Good evening All,
I am trying to read experimental file from my system using the DSSAT R package and I get the following error below: I don't know if there is any expert here that can help me; Here is my reprex:
# Load Required Packages
library(DSSAT)
#> When using the 'DSSAT' package for publications please cite all of the
#> following:
#>
#> Alderman, P.D. 2023. DSSAT: A Comprehensive R Interface for the DSSAT
#> Cropping Systems Model. R package version 0.0.8. DOI:
#> 10.5281/zenodo.4091381. https://CRAN.R-project.org/package=DSSAT.
#>
#> Alderman, P.D. 2020. "A Comprehensive R Interface for the DSSAT
#> Cropping Systems Model." Computers and Electronics in Agriculture
#> 172: 105325. DOI: 10.1016/j.compag.2020.105325.
#>
#> Jones, J.W., G. Hoogenboom, C.H. Porter, K.J. Boote, W.D. Batchelor,
#> L.A. Hunt, P.W. Wilkens, U. Singh, A.J. Gijsman, and J.T. Ritchie.
#> 2003. "The DSSAT Cropping System Model." European Journal of Agronomy
#> 18 (3-4): 235-265.
#>
#> Hoogenboom, G., C.H. Porter, K.J. Boote, V. Shelia, P.W. Wilkens, U.
#> Singh, J.W. White, S. Asseng, J.I. Lizaso, L.P. Moreno, W. Pavan, R.
#> Ogoshi, L.A. Hunt, G.Y. Tsuji, and J.W. Jones. 2019. "The DSSAT Crop
#> Modeling Ecosystem." In: Advances in Crop Modeling for a Sustainable
#> Agriculture, edited by Kenneth J Boote, 173–216. Cambridge, United
#> Kingdom: Burleigh Dodds Science Publishing.
#>
#> Hoogenboom, G., C.H. Porter, V. Shelia, K.J. Boote, U. Singh, J.W.
#> White, W. Pavan, F.A.A. Oliveira, L.P. Moreno-Cadena, J.I. Lizaso, S.
#> Asseng, D.N.L. Pequeno, B.A. Kimball, P.D. Alderman, K.R. Thorp, M.R.
#> Jones, S.V. Cuadra, M.S. Vianna, F.J. Villalobos, T.B. Ferreira, J.
#> Koo, L.A. Hunt, and J.W. Jones. <YEAR>. Decision Support System for
#> Agrotechnology Transfer (DSSAT) Version <VERSION>. Gainesville,
#> Florida, USA: DSSAT Foundation. https://DSSAT.net.
#> For BibTeX entries use toBibtex(citation("DSSAT"))
#>
#> A DSSAT-CSM executable was found here:
#>
#>
#>
#> If this is not the correct executable, please use
#>
#> options(DSSAT.CSM="C:\ \ path\ to\ executable")
#>
#> to set the proper location and file name for DSSAT-CSM.
library(tidyverse)
# Define the Location to the DSSAT Executable file
options(DSSAT.CSM = 'C:\\DSSAT48\\DSCSM048.EXE')
## Set the working directory to read in the potatoes files
setwd("C:/DSSAT48/Potato/")
# Read the Potatoes file_x file
## Potato Data Set
x <-
list(
GENERAL = structure(
list(
PEOPLE = NA_character_,
ADDRESS = NA_character_,
SITE = NA_character_
),
class = c("DSSAT_tbl", "tbl_df", "tbl",
"data.frame"),
row.names = c(NA, -1L),
tier_info = list("PEOPLE",
"ADDRESS", "SITE")
),
`TREATMENTS -------------FACTOR LEVELS------------` = structure(
list(
N = 1:3,
R = c(1L, 1L, 1L),
O = c(0L, 0L, 0L),
C = c(0L,
0L, 0L),
TNAME = c(
"Radiation=100% Deficit=2.",
"Radiation= 79% Deficit=2.",
"Radiation= 66% Deficit=2."
),
CU = c(1L, 1L, 1L),
FL = c(1L,
1L, 1L),
SA = c(0L, 0L, 0L),
IC = c(1L, 1L, 1L),
MP = c(1L,
1L, 1L),
MI = c(0L, 0L, 0L),
MF = c(1L, 1L, 1L),
MR = c(1L,
1L, 1L),
MC = c(0L, 0L, 0L),
MT = c(0L, 0L, 0L),
ME = 1:3,
MH = c(1L, 1L, 1L),
SM = c(1L, 1L, 1L)
),
class = c("DSSAT_tbl",
"tbl_df", "tbl", "data.frame"),
row.names = c(NA, -3L)
),
CULTIVARS = structure(
list(
C = 1L,
CR = "PT",
INGENO = "IB0002",
CNAME = "SEBAGO"
),
class = c("DSSAT_tbl",
"tbl_df", "tbl", "data.frame"),
row.names = c(NA, -1L)
),
FIELDS = structure(
list(
L = 1L,
ID_FIELD = "AUCB0001",
WSTA = "AUCB",
FLSA = "0",
FLOB = 0L,
FLDT = "IB000",
FLDD = 0L,
FLDS = 0L,
FLST = 0L,
SLTX = NA_real_,
SLDP = 0L,
ID_SOIL = "IBPT910002",
FLNAME = NA_character_,
XCRD = 0L,
YCRD = 0L,
ELEV = 0L,
AREA = 0L,
SLEN = 0L,
FLWR = 0L,
SLAS = 0L,
FLHST = NA_character_,
FHDUR = NA_real_
),
class = c("DSSAT_tbl",
"tbl_df", "tbl", "data.frame"),
row.names = c(NA, -1L),
tier_info = list(
c(
"L",
"ID_FIELD",
"WSTA",
"FLSA",
"FLOB",
"FLDT",
"FLDD",
"FLDS",
"FLST",
"SLTX",
"SLDP",
"ID_SOIL",
"FLNAME"
),
c(
"L",
"XCRD",
"YCRD",
"ELEV",
"AREA",
"SLEN",
"FLWR",
"SLAS",
"FLHST",
"FHDUR"
)
)
),
`INITIAL CONDITIONS` = structure(
list(
C = 1L,
PCR = "PT",
ICDAT = structure(
18748800,
tzone = "UTC",
class = c("POSIXct",
"POSIXt")
),
ICRT = 10L,
ICND = 0L,
ICRN = 1L,
ICRE = 1L,
ICWD = NA_real_,
ICRES = 10L,
ICREN = 1.14,
ICREP = 0L,
ICRIP = 100L,
ICRID = 15L,
ICNAME = NA_character_,
ICBL = list(c(10L, 25L,
40L, 65L)),
SH2O = list(c(0.3, 0.3, 0.3, 0.3)),
SNH4 = list(c(3.4, 3.2, 2.5, 2.2)),
SNO3 = list(c(9.8, 7.3, 5.1,
4.7))
),
class = c("DSSAT_tbl", "tbl_df", "tbl", "data.frame"),
row.names = c(NA, -1L),
tier_info = list(
c(
"C",
"PCR",
"ICDAT",
"ICRT",
"ICND",
"ICRN",
"ICRE",
"ICWD",
"ICRES",
"ICREN",
"ICREP",
"ICRIP",
"ICRID",
"ICNAME"
),
c("C", "ICBL", "SH2O", "SNH4", "SNO3")
)
),
`PLANTING DETAILS` = structure(
list(
P = 1L,
PDATE = structure(
19094400,
class = c("POSIXct",
"POSIXt"),
tzone = "UTC"
),
EDATE = structure(
23500800,
class = c("POSIXct",
"POSIXt"),
tzone = "UTC"
),
PPOP = 10L,
PPOE = 10L,
PLME = "S",
PLDS = "R",
PLRS = 71L,
PLRD = 0L,
PLDP = 8L,
PLWT = 1500L,
PAGE = NA_real_,
PENV = NA_real_,
PLPH = NA_real_,
SPRL = 2L,
PLNAME = NA_real_
),
class = c("DSSAT_tbl", "tbl_df", "tbl",
"data.frame"),
row.names = c(NA, -1L)
),
`FERTILIZERS (INORGANIC)` = structure(
list(
F = c(1L, 1L),
FDATE = structure(
c(18921600, 24105600),
class = c("POSIXct",
"POSIXt"),
tzone = "UTC"
),
FMCD = c("FE002", "FE002"),
FACD = c(NA_real_,
NA_real_),
FDEP = c(10L, 1L),
FAMN = c(300L, 125L),
FAMP = c(0L,
NA),
FAMK = c(0L, NA),
FAMC = c(0L, NA),
FAMO = c(0L, NA),
FOCD = c(NA_real_, NA_real_),
FERNAME = c(NA_real_, NA_real_)
),
class = c("DSSAT_tbl", "tbl_df", "tbl", "data.frame"),
row.names = c(NA,
-2L)
),
`RESIDUES AND ORGANIC FERTILIZER` = structure(
list(
R = 1L,
RDATE = structure(
18748800,
class = c("POSIXct", "POSIXt"),
tzone = "UTC"
),
RCOD = "RE001",
RAMT = 10L,
RESN = 1.14,
RESP = 0L,
RESK = 0L,
RINP = 100L,
RDEP = 15L,
RMET = NA_real_,
RENAME = NA_real_
),
class = c("DSSAT_tbl", "tbl_df", "tbl",
"data.frame"),
row.names = c(NA, -1L)
),
`ENVIRONMENT MODIFICATIONS` = structure(
list(
E = 1:3,
ODATE = structure(
c(23500800, 23500800, 23500800),
class = c("POSIXct", "POSIXt"),
tzone = "UTC"
),
EDAY = c("A 0",
"A 0", "A 0"),
ERAD = c("A 0", "M .79", "M .66"),
EMAX = c("A 0",
"M .79", "M .66"),
EMIN = c("A 0", "M .79", "M .66"),
ERAIN = c("A 0.0",
"A 0.0", "A 0.0"),
ECO2 = c("A 0", "A 0", "A 0"),
EDEW = c("A 0",
"A 0", "A 0"),
EWIND = c("A 0", "A 0", "A 0"),
ENVNAME = c("", "", "")
),
class = c("DSSAT_tbl", "tbl_df",
"tbl", "data.frame"),
row.names = c(NA, -3L)
),
`HARVEST DETAILS` = structure(
list(
H = 1L,
HDATE = structure(
30672000,
class = c("POSIXct",
"POSIXt"),
tzone = "UTC"
),
HSTG = "GS000",
HCOM = NA_real_,
HSIZE = NA_real_,
HPC = NA_real_,
HBPC = 0L,
HNAME = NA_real_
),
class = c("DSSAT_tbl",
"tbl_df", "tbl", "data.frame"),
row.names = c(NA, -1L)
),
`SIMULATION CONTROLS` = structure(
list(
N = 1L,
GENERAL = "GE",
NYERS = 1L,
NREPS = 1L,
START = "S",
SDATE = structure(
18748800,
tzone = "UTC",
class = c("POSIXct",
"POSIXt")
),
RSEED = 2150L,
SNAME = "Australia, 1970: solar r",
SMODEL = "",
OPTIONS = "OP",
WATER = "Y",
NITRO = "Y",
SYMBI = "N",
PHOSP = "N",
POTAS = "N",
DISES = "N",
CHEM = "N",
TILL = "Y",
CO2 = "M",
METHODS = "ME",
WTHER = "M",
INCON = "M",
LIGHT = "E",
EVAPO = "R",
INFIL = "S",
PHOTO = "R",
HYDRO = "R",
NSWIT = 1L,
MESOM = "G",
MESEV = "S",
MESOL = 2L,
MANAGEMENT = "MA",
PLANT = "R",
IRRIG = "A",
FERTI = "R",
RESID = "R",
HARVS = "R",
OUTPUTS = "OU",
FNAME = "N",
OVVEW = "Y",
SUMRY = "Y",
FROPT = 1L,
GROUT = "Y",
CAOUT = "N",
WAOUT = "Y",
NIOUT = "Y",
MIOUT = "N",
DIOUT = "N",
VBOSE = "Y",
CHOUT = "N",
OPOUT = "N",
FMOPT = "A",
PLANTING = "PL",
PFRST = structure(
18489600,
tzone = "UTC",
class = c("POSIXct",
"POSIXt")
),
PLAST = structure(
19699200,
tzone = "UTC",
class = c("POSIXct",
"POSIXt")
),
PH2OL = 40L,
PH2OU = 100L,
PH2OD = 30L,
PSTMX = 40L,
PSTMN = 10L,
IRRIGATION = "IR",
IMDEP = 30L,
ITHRL = 80L,
ITHRU = 100L,
IROFF = "IB001",
IMETH = "IBI01",
IRAMT = 10L,
IREFF = 1L,
NITROGEN = "NI",
NMDEP = 30L,
NMTHR = 50L,
NAMNT = 25L,
NCODE = "IB001",
NAOFF = "IB001",
RESIDUES = "RE",
RIPCN = 100L,
RTIME = 1L,
RIDEP = 20L,
HARVEST = "HA",
HFRST = structure(
NA_real_,
tzone = "UTC",
class = c("POSIXct",
"POSIXt")
),
HLAST = structure(
50630400,
tzone = "UTC",
class = c("POSIXct",
"POSIXt")
),
HPCNP = 100L,
HPCNR = 0L
),
class = c("DSSAT_tbl",
"tbl_df", "tbl", "data.frame"),
row.names = c(NA, -1L),
tier_info = list(
c(
"N",
"GENERAL",
"NYERS",
"NREPS",
"START",
"SDATE",
"RSEED",
"SNAME",
"SMODEL"
),
c(
"N",
"OPTIONS",
"WATER",
"NITRO",
"SYMBI",
"PHOSP",
"POTAS",
"DISES",
"CHEM",
"TILL",
"CO2"
),
c(
"N",
"METHODS",
"WTHER",
"INCON",
"LIGHT",
"EVAPO",
"INFIL",
"PHOTO",
"HYDRO",
"NSWIT",
"MESOM",
"MESEV",
"MESOL"
),
c("N", "MANAGEMENT",
"PLANT", "IRRIG", "FERTI", "RESID", "HARVS"),
c(
"N",
"OUTPUTS",
"FNAME",
"OVVEW",
"SUMRY",
"FROPT",
"GROUT",
"CAOUT",
"WAOUT",
"NIOUT",
"MIOUT",
"DIOUT",
"VBOSE",
"CHOUT",
"OPOUT",
"FMOPT"
),
c(
"N",
"PLANTING",
"PFRST",
"PLAST",
"PH2OL",
"PH2OU",
"PH2OD",
"PSTMX",
"PSTMN"
),
c(
"N",
"IRRIGATION",
"IMDEP",
"ITHRL",
"ITHRU",
"IROFF",
"IMETH",
"IRAMT",
"IREFF"
),
c("N",
"NITROGEN", "NMDEP", "NMTHR", "NAMNT", "NCODE", "NAOFF"),
c("N", "RESIDUES", "RIPCN", "RTIME", "RIDEP"),
c("N", "HARVEST",
"HFRST", "HLAST", "HPCNP", "HPCNR")
)
)
)
x <- read_filex(file_name = 'AUCB7001.PTX') # This is the dataset that I provide above
# Write the Potatoes file_x file
write_filex(filex = x,file_name = 'AUCB7001.PTX')
#> Error in `map()`:
#> ℹ In index: 4.
#> Caused by error in `all_of()`:
#> ! Can't subset columns that don't exist.
#> ✖ Columns `PAREA`, `PRNO`, `PLEN`, `PLDR`, `PLSP`, etc. don't exist.
#> Backtrace:
#> ▆
#> 1. ├─DSSAT::write_filex(filex = x, file_name = "AUCB7001.PTX")
#> 2. │ ├─base::unlist(...)
#> 3. │ └─base::lapply(...)
#> 4. │ └─DSSAT (local) FUN(X[[i]], ...)
#> 5. │ └─DSSAT::write_tier(...)
#> 6. │ └─... %>% unlist()
#> 7. ├─base::unlist(.)
#> 8. ├─purrr::map(...)
#> 9. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> 10. │ ├─purrr:::with_indexed_errors(...)
#> 11. │ │ └─base::withCallingHandlers(...)
#> 12. │ ├─purrr:::call_with_cleanup(...)
#> 13. │ └─DSSAT (local) .f(.x[[i]], ...)
#> 14. │ └─tier_data %>% select(all_of(tier_names))
#> 15. ├─dplyr::select(., all_of(tier_names))
#> 16. ├─dplyr:::select.data.frame(., all_of(tier_names))
#> 17. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
#> 18. │ └─tidyselect:::eval_select_impl(...)
#> 19. │ ├─tidyselect:::with_subscript_errors(...)
#> 20. │ │ └─rlang::try_fetch(...)
#> 21. │ │ └─base::withCallingHandlers(...)
#> 22. │ └─tidyselect:::vars_select_eval(...)
#> 23. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
#> 24. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
#> 25. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
#> 26. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
#> 27. │ └─tidyselect:::eval_context(expr, context_mask, call = error_call)
#> 28. │ ├─tidyselect:::with_chained_errors(...)
#> 29. │ │ └─rlang::try_fetch(...)
#> 30. │ │ ├─base::tryCatch(...)
#> 31. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> 32. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> 33. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> 34. │ │ └─base::withCallingHandlers(...)
#> 35. │ └─rlang::eval_tidy(as_quosure(expr, env), context_mask)
#> 36. ├─tidyselect::all_of(tier_names)
#> 37. │ └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
#> 38. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
#> 39. │ └─vctrs::vec_as_location(...)
#> 40. └─vctrs (local) `<fn>`()
#> 41. └─vctrs:::stop_subscript_oob(...)
#> 42. └─vctrs:::stop_subscript(...)
#> 43. └─rlang::abort(...)
Created on 2023-11-11 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.3.1 (2023-06-16 ucrt)
#> os Windows 10 x64 (build 19045)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.utf8
#> ctype English_United States.utf8
#> tz Africa/Lagos
#> date 2023-11-11
#> pandoc 3.1.8 @ C:/PROGRA~1/Pandoc/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> bit 4.0.5 2022-11-15 [2] CRAN (R 4.3.0)
#> bit64 4.0.5 2020-08-30 [2] CRAN (R 4.3.0)
#> cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.1)
#> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.1)
#> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.1)
#> digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.1)
#> dplyr * 1.1.3 2023-09-03 [1] CRAN (R 4.3.1)
#> DSSAT * 0.0.8 2023-11-11 [1] Github (palderman/DSSAT@81a583f)
#> evaluate 0.21 2023-05-05 [1] CRAN (R 4.3.1)
#> fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.1)
#> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.1)
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#> fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.1)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.1)
#> ggplot2 * 3.4.3 2023-08-14 [1] CRAN (R 4.3.1)
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#> htmltools 0.5.6 2023-08-10 [1] CRAN (R 4.3.1)
#> knitr 1.43 2023-05-25 [1] CRAN (R 4.3.1)
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#> lubridate * 1.9.2 2023-02-10 [2] CRAN (R 4.3.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.1)
#> munsell 0.5.0 2018-06-12 [2] CRAN (R 4.3.0)
#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.1)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.1)
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#> vroom 1.6.3 2023-04-28 [2] CRAN (R 4.3.0)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.3.1)
#> xfun 0.40 2023-08-09 [1] CRAN (R 4.3.1)
#> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0)
#>
#> [1] C:/Users/USER/AppData/Local/R/win-library/4.3
#> [2] C:/Program Files/R/R-4.3.1/library
#>
#> ──────────────────────────────────────────────────────────────────────────────