diff --git a/README.Rmd b/README.Rmd
index bf5d8ef..8825425 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -34,6 +34,7 @@ print(alig)
Plot alignments
```{r define-demo-plot-alignments, eval=TRUE, include = TRUE}
library(dtwSat)
+library(ggplot2)
library(gridExtra)
gp1 = plot(alig, type="alignment", attribute="evi", alignment=1, shift=0.5) +
ggtitle("Alignment 1") +
@@ -48,61 +49,66 @@ grid.arrange(gp1,gp2,nrow=2)
Plot path for all classese
```{r define-demo-plot-paths, eval=TRUE, include = TRUE}
library(dtwSat)
+library(ggplot)
library(gridExtra)
gp.list = lapply(query.list, function(query){
- alig = twdtw(query, template, weight = "logistic", alpha = 0.1, beta = 50,
- alignments = 4, keep = TRUE)
+ alig = twdtw(query, template, weight = "logistic", alpha = 0.1,
+ beta = 100, alignments = 4, keep = TRUE)
plot(alig, normalize = TRUE, show.dist = TRUE) +
- ggtitle(names(query.list)[2]) +
theme(axis.title.x=element_blank(),
legend.position="none")
})
-grid.arrange(gp.list[[1]],
- gp.list[[2]],
- gp.list[[3]],
+grid.arrange(gp.list[[1]] + ggtitle(names(query.list)[1]),
+ gp.list[[2]] + ggtitle(names(query.list)[2]),
+ gp.list[[3]] + ggtitle(names(query.list)[3]),
nrow=3)
```
-
-
- - Plot classification:
-
- malig = mtwdtw(query.list, template, weight = "logistic",
- alpha = 0.1, beta = 100)
+Plot classification
+```{r define-demo-plot-classification, eval=TRUE, include = TRUE}
+library(dtwSat)
+library(ggplot2)
+library(gridExtra)
+malig = mtwdtw(query.list, template, weight = "logistic",
+ alpha = 0.1, beta = 100)
- gp = plot(x=malig, type="classify", attribute="evi", from=as.Date("2009-09-01"),
- to=as.Date("2013-09-01"), by = "6 month",
- normalized=TRUE, overlap=.7)
- gp
-
-
-
-
-
-
-
- - Plot alignments:
- df = data.frame(Time=index(template), value=template$evi, variable="Raw")
- df = rbind( df, data.frame(Time=index(sy), value=sy$evi, variable="Wavelet filter") )
- gp = ggplot(df, aes(x=Time, y=value, group=variable, colour=variable)) +
- geom_line() +
- theme(legend.position="bottom") +
+gp1 = plot(x=malig, type="classify", from=as.Date("2009-09-01"),
+ to=as.Date("2013-09-01"), by = "6 month",
+ normalized=TRUE, overlap=.7)
+
+gp2 = plot(x=malig, type="classify", attribute = c("evi","ndvi"),
+ from=as.Date("2009-09-01"), to=as.Date("2013-09-01"),
+ by = "6 month", normalized=TRUE, overlap=.7)
+
+grid.arrange(gp1,gp2,nrow=2)
+```
+
+
+
+Plot wavelet smoothing
+```{r define-demo-plot-smoothing, eval=TRUE, include = TRUE}
+library(dtwSat)
+library(ggplot2)
+library(reshape2)
+library(gridExtra)
+sy = waveletSmoothing(x=template, frequency=8, wf = "la8", J=1,
+ boundary = "periodic")
+df1 = data.frame(Time=index(template), value=template$evi, variable="Raw")
+df1 = rbind(df1, data.frame(Time=index(sy), value=sy$evi, variable="Wavelet filter") )
+gp1 = ggplot(df1, aes(x=Time, y=value, group=variable, colour=variable)) +
+ geom_line() +
+ # theme(legend.position="bottom") +
ylab("EVI")
- gp
-
-
-
-
-
-
-How to build the package:
-
- - Clone the project:
git clone https//github.com/vwmaus/dtwSat.git.
- - Open Rstudio, go to File - Open Project and pick the file
dtwSat.Rproj.
- - Install the required packages
install.packages(c("roxygen2", "testthat")).
- - Go to the Build tab in the upper-right panel and press the button Build & Reload. After this the package is ready to use.
- - You can also create a source package: Go to the Build tab, display the menu More and select the option Build Source Package.
-
+
+df2 = melt(data.frame(Time=index(sy), sy), id="Time")
+gp2 = ggplot(df2, aes(x=Time, y=value, group=variable, colour=variable)) +
+ geom_line() +
+ ylab("Value")
+gp2
+
+grid.arrange(gp1,gp2,nrow=2)
+```
+
```{r, echo = FALSE}
diff --git a/README.md b/README.md
index 1dc1c6a..b4fcf84 100644
--- a/README.md
+++ b/README.md
@@ -54,6 +54,7 @@ Plot alignments
```r
library(dtwSat)
+library(ggplot2)
library(gridExtra)
gp1 = plot(alig, type="alignment", attribute="evi", alignment=1, shift=0.5) +
ggtitle("Alignment 1") +
@@ -71,63 +72,85 @@ Plot path for all classese
```r
library(dtwSat)
+library(ggplot)
+```
+
+```
+## Error in library(ggplot): there is no package called 'ggplot'
+```
+
+```r
library(gridExtra)
gp.list = lapply(query.list, function(query){
- alig = twdtw(query, template, weight = "logistic", alpha = 0.1, beta = 50,
- alignments = 4, keep = TRUE)
+ alig = twdtw(query, template, weight = "logistic", alpha = 0.1,
+ beta = 100, alignments = 4, keep = TRUE)
plot(alig, normalize = TRUE, show.dist = TRUE) +
- ggtitle(names(query.list)[2]) +
theme(axis.title.x=element_blank(),
legend.position="none")
})
-grid.arrange(gp.list[[1]],
- gp.list[[2]],
- gp.list[[3]],
+grid.arrange(gp.list[[1]] + ggtitle(names(query.list)[1]),
+ gp.list[[2]] + ggtitle(names(query.list)[2]),
+ gp.list[[3]] + ggtitle(names(query.list)[3]),
nrow=3)
```
+Plot classification
-
- - Plot classification:
-
- malig = mtwdtw(query.list, template, weight = "logistic",
- alpha = 0.1, beta = 100)
+```r
+library(dtwSat)
+library(ggplot2)
+library(gridExtra)
+malig = mtwdtw(query.list, template, weight = "logistic",
+ alpha = 0.1, beta = 100)
- gp = plot(x=malig, type="classify", attribute="evi", from=as.Date("2009-09-01"),
- to=as.Date("2013-09-01"), by = "6 month",
- normalized=TRUE, overlap=.7)
- gp
-
-
-
-
-
-
-
- - Plot alignments:
- df = data.frame(Time=index(template), value=template$evi, variable="Raw")
- df = rbind( df, data.frame(Time=index(sy), value=sy$evi, variable="Wavelet filter") )
- gp = ggplot(df, aes(x=Time, y=value, group=variable, colour=variable)) +
- geom_line() +
- theme(legend.position="bottom") +
+gp1 = plot(x=malig, type="classify", from=as.Date("2009-09-01"),
+ to=as.Date("2013-09-01"), by = "6 month",
+ normalized=TRUE, overlap=.7)
+
+gp2 = plot(x=malig, type="classify", attribute = c("evi","ndvi"),
+ from=as.Date("2009-09-01"), to=as.Date("2013-09-01"),
+ by = "6 month", normalized=TRUE, overlap=.7)
+
+grid.arrange(gp1,gp2,nrow=2)
+```
+
+
+
+
+
+Plot wavelet smoothing
+
+```r
+library(dtwSat)
+library(ggplot2)
+library(reshape2)
+library(gridExtra)
+sy = waveletSmoothing(x=template, frequency=8, wf = "la8", J=1,
+ boundary = "periodic")
+df1 = data.frame(Time=index(template), value=template$evi, variable="Raw")
+df1 = rbind(df1, data.frame(Time=index(sy), value=sy$evi, variable="Wavelet filter") )
+gp1 = ggplot(df1, aes(x=Time, y=value, group=variable, colour=variable)) +
+ geom_line() +
+ # theme(legend.position="bottom") +
ylab("EVI")
- gp
-
-
-
-
-
-
-How to build the package:
-
- - Clone the project:
git clone https//github.com/vwmaus/dtwSat.git.
- - Open Rstudio, go to File - Open Project and pick the file
dtwSat.Rproj.
- - Install the required packages
install.packages(c("roxygen2", "testthat")).
- - Go to the Build tab in the upper-right panel and press the button Build & Reload. After this the package is ready to use.
- - You can also create a source package: Go to the Build tab, display the menu More and select the option Build Source Package.
-
+
+df2 = melt(data.frame(Time=index(sy), sy), id="Time")
+gp2 = ggplot(df2, aes(x=Time, y=value, group=variable, colour=variable)) +
+ geom_line() +
+ ylab("Value")
+gp2
+```
+
+
+
+```r
+grid.arrange(gp1,gp2,nrow=2)
+```
+
+
+
diff --git a/figure/define-demo-plot-classification-1.png b/figure/define-demo-plot-classification-1.png
new file mode 100644
index 0000000..8e3720c
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diff --git a/figure/define-demo-plot-paths-1.png b/figure/define-demo-plot-paths-1.png
index 89e22f5..dac06d9 100644
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diff --git a/figure/define-demo-plot-smoothing-1.png b/figure/define-demo-plot-smoothing-1.png
new file mode 100644
index 0000000..2df6a17
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diff --git a/figure/define-demo-plot-smoothing-2.png b/figure/define-demo-plot-smoothing-2.png
new file mode 100644
index 0000000..b828866
Binary files /dev/null and b/figure/define-demo-plot-smoothing-2.png differ
diff --git a/tests/testthat/test_dtwSat.R b/tests/testthat/test_dtwSat.R
index aafdfb9..b0899a0 100644
--- a/tests/testthat/test_dtwSat.R
+++ b/tests/testthat/test_dtwSat.R
@@ -51,6 +51,7 @@ sy = waveletSmoothing(x=template, frequency=8, wf = "la8", J=1,
# Plot raw EVI and filtered EVI
+
df = data.frame(Time=index(template), value=template$evi, variable="Raw")
df = rbind( df, data.frame(Time=index(sy), value=sy$evi, variable="Wavelet filter") )
gp = ggplot(df, aes(x=Time, y=value, group=variable, colour=variable)) +