-
Notifications
You must be signed in to change notification settings - Fork 35
/
SS_writepar_3.30.R
136 lines (117 loc) · 4.42 KB
/
SS_writepar_3.30.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
#' write .par file from SS version 3.30
#'
#' Write Stock Synthesis (version 3.30) parameter file from list object in R to file.
#'
#'
#' @param parlist List object created by [SS_readpar_3.30()].
#' @param outfile Filename for where to write new parameter file.
#' @param overwrite Should existing files be overwritten? Default=TRUE.
#' @template verbose
#' @author Nathan R. Vaughan
#' @export
#' @seealso [SS_readpar_3.30()],
#' [SS_readctl()],
#' [SS_readdat()]
#' [SS_readstarter()],
#' [SS_readforecast()],
#' [SS_writectl()],
#' [SS_writedat()],
#' [SS_writestarter()],
#' [SS_writeforecast()]
SS_writepar_3.30 <- function(parlist, outfile, overwrite = TRUE, verbose = FALSE) {
# function to write Stock Synthesis parameter files
if (verbose) message("running SS_writepar_3.30")
if (file.exists(outfile)) {
if (!overwrite) {
message("File exists and input 'overwrite'=FALSE:", outfile)
return()
} else {
file.remove(outfile)
}
}
if (verbose) message("Opening connection to ", outfile)
zz <- file(outfile, open = "at") # open = "at" means open for appending in text mode.
on.exit(close(zz)) # Needed in case the function exits early.
if (!is.null(parlist[["headerlines"]])) {
writeLines(paste0(parlist[["headerlines"]][1]), con = zz)
writeLines(paste0(parlist[["headerlines"]][2]), con = zz)
writeLines(paste0(parlist[["headerlines"]][3]), con = zz)
}
if (!is.null(parlist[["MG_parms"]])) {
for (i in seq_along(parlist[["MG_parms"]][, 1])) {
writeLines(paste0("# MGparm[", i, "]:"), con = zz)
writeLines(paste0(parlist[["MG_parms"]][i, 2]), con = zz)
}
}
if (!is.null(parlist[["SR_parms"]])) {
for (i in seq_along(parlist[["SR_parms"]][, 1])) {
writeLines(paste0("# SR_parm[", i, "]:"), con = zz)
writeLines(paste0(parlist[["SR_parms"]][i, 2]), con = zz)
}
}
if (!is.null(parlist[["recdev_cycle_parm"]])) {
for (i in seq_along(parlist[["recdev_cycle_parm"]][, 1])) {
writeLines(paste0("# recdev_cycle_parm[", i, "]:"), con = zz)
writeLines(paste0(parlist[["recdev_cycle_parm"]][i, 2]), con = zz)
}
}
if (!is.null(parlist[["recdev_early"]])) {
writeLines(paste0("# recdev_early:"), con = zz)
writeLines(paste0(parlist[["recdev_early"]][, 2], collapse = " "), con = zz)
}
if (!is.null(parlist[["recdev1"]])) {
writeLines(paste0("# recdev1:"), con = zz)
writeLines(paste0(parlist[["recdev1"]][, 2], collapse = " "), con = zz)
}
if (!is.null(parlist[["recdev2"]])) {
writeLines(paste0("# recdev2:"), con = zz)
writeLines(paste0(parlist[["recdev2"]][, 2], collapse = " "), con = zz)
}
if (!is.null(parlist[["recdev_forecast"]])) {
writeLines(paste0("# Fcast_recruitments:"), con = zz)
writeLines(paste0(parlist[["recdev_forecast"]][, 2], collapse = " "), con = zz)
}
if (!is.null(parlist[["Fcast_impl_error"]])) {
writeLines(paste0("# Fcast_impl_error:"), con = zz)
writeLines(paste0(parlist[["Fcast_impl_error"]][, 2], collapse = " "), con = zz)
}
if (!is.null(parlist[["init_F"]])) {
for (i in seq_along(parlist[["init_F"]])) {
writeLines(paste0("# init_F[", i, "]:"), con = zz)
writeLines(paste0(parlist[["init_F"]][i]), con = zz)
}
}
if (!is.null(parlist[["F_rate"]])) {
for (i in seq_along(parlist[["F_rate"]][, 1])) {
writeLines(paste0("# F_rate[", i, "]:"), con = zz)
writeLines(paste0(parlist[["F_rate"]][i, 4]), con = zz)
}
}
if (!is.null(parlist[["Q_parms"]])) {
for (i in seq_along(parlist[["Q_parms"]][, 1])) {
writeLines(paste0("# Q_parm[", i, "]:"), con = zz)
writeLines(paste0(parlist[["Q_parms"]][i, 2]), con = zz)
}
}
if (!is.null(parlist[["S_parms"]])) {
for (i in seq_along(parlist[["S_parms"]][, 1])) {
writeLines(paste0("# selparm[", i, "]:"), con = zz)
writeLines(paste0(parlist[["S_parms"]][i, 2]), con = zz)
}
}
if (!is.null(parlist[["TG_parms"]])) {
for (i in seq_along(parlist[["TG_parms"]][, 1])) {
writeLines(paste0("# TG_parm[", i, "]:"), con = zz)
writeLines(paste0(parlist[["TG_parms"]][i, 2]), con = zz)
}
}
if (!is.null(parlist[["parm_devs"]])) {
for (i in seq_along(parlist[["parm_devs"]])) {
writeLines(paste0("# parm_dev[", i, "]:"), con = zz)
writeLines(paste0(parlist[["parm_devs"]][[i]][, 2], collapse = " "), con = zz)
}
}
writeLines(paste0("# checksum999:"), con = zz)
writeLines(paste0(999), con = zz)
return(parlist)
}