Last updated: 2022-03-08
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Knit directory: HenriqueDGen/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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/lbd54/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"))
# 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))
saveRDS(PhenoData2, here::here("output", "DadosFenotipicosv2.RDS"))Anthracnosis (Anth), White Leaf spot (WhLS), Brown Leaf spot (BrLS), Blight Leaf Spot (BlLS).
library(reshape2)
Attaching package: 'reshape2'The following object is masked from 'package:tidyr':
smithsDadosProdutivos <- read.table(here::here("data", "Dados Produtivos 2011-2021.CSV"), header = T, sep = ",",
na.strings = "NA")
head(DadosProdutivos) Ano Campo Local Genotipos.BGM Genotipos Delineamento Controle Bloco
1 2011 Agroverde1 CNPMF BGM-0023 BGM-0023 DBC 0 1
2 2011 Agroverde1 CNPMF BGM-0023 BGM-0023 DBC 0 2
3 2011 Agroverde1 CNPMF BGM-0023 BGM-0023 DBC 0 3
4 2011 Agroverde1 CNPMF BGM-0025 BGM-0025 DBC 0 1
5 2011 Agroverde1 CNPMF BGM-0025 BGM-0025 DBC 0 2
6 2011 Agroverde1 CNPMF BGM-0025 BGM-0025 DBC 0 3
Linha Coluna Stand AP APsF DMC PTR PRC PRNC PPA NR Vigor Vigor45D
1 27 7 18 128 NA NA 47.81 41.56 6.25 46.88 NA NA NA
2 25 14 17 229 NA NA 45.94 35.06 10.88 49.06 NA NA NA
3 16 24 20 268 NA NA 71.25 59.95 11.30 56.56 NA NA NA
4 7 2 16 174 NA NA 21.25 13.96 7.29 21.25 NA NA NA
5 4 11 17 202 NA NA 25.00 19.91 5.09 27.50 NA NA NA
6 3 20 17 230 NA NA 16.25 9.19 7.06 29.38 NA NA NA
Vigor6M Vigor12M
1 NA NA
2 NA NA
3 NA NA
4 NA NA
5 NA NA
6 NA NAcolnames(DadosProdutivos)[c(4,12:23)] <- c("Genotipo_BGM","AP", "APsF","DMC",
"PTR","PRC", "PRNC","PPA","NR","Vigor","Vigor45D","Vigor6M","Vigor12M")
DadosPhen2 <- DadosProdutivos %>% dplyr::select(-c(AP, APsF, DMC, PRC, PRNC))
head(DadosPhen2) Ano Campo Local Genotipo_BGM Genotipos Delineamento Controle Bloco
1 2011 Agroverde1 CNPMF BGM-0023 BGM-0023 DBC 0 1
2 2011 Agroverde1 CNPMF BGM-0023 BGM-0023 DBC 0 2
3 2011 Agroverde1 CNPMF BGM-0023 BGM-0023 DBC 0 3
4 2011 Agroverde1 CNPMF BGM-0025 BGM-0025 DBC 0 1
5 2011 Agroverde1 CNPMF BGM-0025 BGM-0025 DBC 0 2
6 2011 Agroverde1 CNPMF BGM-0025 BGM-0025 DBC 0 3
Linha Coluna Stand PTR PPA NR Vigor Vigor45D Vigor6M Vigor12M
1 27 7 18 47.81 46.88 NA NA NA NA NA
2 25 14 17 45.94 49.06 NA NA NA NA NA
3 16 24 20 71.25 56.56 NA NA NA NA NA
4 7 2 16 21.25 21.25 NA NA NA NA NA
5 4 11 17 25.00 27.50 NA NA NA NA NA
6 3 20 17 16.25 29.38 NA NA NA NA NADadosPhenfin <- reshape2::melt(data = DadosPhen2,id.vars = c("Ano","Campo","Local","Delineamento","Controle","Genotipo_BGM","Genotipos","Bloco","Linha", "Coluna", "Stand"),
variable.name = "Trait",
value.name = "Value") %>%
filter(!is.na(Value)) %>%
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),
y = Value, .keep = "unused") %>% dplyr::select(-c("Genotipos")) %>%
filter(Trait != "NR" | (Trait=="NR" & y < 30))
head(DadosPhenfin) Ano Campo Local Linha Coluna Stand Trait trial studyDesign clone rep
1 2011 Agroverde1 CNPMF 27 7 18 PTR 1 DBC BGM-0023 1
2 2011 Agroverde1 CNPMF 25 14 17 PTR 1 DBC BGM-0023 2
3 2011 Agroverde1 CNPMF 16 24 20 PTR 1 DBC BGM-0023 3
4 2011 Agroverde1 CNPMF 7 2 16 PTR 1 DBC BGM-0025 1
5 2011 Agroverde1 CNPMF 4 11 17 PTR 1 DBC BGM-0025 2
6 2011 Agroverde1 CNPMF 3 20 17 PTR 1 DBC BGM-0025 3
check new y
1 999 1 47.81
2 999 1 45.94
3 999 1 71.25
4 999 1 21.25
5 999 1 25.00
6 999 1 16.25saveRDS(object = DadosPhenfin, file = here::here("output", "DadosFenotipicos.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] reshape2_1.4.4 reactable_0.2.3 here_1.0.1 forcats_0.5.1
[5] stringr_1.4.0 dplyr_1.0.8 purrr_0.3.4 readr_2.1.2
[9] tidyr_1.2.0 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 plyr_1.8.6 reactR_0.4.4
[9] R6_2.5.1 cellranger_1.1.0 backports_1.4.1 reprex_2.0.1
[13] evaluate_0.15 httr_1.4.2 pillar_1.7.0 rlang_1.0.1
[17] readxl_1.3.1 rstudioapi_0.13 whisker_0.4 jquerylib_0.1.4
[21] rmarkdown_2.11 htmlwidgets_1.5.4 munsell_0.5.0 broom_0.7.12
[25] compiler_4.1.2 httpuv_1.6.5 modelr_0.1.8 xfun_0.29
[29] pkgconfig_2.0.3 htmltools_0.5.2 tidyselect_1.1.1 workflowr_1.7.0
[33] fansi_1.0.2 crayon_1.5.0 tzdb_0.2.0 dbplyr_2.1.1
[37] withr_2.4.3 later_1.3.0 grid_4.1.2 jsonlite_1.7.3
[41] gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2 git2r_0.29.0
[45] magrittr_2.0.2 scales_1.1.1 cli_3.2.0 stringi_1.7.6
[49] fs_1.5.2 promises_1.2.0.1 xml2_1.3.3 bslib_0.3.1
[53] ellipsis_0.3.2 generics_0.1.2 vctrs_0.3.8 tools_4.1.2
[57] glue_1.6.1 crosstalk_1.2.0 hms_1.1.1 fastmap_1.1.0
[61] yaml_2.3.4 colorspace_2.0-2 rvest_1.0.2 knitr_1.37
[65] haven_2.4.3 sass_0.4.0