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Replace ProSpectSEDlike manual parameter plumbing with ParmOff #31

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Replace ProSpectSEDlike manual parameter plumbing with ParmOff #31

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1af9f58
Use ParmOff in ProSpectSEDlike for bounds/logged and function dispatch
Copilot May 14, 2026
3444d84
Fix!
asgr May 14, 2026
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115 changes: 68 additions & 47 deletions R/ProSpect.R
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Original file line number Diff line number Diff line change
Expand Up @@ -533,6 +533,21 @@ ProSpectSEDlike = function(parm = c(8, 9, 10, 10, 0, -0.5, 0.2), Data) {
}

names(parm) = Data$parm.names

if (!requireNamespace("ParmOff", quietly = TRUE)) {
stop("The ParmOff package is needed for parameter mapping in ProSpectSEDlike. Please install it from GitHub/asgr/ParmOff.", call. = FALSE)
}

logged_parm_names = NULL
if (!is.null(Data$logged)) {
if (length(Data$logged) == 1) {
if (Data$logged) {
logged_parm_names = Data$parm.names
}
} else {
logged_parm_names = Data$parm.names[Data$logged]
}
}

if(is.null(Data$photom) & isTRUE(Data$mode == 'photom')){
Data$photom = Data$flux
Expand Down Expand Up @@ -573,7 +588,7 @@ ProSpectSEDlike = function(parm = c(8, 9, 10, 10, 0, -0.5, 0.2), Data) {
z_genSF = Data$arglist$z_genSF ## What redshift should we start star formation?

ztest = parm["z"]
if(Data$logged[Data$parm.names == "z"]){
if("z" %in% logged_parm_names){
ztest = 10^ztest
}

Expand Down Expand Up @@ -622,31 +637,6 @@ ProSpectSEDlike = function(parm = c(8, 9, 10, 10, 0, -0.5, 0.2), Data) {
parm = Data$constraints(parm)
}

if (!is.null(Data$intervals)) {
#parm[parm < Data$intervals$lo] = Data$intervals$lo[parm < Data$intervals$lo]
#parm[parm > Data$intervals$hi] = Data$intervals$hi[parm > Data$intervals$hi]
parm = pmin(pmax(parm, Data$intervals$lo), Data$intervals$hi)
}

if (!is.null(Data$logged)) {
if (length(Data$logged) == 1) {
if (Data$logged) {
parmlist = 10 ^ parm
} else{
parmlist = parm
}
} else{
parmlist = parm
parmlist[Data$logged] = 10 ^ parm[Data$logged]
}
} else{
parmlist = parm
}

if (Data$verbose) {
message(parmlist)
}

if('scat_scale' %in% Data$parm.names){
sel = which('scat_scale' == Data$parm.names)
scat_scale = parmlist[sel]
Expand All @@ -655,6 +645,33 @@ ProSpectSEDlike = function(parm = c(8, 9, 10, 10, 0, -0.5, 0.2), Data) {
}else{
scat_scale = 1
}

parm_lower = NULL
parm_upper = NULL
if (!is.null(Data$intervals)) {
parm_lower = as.list(Data$intervals$lo)
parm_upper = as.list(Data$intervals$hi)
names(parm_lower) = Data$parm.names
names(parm_upper) = Data$parm.names
}

parmlist = ParmOff::ParmOff(
.func = ProSpectSED,
.args = parm,
.lower = parm_lower,
.upper = parm_upper,
.logged = logged_parm_names,
.return = 'args',
.check = FALSE
)$current_args
if(any(lengths(parmlist) != 1L)){
stop('All fitting parameters must be scalar values.')
}
parmlist = unlist(parmlist, recursive = FALSE, use.names = TRUE)

if (Data$verbose) {
message(parmlist)
}

Monitor = {}

Expand All @@ -666,20 +683,22 @@ ProSpectSEDlike = function(parm = c(8, 9, 10, 10, 0, -0.5, 0.2), Data) {
}

if (returnall) {
SEDout = do.call(
'ProSpectSED',
args = c(
parmlist,
list(SFH = quote(Data$SFH)),
list(speclib = quote(Data$speclib)),
list(Dale = quote(Data$Dale)),
list(AGN = quote(Data$AGN)),
list(filtout = quote(filtout)),
SEDout = ParmOff::ParmOff(
.func = ProSpectSED,
.args = c(
as.list(parmlist),
list(SFH = Data$SFH),
list(speclib = Data$speclib),
list(Dale = Data$Dale),
list(AGN = Data$AGN),
list(filtout = filtout),
list(filters = NULL),
list(returnall = TRUE),
list(Dale_M2L_func = quote(Data$Dale_M2L_func)),
list(Dale_M2L_func = Data$Dale_M2L_func),
Data$arglist
)
),
.return = 'func',
.check = FALSE
)
if(is.null(Data$filtout) | isTRUE(Data$mode == 'spec') | isTRUE(Data$mode == 'both')){
#this means we are in spec-z mode
Expand Down Expand Up @@ -718,19 +737,21 @@ ProSpectSEDlike = function(parm = c(8, 9, 10, 10, 0, -0.5, 0.2), Data) {
}
} else{

Photom = do.call(
'ProSpectSED',
args = c(
parmlist,
list(SFH = quote(Data$SFH)),
list(speclib = quote(Data$speclib)),
list(Dale = quote(Data$Dale)),
list(AGN = quote(Data$AGN)),
list(filtout = quote(filtout)),
Photom = ParmOff::ParmOff(
.func = ProSpectSED,
.args = c(
as.list(parmlist),
list(SFH = Data$SFH),
list(speclib = Data$speclib),
list(Dale = Data$Dale),
list(AGN = Data$AGN),
list(filtout = filtout),
list(filters = NULL),
list(returnall = FALSE),
Data$arglist
)
),
.return = 'func',
.check = FALSE
)

if(is.null(filtout)){
Expand Down
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