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more optimizations to SPC methods #135
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@brownag
brownag committed May 25, 2020
1 parent efb0909 commit 6f47409
Showing 1 changed file with 32 additions and 29 deletions.
61 changes: 32 additions & 29 deletions R/SoilProfileCollection-methods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -308,10 +308,10 @@ definition=function(x, v=NULL) {
# optionally use a horizon-level property refine calculation
if(!missing(v)) {
# combine bottom depths with IDs and variable
h <- horizons(x)[, c(hz_bottom_depths, idname(x), v)]
h <- x@horizons[, c(hz_bottom_depths, idname(x), v)]
} else {
# combine bottom depths with IDs
h <- horizons(x)[, c(hz_bottom_depths, idname(x))]
h <- x@horizons[, c(hz_bottom_depths, idname(x))]
}

# filter out missing data
Expand All @@ -333,10 +333,10 @@ definition=function(x, v=NULL){
# optionally use a horizon-level property refine calculation
if(!missing(v)) {
# combine bottom depths with IDs and variable
h <- horizons(x)[, c(hz_bottom_depths, idname(x), v)]
h <- x@horizons[, c(hz_bottom_depths, idname(x), v)]
} else {
# combine bottom depths with IDs
h <- horizons(x)[, c(hz_bottom_depths, idname(x))]
h <- x@horizons[, c(hz_bottom_depths, idname(x))]
}

# filter out missing data
Expand All @@ -352,7 +352,9 @@ definition=function(x, v=NULL){
# overload length() to give us the number of profiles in the collection
setMethod(f='length', signature='SoilProfileCollection',
definition=function(x){
l <- length(profile_id(x))
# faster replacement for profile_id()
# which calls unique(horizons(x)[[idname(x)]]) -- expensive
l <- length(x@site[[idname(x)]])#profile_id(x))
return(l)
}
)
Expand Down Expand Up @@ -411,11 +413,11 @@ setMethod("$", "SoilProfileCollection",

# get column from horizon data
if (name %in% h.names) {
res <- horizons(x)[[name]]
res <- x@horizons[[name]]
} else {
# otherwise check site data
if (name %in% s.names) {
res <- site(x)[[name]]
res <- x@site[[name]]
} else {
# if still missing return NULL
res <- NULL
Expand All @@ -431,37 +433,37 @@ setMethod("$", "SoilProfileCollection",
setReplaceMethod("$", "SoilProfileCollection",
function(x, name, value) {
# extract hz and site data
h <- horizons(x)
s <- site(x)
h <- x@horizons
s <- x@site

# working with horizon data
if (name %in% names(h)) {
h[[name]] <- value
slot(x, 'horizons') <- h
x@horizons <- h
return(x)
}

# working with site data
if(name %in% names(s)) {
s[[name]] <- value
slot(x, 'site') <- s
x@site <- s
return(x)
}

# ambiguous: use length of replacement to determing: horizon / site
# ambiguous: use length of replacement to determine: horizon / site
n.site <- nrow(s)
n.hz <- nrow(h)
l <- length(value)

if(l == n.hz) {
h[[name]] <- value
slot(x, 'horizons') <- h
x@horizons <- h
return(x)
}

if(l == n.site) {
s[[name]] <- value
slot(x, 'site') <- s
x@site <- s
return(x)
}

Expand All @@ -472,17 +474,20 @@ setReplaceMethod("$", "SoilProfileCollection",

setReplaceMethod("[[", signature=c(x="SoilProfileCollection", i="character", j="ANY"),
function(x, i, j, ...) {
lv <- length(value)
lx <- length(x)
nx <- nrow(x)
hznames <- horizonNames(x)
stnames <- siteNames(x)
# default to creating site var, as long as its not in horizon names
if((!i %in% horizonNames(x)) & (i %in% siteNames(x) |
length(value) == length(x))) {
if(length(value) == length(x)) {
if((!i %in% hznames) & (i %in% stnames | lv == lx)) {
if(lv == lx) {
x@site[,i] <- value
} else {
stop("replacement length does not match number of profiles!", call. = FALSE)
}
} else if (i %in% horizonNames(x) |
length(value) == nrow(x)) {
if(length(value) == nrow(x)) {
} else if (i %in% hznames | lv == nx) {
if(lv == nx) {
x@horizons[,i] <- value
} else {
stop("replacement length does not match number of horizons!", call. = FALSE)
Expand Down Expand Up @@ -786,19 +791,20 @@ setMethod("[", signature=c("SoilProfileCollection", i="ANY", j="ANY"),
#### TODO: implicit sub-setting of horizon records should affect all slots
#### https://github.com/ncss-tech/aqp/issues/89

# extract requested profile IDs
p.ids <- profile_id(x)[i]

# extract all horizon data
# extract all site and horizon data
h <- horizons(x)
s.all <- site(x)

# extract requested profile IDs
p.ids <- s.all[[idname(x)]][unique(i)]

# keep only the requested horizon data (filtered by profile ID)
h <- h[h[[idname(x)]] %in% p.ids, ]

# keep only the requested site data, (filtered by profile ID)
s.all <- site(x)
s.i <- which(s.all[[idname(x)]] %in% p.ids)
s <- s.all[s.i, , drop=FALSE] # need to use drop=FALSE when @site contains only a single column
s <- s.all[s.i, , drop=FALSE]
# need to use drop=FALSE when @site contains only a single column

# subset spatial data, but only if valid
if(validSpatialData(x)) {
Expand All @@ -808,7 +814,6 @@ setMethod("[", signature=c("SoilProfileCollection", i="ANY", j="ANY"),
else {
sp <- x@sp
}


# subset diagnostic data, but only if it exists
# note that not all profiles have diagnostic hz data
Expand Down Expand Up @@ -852,7 +857,6 @@ setMethod("[", signature=c("SoilProfileCollection", i="ANY", j="ANY"),
# put it all back together and replace what we started with
h <- do.call('rbind', hh)
}


# if there is REAL data in @sp, and we only have 1 row of hz per coordinate- return SPDF
# valid spatial data is now tested via validSpatialData()
Expand Down Expand Up @@ -897,7 +901,6 @@ setMethod("[", signature=c("SoilProfileCollection", i="ANY", j="ANY"),
suppressMessages(hzdesgnname(res) <- hzdesgnname(x))
suppressMessages(hztexclname(res) <- hztexclname(x))


## integrity checks: these will be implicit in the aqp 2.0 SPC

# https://github.com/ncss-tech/aqp/issues/89
Expand Down

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