Last updated: 2022-01-26
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Knit directory: HenriqueDGen/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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. In this work we used a natural logarithm transformation for Affected area by Anthracnosis at the innoculated area at stem in cassava plants (AnAr).
suppressMessages(library(tidyverse))Warning: package 'tibble' was built under R version 4.1.1Warning: package 'readr' was built under R version 4.1.1library(here)Warning: package 'here' was built under R version 4.1.2here() starts at C:/Users/jhenr/OneDrive/Documentos/GitHub/HenriqueDGensuppressMessages(library(reactable))Warning: package 'reactable' was built under R version 4.1.2# 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$accession_name %in% control, 0, 1)
# Change the Disease names to english abbreviations
colnames(PhenoData)[7:11] <- c("Anth", "WhLS", "BrLS", "BlLS", "AnAr")
# Natural logarithm transformation for Anthracnosis Area
PhenoData$AnAr <- log(PhenoData$AnAr)Anthracnosis (Anth), White Leaf spot (WhLS), Brown Leaf spot (BrLS), Blight Leaf Spot (BlLS), Affected area by Anthracnosis at the innoculated area at stem in cassava plants (AnAr).
lnfUtl <- colnames(PhenoData)[c(1:4, 12:13)]
PhenoData$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), Affected area by Anthracnosis at the innoculated area at stem in cassava plants (AnAr).
saveRDS(PhenoData2, here::here("output", "DadosFenotipicosv2.RDS"))# Rodar o script aqui dentro
#install.packages("reshape2")
library(reshape2)Warning: package 'reshape2' was built under R version 4.1.2
Attaching package: 'reshape2'The following object is masked from 'package:tidyr':
smithsDadosProdutivos <- read.table(here::here("data", "Dados Produtivos 2011-2021.CSV1.CSV"), header = T, sep = ";")
head(DadosProdutivos) Ano Campo Local Genotipos.BGM Genotipos Bloco Linha
1 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0023 BGM-0023 1 27
2 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0023 BGM-0023 2 25
3 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0023 BGM-0023 3 16
4 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0025 BGM-0025 1 7
5 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0025 BGM-0025 2 4
6 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0025 BGM-0025 3 3
Coluna Stand AP APsF DMC PTR PRC PRNC PPA Vigor Vigor45D Vigor6M
1 7 18 128 NA NA 47.81 41.56 6.25 46.88 NA <NA> NA
2 14 17 229 NA NA 45.94 35.06 10.88 49.06 NA <NA> NA
3 24 20 268 NA NA 71.25 59.95 11.30 56.56 NA <NA> NA
4 2 16 174 NA NA 21.25 13.96 7.29 21.25 NA <NA> NA
5 11 17 202 NA NA 25.00 19.91 5.09 27.50 NA <NA> NA
6 20 17 230 NA NA 16.25 9.19 7.06 29.38 NA <NA> NA
Vigor12M
1 NA
2 NA
3 NA
4 NA
5 NA
6 NAcolnames(DadosProdutivos)[c(4,10:20)] <- c("Genotipo-BGM","AP", "APsF","DMC",
"PTR","PRC", "PRNC","PPA","Vigor","Vigor45D","Vigor6M","Vigor12M")
DadosProdutivos2 <- DadosProdutivos[,1:16]
DadosProdutivosfin <- reshape2::melt(data = DadosProdutivos2,id.vars = c("Ano","Campo","Local","Genotipo-BGM","Genotipos","Bloco","Linha", "Coluna"),
variable.name = "Trait",
value.name = "Value") %>% filter(!is.na(Value))
saveRDS(object = DadosProdutivosfin, file = here::here("output", "DadosProdutivos.rds"))
DadosVigor <- DadosProdutivos[,c(1:8,17:20)]
head(DadosVigor) Ano Campo Local Genotipo-BGM Genotipos Bloco Linha
1 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0023 BGM-0023 1 27
2 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0023 BGM-0023 2 25
3 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0023 BGM-0023 3 16
4 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0025 BGM-0025 1 7
5 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0025 BGM-0025 2 4
6 2011 Agroverde1 CNPMF (Cruz das Almas) BGM-0025 BGM-0025 3 3
Coluna Vigor Vigor45D Vigor6M Vigor12M
1 7 NA <NA> NA NA
2 14 NA <NA> NA NA
3 24 NA <NA> NA NA
4 2 NA <NA> NA NA
5 11 NA <NA> NA NA
6 20 NA <NA> NA NADadosVigorFin <- 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) Ano Campo Local Genotipo-BGM Genotipos
1 2021 BR.BAG.20.Rec UFRB-Candial (Cruz das Almas) 4271 4271
2 2021 BR.BAG.20.Rec UFRB-Candial (Cruz das Almas) 4271 4271
3 2021 BR.BAG.20.Rec UFRB-Candial (Cruz das Almas) 01/03/2011 01/03/2011
4 2021 BR.BAG.20.Rec UFRB-Candial (Cruz das Almas) 11-CONQUISTA2 11-CONQUISTA2
5 2021 BR.BAG.20.Rec UFRB-Candial (Cruz das Almas) 2011-24-156 2011-24-156
6 2021 BR.BAG.20.Rec UFRB-Candial (Cruz das Almas) 2011-24-156 2011-24-156
Bloco Linha Coluna Epoca Value
1 1 10 10 Vigor 3
2 1 9 10 Vigor 3
3 1 1 1 Vigor 3
4 1 3 1 Vigor 3
5 1 10 11 Vigor 3
6 2 7 17 Vigor 3saveRDS(object = DadosVigorFin, file = here::here("output", "DadosVigor.rds"))
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.1252
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_1.0.7 purrr_0.3.4 readr_2.0.1
[9] tidyr_1.1.3 tibble_3.1.4 ggplot2_3.3.5 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 lubridate_1.7.10 assertthat_0.2.1 rprojroot_2.0.2
[5] digest_0.6.27 utf8_1.2.2 plyr_1.8.6 reactR_0.4.4
[9] R6_2.5.1 cellranger_1.1.0 backports_1.2.1 reprex_2.0.1
[13] evaluate_0.14 httr_1.4.2 pillar_1.6.2 rlang_0.4.11
[17] readxl_1.3.1 rstudioapi_0.13 whisker_0.4 rmarkdown_2.10
[21] htmlwidgets_1.5.4 munsell_0.5.0 broom_0.7.9 compiler_4.1.0
[25] httpuv_1.6.3 modelr_0.1.8 xfun_0.25 pkgconfig_2.0.3
[29] htmltools_0.5.2 tidyselect_1.1.1 workflowr_1.6.2 fansi_0.5.0
[33] crayon_1.4.1 tzdb_0.1.2 dbplyr_2.1.1 withr_2.4.2
[37] later_1.3.0 grid_4.1.0 jsonlite_1.7.2 gtable_0.3.0
[41] lifecycle_1.0.0 DBI_1.1.1 git2r_0.28.0 magrittr_2.0.1
[45] scales_1.1.1 cli_3.0.1 stringi_1.7.4 fs_1.5.0
[49] promises_1.2.0.1 xml2_1.3.2 ellipsis_0.3.2 generics_0.1.0
[53] vctrs_0.3.8 tools_4.1.0 glue_1.4.2 hms_1.1.0
[57] fastmap_1.1.0 yaml_2.2.1 colorspace_2.0-2 rvest_1.0.1
[61] knitr_1.33 haven_2.4.3