Last updated: 2021-10-15
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Knit directory: CassavaArchitectureGP/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5d56695 | LucianoRogerio | 2021-10-11 | Add of the First Branch height measure at 9 MAP and new table for the number of trials for each Institute |
| html | 5d56695 | LucianoRogerio | 2021-10-11 | Add of the First Branch height measure at 9 MAP and new table for the number of trials for each Institute |
| Rmd | 0d2341c | LucianoRogerio | 2021-09-09 | Small changes at writing |
| html | 0d2341c | LucianoRogerio | 2021-09-09 | Small changes at writing |
| Rmd | 1b63c8c | LucianoRogerio | 2021-07-28 | Add Home button to the PhenData html Page |
| html | 1b63c8c | LucianoRogerio | 2021-07-28 | Add Home button to the PhenData html Page |
| html | 2b49915 | LucianoRogerio | 2021-07-22 | Build site. |
| Rmd | 7f7b622 | LucianoRogerio | 2021-07-22 | Update PhenDataRmd |
| html | 7f7b622 | LucianoRogerio | 2021-07-22 | Update PhenDataRmd |
| Rmd | 6d25535 | LucianoRogerio | 2021-07-22 | Update PhenDataRmd |
| html | 6d25535 | LucianoRogerio | 2021-07-22 | Update PhenDataRmd |
| Rmd | 3e1bc0d | LucianoRogerio | 2021-07-22 | PhenD update |
| html | 3e1bc0d | LucianoRogerio | 2021-07-22 | PhenD update |
| html | 7a63d40 | LucianoRogerio | 2021-07-22 | Build site. |
| html | d25ce40 | LucianoRogerio | 2021-07-22 | Build site. |
| Rmd | 73f4e1f | LucianoRogerio | 2021-07-22 | wflow_publish("analysis/PhenData.Rmd") |
| html | ce3ca50 | LucianoRogerio | 2021-07-21 | Build site. |
| Rmd | e7db3e0 | LucianoRogerio | 2021-07-21 | Publish the update 1 Phenotypic data CassavaArchitectureGP |
Wrong section? get back to home.
Initialy we are going to download phenotypic data from Cassavabase. In this case we are going to download the data from traits related to plant Architecture, as the following table:
| Trait | Cassavabase code | Description |
|---|---|---|
| plant architecture visual rating 1-5 | CO_334:0000099 | Plant architecture on a 1-5 scale with 1 = excellent, 2 good, 3 = fair, 4 = bad, and 5 = very bad |
| plant architecture visual rating 1-5 at month 8 | COMP:0000119 | |
| flowering ability visual assessment 0-3 | CO_334:0000233 | Presence of flowers (0=none; 1=little; 2=intermediate; 3=many). |
| flower visual rating 0&1 | CO_334:0000111 | Visual rating of flowers (50%) in plant with 0 = absent and 1 = present. |
| initial plant vigor assessment 1-5 | CO_334:0000220 | Visual assessment of plant vigor during establishment (1=very little vigor, and 5 = very vigorous). as being evaluated by CIAT. |
| initial vigor assessment 1-7 | CO_334:0000009 | Visual assessment of plant vigor during establishment scored one month after planting. 3 = Not vigorous, 5 = Medium vigor, 7 = highly vigorous. |
| number of forks counting | CO_334:0000146 | Number of branches (2 forks/branches (dichotomous), 3 forks/branches (trichotomous), or 4 forks/branches (tetrachotomous)) at every branching level. |
| number of forks on branching level 1 counting | CO_334:0000522 | Number of forks (2 forks/branches (dichotomous), 3 forks/branches (trichotomous), or 4 forks/branches (tetrachotomous)) on the first branching level. |
| number of forks on branching level 2 counting | CO_334:0000523 | Number of forks (2 forks/branches (dichotomous), 3 forks/branches (trichotomous), or 4 forks/branches (tetrachotomous)) on the second branching level. |
| number of forks on branching level 3 counting | CO_334:0000524 | Number of forks (2 forks/branches (dichotomous), 3 forks/branches (trichotomous), or 4 forks/branches (tetrachotomous)) on the third branching level. |
| number of nodes at branching level 1 counting | CO_334:0000352 | Number of nodes at the first branching level. |
| number of nodes at branching level 2 counting | CO_334:0000363 | Number of nodes at the second branching level. |
| number of nodes at branching level 3 counting | CO_334:0000368 | Number of nodes at the third branching level. |
| first apical branch height measurement in cm | CO_334:0000106 | Height of first apical branch (ground level to point of first Apical branch, 9 months after planting) in cm |
| plant height measurement in cm | CO_334:0000018 | Vertical height of plants from the ground to top of the canopy measured in centimeter (cm). |
| plant height measurement in cm at month 12 | COMP:0000181 | |
| plant height with leaf in cm | CO_334:0000123 | Portion of the stem with leaves measured as the distance in centimeter from the point of attachment of the oldest leaf to the youngest leaf (apical leaf portion). |
| plant height without leaf | CO_334:0000125 | Portion of stem with no leaf measured in centimeter (cm) by deducting plant height with leaf from plant height. |
| plant height without leaf at month 12 | COMP:0000182 | |
| stalk length evaluation | CO_334:0000227 | Visual assessment of the average length of the stalks (1=short; 2=intermediate; 3=long) |
| stem diameter measurement in cm | CO_334:0000257 | Measurement of stem diameter taken on the middle of the plant in centimeter (cm) using the vernier caliper. |
| stem diameter measurement in cm at month 5 | COMP:0000129 | |
| stem diameter measurement in cm at month 6 | COMP:0000130 |
Use the following filters:
TraitsLucianoGSTrial Types:
Years from 2010 to 2021.trials available at cassavabase after the filter.library(tidyverse); library(reactable); library(here)
PhenoData <- readRDS(here("data","phenotypePAGP.RDS"))
PhenoData %>% group_by(programName, studyYear) %>% summarise(n_trials = unique(studyName)) -> PhenoData2
cat("Table 2. Number of trial per Institute in Cassavabase with Cassava Plant Shape Traits.", "\n")Table 2. Number of trial per Institute in Cassavabase with Cassava Plant Shape Traits. table(PhenoData2$programName, PhenoData2$studyYear)
2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021
CIAT 62 58 99 58 74 58 9 42 34 69 29 1
Embrapa 0 0 0 0 0 0 0 0 0 2 0 0
IITA 58 41 65 84 74 100 116 116 110 80 39 1
NaCRRI 0 0 1 2 0 4 13 5 6 22 12 0
NRCRI 6 5 4 12 1 5 3 7 24 28 0 0
TARI 0 0 0 0 0 0 0 4 6 0 0 0cat("Table 3. Plot number of the trials available in Cassavabase with Cassava Plant Shape traits.", "\n")Table 3. Plot number of the trials available in Cassavabase with Cassava Plant Shape traits. PhenoData %>% group_by(programName, studyYear) %>% count(studyName) %>%
reactable(defaultPageSize = 50)The heritability and Reliability were estimated for each trial. We will proceed with the trails with reliability bigger than 0.2.
sessionInfo()R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
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] here_1.0.1 reactable_0.2.3 forcats_0.5.1 stringr_1.4.0
[5] dplyr_1.0.7 purrr_0.3.4 readr_2.0.2 tidyr_1.1.4
[9] tibble_3.1.5 ggplot2_3.3.5 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 lubridate_1.8.0 assertthat_0.2.1 rprojroot_2.0.2
[5] digest_0.6.28 utf8_1.2.2 reactR_0.4.4 R6_2.5.1
[9] cellranger_1.1.0 backports_1.2.1 reprex_2.0.1 evaluate_0.14
[13] httr_1.4.2 pillar_1.6.3 rlang_0.4.11 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_0.7.9 compiler_4.1.1
[25] httpuv_1.6.3 modelr_0.1.8 xfun_0.26 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_4.1.1 jsonlite_1.7.2 gtable_0.3.0
[41] lifecycle_1.0.1 DBI_1.1.1 git2r_0.28.0 magrittr_2.0.1
[45] scales_1.1.1 cli_3.0.1 stringi_1.7.5 fs_1.5.0
[49] promises_1.2.0.1 xml2_1.3.2 bslib_0.3.1 ellipsis_0.3.2
[53] generics_0.1.0 vctrs_0.3.8 tools_4.1.1 glue_1.4.2
[57] crosstalk_1.1.1 hms_1.1.1 fastmap_1.1.0 yaml_2.2.1
[61] colorspace_2.0-2 rvest_1.0.1 knitr_1.36 haven_2.4.3
[65] sass_0.4.0