1.0.4 crosstalk_1.2.0 scales_1.2.1
[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 ellipsis_0.3.2
[25] munsell_0.5.0 reactR_0.4.4 withr_2.5.0 cachem_1.0.8
[29] yaml_2.3.7 tools_4.3.1 tzdb_0.4.0 colorspace_2.1-0
[33] httpuv_1.6.11 vctrs_0.6.3 R6_2.5.1 lifecycle_1.0.3
[37] git2r_0.32.0 htmlwidgets_1.6.2 fs_1.6.3 pkgconfig_2.0.3
[41] pillar_1.9.0 bslib_0.5.1 later_1.3.1 gtable_0.3.3
[45] glue_1.6.2 Rcpp_1.0.11 xfun_0.40 tidyselect_1.2.0
[49] rstudioapi_0.15.0 knitr_1.43 htmltools_0.5.6 rmarkdown_2.24
[53] compiler_4.3.1