Package: expDB 0.1.0

expDB: Database for Experiment Dataset

A 'SQLite' database is designed to store all information of experiment-based data including metadata, experiment design, managements, phenotypic values and climate records. The dataset can be imported from an 'Excel' file.

Authors:Bangyou Zheng [aut, cre]

expDB_0.1.0.tar.gz
expDB_0.1.0.zip(r-4.5)expDB_0.1.0.zip(r-4.4)expDB_0.1.0.zip(r-4.3)
expDB_0.1.0.tgz(r-4.4-any)expDB_0.1.0.tgz(r-4.3-any)
expDB_0.1.0.tar.gz(r-4.5-noble)expDB_0.1.0.tar.gz(r-4.4-noble)
expDB_0.1.0.tgz(r-4.4-emscripten)expDB_0.1.0.tgz(r-4.3-emscripten)
expDB.pdf |expDB.html✨
expDB/json (API)

# Install 'expDB' in R:

install.packages('expDB', repos = c('https://byzheng.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/byzheng/expdb/issues

On CRAN:

51 exports 0.84 score 114 dependencies 4 scripts 283 downloads

Last updated 9 months agofrom:331dd2e7f0. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 09 2024
R-4.5-win	NOTE	Sep 09 2024
R-4.5-linux	NOTE	Sep 09 2024
R-4.4-win	NOTE	Sep 09 2024
R-4.4-mac	NOTE	Sep 09 2024
R-4.3-win	NOTE	Sep 09 2024
R-4.3-mac	NOTE	Sep 09 2024

Exports:dbAddDesigns dbAddFertilization dbAddGene dbAddGeneAllele dbAddGenotype dbAddIrrigatons dbAddLog dbAddMethods dbAddMets dbAddNodes dbAddPhenotype dbAddResearcher dbAddSites dbAddSource dbAddTraits dbAddTrials dbAddTrialSoil dbAddWeather dbExportMet dbGenotypeCheckName dbGetDryWeightPerStem dbGetFertilization dbGetFieldMaturity dbGetFieldPopulation dbGetFieldStemNumber dbGetFieldTillerNumber dbGetGene dbGetGenotype dbGetIrrigation dbGetLog dbGetMetInfo dbGetOrganFinalLeafNumber dbGetOrganHaunIndex dbGetPhenotype dbGetPlantFlowering dbGetPlantHeading dbGetPlantStemElongation dbGetPlantStemNumber dbGetPlantTillerNumber dbGetSites dbGetSource dbGetTraits dbGetTrials dbGetWeather dbGetZadoksStage dbImportXLSX dbListTrials expdbConnect expdbCreateDB expdbDisconnect harvestQuadratDetail

Dependencies:askpass backports base64enc bit bit64 blob broom bslib cachem callr cellranger cli clipr colorspace conflicted cpp11 crayon curl data.table DBI dbplyr digest dplyr dtplyr evaluate fansi farver fastmap fontawesome forcats fs gargle generics ggplot2 glue googledrive googlesheets4 gtable haven highr hms htmltools httr ids isoband jquerylib jsonlite knitr labeling lattice lifecycle lubridate magrittr MASS Matrix memoise mgcv mime modelr munsell nlme openssl pillar pkgconfig plogr plyr png prettyunits processx progress ps purrr R6 ragg rappdirs RColorBrewer Rcpp readr readxl rematch rematch2 reprex reshape2 rlang rmarkdown RSQLite rstudioapi rvest sass scales selectr settings stringi stringr sys systemfonts textshaping tibble tidyr tidyselect tidyverse timechange tinytex tzdb utf8 uuid vctrs viridisLite vroom weaana withr xfun xml2 yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add design for a trial	dbAddDesigns
Insert or Update fertilization into expDB	dbAddFertilization
Add gene information into database	dbAddGene
Add gene allele information into database	dbAddGeneAllele
Add genotypes into expDB	dbAddGenotype
Insert or Update irrigation into expDB	dbAddIrrigatons
Add log from expDB	dbAddLog
Insert or Update methods into expDB	dbAddMethods
Insert and update met into expDB	dbAddMets
Add nodes into expDB	dbAddNodes
Add design for a trial	dbAddPhenotype
Insert and update researcher into expDB	dbAddResearcher
Insert or update site into expDB	dbAddSites
Insert and update source into expDB	dbAddSource
Insert or update trait into expDB	dbAddTraits
Insert or Update trial into expDB	dbAddTrials
Add soil for a trial	dbAddTrialSoil
Add weather records into expDB	dbAddWeather
Append a table into db and check the column name	dbAppendTable
Export trials weather records to met file	dbExportMet
Check genotype names	dbGenotypeCheckName
Get the dry weight per stem	dbGetDryWeightPerStem
Get fertilization from database	dbGetFertilization
Estimation of maturity	dbGetFieldMaturity
Estimation of plant populations	dbGetFieldPopulation
Estimation of stem number per unit area	dbGetFieldStemNumber
Estimation of tiller number per unit area	dbGetFieldTillerNumber
Get the gene information	dbGetGene
Get the genotype information	dbGetGenotype
Get irrigation from database	dbGetIrrigation
Get log from expDB	dbGetLog
Get met information	dbGetMetInfo
Get the final leaf number	dbGetOrganFinalLeafNumber
Get Haun Index	dbGetOrganHaunIndex
Get phenotype values through a group of conditions	dbGetPhenotype
Estimation of flowering time	dbGetPlantFlowering
Estimation of heading time	dbGetPlantHeading
Estimation of stem elongation	dbGetPlantStemElongation
Estimation of stem number per plant	dbGetPlantStemNumber
Estimation of tiller number per plant	dbGetPlantTillerNumber
Get site into expDB	dbGetSites
Get source from expDB	dbGetSource
Get trait list	dbGetTraits
Get trials by a groups of conditions.	dbGetTrials
Get weather records from expDB	dbGetWeather
Obtain the key phenology stage	dbGetZadoksStage
Import data from excel file	dbImportXLSX
Insert new rows or update existing rows to a specific table according to a specific column (unique) by each row	dbInsertUpdateByRow
List all trials	dbListTrials
Connect to expDB	expdbConnect
create to expDB	expdbCreateDB
Didconnect to expDB	expdbDisconnect
Get index id by unique_columns.	getIdByUniqueIndex
Process quadrat (detail) harvestQuadratDetail	harvestQuadratDetail