| Type: | Package |
| Title: | A Comprehensive R Interface for the DSSAT Cropping Systems Model |
| Version: | 0.0.9 |
| Date: | 2024-01-19 |
| Author: | Phillip D. Alderman [aut, cre] |
| Maintainer: | Phillip D. Alderman <phillip.alderman@okstate.edu> |
| Description: | The purpose of this package is to provide a comprehensive R interface to the Decision Support System for Agrotechnology Transfer Cropping Systems Model (DSSAT-CSM; see https://dssat.net for more information). The package provides cross-platform functions to read and write input files, run DSSAT-CSM, and read output files. |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| Imports: | dplyr (≥ 1.0.0), glue, lubridate, magrittr, methods, purrr, readr, rlang, stringr, tibble, tidyr, tidyselect, utils |
| RoxygenNote: | 7.2.3 |
| Suggests: | knitr, rmarkdown |
| BugReports: | https://github.com/palderman/DSSAT/issues |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2024-02-19 18:16:33 UTC; palderman |
| Repository: | CRAN |
| Date/Publication: | 2024-02-19 18:30:02 UTC |
Adds width as a attribute to each column from a list of tibbles
Description
Adds width as a attribute to each column from a list of tibbles
Usage
add_col_widths(tbl_list, fwf_pos)
Arguments
tbl_list |
a list of tibbles |
fwf_pos |
a list of returns from |
Value
a tibble containing the data from the raw DSSAT file
Adds variable format information to a tibble
Description
Adds variable format information to a tibble
Usage
add_v_fmt(input_tbl, v_fmt = NULL)
Arguments
input_tbl |
a tibble |
v_fmt |
a named vector containing variable format information to be added to 'input_tbl' |
Value
a tibble containing the original tibble with an additional attribute that contains variable format information
Examples
# Extract file path for sample ecotype file
sample_eco_file <- system.file('extdata','SAMPLE.ECO',package='DSSAT')
# Read sample ecotype file
eco <- read_eco(sample_eco_file)
# Replace formats for TSEN and CDAY parameters
eco <- add_v_fmt(eco,v_fmt=c(TSEN='%6.1f',CDAY='%6.1f'))
Convert tibble to DSSAT_tbl
Description
Convert tibble to DSSAT_tbl
Usage
as_DSSAT_tbl(tbl_in, v_fmt = NULL, tier_info = NULL)
Arguments
tbl_in |
a tibble |
v_fmt |
a character vector specifying the sprintf() format for each column |
tier_info |
a list of character vectors storing the history of which original table that columns came from for tibbles that are comprised of multiple joined tables |
Value
a tibble of class DSSAT_tbl
Calculate long-term temperature amplitude (AMP)
Description
Calculate long-term temperature amplitude (AMP)
Usage
calc_AMP(wth)
Arguments
wth |
a data frame that contains weather data formatted as would be generated using read_wth, namely including columns DATE, TMAX and TMIN. |
Calculate long-term temperature average (TAV)
Description
Calculate long-term temperature average (TAV)
Usage
calc_TAV(wth)
Arguments
wth |
a data frame that contains weather data formatted as would be generated using read_wth, namely including columns TMAX and TMIN. |
Clear output files
Description
A function to delete DSSAT output files (\*.OUT) and intermediate files (\*.INH, \*.INP and \*.LST) from a directory
Usage
clear_output(dir_name = getwd(), file_ext = c("OUT", "LST", "INP", "INH"))
Arguments
dir_name |
a length-one character vector indicating the directory in which to delete output files (by default the current working directory) |
file_ext |
a character vector of file extensions to delete |
Efficiently combine data from two data tiers into one
Description
Efficiently combine data from two data tiers into one
Usage
combine_tiers(tier1, tier2, use_collapse_rows = FALSE, force_bind_rows = FALSE)
Arguments
tier1, tier2 |
a tibble for each tier of data |
use_collapse_rows |
a length-one logical vector that indicates whether rows should be collapsed before join |
Value
a tibble containing the data from the combined tiers
Converts a column to POSIXct
Description
Converts a column to POSIXct
Usage
convert_to_date(d)
Arguments
d |
a numeric or character vector |
Value
a POSIXct vector
Examples
convert_to_date('2018031')
Converts header line into a vector of column names
Description
Converts header line into a vector of column names
Usage
header_to_fwf_position(
header,
left_justified = "EXCODE",
col_types = NULL,
col_names = NULL,
read_only = NULL
)
Arguments
header |
A length-one character vector of a header line from a DSSAT format output file |
left_justified |
A character vector of column names that should be left justified |
Value
a tibble containing the begin position, end position, and name for each column from the original header line
Examples
header_line <-
"@YEAR DOY DAS SRAA ES1D ES2D ES3D ES4D ES5D ES6D ES7D ES8D"
DSSAT:::header_to_fwf_position(header_line)
Convenience function that allows mutating a subset of rows
Description
Convenience function that allows mutating a subset of rows
Usage
mutate_cond(.data, condition, ..., envir = parent.frame())
Arguments
.data |
a tibble |
condition |
a logical vector for subsetting rows of '.data' |
... |
Name-value pairs of expressions to be evaluated by 'mutate()' |
envir |
environment within which expressions should be evaluated |
Details
Original code taken from https://stackoverflow.com/questions/34096162/dplyr-mutate-replace-several-columns-on-a-subset-of-rows
Value
a tibble with specified rows modified
Convert column names to a regex
Description
Convert column names to a regex
Usage
name_to_regex(cnames)
Arguments
cnames |
A character vector that contains column names |
Value
A character vector with escaped special characters (e.g. parentheses, periods, asterisks)
Examples
name_to_regex("TB(1)")
Extracts run number, model code, experiment code, treatment number and data headline from DSSAT output header
Description
Extracts run number, model code, experiment code, treatment number and data headline from DSSAT output header
Usage
process_dssat_output_header(raw_lines)
Arguments
raw_lines |
a character vector that includes the contents of a single tier of data (including version stamp and header information) from a DSSAT output file |
Value
a list containing the data headline, model code, experiment code, treatment number, and run number extracted from the raw output
Examples
sample_data_tier <- c(
"*DSSAT Cropping System Model Ver. 4.6.0.030 -forage MAR 27, 2014; 06:11:48",
"",
"*RUN 1 : 0 KG N/HA PRFRM046 UFGA0601 1 ",
"MODEL : PRFRM046 - Tifton 85 bermud ",
"EXPERIMENT : UFGA0601 G0 NITROGEN RESPONSE OF TIFTON 85 BERMUDAGRASS REGROW",
"DATA PATH : ",
" TREATMENT 1 : 0 KG N/HA PRFRM046 ",
"",
"",
"! Soil evaporation (mm/d) by soil depth (cm):",
"! 0-5 5-15 15-23 23-32 32-41 41-51 51-61 61-71",
"@YEAR DOY DAS SRAA ES1D ES2D ES3D ES4D ES5D ES6D ES7D ES8D",
" 2006 001 1 7.40 0.508 0.175 0.060 0.101 0.083 0.110 0.098 0.035",
" 2006 002 2 8.40 0.849 0.263 0.064 0.104 0.086 0.113 0.101 0.036",
" 2006 003 3 13.10 1.148 0.549 0.091 0.132 0.108 0.144 0.128 0.046")
DSSAT:::process_dssat_output_header(sample_data_tier)
Reads parameters from a single DSSAT CASUPRO ecotype parameter file (*.ECO)
Description
Reads parameters from a single DSSAT CASUPRO ecotype parameter file (*.ECO)
Usage
read_casupro_eco(raw_lines)
Value
a tibble containing the data from the raw DSSAT file
Examples
sample_eco <- c('CA0001 (CP 80-1743; CP 88-1762)',
'!-------------------',
' KCAN_ECO 0.80 Superseeds KCAN from .SPE file',
' SMAX 20 Maximum number of stalks a variety can yield per stubble or plant',
'!-------------------',
' CAB 8 Number of leaves in spindle cluster at top of stalk ("cabbage"). ',
' CanLmtFac 0.010 Proportion of stalk leaf area moved up each day to keep de-popula',
' LfShdFac 0.35 Proportion of a stalks new leaf area that shades (displaces to t',
' MINSHD 0.15 Minimum value allowed for FRSHAV (Average of daylight fraction of',
'!-------------------',
' StkSenFrac .00005 Threshold maintenance respiration deficit to stalk dry weight rat',
' SENDAY 0.05 Maximum fraction of existing leaf weight which can be senesced on')
read_casupro_eco(sample_eco)
Reads parameters from a single DSSAT cultivar parameter file (*.CUL)
Description
Reads parameters from a single DSSAT cultivar parameter file (*.CUL)
Usage
read_cul(
file_name,
col_types = NULL,
col_names = NULL,
left_justified = c("VAR#", "VARNAME\\.*", "VAR-NAME\\.*", "VRNAME\\.*"),
use_std_fmt = TRUE
)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
left_justified |
A character vector of column names that should be left justified |
use_std_fmt |
logical value indicating whether to read FileX using the standard column formats. If FALSE, column formats will be inferred from tier headers |
Value
a tibble containing the data from the raw DSSAT output
Examples
# Extract file path for sample cultivar file path
sample_cul_file <- system.file('extdata','SAMPLE.CUL',package='DSSAT')
# Read sample cultivar file
cul <- read_cul(sample_cul_file)
Reads data from a single DSSAT file
Description
Reads data from a single DSSAT file
Usage
read_dssat(
file_name,
col_types = NULL,
col_names = NULL,
na_strings = NULL,
left_justified = "EXCODE",
guess_max = 10
)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
na_strings |
A character vector containing strings that should be interpreted as missing values |
left_justified |
A character vector of column names that should be left justified |
guess_max |
An integer indicating the maximum number of lines that should be used to guess the type of a column |
Value
a tibble containing the data from the raw DSSAT output
Examples
# Extract file path for sample output file path
sample_output <- system.file('extdata','SAMPLE.OUT',package='DSSAT')
read_dssat(sample_output)
Reads data from a single DSSAT batch file
Description
Reads data from a single DSSAT batch file
Usage
read_dssbatch(file_name = "DSSBatch.V47")
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT batch file |
Value
a tibble containing the data from the DSSAT batch file
Examples
# Create example batch file path
batch_file_path <- paste0(tempdir(),'/DSSBatch.V47')
# Write example batch file
write_dssbatch(x='UFGA0601.BMX',trtno=1:4,file_name = batch_file_path)
# Read example batch file
dssbatch <- read_dssbatch(batch_file_path)
Reads parameters from a single DSSAT ecotype parameter file (*.ECO)
Description
Reads parameters from a single DSSAT ecotype parameter file (*.ECO)
Usage
read_eco(
file_name,
col_types = NULL,
col_names = NULL,
left_justified = c("ECO ", "ECO#", "ECONAME\\.*", "ECO-NAME\\.*")
)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
left_justified |
A character vector of column names that should be left justified |
Value
a tibble containing the data from the raw DSSAT file
Examples
# Extract file path for sample ecotype file path
sample_eco <- system.file('extdata','SAMPLE.ECO',package='DSSAT')
eco <- read_eco(sample_eco)
Reads data from a single DSSAT file A
Description
Reads data from a single DSSAT file A
Usage
read_filea(file_name, col_types = NULL, col_names = NULL, na_strings = NULL)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
na_strings |
a character vector of string to represent missing values |
Value
a tibble containing the data from the raw DSSAT file
Examples
# Extract FileA path for sample file
sample_filea <- system.file('extdata','SAMPLE.CRA',package='DSSAT')
filea <- read_filea(sample_filea)
Reads time series data from a single DSSAT file T
Description
Reads time series data from a single DSSAT file T
Usage
read_filet(file_name, col_types = NULL, col_names = NULL, na_strings = NULL)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
na_strings |
a character vector of string to represent missing values |
Value
a tibble containing the data from the raw DSSAT file
Examples
# Extract FileT path for sample file
sample_filet <- system.file('extdata','SAMPLE.CRT',package='DSSAT')
read_filet(sample_filet)
Reads input data from a single DSSAT experiment file (*.*X)
Description
Reads input data from a single DSSAT experiment file (*.*X)
Usage
read_filex(
file_name,
col_types = NULL,
col_names = NULL,
na_strings = NULL,
store_v_fmt = FALSE,
use_std_fmt = FALSE
)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
na_strings |
A character vector containing strings that should be interpreted as missing values |
store_v_fmt |
a logical value indicating whether or not to store the format for variables being read |
use_std_fmt |
logical value indicating whether to read FileX using the standard column formats. If FALSE, column formats will be inferred from tier headers |
Value
a tibble containing the data from the raw DSSAT file
Read multiple File X
Description
Read multiple File X
Usage
read_filex_multiple(
file_name,
col_types = NULL,
col_names = NULL,
na_strings = NULL,
store_v_fmt = FALSE,
use_std_fmt = TRUE
)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
na_strings |
A character vector containing strings that should be interpreted as missing values |
store_v_fmt |
a logical value indicating whether or not to store the format for variables being read |
use_std_fmt |
logical value indicating whether to read FileX using the standard column formats. If FALSE, column formats will be inferred from tier headers |
Reads data from a single DSSAT output file
Description
Reads data from a single DSSAT output file
Usage
read_output(
file_name,
col_types = NULL,
col_names = NULL,
left_justified = NULL,
read_only = NULL,
store_v_fmt = FALSE
)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
left_justified |
A character vector of column names that should be left justified |
read_only |
NULL or a character vector of column names that should be read in; If non-NULL only the columns listed will be read in. |
store_v_fmt |
a logical value indicating whether or not to store the format for variables being read |
Value
a tibble containing the data from the raw DSSAT output
Examples
# Extract file path for sample output file path
sample_output <- system.file('extdata','SAMPLE.OUT',package='DSSAT')
out <- read_output(sample_output)
Reads input data from a single DSSAT pest file (*.PST)
Description
Reads input data from a single DSSAT pest file (*.PST)
Usage
read_pest(file_name, col_types = NULL, col_names = NULL)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
Value
a tibble containing the data from the raw DSSAT file
Reads a single DSSAT formatted soil profile from a raw character vector
Description
Reads a single DSSAT formatted soil profile from a raw character vector
Usage
read_soil_profile(
raw_lines,
left_justified = NULL,
col_types = NULL,
col_names = NULL
)
Arguments
raw_lines |
a character vector that includes the contents of a single tier of data (including headline, but excluding version stamp and other header information) from a DSSAT output file |
left_justified |
A character vector of column names that should be left justified |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
Value
a list containing tibbles for each tier of a DSSAT formatted soil profile
Examples
sample_sol <- c(
"*IB00000001 IBSNAT SIC 210 DEFAULT - DEEP SILTY CLAY",
"@SITE COUNTRY LAT LONG SCS FAMILY",
" Generic Generic -99 -99 Generic",
"@ SCOM SALB SLU1 SLDR SLRO SLNF SLPF SMHB SMPX SMKE",
" -99 0.11 6.0 0.30 85.0 1.00 1.00 IB001 IB001 IB001",
"@ SLB SLMH SLLL SDUL SSAT SRGF SSKS SBDM SLOC SLCL SLSI SLCF SLNI SLHW SLHB",
" 5 -99 0.228 0.385 0.481 1.000 -99 1.30 1.75 50.0 45.0 0.0 0.170 6.5 -99",
" 15 -99 0.228 0.385 0.481 1.000 -99 1.30 1.75 50.0 45.0 0.0 0.170 6.5 -99",
" 30 -99 0.249 0.406 0.482 0.638 -99 1.30 1.60 50.0 45.0 0.0 0.170 6.5 -99",
" 45 -99 0.249 0.406 0.465 0.472 -99 1.35 1.45 50.0 45.0 0.0 0.140 6.5 -99",
" 60 -99 0.249 0.406 0.465 0.350 -99 1.35 1.45 50.0 45.0 0.0 0.140 6.5 -99",
" 90 -99 0.308 0.456 0.468 0.223 -99 1.35 1.10 50.0 45.0 0.0 0.110 6.5 -99",
" 120 -99 0.207 0.341 0.452 0.122 -99 1.40 0.65 50.0 45.0 0.0 0.060 6.5 -99",
" 150 -99 0.243 0.365 0.455 0.067 -99 1.40 0.30 50.0 45.0 0.0 0.030 6.5 -99",
" 180 -99 0.259 0.361 0.457 0.037 -99 1.40 0.10 50.0 45.0 0.0 0.010 6.5 -99",
" 210 -99 0.259 0.361 0.457 0.020 -99 1.40 0.01 50.0 45.0 0.0 0.000 6.5 -99")
read_soil_profile(sample_sol)
Reads soil parameters from a single DSSAT soil parameter file (*.SOL)
Description
Reads soil parameters from a single DSSAT soil parameter file (*.SOL)
Usage
read_sol(
file_name,
id_soil = NULL,
left_justified = NULL,
col_types = NULL,
col_names = NULL
)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
id_soil |
a length-one character vector containing the soil ID code for a single soil profile |
left_justified |
A character vector of column names that should be left justified |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
Value
a tibble containing the data from the raw DSSAT file
Examples
# Extract file path for sample soil file
sample_sol <- system.file('extdata','SAMPLE.SOL',package='DSSAT')
sol <- read_sol(sample_sol)
Reads and combines data and header information from a single tier of a DSSAT output file
Description
Reads and combines data and header information from a single tier of a DSSAT output file
Usage
read_tier(
raw_lines,
col_types = NULL,
col_names = NULL,
na_strings = NULL,
left_justified = "EXCODE",
guess_max = 1000,
store_v_fmt = TRUE,
read_only = NULL
)
Arguments
raw_lines |
a character vector that includes the contents of a single tier of data (including headline, but excluding version stamp and other header information) from a DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
na_strings |
a character vector of string to represent missing values |
left_justified |
A character vector of column names that should be left justified |
guess_max |
An integer indicating the maximum number of lines that should be used to guess the type of a column |
store_v_fmt |
a logical value indicating whether or not to store the format for variables being read |
read_only |
NULL or a character vector of column names that should be read in; If non-NULL only the columns listed will be read in. |
Value
a tibble containing the data from the raw DSSAT output
Examples
sample_data_tier <- c(
"*DSSAT Cropping System Model Ver. 4.6.0.030 -forage MAR 27, 2014; 06:11:48",
"",
"*RUN 1 : 0 KG N/HA PRFRM046 UFGA0601 1 ",
"MODEL : PRFRM046 - Tifton 85 bermud ",
"EXPERIMENT : UFGA0601 G0 NITROGEN RESPONSE OF TIFTON 85 BERMUDAGRASS REGROW",
"DATA PATH : ",
" TREATMENT 1 : 0 KG N/HA PRFRM046 ",
"",
"",
"! Soil evaporation (mm/d) by soil depth (cm):",
"! 0-5 5-15 15-23 23-32 32-41 41-51 51-61 61-71",
"@YEAR DOY DAS SRAA ES1D ES2D ES3D ES4D ES5D ES6D ES7D ES8D",
" 2006 001 1 7.40 0.508 0.175 0.060 0.101 0.083 0.110 0.098 0.035",
" 2006 002 2 8.40 0.849 0.263 0.064 0.104 0.086 0.113 0.101 0.036",
" 2006 003 3 13.10 1.148 0.549 0.091 0.132 0.108 0.144 0.128 0.046")
read_tier(sample_data_tier)
Reads data from a single tier of a DSSAT output file
Description
Reads data from a single tier of a DSSAT output file
Usage
read_tier_data(
raw_lines,
col_types = NULL,
col_names = NULL,
na_strings = NULL,
left_justified = "EXCODE",
guess_max = 1000,
join_tiers = TRUE,
store_v_fmt = TRUE,
read_only = NULL,
tier_fmt = NULL,
convert_date_cols = TRUE
)
Arguments
raw_lines |
a character vector that includes the contents of a single tier of data (including headline, but excluding version stamp and other header information) from a DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
na_strings |
a character vector of string to represent missing values |
left_justified |
A character vector of column names that should be left justified |
guess_max |
An integer indicating the maximum number of lines that should be used to guess the type of a column |
join_tiers |
A logical indicating whether the multiple tiers should be combined into a single tibble |
store_v_fmt |
a logical value indicating whether or not to store the format for variables being read |
read_only |
NULL or a character vector of column names that should be read in; If non-NULL only the columns listed will be read in. |
convert_date_cols |
A logical value indicating whether to convert columns expected to be dates into date-time format. If TRUE, any column that matches the following regular expression will be converted: "(DATE)|((?<!(L)|(SS))AT$)|(PFRST)|(PLAST)|(HFRST)|(HLAST)" |
Value
a tibble or list of tibbles containing the data from the raw DSSAT output
Examples
sample_data_tier <- c(
"@YEAR DOY DAS SRAA ES1D ES2D ES3D ES4D ES5D ES6D ES7D ES8D",
" 2006 001 1 7.40 0.508 0.175 0.060 0.101 0.083 0.110 0.098 0.035",
" 2006 002 2 8.40 0.849 0.263 0.064 0.104 0.086 0.113 0.101 0.036",
" 2006 003 3 13.10 1.148 0.549 0.091 0.132 0.108 0.144 0.128 0.046")
read_tier_data(sample_data_tier)
Reads weather input data from a single DSSAT weather file (*.WTH)
Description
Reads weather input data from a single DSSAT weather file (*.WTH)
Usage
read_wth(file_name, col_types = NULL, col_names = NULL)
Arguments
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
col_types |
One of NULL, a cols() specification, or a string.
See |
col_names |
A character vector of column names; primarily helpful for cases where there are no white spaces between column names within the header line |
Value
a tibble containing the data from the raw DSSAT file
Examples
# Extract file path for sample weather file
sample_wth <- system.file('extdata','SAMPLE.WTH',package='DSSAT')
read_wth(sample_wth)
Writes data from a single DSSAT data tier
Description
Writes data from a single DSSAT data tier
Usage
run_dssat(run_mode = "B", file_name = NULL, suppress_output = FALSE, wd = NULL)
Arguments
run_mode |
a length-one character vector that specifies the run mode that should be used for the DSSAT simulation. One of: A - Run all treatments. User specifies fileX on the command line and the model runs all treatments B - Batch mode. User defines fileX and treatment numbers in Batch file C - Command line mode. Use input from the command line. D - Debug mode. Model skips input module and reads temp file from the command line E - Sensitivity analysis. User defines fileX and treatment number in Batch file F - Farm model. Use Batch file to define experiment G - Gencalc. Use Command line to define experiment and treatment I - Interactive mode. Use model interface for exp. & trtno. L - Gene based model (Locus). Use Batch file to define experiment N - Seasonal analysis. Use Batch file to define experiment and treatments Q - Sequence analysis. Use Batch file to define experiment S - Spatial. Use Batch file to define experiment T - Gencalc. Use Batch file to define experiments and treatment |
file_name |
a length-one character vector that specifies the file name to be used for simulation. Usually the name of a batch file or file X. |
suppress_output |
a logical value indicating whether to suppress DSSAT-CSM output from being printed to the console |
wd |
an optional character string that specifies the working directory within which to run DSSAT-CSM. If left NULL, DSSAT-CSM will be run in the current working directory |
Value
Invisibly returns the console output from running DSSAT-CSM
Examples
## Not run:
run_dssat()
## End(Not run)
Splice column name into vector of column names
Description
Splice column name into vector of column names
Usage
splice_in_col_name(col_names, new_name)
Arguments
col_names |
A length-one character vector of a header line from a DSSAT format output file |
new_name |
A length-one character vector that contains a
column name suspected to be a substring of one of the existing
elements of the |
Value
If new_name matches a substring, the function will
return a new character vector with it spliced into the existing
col_names in the position immediately before the element
that contained the matching substring. Otherwise the original
col_names will be returned.
Examples
cnames <-
c("@VAR#","VAR-NAME........","EXPNO","ECO#","TB(1)TO1(1)TO2(1)","TM(1)")
DSSAT:::splice_in_col_name(cnames,"TB(1)")
Writes parameters to a single DSSAT CASUPRO ecotype parameter file (*.ECO)
Description
Writes parameters to a single DSSAT CASUPRO ecotype parameter file (*.ECO)
Usage
write_casupro_eco(eco)
Examples
sample_eco <- c('CA0001 (CP 80-1743; CP 88-1762)',
'!-------------------',
' KCAN_ECO 0.80 Superseeds KCAN from .SPE file',
' SMAX 20 Maximum number of stalks a variety can yield per stubble or plan',
'!-------------------',
' CAB 8 Number of leaves in spindle cluster at top of stalk ("cabbage").',
' CanLmtFac 0.010 Proportion of stalk leaf area moved up each day to keep de-popul',
' LfShdFac 0.35 Proportion of a stalks new leaf area that shades (displaces to ',
' MINSHD 0.15 Minimum value allowed for FRSHAV (Average of daylight fraction o',
'!-------------------',
' StkSenFrac .00005 Threshold maintenance respiration deficit to stalk dry weight ra',
' SENDAY 0.05 Maximum fraction of existing leaf weight which can be senesced o')
eco <- read_casupro_eco(sample_eco)
write_casupro_eco(eco)
Reads parameters from a single DSSAT cultivar parameter file (*.CUL)
Description
Reads parameters from a single DSSAT cultivar parameter file (*.CUL)
Usage
write_cul(cul, file_name)
Arguments
cul |
a DSSAT_tbl containing the contents of a DSSAT cultivar parameter file |
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
Value
a tibble containing the data from the raw DSSAT output
Examples
# Extract file path for sample cultivar file path
sample_cul_file <- system.file('extdata','SAMPLE.CUL',package='DSSAT')
# Read sample cultivar file
cul <- read_cul(sample_cul_file)
# Create example cultivar file path
sample_cul_file2 <- paste0(tempdir(),'/SAMPLE.CUL')
# Write out sample cultivar file
write_cul(cul,sample_cul_file2)
Constructs and writes a DSSAT simulation batch file
Description
Constructs and writes a DSSAT simulation batch file
Usage
write_dssbatch(x, trtno = 1, rp = 1, sq = 0, op = 0, co = 0, file_name = NULL)
Arguments
x |
a tibble/data frame or character vector; if a tibble, it should contain all required columns of a DSSAT batch file (FILEX, TRTNO, RP, SQ, OP, CO); if a character vector, it should contain FileX file names |
trtno, rp, sq, op, co |
a numeric vector |
file_name |
an optional character vector of the intended batch file name |
Value
invisibly returns a character vector containing the content of a DSSAT batch file
Examples
# Create example batch file path
batch_file_path <- paste0(tempdir(),'/DSSBatch.V47')
# Write example batch file
write_dssbatch(x='UFGA0601.BMX', trtno=1:4, file_name = batch_file_path)
# Construct tibble for DSSAT batch file
batch_tbl <- data.frame(FILEX='UFGA0601.BMX',
TRTNO=1:4,
RP=1,
SQ=0,
OP=0,
CO=0)
# Write example batch file
write_dssbatch(batch_tbl, file_name = batch_file_path)
tbl_df method for write_dssbatch()
Description
tbl_df method for write_dssbatch()
Usage
## S3 method for class 'data.frame'
write_dssbatch(x, trtno = 1, rp = 1, sq = 0, op = 0, co = 0, file_name = NULL)
Arguments
x |
a tibble/data frame or character vector; if a tibble, it should contain all required columns of a DSSAT batch file (FILEX, TRTNO, RP, SQ, OP, CO); if a character vector, it should contain FileX file names |
trtno, rp, sq, op, co |
a numeric vector |
file_name |
an optional character vector of the intended batch file name |
Default method for write_dssbatch()
Description
Default method for write_dssbatch()
Usage
## Default S3 method:
write_dssbatch(x, trtno = 1, rp = 1, sq = 0, op = 0, co = 0, file_name = NULL)
Arguments
x |
a tibble/data frame or character vector; if a tibble, it should contain all required columns of a DSSAT batch file (FILEX, TRTNO, RP, SQ, OP, CO); if a character vector, it should contain FileX file names |
trtno, rp, sq, op, co |
a numeric vector |
file_name |
an optional character vector of the intended batch file name |
tbl_df method for write_dssbatch()
Description
tbl_df method for write_dssbatch()
Usage
## S3 method for class 'tbl_df'
write_dssbatch(x, trtno = 1, rp = 1, sq = 0, op = 0, co = 0, file_name = NULL)
Arguments
x |
a tibble/data frame or character vector; if a tibble, it should contain all required columns of a DSSAT batch file (FILEX, TRTNO, RP, SQ, OP, CO); if a character vector, it should contain FileX file names |
trtno, rp, sq, op, co |
a numeric vector |
file_name |
an optional character vector of the intended batch file name |
Reads parameters from a single DSSAT ecotype parameter file (*.ECO)
Description
Reads parameters from a single DSSAT ecotype parameter file (*.ECO)
Usage
write_eco(eco, file_name)
Arguments
eco |
a DSSAT_tbl containing the contents of a DSSAT ecotype parameter file |
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
Value
a tibble containing the data from the raw DSSAT output
Examples
# Extract file path for sample ecotype file path
sample_eco_file <- system.file('extdata','SAMPLE.ECO',package='DSSAT')
# Read sample ecotype file
eco <- read_eco(sample_eco_file)
# Create example ecotype file path
sample_eco_file2 <- paste0(tempdir(),'/SAMPLE.ECO')
# Write out sample ecotype file
write_eco(eco,sample_eco_file2)
Writes data to a single DSSAT file A
Description
Writes data to a single DSSAT file A
Usage
write_filea(filea, file_name, drop_duplicate_rows = TRUE)
Arguments
filea |
a tibble containing the data to write to a DSSAT file A |
file_name |
a character vector of length one that contains the name of a single DSSAT file into which 'filea' will be written |
drop_duplicate_rows |
a logical value indicating whether duplicate rows should be dropped from tier_data |
Examples
# Extract FileA path for sample file
sample_filea <- system.file('extdata','SAMPLE.CRA',package='DSSAT')
filea <- read_filea(sample_filea)
# Create example FileA file path
sample_filea2 <- paste0(tempdir(),'/SAMPLE.CRA')
# Write out sample FileA
write_filea(filea,sample_filea2)
Writes data to a single DSSAT file T
Description
Writes data to a single DSSAT file T
Usage
write_filet(filet, file_name, drop_duplicate_rows = TRUE)
Arguments
filet |
a tibble containing the data to write to a DSSAT file T |
file_name |
a character vector of length one that contains the name of a single DSSAT file into which 'filet' will be written |
drop_duplicate_rows |
a logical value indicating whether duplicate rows should be dropped from tier_data |
Examples
# Extract FileT path for sample file
sample_filet <- system.file('extdata','SAMPLE.CRT',package='DSSAT')
filet <- read_filet(sample_filet)
# Create example FileT file path
sample_filet2 <- paste0(tempdir(),'/SAMPLE.CRT')
# Write out sample FileA
write_filet(filet,sample_filet2)
Writes data to a single DSSAT FileX
Description
Writes data to a single DSSAT FileX
Usage
write_filex(filex, file_name, drop_duplicate_rows = TRUE, force_std_fmt = TRUE)
Arguments
filex |
a list of tibbles containing the data to write to a DSSAT file X |
file_name |
a character vector of length one that contains the name of a single DSSAT file into which 'filet' will be written |
drop_duplicate_rows |
a logical value indicating whether duplicate rows should be dropped from tier_data |
force_std_fmt |
a logical value indicating whether to override the variable format stored within the FileX object with standard DSSAT formatting |
Writes soil parameters to a single DSSAT soil parameter file (*.SOL)
Description
Writes soil parameters to a single DSSAT soil parameter file (*.SOL)
Usage
write_sol(sol, file_name, title = NULL, append = TRUE, force_std_fmt = TRUE)
Arguments
sol |
a tibble of soil profiles that have been read in by read_sol() |
file_name |
a character vector of length one that contains the name of a single DSSAT output file |
title |
a length-one character vector that contains the title of the soil file |
append |
TRUE or FALSE indicating whether soil profile should be appended to file_name. If FALSE, the soil profile will be written to a new file and will overwrite file_name (if it exists). |
force_std_fmt |
a logical value indicating whether to override the variable format stored within the FileX object with standard DSSAT formatting |
Value
Invisibly returns NULL
Examples
# Extract file path for sample soil file
sample_sol <- system.file('extdata','SAMPLE.SOL',package='DSSAT')
# Read sample soil file
sol <- read_sol(sample_sol)
# Create example soil file path
sample_sol2 <- paste0(tempdir(),'/SAMPLE.SOL')
# Write example soil file
write_sol(sol,sample_sol2)
Writes data from a single DSSAT data tier
Description
Writes data from a single DSSAT data tier
Usage
write_tier(
tier_data,
pad_name = NULL,
drop_duplicate_rows = FALSE,
drop_na_rows = TRUE
)
Arguments
tier_data |
a tibble containing the data to write out |
pad_name |
a character vector of column names for which to add leading spaces/trailing periods |
drop_duplicate_rows |
a logical value indicating whether duplicate rows should be dropped from tier_data |
drop_na_rows |
a logical value indicating whether rows containing all NA values should be dropped from tier_data |
Value
a character vector
Examples
tier_data <- data.frame(TRNO=1:4,HWAM=rnorm(4,2000,250))
tier_data <- add_v_fmt(tier_data,v_fmt=c(TRNO='%6.0f', HWAM='%6.0f'))
output <- write_tier(tier_data)
Writes data to a single DSSAT weather file
Description
Writes data to a single DSSAT weather file
Usage
write_wth(
wth,
file_name,
force_std_fmt = TRUE,
location = NULL,
comments = NULL,
INSI = NULL,
LAT = NULL,
LONG = NULL,
ELEV = NULL,
TAV = NULL,
AMP = NULL,
REFHT = NULL,
WNDHT = NULL,
CO2 = NULL
)
Arguments
wth |
a tibble containing the data to write to a DSSAT weather file |
file_name |
a character vector of length one that contains the name of a single DSSAT file into which 'wth' will be written |
force_std_fmt |
a logical value indicating whether to override the variable format stored within the 'wth' object with standard DSSAT formatting |
location |
a character value that gives the location for the weather file header line |
comments |
a character vector containing any comments to be included in the weather file |
INSI |
Institute and site code (four-digit character code) |
LAT |
Latitude in decimal degrees |
LONG |
Longitude in decimal degrees |
ELEV |
Elevation in meters |
TAV |
Long-term average air temperature at reference height (typically 2 meters) |
AMP |
Long-term monthly air temperature amplitude at reference height (typically 2 meters) |
REFHT |
reference height for air temperature measurements |
WNDHT |
reference height for wind speed measurements |
CO2 |
carbon dioxide concentration in parts per million |