Last updated: 2022-03-01
Checks: 6 1
Knit directory: HenriqueDGen/
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File | Version | Author | Date | Message |
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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/lbd54/Documents/GitHub/HenriqueDGen
suppressMessages(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"))
# 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$accession_name %in% control, 0, 1)
# Change the Disease names to english abbreviations
colnames(PhenoData)[7:10] <- c("Anth", "WhLS", "BrLS", "BlLS")
Anthracnosis (Anth), White Leaf spot (WhLS), Brown Leaf spot (BrLS), Blight Leaf Spot (BlLS).
lnfUtl <- colnames(PhenoData)[c(1:4, 11:12)]
PhenoData$talhao_number <- NULL
PhenoData$Idade <- NULL
traits <- colnames(PhenoData)[!colnames(PhenoData) %in% lnfUtl]
PhenoData2 <- PhenoData %>% gather(key = traits, value = Y, -all_of(lnfUtl))
Anthracnosis (Anth), White Leaf spot (WhLS), Brown Leaf spot (BrLS), Blight Leaf Spot (BlLS).
saveRDS(PhenoData2, here::here("output", "DadosFenotipicosv2.RDS"))
-[ ] Adicionar a informação de delineamento experimental - DBC - Delineamento em Blocos Casualizados - possui repetição para todos os clones - DBA - Delineamento em Blocos Aumentados - possui repetição apenas para os controles -[ ] Adicionar a informação de qual clone foi utilizado como controle nos ensaios DBA. - é controle recebe 1. - ñ é controle recebe 0. inserir 0 para todas as células dos ensaios DBC.
library(reshape2)
DadosProdutivos <- read.table(here::here("data", "Dados Produtivos 2011-2021.CSV"), header = T, sep = ";")
head(DadosProdutivos)
colnames(DadosProdutivos)[c(4,10:21)] <- c("Genotipo-BGM","AP", "APsF","DMC",
"PTR","PRC", "PRNC","PPA","Vigor","Vigor45D","Vigor6M","Vigor12M","NR")
DadosProdutivos2 <- DadosProdutivos[,c(1:16,21)] %>% select(-c(AP, APsF, DMC, PRC, PRNC))
head(DadosProdutivos2)
DadosProdutivosfin <- reshape2::melt(data = DadosProdutivos2,id.vars = c("Ano","Campo","Local","Genotipo-BGM","Genotipos","Bloco","Linha", "Coluna", "Stand"),
variable.name = "Trait",
value.name = "Value") %>%
filter(!is.na(Value)) %>%
mutate(Ano = Ano,
Campo = Campo,
Local = Local,
trial = match(paste(Ano, Campo, Local, sep = "."), unique(paste(Ano, Campo, Local, sep = "."))),
studyDesign = Delineamento,
clone = 'Genotipos-BGM',
rep = Bloco,
check = ifelse(Controle == "1", clone, "999"),
check = ifelse(clone %in% unique(check), clone, "999"),
new = ifelse(check != "999", 0, 1),
y = Value, .keep = "unused")
saveRDS(object = DadosProdutivosfin, file = here::here("output", "DadosProdutivos.rds"))
DadosVigor <- DadosProdutivos[,c(1:8,17:20)]
head(DadosVigor)
DadosVigorFin <- reshape2::melt(data = DadosVigor, id.vars = c("Ano","Campo","Local","Genotipo-BGM",
"Genotipos","Bloco","Linha","Coluna"),
variable.name = "Epoca",
value.name = "Value") %>% filter(!is.na(Value))
head(DadosVigorFin)
saveRDS(object = DadosVigorFin, file = here::here("output", "DadosVigor.rds"))
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reactable_0.2.3 here_1.0.1 forcats_0.5.1 stringr_1.4.0
[5] dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
[9] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8 lubridate_1.8.0 assertthat_0.2.1 rprojroot_2.0.2
[5] digest_0.6.29 utf8_1.2.2 reactR_0.4.4 R6_2.5.1
[9] cellranger_1.1.0 backports_1.4.1 reprex_2.0.1 evaluate_0.15
[13] httr_1.4.2 pillar_1.7.0 rlang_1.0.1 readxl_1.3.1
[17] rstudioapi_0.13 whisker_0.4 jquerylib_0.1.4 rmarkdown_2.11
[21] htmlwidgets_1.5.4 munsell_0.5.0 broom_0.7.12 compiler_4.1.2
[25] httpuv_1.6.5 modelr_0.1.8 xfun_0.29 pkgconfig_2.0.3
[29] htmltools_0.5.2 tidyselect_1.1.1 workflowr_1.7.0 fansi_1.0.2
[33] crayon_1.5.0 tzdb_0.2.0 dbplyr_2.1.1 withr_2.4.3
[37] later_1.3.0 grid_4.1.2 jsonlite_1.7.3 gtable_0.3.0
[41] lifecycle_1.0.1 DBI_1.1.2 git2r_0.29.0 magrittr_2.0.2
[45] scales_1.1.1 cli_3.2.0 stringi_1.7.6 fs_1.5.2
[49] promises_1.2.0.1 xml2_1.3.3 bslib_0.3.1 ellipsis_0.3.2
[53] generics_0.1.2 vctrs_0.3.8 tools_4.1.2 glue_1.6.1
[57] crosstalk_1.2.0 hms_1.1.1 fastmap_1.1.0 yaml_2.3.4
[61] colorspace_2.0-2 rvest_1.0.2 knitr_1.37 haven_2.4.3
[65] sass_0.4.0