Example 1
Let’s first start by using the sample data from FIESTA. Here, in it’s most simple form, we get summed live basal area and net cubic-foot volume by plot.
Note: datSum_opts has several parameter options, such as TPA and rounding (See datSum_options() for other parameters).
What is TPA? TPA is Trees Per Acre (TPA_UNADJ). The TPA_UNADJ variable is an acre-level expansion factor for measured trees. For FIA’s annual inventory, fixed plot design: TPA equals the inverse of the plot area (TPA = 1 / (Number of plots * area of plot).
FIA’s fixed plot design includes 4 subplots that are 24ft (7.3m) radius (0.04154 acres) and 4 microplots that are 6.8ft (2.1m) radius (0.00333 acres). Trees 5.0in (61cm) and greater are measured on the subplots and trees less than 5.0in are measured on the microplots. TPA for trees measured on the subplots is 6.018 (1 / (4 * 0.04143) and TPA for trees measured on the microplots is 74.965 (1 / 4 * 0.00333)). So, if we set TPA = TRUE, each tree 5.0in and greater represents 6.018 trees and each tree less than 5.0in represents 74.965 trees.
In FIESTA, TPA is default to TRUE. This means anything in the tsumvarlst (except TPA_UNADJ) is multiplied by TPA_UNADJ. If TPA = FALSE, we simply get a sum of the count of trees measured on the FIA plots.
sumdat1 <- datSumTree(tree = WYtree,
tsumvarlst = c("BA", "VOLCFNET"),
tfilter = "STATUSCD == 1")## Warning: no DISPLAY variable so Tk is not available
## Returned list items
names(sumdat1)## [1] "treedat" "sumvars" "tsumuniqueid" "treeqry" "tfilter"
## [6] "tround"
## The first six rows of the summarized data table.
head(sumdat1$treedat)## Key: <PLT_CN>
## PLT_CN BA_TPA_live VOLCFNET_TPA_live
## <char> <num> <num>
## 1: 40404729010690 14.27414 41.80061
## 2: 40404730010690 119.74279 1563.03478
## 3: 40404737010690 4.39131 25.08993
## 4: 40404738010690 17.71590 137.52138
## 5: 40404742010690 31.15636 448.67475
## 6: 40404743010690 70.82421 907.80021
## The summarized variable names
sumdat1$sumvars## [1] "BA_TPA_live" "VOLCFNET_TPA_live"
## The query used to get data (use message to output in pretty format)
message(sumdat1$treeqry)## WITH tdat AS
## (SELECT 'TREE' src, t.PLT_CN, t.CONDID, t.SUBP, t.TREE, t.BA, t.VOLCFNET, t.TPA_UNADJ
## FROM treex t
## WHERE STATUSCD = 1)
## -------------------------------------------
## SELECT tdat.PLT_CN,
## COALESCE(SUM(BA * TPA_UNADJ),0) AS BA_TPA_live,
## COALESCE(SUM(VOLCFNET * TPA_UNADJ),0) AS VOLCFNET_TPA_live
## FROM tdat
## GROUP BY tdat.PLT_CNExample 2
So, let’s now get a little more familiar with this function by showing what else it can do.
This time we will do the following things: 1) Add custom names
(tsumvarnmlst) 2) summarize by plot and species
(bydomainlst) 3) Add a derived variable
(tderive) 4) Exclude woodland species
(woodland) 5) Include seedlings (seedlings) 6)
include a per acre count (i.e., TPA_UNADJ)
Note: Derived variables are not multiplied by TPA_UNADJ when the
default is set (datSum_opts(TPA = TRUE)). Therefore, you
must include it in the derived statement if it is desired. Furthermore
variables defined in tderive should not be included in
tsumvarlst.
Notice that the definitions for the derived variables are written in SQL syntax. This is required so that the statement can be appropriately plugged into the query that is used to generate collect the data.
sumdat2 <-
datSumTree(tree = WYtree,
seed = WYseed,
tsumvarlst = c("BA", "VOLCFNET", "TPA_UNADJ"),
tsumvarnmlst = c("BA_LIVE", "VOLNET_LIVE", "COUNT"),
bydomainlst = "SPCD",
tderive = list(SDI = '(POWER(DIA / 10, 1.605)) * TPA_UNADJ'),
woodland = "N",
seedlings = "Y",
tfilter = "STATUSCD == 1")
## Returned list items
names(sumdat2)## [1] "treedat" "sumvars" "tsumuniqueid" "treeqry" "tfilter"
## [6] "tdomainlst" "pcdomainlst" "tround"
## The first six rows of the summarized data table.
head(sumdat2$treedat)## Key: <PLT_CN>
## PLT_CN SPCD COUNT_TREE BA_LIVE VOLNET_LIVE SDI COUNT_SEED
## <char> <num> <num> <num> <num> <num> <num>
## 1: 40404729010690 113 18.05414 6.02915 41.80061 12.00007 74.96528
## 2: 40404730010690 108 6.01805 1.60830 21.73192 3.39498 0.00000
## 3: 40404730010690 113 36.10828 12.56114 124.99617 24.57426 0.00000
## 4: 40404730010690 122 135.14574 41.04085 612.11646 73.29117 0.00000
## 5: 40404730010690 202 138.41506 64.53249 804.19022 118.74775 224.89585
## 6: 40404737010690 113 6.01805 1.94604 10.21924 3.95615 0.00000
## COUNT
## <num>
## 1: 93.01942
## 2: 6.01805
## 3: 36.10828
## 4: 135.14574
## 5: 363.31090
## 6: 6.01805
## The summarized variable names
sumdat2$sumvars## [1] "COUNT_TREE" "COUNT_SEED" "COUNT" "BA_LIVE" "VOLNET_LIVE"
## [6] "SDI"
## The query used to get data (use message to output in pretty format)
message(sumdat2$treeqry)## WITH tdat AS
## (SELECT 'TREE' src, t.PLT_CN, t.CONDID, t.SUBP, t.TREE, t.SPCD, t.TPA_UNADJ, t.BA, t.VOLCFNET, t.DIA
## FROM treex t
## JOIN ref_species ref ON (ref.SPCD = t.SPCD)
## WHERE STATUSCD = 1 AND WOODLAND = 'N'
## UNION
## SELECT 'SEED' src, s.PLT_CN, s.CONDID, s.SUBP, 0, s.SPCD, s.TPA_UNADJ, 'null', 'null', 'null'
## FROM seedx s
## JOIN ref_species ref ON (ref.SPCD = s.SPCD)
## WHERE WOODLAND = 'N')
## -------------------------------------------
## SELECT tdat.PLT_CN, SPCD,
## COALESCE(SUM(CASE WHEN src = 'TREE' THEN TPA_UNADJ ELSE 0 END),0) AS COUNT_TREE,
## COALESCE(SUM(CASE WHEN src = 'TREE' THEN BA * TPA_UNADJ ELSE 0 END),0) AS BA_LIVE,
## COALESCE(SUM(CASE WHEN src = 'TREE' THEN VOLCFNET * TPA_UNADJ ELSE 0 END),0) AS VOLNET_LIVE,
## COALESCE(SUM(CASE WHEN src = 'TREE' THEN (POWER(DIA / 10, 1.605)) * TPA_UNADJ ELSE 0 END),0) AS SDI,
## COALESCE(SUM(CASE WHEN src = 'SEED' THEN TPA_UNADJ ELSE 0 END),0) AS COUNT_SEED,
## COALESCE(SUM(TPA_UNADJ),0) AS COUNT
## FROM tdat
## GROUP BY tdat.PLT_CN, SPCDExample 3:
Now, let’s go further and include classified domains to summarize by. 1) Classify species into 3 classes (C-Conifer;W-Woodland;H-Hardwood) 2) Specify diameter breaks 3) Add species look up table and diameter breaks to domclassify, while also adding variables classified to bydomainlst.
## First, find unique species in WYtree
spcdlst <- sort(unique(WYtree$SPCD))
## specify new class values for each unique species in WYtree
spcdlut <- data.frame(SPCD = spcdlst,
SPCDCL = c("C","W","W","C","C","C","W","C","C","C","C","H","H","W","H","H","H","H","H"))
## Next, find unique diameters in WYtree
dialst <- sort(unique(WYtree$DIA))
## specify break values to define new diameter class
diabrks <- c(0,20,40,80)
sumdat3 <-
datSumTree(tree = WYtree,
seed = WYseed,
tsumvarlst = c("BA", "VOLCFNET", "TPA_UNADJ"),
tsumvarnmlst = c("BA_LIVE", "VOLNET_LIVE", "COUNT"),
bydomainlst = c("SPCD", "DIA"),
tderive = list(SDI = '(POWER(DIA / 10, 1.605)) * TPA_UNADJ'),
domclassify = list(SPCD = spcdlut, DIA = diabrks),
woodland = "N",
seedlings = "Y",
tfilter = "STATUSCD == 1")
## Returned list items
names(sumdat3)## [1] "treedat" "sumvars" "tsumuniqueid" "treeqry"
## [5] "tfilter" "tdomainlst" "pcdomainlst" "classifynmlst"
## [9] "tround"
## The first six rows of the summarized data table.
head(sumdat3$treedat)## Key: <PLT_CN>
## PLT_CN SPCDCL DIACL COUNT_TREE BA_LIVE VOLNET_LIVE SDI
## <char> <char> <char> <num> <num> <num> <num>
## 1: 40404729010690 C 0-20 6.01805 0.88752 3.79245 2.10689
## 2: 40404729010690 C 0-20 6.01805 2.54177 14.99432 4.90174
## 3: 40404729010690 C 0-20 6.01805 2.59986 23.01384 4.99145
## 4: 40404729010690 C 80+ 0.00000 0.00000 0.00000 0.00000
## 5: 40404730010690 C 0-20 74.96528 3.67975 0.00000 10.85525
## 6: 40404730010690 C 0-20 6.01805 0.85371 6.26437 2.04223
## COUNT_SEED COUNT
## <num> <num>
## 1: 0.00000 6.01805
## 2: 0.00000 6.01805
## 3: 0.00000 6.01805
## 4: 74.96528 74.96528
## 5: 0.00000 74.96528
## 6: 0.00000 6.01805
## The summarized variable names
sumdat3$sumvars## [1] "COUNT_TREE" "COUNT_SEED" "COUNT" "BA_LIVE" "VOLNET_LIVE"
## [6] "SDI"
## The query used to get data (use message to output in pretty format)
message(sumdat3$treeqry)## WITH tdat AS
## (SELECT 'TREE' src, t.PLT_CN, t.CONDID, t.SUBP, t.TREE, t.SPCD, t.TPA_UNADJ, t.DIA, t.BA, t.VOLCFNET
## FROM treex t
## JOIN ref_species ref ON (ref.SPCD = t.SPCD)
## WHERE STATUSCD = 1 AND WOODLAND = 'N'
## UNION
## SELECT 'SEED' src, s.PLT_CN, s.CONDID, s.SUBP, 0, s.SPCD, s.TPA_UNADJ, 'null', 'null', 'null'
## FROM seedx s
## JOIN ref_species ref ON (ref.SPCD = s.SPCD)
## WHERE WOODLAND = 'N')
## -------------------------------------------
## SELECT tdat.PLT_CN,
## (CASE
## WHEN tdat.SPCD = 19 THEN 'C'
## WHEN tdat.SPCD = 65 THEN 'W'
## WHEN tdat.SPCD = 66 THEN 'W'
## WHEN tdat.SPCD = 93 THEN 'C'
## WHEN tdat.SPCD = 96 THEN 'C'
## WHEN tdat.SPCD = 101 THEN 'C'
## WHEN tdat.SPCD = 106 THEN 'W'
## WHEN tdat.SPCD = 108 THEN 'C'
## WHEN tdat.SPCD = 113 THEN 'C'
## WHEN tdat.SPCD = 122 THEN 'C'
## WHEN tdat.SPCD = 202 THEN 'C'
## WHEN tdat.SPCD = 313 THEN 'H'
## WHEN tdat.SPCD = 375 THEN 'H'
## WHEN tdat.SPCD = 475 THEN 'W'
## WHEN tdat.SPCD = 544 THEN 'H'
## WHEN tdat.SPCD = 745 THEN 'H'
## WHEN tdat.SPCD = 746 THEN 'H'
## WHEN tdat.SPCD = 749 THEN 'H'
## WHEN tdat.SPCD = 823 THEN 'H' END) AS SPCDCL,
## (CASE
## WHEN tdat.DIA IS NULL THEN '<1'
## WHEN tdat.DIA >= 0 AND tdat.DIA < 20 THEN '0-20'
## WHEN tdat.DIA >= 20 AND tdat.DIA < 40 THEN '20-40'
## WHEN tdat.DIA >= 40 AND tdat.DIA < 80 THEN '40-80'
## WHEN tdat.DIA >= 80 THEN '80+' END) AS DIACL,
## COALESCE(SUM(CASE WHEN src = 'TREE' THEN TPA_UNADJ ELSE 0 END),0) AS COUNT_TREE,
## COALESCE(SUM(CASE WHEN src = 'TREE' THEN BA * TPA_UNADJ ELSE 0 END),0) AS BA_LIVE,
## COALESCE(SUM(CASE WHEN src = 'TREE' THEN VOLCFNET * TPA_UNADJ ELSE 0 END),0) AS VOLNET_LIVE,
## COALESCE(SUM(CASE WHEN src = 'TREE' THEN (POWER(DIA / 10, 1.605)) * TPA_UNADJ ELSE 0 END),0) AS SDI,
## COALESCE(SUM(CASE WHEN src = 'SEED' THEN TPA_UNADJ ELSE 0 END),0) AS COUNT_SEED,
## COALESCE(SUM(TPA_UNADJ),0) AS COUNT
## FROM tdat
## GROUP BY tdat.PLT_CN, DIAExample 4:
Lastly, let’s play around with some additional derived variables:
sumdat4 <-
datSumTree(tree = WYtree,
tderive = list(LIVE_BA = "SUM(power(DIA, 2) * 0.005454 * TPA_UNADJ * (CASE WHEN STATUSCD = 1 THEN 1 ELSE 0 END))",
DEAD_BA = "SUM(power(DIA, 2) * 0.005454 * TPA_UNADJ * (CASE WHEN STATUSCD = 2 THEN 1 ELSE 0 END))",
SDI = "SUM((POWER(DIA / 10, 1.605)) * TPA_UNADJ)",
QMD = "sqrt(SUM(power(DIA, 2) * 0.005454 * TPA_UNADJ) / (SUM(TPA_UNADJ) * 0.005454))",
MEAN_DIA = "AVG(DIA)",
MEDIAN_DIA = "MEDIAN(DIA)",
LIVELESS20 = "SUM(TPA_UNADJ * (CASE WHEN DIA < 10 THEN 1 ELSE 0 END))",
LIVE10to30 = "SUM(TPA_UNADJ * (CASE WHEN DIA > 10 AND DIA <= 30 THEN 1 ELSE 0 END))"))
## Returned list items
names(sumdat4)## [1] "treedat" "sumvars" "tsumuniqueid" "treeqry" "tround"
## The first six rows of the summarized data table.
head(sumdat4$treedat)## Key: <PLT_CN>
## PLT_CN LIVE_BA DEAD_BA SDI QMD MEAN_DIA MEDIAN_DIA
## <char> <num> <num> <num> <num> <num> <num>
## 1: 40404729010690 14.27414 2.83356 32.50917 8.62902 8.31429 8.80
## 2: 40404730010690 119.74279 7.48450 234.13906 8.36041 8.65455 7.60
## 3: 40404737010690 4.39131 4.49306 17.14599 8.22618 7.90000 7.00
## 4: 40404738010690 17.71590 19.05506 67.95588 8.94547 8.45714 7.65
## 5: 40404742010690 31.15636 0.00000 53.66041 11.64499 11.60000 11.40
## 6: 40404743010690 70.82421 5.10750 146.05962 7.09833 8.69565 7.50
## LIVELESS20 LIVE10to30
## <num> <num>
## 1: 30.09023 12.03609
## 2: 249.48862 78.23460
## 3: 18.05414 6.01805
## 4: 60.18046 18.05414
## 5: 6.01805 36.10828
## 6: 222.14712 54.16241
## The summarized variable names
sumdat4$sumvars## [1] "LIVE_BA" "DEAD_BA" "SDI" "QMD" "MEAN_DIA"
## [6] "MEDIAN_DIA" "LIVELESS20" "LIVE10to30"
## The query used to get data (use message to output in pretty format)
message(sumdat4$treeqry)## WITH tdat AS
## (SELECT 'TREE' src, t.PLT_CN, t.CONDID, t.SUBP, t.TREE, t.STATUSCD, t.DIA, t.TPA_UNADJ
## FROM treex t)
## -------------------------------------------
## SELECT tdat.PLT_CN,
## SUM(power(DIA, 2) * 0.005454 * TPA_UNADJ * (CASE WHEN STATUSCD = 1 THEN 1 ELSE 0 END)) AS LIVE_BA,
## SUM(power(DIA, 2) * 0.005454 * TPA_UNADJ * (CASE WHEN STATUSCD = 2 THEN 1 ELSE 0 END)) AS DEAD_BA,
## SUM((POWER(DIA / 10, 1.605)) * TPA_UNADJ) AS SDI,
## sqrt(SUM(power(DIA, 2) * 0.005454 * TPA_UNADJ) / (SUM(TPA_UNADJ) * 0.005454)) AS QMD,
## AVG(DIA) AS MEAN_DIA,
## MEDIAN(DIA) AS MEDIAN_DIA,
## SUM(TPA_UNADJ * (CASE WHEN DIA < 10 THEN 1 ELSE 0 END)) AS LIVELESS20,
## SUM(TPA_UNADJ * (CASE WHEN DIA > 10 AND DIA <= 30 THEN 1 ELSE 0 END)) AS LIVE10to30
## FROM tdat
## GROUP BY tdat.PLT_CN