| Type: | Package |
| Title: | Database for Experiment Dataset |
| Version: | 0.3.0 |
| Maintainer: | Bangyou Zheng <bangyou.zheng@csiro.au> |
| Description: | 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. |
| License: | MIT + file LICENSE |
| URL: | https://expdb.bangyou.me/, https://github.com/byzheng/expdb |
| BugReports: | https://github.com/byzheng/expdb/issues |
| Encoding: | UTF-8 |
| Imports: | DBI, RSQLite, utils, readxl, png, grid, tibble, lubridate, dplyr, methods, weaana (≥ 0.1.1), tidyr, magrittr, stats, reshape2, stringr, rlang |
| RoxygenNote: | 7.3.2 |
| Suggests: | testthat |
| NeedsCompilation: | no |
| Packaged: | 2025-09-23 11:46:13 UTC; zhe00a |
| Author: | Bangyou Zheng [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2025-09-23 12:00:02 UTC |
Approximate Date for a Target Zadoks Stage
Description
This function estimates the date corresponding to a specified target Zadoks stage by interpolating between known Zadoks stages and their associated dates. Phenology Analysis Functions
Usage
approx_zadoks(zadoks, date, target)
Arguments
zadoks |
A numeric vector of Zadoks growth stages (should be between 51 and 69). |
date |
A vector of dates (class |
target |
A single numeric value indicating the target Zadoks stage for which to estimate the date. |
Details
This module provides methods for analyzing phenological data, particularly focusing on the Zadoks scale.
The following two methods are implemented:
1. **Relative Date for Observed Target (Zadoks Rounded):** - If the target phenological stage is observed in the dataset (after rounding Zadoks values), the function will use the relative date corresponding to this observation. This allows for precise tracking of phenological events based on actual recorded data.
2. **Linear Interpolation for Target within Observed Range:** - If the target Zadoks stage is not directly observed but falls within the range of observed stages, the function estimates the date using linear interpolation between the nearest observed stages. This provides an approximate date for the target stage based on the trend of observed data.
Value
A Date object representing the interpolated date for the target Zadoks stage,
or NA if the target is outside the observed range.
Note
Ensure that the input data includes Zadoks stage observations and corresponding dates for accurate analysis.
Examples
zadoks <- c(51, 54, 55, 59)
date <- as.Date(c("2020-08-15", "2020-08-17", "2020-08-18", "2020-08-21"))
target <- 55
approx_zadoks(zadoks, date, target)
approx_zadoks(zadoks[-3], date[-3], target)
Add design for a trial
Description
Add design for a trial
Usage
dbAddDesigns(con, data, extra_design = NULL)
Arguments
con |
a connection object as produced by dbConnect |
data |
Trial design |
extra_design |
The extra columns for design |
Value
no return values
Insert or Update fertilization into expDB
Description
Insert or Update fertilization into expDB
Usage
dbAddFertilization(con, data)
Arguments
con |
a connection object as produced by dbConnect |
data |
A data frame includes all columns |
Value
no return values
Add gene information into database
Description
Add gene information into database
Usage
dbAddGene(con, genes)
Arguments
con |
a connection object as produced by dbConnect |
genes |
A data.frame of genes |
Value
No return values
Add gene allele information into database
Description
Add gene allele information into database
Usage
dbAddGeneAllele(con, genes)
Arguments
con |
a connection object as produced by dbConnect |
genes |
A data.frame of genes |
Value
No return values
Add genotypes into expDB
Description
Add genotypes into expDB
Usage
dbAddGenotype(con, genotypes)
Arguments
con |
a connection object as produced by dbConnect |
genotypes |
A string vector of genotypes |
Value
No return values
Insert or Update irrigation into expDB
Description
Insert or Update irrigation into expDB
Usage
dbAddIrrigatons(con, data)
Arguments
con |
a connection object as produced by dbConnect |
data |
A data frame includes all columns |
Value
no return values
Add log from expDB
Description
Add log from expDB
Usage
dbAddLog(con, msg, date = format(Sys.time(), format = "%Y-%m-%d"))
Arguments
con |
a connection object as produced by dbConnect |
msg |
Add message into expdb |
date |
Create time of message |
Value
No return values
Insert or Update methods into expDB
Description
Insert or Update methods into expDB
Usage
dbAddMethods(con, data)
Arguments
con |
a connection object as produced by dbConnect |
data |
A data frame includes all columns |
Value
no return values
Insert and update met into expDB
Description
Insert and update met into expDB
Usage
dbAddMets(con, data)
Arguments
con |
a connection object as produced by dbConnect |
data |
Met design |
Value
no return values
Add nodes into expDB
Description
Add nodes into expDB
Usage
dbAddNodes(con, data)
Arguments
con |
a connection object as produced by dbConnect |
data |
phenotype value |
Value
no return values
Add design for a trial
Description
Add design for a trial
Usage
dbAddPhenotype(con, data)
Arguments
con |
a connection object as produced by dbConnect |
data |
phenotype value |
Value
no return values
Insert and update researcher into expDB
Description
Insert and update researcher into expDB
Usage
dbAddResearcher(con, data)
Arguments
con |
A connection object as produced by dbConnect |
data |
A data frame includes all columns |
Value
no return values
Insert or update site into expDB
Description
Insert or update site into expDB
Usage
dbAddSites(con, data)
Arguments
con |
a connection object as produced by dbConnect |
data |
A data frame includes all columns |
Value
no return values
Insert and update source into expDB
Description
Insert and update source into expDB
Usage
dbAddSource(con, data)
Arguments
con |
A connection object as produced by dbConnect |
data |
A data frame includes all columns |
Value
no return values
Insert or update trait into expDB
Description
Insert or update trait into expDB
Usage
dbAddTraits(con, data)
Arguments
con |
a connection object as produced by dbConnect |
data |
A data frame includes all columns |
Value
no return values
Add soil for a trial
Description
Add soil for a trial
Usage
dbAddTrialSoil(
con,
data,
units = list(thickness = "cm", no3 = "kg/ha", nh4 = "kg/ha")
)
Arguments
con |
a connection object as produced by dbConnect |
data |
Soil profiles for trials |
units |
a list for the unit |
Value
no return values
Insert or Update trial into expDB
Description
Insert or Update trial into expDB
Usage
dbAddTrials(con, data)
Arguments
con |
a connection object as produced by dbConnect |
data |
A data frame includes all columns |
Value
no return values
Add weather records into expDB
Description
Add weather records into expDB
Usage
dbAddWeather(con, data, name = NULL)
Arguments
con |
a connection object as produced by dbConnect |
data |
A string character for the path to met file, a WeaAna object, or a data frame. |
name |
The met name in the database if data is a data frame. |
Value
no return values
Append a table into db and check the column name
Description
Append a table into db and check the column name
Usage
dbAppendTable(con, table, data)
Arguments
con |
A connection object as produced by dbConnect |
table |
The target table name |
data |
A data frame to write into table |
Export trials weather records to met file
Description
Export trials weather records to met file
Usage
dbExportMet(con, output, na = NA, ...)
Arguments
con |
a connection object as produced by dbConnect |
output |
The folder of output files |
na |
The character for missing value with default NA |
... |
All other arguments to define range of export trials. All trials will be export if there are not arguments. Supported arguments include trial (or trialcode) |
Value
Write weather records into files. No return values.
Check genotype names
Description
Check genotype names
Usage
dbGenotypeCheckName(con, genotype)
Arguments
con |
a connection object as produced by dbConnect |
genotype |
The genotype name will be checked |
Value
A vector with check genotype names
Get the dry weight per stem
Description
Get the dry weight per stem
Usage
dbGetDryWeightPerStem(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
... |
Arguments pass to dbGetTrials |
Value
A data.frame for selected dry weight per stem
Get fertilization from database
Description
Get fertilization from database
Usage
dbGetFertilization(con, ...)
Arguments
con |
a connection object as produced by dbConnect |
... |
Other arguments to specify meta data |
Value
a data.frame for fertilization information
Estimation of maturity
Description
Estimation of maturity
Usage
dbGetFieldMaturity(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
... |
Arguments pass to dbGetTrials |
Value
A data.frame for selected maturity time
Estimation of plant populations
Description
Estimation of plant populations
Usage
dbGetFieldPopulation(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
... |
Arguments pass to dbGetTrials |
Value
A data.frame for selected field population
Estimation of stem number per unit area
Description
Estimation of stem number per unit area
Usage
dbGetFieldStemNumber(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
... |
Arguments pass to dbGetTrials |
Value
A data.frame for selected stem number
Estimation of tiller number per unit area
Description
Estimation of tiller number per unit area
Usage
dbGetFieldTillerNumber(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
... |
Arguments pass to dbGetTrials |
Value
A data.frame for selected tiller number
Get the gene information
Description
Get the gene information
Usage
dbGetGene(con)
Arguments
con |
a connection object as produced by dbConnect |
Value
a data.frame with all gene information
Get the genotype information
Description
Get the genotype information
Usage
dbGetGenotype(con, name_only = FALSE)
Arguments
con |
a connection object as produced by dbConnect |
name_only |
Only return the name of genotypes |
Value
data.frame with genotype information or a vector with genotype name if name_only = TRUE.
Get irrigation from database
Description
Get irrigation from database
Usage
dbGetIrrigation(con, ...)
Arguments
con |
a connection object as produced by dbConnect |
... |
Other arguments to specify meta data |
Value
a data frame for irrigation information
Get log from expDB
Description
Get log from expDB
Usage
dbGetLog(con)
Arguments
con |
a connection object as produced by dbConnect |
Value
A data.frame with all logs
Get met information
Description
Get met information
Usage
dbGetMetInfo(con, name)
Arguments
con |
a connection object as produced by dbConnect |
name |
The met name |
Value
a data.frame for met information
Get the final leaf number
Description
The final leaf number is first retrived from trait "O_FinalLeafNumber", then calculated from trait "O_HaunIndex" if "O_FinalLeafNumber" is not observed. Final leaf number equals the maximum value of "O_HaunIndex", which should be an integer.
Usage
dbGetOrganFinalLeafNumber(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments |
... |
Arguments to specific trials. |
Value
A data.frame for selected final leaf number
Get Haun Index
Description
The Haun Index is retrived from trait "O_HaunIndex", extending the final observationa
Usage
dbGetOrganHaunIndex(con, trials = NULL, avg = TRUE, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments |
avg |
Whether to calculate the average value |
... |
Arguments to specific trials. |
Value
A data.frame for selected Haun Index
Get phenotype values through a group of conditions
Description
Get phenotype values through a group of conditions
Usage
dbGetPhenotype(
con,
traits = NULL,
direction = "long",
tt = FALSE,
gene = FALSE,
...
)
Arguments
con |
a connection object as produced by dbConnect |
traits |
A list of traits. All traits will be returned if NULL |
direction |
One of 'long' or 'wide' for reshape function |
tt |
Whether to calculate thermal time |
gene |
Whether to get gene information |
... |
All other arguments to define range of export trials |
Value
a data.frame for selected phenotypic values
Estimation of flowering time
Description
Estimation of flowering time
Usage
dbGetPlantFlowering(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
... |
Arguments pass to dbGetTrials |
Value
A data.frame for selected flowering time
Estimation of heading time
Description
Estimation of heading time
Usage
dbGetPlantHeading(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
... |
Arguments pass to dbGetTrials |
Value
A data.frame for selected heading time
Estimation of stem elongation
Description
Estimation of stem elongation
Usage
dbGetPlantStemElongation(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
... |
Arguments pass to dbGetTrials |
Value
A data.frame for selected stem elongation stage
Estimation of stem number per plant
Description
Estimation of stem number per plant
Usage
dbGetPlantStemNumber(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
... |
Arguments pass to dbGetTrials |
Value
A data.frame for selected stem number for individual plant
Estimation of tiller number per plant
Description
Estimation of tiller number per plant
Usage
dbGetPlantTillerNumber(con, trials = NULL, ...)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
... |
Arguments pass to dbGetTrials |
Value
A data.frame for selected tiller number for individual plant
Get site into expDB
Description
Get site into expDB
Usage
dbGetSites(con)
Arguments
con |
a connection object as produced by dbConnect |
Value
a data.frame for all sites in the data base
Get source from expDB
Description
Get source from expDB
Usage
dbGetSource(con)
Arguments
con |
a connection object as produced by dbConnect |
Value
A data.frame for all source in the data base
Get trait list
Description
Get trait list
Usage
dbGetTraits(con)
Arguments
con |
a connection object as produced by dbConnect |
Value
a data.frame for all traits in the data base
Get trials by a groups of conditions.
Description
Get trials by a groups of conditions.
Usage
dbGetTrials(con, design = TRUE, ...)
Arguments
con |
a connection object as produced by dbConnect |
design |
Whether include design |
... |
All other arguments to define range of export trials. All trials will be export if there are not arguments. Supported arguments include trial (or trialcode) |
Value
A data.frame for selected trials
Get weather records from expDB
Description
Get weather records from expDB
Usage
dbGetWeather(con, name, format = "data_frame", na = NA_character_, tz = "UTC")
Arguments
con |
a connection object as produced by dbConnect |
name |
The met name |
format |
The format of export dataset. |
na |
The character for missing value with default NA |
tz |
Time zone applied for hourly temperature |
Value
a data.frame for all weather records
Obtain the key phenology stage
Description
Obtain the key phenology stage
Usage
dbGetZadoksStage(con, trials, key_stage)
Arguments
con |
a connection object as produced by dbConnect |
trials |
A data.frame to specify trials. If not NULL, other arguments will be ignored. |
key_stage |
The key zadoks stage |
Value
A data.frame for selected Zadoks stage
Import data from excel file
Description
Import data from excel file
Usage
dbImportXLSX(con, xlsx, ignore_genotype = TRUE, ignore_trait = TRUE, ...)
Arguments
con |
a connection object as produced by dbConnect |
xlsx |
The path to excel file |
ignore_genotype |
Ignore genotype tables when importing |
ignore_trait |
Ignore trait table when importing |
... |
Other arguments. Supported arguments include
|
Value
No return values
Insert new rows or update existing rows to a specific table according to a specific column (unique) by each row
Description
Insert new rows or update existing rows to a specific table according to a specific column (unique) by each row
Usage
dbInsertUpdateByRow(con, table, data, unique_col = "name")
Arguments
con |
A connection object as produced by dbConnect |
table |
The target table name |
data |
A data frame to write into table |
unique_col |
A character vector to indentify each row in the table |
List all trials
Description
List all trials
Usage
dbListTrials(con)
Arguments
con |
a connection object as produced by dbConnect |
Value
A data.frame for all trials in the data base
Connect to expDB
Description
Connect to expDB
Usage
expdbConnect(filename)
Arguments
filename |
The filename of SQLite |
Value
a connection object as produced by dbConnect
Examples
## Not run:
con <- connect('filename')
## End(Not run)
create to expDB
Description
create to expDB
Usage
expdbCreateDB(filename, system_traits = TRUE)
Arguments
filename |
The filename of new expDB |
system_traits |
Whether to import system traits |
Value
a connection object as produced by dbConnect
Didconnect to expDB
Description
Didconnect to expDB
Usage
expdbDisconnect(con)
Arguments
con |
a connection object as produced by dbConnect. |
Value
no return values
Examples
## Not run:
con <- connect('filename')
disconnect(con)
## End(Not run)
Get index id by unique_columns.
Description
Get index id by unique_columns.
Usage
getIdByUniqueIndex(
con,
table,
data,
unique_col = "name",
data_col = unique_col,
ignore_case = FALSE
)
Arguments
con |
a connection object as produced by dbConnect |
table |
the table name |
data |
A data frame to write into table |
unique_col |
A character vector to identify each row in the table |
data_col |
The column names in the data.frame |
ignore_case |
Whether ignore_case |
Value
id of unique_col
Process quadrat (detail) harvestQuadratDetail
Description
Process quadrat (detail) harvestQuadratDetail
Usage
harvestQuadratDetail(con, records)
Arguments
con |
a connection object as produced by dbConnect |
records |
Phenotype records |
Value
no return values