Last updated: 2021-07-22
Checks: 6 1
Knit directory: CassavaArchitectureGP/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.
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(20210721) 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 09489e4. 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: .Rhistory
Ignored: .Rproj.user/
Unstaged changes:
Modified: analysis/PhenData.Rmd
Modified: data/phenotypePAGP.RDS
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/PhenData.Rmd) and HTML (docs/PhenData.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 |
|---|---|---|---|---|
| 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 |
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. |
| 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: 1. Select the trait list TraitsLucianoGS 2. Select the following Trial Types: - Clonal Evaluation; - Preliminary Yield Trial; - Advanced Yield Trial; - Uniform Yield Trial; - Regional Trials; - phenotyping_trial. 3. Select Years from 2010 to 2021. 4. Select all the trials available at cassavabase after the filter.
library(tidyverse); library(reactable)-- Attaching packages --------------------------------------- tidyverse 1.3.1 --v ggplot2 3.3.5 v purrr 0.3.4
v tibble 3.1.2 v dplyr 1.0.7
v tidyr 1.1.3 v stringr 1.4.0
v readr 1.4.0 v forcats 0.5.1-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()PhenoData <- readRDS("data/phenotypePAGP.RDS")
PhenoData %>% group_by(studyYear, programName) %>% count(studyName) %>%
reactable(defaultPageSize = 50)
sessionInfo()R version 4.1.0 (2021-05-18)
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] reactable_0.2.3 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[5] purrr_0.3.4 readr_1.4.0 tidyr_1.1.3 tibble_3.1.2
[9] 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_1.2.1 reactR_0.4.4 R6_2.5.0
[9] cellranger_1.1.0 backports_1.2.1 reprex_2.0.0 evaluate_0.14
[13] httr_1.4.2 pillar_1.6.1 rlang_0.4.11 readxl_1.3.1
[17] rstudioapi_0.13 whisker_0.4 jquerylib_0.1.4 rmarkdown_2.9
[21] htmlwidgets_1.5.3 munsell_0.5.0 broom_0.7.8 compiler_4.1.0
[25] httpuv_1.6.1 modelr_0.1.8 xfun_0.24 pkgconfig_2.0.3
[29] htmltools_0.5.1.1 tidyselect_1.1.1 workflowr_1.6.2 fansi_0.5.0
[33] crayon_1.4.1 dbplyr_2.1.1 withr_2.4.2 later_1.2.0
[37] grid_4.1.0 jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.0
[41] DBI_1.1.1 git2r_0.28.0 magrittr_2.0.1 scales_1.1.1
[45] cli_3.0.1 stringi_1.7.3 fs_1.5.0 promises_1.2.0.1
[49] xml2_1.3.2 bslib_0.2.5.1 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] crosstalk_1.1.1 yaml_2.2.1 colorspace_2.0-2 rvest_1.0.0
[61] knitr_1.33 haven_2.4.1 sass_0.4.0