WebSVN - public iLand - Diff - Rev 1054 and 1104 - /R


Redirecting to URL 'https://iland.boku.ac.at/svn/iland/tags/release_1.0/R_analysis/stacked.timeseries.R':
### 
### load some useful tools/functions
#source("sql_tools.R")
library(RSQLite)

# connect to an existing database
db.conn <<- dbConnect(RSQLite::SQLite(), dbname="e:/Daten/iLand/projects/HJA_WS12_v2/output/HJA_WS12.sqlite" )

### load data from the iLand output table
stand <- dbReadTable(db.conn, "stand")
# alternatively (using sql_tools): stand <- query("select * from stand")

summary(stand)

## stacked bar chart, e.g. for basal area
library(ggplot2)

head(stand)
# aggregate to values for each species and year (i.e. averaging over all the resource units)
stand.avg <- aggregate(stand, list(year=stand$year, species=stand$species), FUN="mean")
head(stand.avg)

#### provide fixed colors for species (in form of key-value pairs; the key is the species code, value is the color)
cols.species <- c("Tshe"="#101010", 
                  "Abam"="#202020", 
                  "Alru" =  "#303030", 
                  "Thpl" = "#404040", 
                  "Psme" = "#505050", 
                  "Acma" = "#606060", 
                  "var2" = "#707070", 
                  "var3" = "#808080")

# now we can plot them:
ggplot(stand.avg, aes(x=year,y=basal_area_m2,group=species,fill=species)) + geom_area() + labs(xlab="year", ylab="basal area m2", title="average basal area") + scale_fill_manual(values=cols.species)
## stem numbers
ggplot(stand.avg, aes(x=year,y=count_ha,group=species,fill=species)) + geom_area()
ggplot(stand.avg, aes(x=year,y=cohortCount_ha,group=species,fill=species)) + geom_area()

ggplot(stand.avg, aes(x=year,y=LAI,group=species,fill=species)) + geom_area()

cols <- rainbow(nrow(mtcars))
mtcars$car <- rownames(mtcars)
ggplot(mtcars, aes(mpg, disp, colour = car)) + geom_point() +
  scale_colour_manual(limits = mtcars$car, values = cols) +
  guides(colour = guide_legend(ncol = 3))


### e.g. LAI per resource unit in the first three years
par(mfrow=c(1,3))
for (y in c(1,2,3))
  boxplot(tapply(stand$LAI[stand$year == y], stand$ru[stand$year == y], sum), ylim=c(0,10), main=paste("Year", y))

Rev 1054	Rev 1104
1	Redirecting to URL 'https://iland.boku.ac.at/svn/iland/tags/release_1.0/R_analysis/stacked.timeseries.R':	1	Redirecting to URL 'https://iland.boku.ac.at/svn/iland/tags/release_1.0/R_analysis/stacked.timeseries.R':
2	###	2	###
3	### load some useful tools/functions	3	### load some useful tools/functions
4	#source("sql_tools.R")	4	#source("sql_tools.R")
5	library(RSQLite)	5	library(RSQLite)
6		6
7	# connect to an existing database	7	# connect to an existing database
8	db.conn <<- dbConnect(RSQLite::SQLite(), dbname="e:/Daten/iLand/projects/HJA_WS12_v2/output/HJA_WS12.sqlite" )	8	db.conn <<- dbConnect(RSQLite::SQLite(), dbname="e:/Daten/iLand/projects/HJA_WS12_v2/output/HJA_WS12.sqlite" )
9		9
10	### load data from the iLand output table	10	### load data from the iLand output table
11	stand <- dbReadTable(db.conn, "stand")	11	stand <- dbReadTable(db.conn, "stand")
12	# alternatively (using sql_tools): stand <- query("select * from stand")	12	# alternatively (using sql_tools): stand <- query("select * from stand")
13		13
14	summary(stand)	14	summary(stand)
15		15
16	## stacked bar chart, e.g. for basal area	16	## stacked bar chart, e.g. for basal area
17	library(ggplot2)	17	library(ggplot2)
18		18
19	head(stand)	19	head(stand)
20	# aggregate to values for each species and year (i.e. averaging over all the resource units)	20	# aggregate to values for each species and year (i.e. averaging over all the resource units)
21	stand.avg <- aggregate(stand, list(year=stand$year, species=stand$species), FUN="mean")	21	stand.avg <- aggregate(stand, list(year=stand$year, species=stand$species), FUN="mean")
22	head(stand.avg)	22	head(stand.avg)
23		23
24	#### provide fixed colors for species (in form of key-value pairs; the key is the species code, value is the color)	24	#### provide fixed colors for species (in form of key-value pairs; the key is the species code, value is the color)
25	cols.species <- c("Tshe"="#101010",	25	cols.species <- c("Tshe"="#101010",
26	"Abam"="#202020",	26	"Abam"="#202020",
27	"Alru" = "#303030",	27	"Alru" = "#303030",
28	"Thpl" = "#404040",	28	"Thpl" = "#404040",
29	"Psme" = "#505050",	29	"Psme" = "#505050",
30	"Acma" = "#606060",	30	"Acma" = "#606060",
31	"var2" = "#707070",	31	"var2" = "#707070",
32	"var3" = "#808080")	32	"var3" = "#808080")
33		33
34	# now we can plot them:	34	# now we can plot them:
35	ggplot(stand.avg, aes(x=year,y=basal_area_m2,group=species,fill=species)) + geom_area() + labs(xlab="year", ylab="basal area m2", title="average basal area") + scale_fill_manual(values=cols.species)	35	ggplot(stand.avg, aes(x=year,y=basal_area_m2,group=species,fill=species)) + geom_area() + labs(xlab="year", ylab="basal area m2", title="average basal area") + scale_fill_manual(values=cols.species)
36	## stem numbers	36	## stem numbers
37	ggplot(stand.avg, aes(x=year,y=count_ha,group=species,fill=species)) + geom_area()	37	ggplot(stand.avg, aes(x=year,y=count_ha,group=species,fill=species)) + geom_area()
38	ggplot(stand.avg, aes(x=year,y=cohortCount_ha,group=species,fill=species)) + geom_area()	38	ggplot(stand.avg, aes(x=year,y=cohortCount_ha,group=species,fill=species)) + geom_area()
39		39
40	ggplot(stand.avg, aes(x=year,y=LAI,group=species,fill=species)) + geom_area()	40	ggplot(stand.avg, aes(x=year,y=LAI,group=species,fill=species)) + geom_area()
41		41
42	cols <- rainbow(nrow(mtcars))	42	cols <- rainbow(nrow(mtcars))
43	mtcars$car <- rownames(mtcars)	43	mtcars$car <- rownames(mtcars)
44	ggplot(mtcars, aes(mpg, disp, colour = car)) + geom_point() +	44	ggplot(mtcars, aes(mpg, disp, colour = car)) + geom_point() +
45	scale_colour_manual(limits = mtcars$car, values = cols) +	45	scale_colour_manual(limits = mtcars$car, values = cols) +
46	guides(colour = guide_legend(ncol = 3))	46	guides(colour = guide_legend(ncol = 3))
47		47
48		48
49	### e.g. LAI per resource unit in the first three years	49	### e.g. LAI per resource unit in the first three years
50	par(mfrow=c(1,3))	50	par(mfrow=c(1,3))
51	for (y in c(1,2,3))	51	for (y in c(1,2,3))
52	boxplot(tapply(stand$LAI[stand$year == y], stand$ru[stand$year == y], sum), ylim=c(0,10), main=paste("Year", y))	52	boxplot(tapply(stand$LAI[stand$year == y], stand$ru[stand$year == y], sum), ylim=c(0,10), main=paste("Year", y))

Subversion Repositories public iLand

(root)/R_analysis/stacked.timeseries.R @ 1222 - Rev 1054 → 1104