| Title: | Tools for Reading, Processing and Writing 'DSSAT' Files |
|---|---|
| Description: | Provides methods for reading, displaying, processing and writing files originally arranged for the 'DSSAT-CSM' fixed width format. The 'DSSAT-CSM' cropping system model is described at J.W. Jones, G. Hoogenboomb, C.H. Porter, K.J. Boote, W.D. Batchelor, L.A. Hunt, P.W. Wilkens, U. Singh, A.J. Gijsman, J.T. Ritchie (2003) <doi:10.1016/S1161-0301(02)00107-7>. |
| Authors: | Homero Lozza [aut, cre] |
| Maintainer: | Homero Lozza <[email protected]> |
| License: | GPL (>=2) |
| Version: | 0.3.4 |
| Built: | 2025-03-08 03:14:51 UTC |
| Source: | https://github.com/hlozza/dasst |
The Dasst (DSSAT-style AS Simple Tables) package provides methods for reading, processing and writing files originally formatted for the 'DSSAT-CSM' crop simulation models.
The Dasst package defines the
Dasst class which enables to store
the data encoded for the 'DSSAT-CSM' crop simulation
models as an S4 object, both for the inputs and the
outputs. Several methods are available.
Homero Lozza, [email protected]
Dasst for class definition,
show, summary,
[[ [ methods for content
description, and read.dssat function for
reading files. For other available methods see INDEX
file.
An object example is available at
plantGrowth.
"[" gets a subset of an object of class
Dasst.
x |
An object of class |
i |
An integer or logical vector. This is the subset that will be retrieved from the whole object. |
This method gets a subset of an object of class
Dasst. Shorter objects in the
expression are recycled as often as need be until they
match the length of the longest object.
A new object of class Dasst that
comprises the elements from the selected subset.
data(plantGrowth) length(plantGrowth) plantgro1 <- plantGrowth[1:10] length(plantgro1) class(plantgro1) # Drop contents corresponding to selected orders summary(plantGrowth) plantgro2 <- plantGrowth[-1] summary(plantgro2)data(plantGrowth) length(plantGrowth) plantgro1 <- plantGrowth[1:10] length(plantgro1) class(plantgro1) # Drop contents corresponding to selected orders summary(plantGrowth) plantgro2 <- plantGrowth[-1] summary(plantgro2)
"[[" gets the contents of a table from an object
of class Dasst.
x |
An object of class |
i |
An integer value. Position where values will be retrieved. |
This method gets the contents of the selected table
stored in an object of class Dasst.
Tables are internally stored and retrieved as
data.frame. Rules for subset can be
applied.
The values retrieved from the table at position i as
data.frame.
data(plantGrowth) class(plantGrowth[[1]]) plantGrowth[[1]] plantGrowth[[1]][1:10,]data(plantGrowth) class(plantGrowth[[1]]) plantGrowth[[1]] plantGrowth[[1]][1:10,]
Dasst
"[[<-" sets the contents of a table from an object
of class Dasst.
x |
An object of class |
i |
An integer value. Position where values will be updated. |
value |
Any Values to be stored at the given position. |
This method sets the contents of the selected table
stored in an object of class Dasst.
Tables are internally stored and retrieved as
data.frame. Rules for subset can be
applied.
The actual object of class Dasst.
# Add a row of NA at the end of the table 1 data(plantGrowth) rmax <- nrow(plantGrowth[[1]]) plantGrowth[[1]][rmax + 1, ] <- NA # Edit a subset plantGrowth[[1]][131:132,2:4] plantGrowth[[1]][131:132,2:4] <- matrix(rep(100,6),nrow=2) plantGrowth[[1]][131:132,2:4] # Remove the last rows # No need to subset left hand side. Dimension are automatically adjusted. tail(plantGrowth[[1]]) plantGrowth[[1]] <- plantGrowth[[1]][c(-131,-132), ] tail(plantGrowth[[1]]) # Column names are also valid plantGrowth[[1]][129:130,"SNW1C"] plantGrowth[[1]][129:130,"SNW1C"] <- 1100:1101 plantGrowth[[1]][129:130,"SNW1C"]# Add a row of NA at the end of the table 1 data(plantGrowth) rmax <- nrow(plantGrowth[[1]]) plantGrowth[[1]][rmax + 1, ] <- NA # Edit a subset plantGrowth[[1]][131:132,2:4] plantGrowth[[1]][131:132,2:4] <- matrix(rep(100,6),nrow=2) plantGrowth[[1]][131:132,2:4] # Remove the last rows # No need to subset left hand side. Dimension are automatically adjusted. tail(plantGrowth[[1]]) plantGrowth[[1]] <- plantGrowth[[1]][c(-131,-132), ] tail(plantGrowth[[1]]) # Column names are also valid plantGrowth[[1]][129:130,"SNW1C"] plantGrowth[[1]][129:130,"SNW1C"] <- 1100:1101 plantGrowth[[1]][129:130,"SNW1C"]
Dasst
"[<-" sets to a subset of an object of class
Dasst an other object of the same
class
x |
An object of class |
i |
An integer or logical vector. This is the subset that will be updated from the whole object. |
value |
An object of class
|
This method sets to a subset of an object of class
Dasst an other object of the same
class. Shorter objects in the expression are recycled as
often as need be until they match the length of the
longest object.
The actual object of class Dasst
that comprises the elements updated from the selected
subset.
# Replace position 1 with the contents of position 30. data(plantGrowth) plantGrowth[[1]][1:10, 1:15] plantGrowth[1] <- plantGrowth[30] plantGrowth[[1]][1:10, 1:15] # Add a copy of the first order at the end extending the object length rmax <- length(plantGrowth) rmax plantGrowth[rmax+1] <- plantGrowth[1] length(plantGrowth) # Copy position 2 into position 31, moving the former position 31 to the 32. plantgro31 <- plantGrowth[31] plantGrowth[31] <- plantGrowth[2] plantGrowth[32] <- plantgro31# Replace position 1 with the contents of position 30. data(plantGrowth) plantGrowth[[1]][1:10, 1:15] plantGrowth[1] <- plantGrowth[30] plantGrowth[[1]][1:10, 1:15] # Add a copy of the first order at the end extending the object length rmax <- length(plantGrowth) rmax plantGrowth[rmax+1] <- plantGrowth[1] length(plantGrowth) # Copy position 2 into position 31, moving the former position 31 to the 32. plantgro31 <- plantGrowth[31] plantGrowth[31] <- plantGrowth[2] plantGrowth[32] <- plantgro31
addDate<- adds a column of class date to tables of
the object of class Dasst.
x |
An object of class |
... |
Other parameters: format, character vector encoding the date format; |
value |
A formula, numeric vector or character vector. Order of the column fields from where dates can be composed. |
This method adds a column of class date to tables of the
object of class Dasst. Dates
expressed as string or integers may be converted and
stored as date objects in a new column whose name begins
with "date_" and follows with the names of column fields
involved in the date extraction.
So far, the new column will not be saved if the write method is invoked.
The actual object.
data(plantGrowth) addDate(plantGrowth) <- ~ YEAR + DOY # or addDate(plantGrowth) <- c("YEAR", "DOY") # or addDate(plantGrowth) <- c(1, 2) # Only one tables 1 and specifying date format addDate(plantGrowth, index=c(1,2), format="%Y%j") <- ~ YEAR + DOYdata(plantGrowth) addDate(plantGrowth) <- ~ YEAR + DOY # or addDate(plantGrowth) <- c("YEAR", "DOY") # or addDate(plantGrowth) <- c(1, 2) # Only one tables 1 and specifying date format addDate(plantGrowth, index=c(1,2), format="%Y%j") <- ~ YEAR + DOY
Coerces an object of class Dasst to
an object of class list.
This function enables the function as to
coerce objects of class Dasst to
belong to class list.
data(plantGrowth) lplantgro <- as(plantGrowth, "list") class(lplantgro)data(plantGrowth) lplantgro <- as(plantGrowth, "list") class(lplantgro)
buildContents generates contents that are inserted
into an object of class Dasst.
buildContents(fileName, section, headerLine, dataLine, table)buildContents(fileName, section, headerLine, dataLine, table)
fileName |
A character string. The file name and path corresponding to the generated contents. |
section |
A character string. The section title corresponding to the generated contents. |
headerLine |
A character string. The header names for the table of data included in the generated contents. |
dataLine |
A character string. A typically formatted line of data. |
table |
A data.frame. The records for the table of
data included in the generated contents are inserted as a
|
This function builds the contents that are inserted into
an object of class Dasst from a
data.frame and ancillary character strings.
The data.frame contains the actual data
that is stored as a table within the object of class
Dasst.
An object of class Dasst.
mydf <- data.frame(a=c(1,2,3), b=c("one","two","three"),c=c(1.1,2.2,3.3)) myObj <- Dasst() myObj[1] <- buildContents("MyTest.OUT","*TestSec", "@ID NAME VALUE"," 1 one 1.100", mydf)mydf <- data.frame(a=c(1,2,3), b=c("one","two","three"),c=c(1.1,2.2,3.3)) myObj <- Dasst() myObj[1] <- buildContents("MyTest.OUT","*TestSec", "@ID NAME VALUE"," 1 one 1.100", mydf)
Dasst.compute<- computes an expression using the columns
of the object of class Dasst.
x |
An object of class |
cocol |
A character string. The name of the new column field. |
value |
A character string. An expression to compute within column fields. |
This method computes an expression taking the values
recorded on each column field used in the expression
belonging to the object of class
Dasst. The result is stored as a new
column table.
So far, the new column will not be saved if the write method is invoked.
The actual object of class Dasst.
data(plantGrowth) compute(plantGrowth, "date_YEAR_DOY") <- "as.Date(paste(YEAR, DOY, sep=\"\"), format=\"%Y%j\")"data(plantGrowth) compute(plantGrowth, "date_YEAR_DOY") <- "as.Date(paste(YEAR, DOY, sep=\"\"), format=\"%Y%j\")"
Dasst is a constructor for the user that returns
an empty object of class Dasst.
Dasst()Dasst()
This function constructs an empty object of class
Dasst. No arguments are required.
An empty object of class Dasst.
Dasst for class definition.
myObj <- Dasst() myObj class(myObj) length(myObj)myObj <- Dasst() myObj class(myObj) length(myObj)
An S4 class that stores information recorded on DSSAT-style files.
fileNames:A character vector containing the names and the paths to the original data files.
sections:A character vector containing the names for each section within the DSSAT-style format specification and structure.
fields:A list of data.frame
containing the names, modes, and widths in characters for
each data field. The number of decimal digits are also
stored in each numeric field.
tables:A
list of data.frame containing the actual
values retrieved from the original file.
show, summary,
[[ [ methods for content
description, and read.dssat function for
reading files. For other available methods see INDEX
file.
An object example is available at
plantGrowth.
gatherTables gathers the result of performing a
certain operation over the tables of an object of class
Dasst.
gatherTables(object, coCol, opCol, operation, ...)gatherTables(object, coCol, opCol, operation, ...)
object |
Object of class
|
coCol |
A character vector. The field names of those columns that will be copied identically into the result. |
opCol |
A character vector. The field names of those columns that will be gather by means of applying the required operation. |
operation |
A function. The function name for the
required operation. i.e. |
... |
Other parameters for the |
This function gathers the result of performing a certain
operation over the tables of an object of class
Dasst. The result is given as a
data.frame.
A data.frame with the values gathered after
the application of the operator to the required columns.
data(plantGrowth) plantgro12 <- gatherTables(plantGrowth[1:10], c("DAP"), c("SWAD","LWAD","GWAD"), mean)data(plantGrowth) plantgro12 <- gatherTables(plantGrowth[1:10], c("DAP"), c("SWAD","LWAD","GWAD"), mean)
Dasst
getAncillary gets ancillary data from an object of
class Dasst connected to the
selected table orders.
x |
An object of class |
i |
An optional integer vector. Orders where to retrieve ancillary data. The default action is to retrieve all the available ancillary data. |
This method gets ancillary data from an object of class
Dasst connected to the selected
table orders. Values are arranged in tables, and the
order is the number assigned successively to each of them
after the data have been stored within the
Dasst object. getAncillary
provides ancillary data such as the file name which was
originally read, and the section and the header which
introduced the values within the file.
An object of class Ancillary which contains the retrieved ancillary data for the selected table orders.
data(plantGrowth) getAncillary(plantGrowth, c(1,3,5))data(plantGrowth) getAncillary(plantGrowth, c(1,3,5))
Dasst.length.Dasst computes the length of an object of
class Dasst.
## S3 method for class 'Dasst' length(x)## S3 method for class 'Dasst' length(x)
x |
Object of class |
This function extends the S3 length generic
function. It computes the length of an object of class
Dasst. The length equals the
quantity of stored tables. The empty object has length
0.
An integer representing the length of the object.
data(plantGrowth) length(plantGrowth)data(plantGrowth) length(plantGrowth)
Dasst.This sets the length of an object of class
Dasst.
## S3 replacement method for class 'Dasst' length(x) <- value## S3 replacement method for class 'Dasst' length(x) <- value
x |
Object of class |
value |
Integer value. Sets the new length of the
|
length<-.Dasst function extends the S3
length generic function. It sets the length
of an object of class Dasst. The
object can be shrinked or extended adding NULL or
NA contents.
An integer value corresponding to the actual length of the object.
data(plantGrowth) length(plantGrowth) length(plantGrowth) <- 8 length(plantGrowth)data(plantGrowth) length(plantGrowth) length(plantGrowth) <- 8 length(plantGrowth)
An example of a Dasst object based
on file PlantGro.OUT. The originally data set can be
found within package directory as
‘extdata/PlantGro.OUT’.
plantGrowth contains the daily plant growth for 3
treatments repeated on 10 years. A summary of its
contents follows
45 fields and 131 records
45 fields and 112 records
45 fields and 124 records
...
45 fields and 123 records
Tables ranging from 1 to 10 have plant output data for treatment 1 which simulates maize growth from 1970 to 1979 (south hemisphere). Treatment 2 adds fertilization with 50kg/ha of urea, and treatment 3 adds fertilization with 100kg/ha of urea.
Dasst for class definition and the
example at read.dssat.
data(plantGrowth) plot(plantGrowth[[1]][,"DAP"],plantGrowth[[1]][,"LAID"]) # Or plot(plantGrowth[[1]][,c("DAP","LAID")])data(plantGrowth) plot(plantGrowth[[1]][,"DAP"],plantGrowth[[1]][,"LAID"]) # Or plot(plantGrowth[[1]][,c("DAP","LAID")])
Ancillary
print.Ancillary prints the contents of an object
of class Ancillary.
## S3 method for class 'Ancillary' print(x, ...)## S3 method for class 'Ancillary' print(x, ...)
x |
Object of class |
... |
Arguments that may be passed to other functions. |
This function extends the S3 print generic
function. It prints the contents of an object of class
Ancillary.
An invisible object.
data(plantGrowth) getAncillary(plantGrowth, 1:5)data(plantGrowth) getAncillary(plantGrowth, 1:5)
print.Dasst prints the contents of an object of
class Dasst.
## S3 method for class 'Dasst' print(x, ix = 1, ...)## S3 method for class 'Dasst' print(x, ix = 1, ...)
x |
Object of class |
ix |
An integer number. The contents of the first
table are print by default. Others table contents can be
display setting this parameter in the range form 1 to
|
... |
Other parameters for the
|
This function extends the S3 print generic
function. It prints the contents of an object of class
Dasst.
An invisible object.
data(plantGrowth) print(plantGrowth)data(plantGrowth) print(plantGrowth)
summary.Dasst
print.summary.Dasst prints the contents of an
object of class summary.Dasst.
## S3 method for class 'summary.Dasst' print(x, ...)## S3 method for class 'summary.Dasst' print(x, ...)
x |
Object of class |
... |
Arguments that may be passed to other functions. |
This function extends the S3 print generic
function. It prints the contents of an object of class
summary.Dasst.
An invisible object.
data(plantGrowth) summary(plantGrowth)data(plantGrowth) summary(plantGrowth)
read.dssat reads the contents of a file or group
of files and stores the contents into an object of class
Dasst.
read.dssat(fileVec, fieldVec = character(), keyVec = character())read.dssat(fileVec, fieldVec = character(), keyVec = character())
fileVec |
A character vector. The names including the paths to the files that will be read. |
fieldVec |
A character vector. An optional parameter. If it is not specified, all column fields are retrieved. Else, the names subset are the only retrieved column fields. |
keyVec |
A character vector. An optional parameter. If it is not specified, only sections satisfying this condition will be retrieved. |
This function reads the contents of a file or group of
files and stores the contents into an object of class
Dasst.
A Dasst object with the structure
and information originally saved in the file using
DSSAT-style format specifications.
dssatfile <- system.file("extdata","PlantGro.OUT",package="Dasst") dssatfile plantgro <- read.dssat(dssatfile) summary(plantgro)dssatfile <- system.file("extdata","PlantGro.OUT",package="Dasst") dssatfile plantgro <- read.dssat(dssatfile) summary(plantgro)
Dasst objectsearchAncillary looks for ancillary data that
satisfies the search criteria and gives the table orders
in the Dasst object for successful
results.
x |
An object of class |
fileKey |
A character string. Search for this pattern within the "filename" slot. |
secKey |
A character string. Search for this pattern within the "section" slot. |
colKey |
A character string. Search for this pattern within the tables column names. |
... |
Other parameters than may be passed to grepl. |
This method searches for character strings or regular
expressions in the ancillary data of the
Dasst object. Patterns are sought
into "fileNames" and "sections" slots, and table column
names. The corresponding table orders whose ancillary
data satisfied the search criteria are gathered in a
vector.
An integer representing the table orders whose ancillary data satisfied the search criteria.
data(plantGrowth) searchAncillary(plantGrowth, secKey="run[[:space:]]*1") searchAncillary(plantGrowth, secKey="run[[:space:]]*1", ignore.case=TRUE)data(plantGrowth) searchAncillary(plantGrowth, secKey="run[[:space:]]*1") searchAncillary(plantGrowth, secKey="run[[:space:]]*1", ignore.case=TRUE)
Dasst
show shows a few contents of an object of class
Dasst.
This method shows the contents of the first table stored
in an object of class Dasst. It
displays values limited to a few records. Use the
print function for more options.
data(plantGrowth) plantGrowthdata(plantGrowth) plantGrowth
stackTables stacks the tables of an object of
class Dasst.
stackTables(object)stackTables(object)
object |
Object of class
|
This function stacks the tables of an object of class
Dasst. The result is given as a
data.frame.
A data.frame composed of the stacked
tables.
data(plantGrowth) nrow(plantGrowth[[1]]) nrow(plantGrowth[[2]]) plantgro12 <- stackTables(plantGrowth[1:2]) nrow(plantgro12)data(plantGrowth) nrow(plantGrowth[[1]]) nrow(plantGrowth[[2]]) plantgro12 <- stackTables(plantGrowth[1:2]) nrow(plantgro12)
Dasst
summary summarizes the contents of an object of
class Dasst.
## S3 method for class 'Dasst' summary(object, ...)## S3 method for class 'Dasst' summary(object, ...)
object |
An object of class
|
... |
Arguments that may be passed to other functions. |
This method summarizes the contents of the object of
object of class Dasst. After reading
a DSSAT file, summary can give an idea of the volume of
information stored in that file.
An object of class summary.Dasst
data(plantGrowth) summary(plantGrowth)data(plantGrowth) summary(plantGrowth)
write.dssat writes to a file the contents of an
object of class Dasst.
write.dssat(object, fnames)write.dssat(object, fnames)
object |
An object of class
|
fnames |
A character vector. The paths to the files
where the contents of the object of class
|
This function writes to a file the contents of an object
of class Dasst striving to maintain
compatibility with the DSSAT-style format specifications.
The fnames vector specifies the paths to the files
where data will be stored. Each table of the
Dasst object may be saved in an
individual file. If the length of fnames vector is
shorter than the length of the object, then the paths
will be recycled as necessary.
If paths contain file names that already exist, first the
original files are saved appending a ‘.bak’
extension. Then, the Dasst object is
saved using these paths.
data(plantGrowth) length(plantGrowth) <- 1 ffn <- paste(tempdir(), "PlantGro.OUT", sep="/") write.dssat(plantGrowth, ffn)data(plantGrowth) length(plantGrowth) <- 1 ffn <- paste(tempdir(), "PlantGro.OUT", sep="/") write.dssat(plantGrowth, ffn)