| Type: | Package |
| Title: | Database for Experiment Dataset |
| Version: | 0.1.0 |
| 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, tidyverse, magrittr, stats, reshape2, stringr, rlang |
| RoxygenNote: | 7.1.2 |
| Suggests: | testthat |
| NeedsCompilation: | no |
| Packaged: | 2021-10-08 05:00:13 UTC; zhe00a |
| Author: | Bangyou Zheng [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2021-10-08 17:40:06 UTC |
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