Preparing release

r-spatial · Oct 11, 2022 · cb685b3 · cb685b3
1 parent 37ea865
commit cb685b3
Show file tree

Hide file tree

Showing 16 changed files with 45 additions and 28 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -30,5 +30,6 @@ dtwSat-Ex_i386.Rout
 dtwSat-Ex_x64.Rout
 examples_i386
 examples_x64
+vignettes/twdtw03-speed.Rmd
 
 ^CRAN-RELEASE$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: dtwSat
 Type: Package
 Title: Time-Weighted Dynamic Time Warping for Satellite Image Time Series Analysis
-Version: 0.2.7.9999
-Date: 2021-12-17
+Version: 0.2.8
+Date: 2022-10-11
 Authors@R:
     c(person(given = "Victor",
              family = "Maus",
@@ -31,7 +31,7 @@ Description: Provides an implementation of the Time-Weighted Dynamic Time
     produce land cover maps, create temporal plots for land cover change, and compute 
     accuracy metrics.
 Depends:
-    R (>= 3.2.0),
+    R (>= 3.5.0),
     zoo,
     raster,
     ggplot2

diff --git a/R/plotCostMatrix.R b/R/plotCostMatrix.R
@@ -48,7 +48,7 @@
 #' log_fun = logisticWeight(-0.1, 100)
 #' ts = twdtwTimeSeries(MOD13Q1.ts.list)
 #' patt = twdtwTimeSeries(MOD13Q1.patterns.list)
-#' mat1 = twdtwApply(x=ts, y=patt, weight.fun=log_fun, keep=TRUE)
+#' mat1 = twdtwApply(x=ts, y=patt, weight.fun=log_fun, keep=TRUE, legacy=TRUE)
 #' 
 #' plotCostMatrix(mat1, matrix.name="costMatrix")
 #' 

diff --git a/R/plotPaths.R b/R/plotPaths.R
@@ -47,7 +47,7 @@
 #' log_fun = logisticWeight(-0.1, 100)
 #' ts = twdtwTimeSeries(MOD13Q1.ts.list)
 #' patt = twdtwTimeSeries(MOD13Q1.patterns.list)
-#' mat1 = twdtwApply(x=ts, y=patt, weight.fun=log_fun, keep=TRUE)
+#' mat1 = twdtwApply(x=ts, y=patt, weight.fun=log_fun, keep=TRUE, legacy=TRUE)
 #' 
 #' plotPaths(mat1)
 #' 

diff --git a/R/twdtw_reduce_time.R b/R/twdtw_reduce_time.R
@@ -127,9 +127,26 @@ twdtwReduceTime = function(x,
   il <- order(aligs[,1], aligs[,2])
 
   # Create classification intervals 
-  if(is.null(breaks)){
-    breaks <- seq(as.Date(from), as.Date(to), by = by) 
-  }
+  # if(is.null(breaks)){
+  #   breaks <- seq(as.Date(from), as.Date(to), by = by) 
+  # }
+  if(is.null(breaks))
+    if( !is.null(from) & !is.null(to) ){
+      breaks = seq(as.Date(from), as.Date(to), by = by)
+    } else {
+      patt_range = lapply(y, function(yy) range(yy$date))
+      patt_diff = trunc(sapply(patt_range, diff)/30)+1
+      min_range = which.min(patt_diff)
+      by = patt_diff[[min_range]]
+      from = patt_range[[min_range]][1]
+      to = from 
+      month(to) = month(to) + by
+      year(from) = year(range(x$date)[1])
+      year(to) = year(range(x$date)[2])
+      if(to<from) year(to) = year(to) + 1
+      breaks = seq(from, to, paste(by,"month"))
+      breaks = as.Date(breaks)
+    }
 
   # Find best macthes for the intervals 
   best_matches <- .bestmatches2(

diff --git a/data/MOD13Q1.patterns.list.RData b/data/MOD13Q1.patterns.list.RData
diff --git a/man/plotCostMatrix.Rd b/man/plotCostMatrix.Rd
diff --git a/man/plotPaths.Rd b/man/plotPaths.Rd
diff --git a/man/twdtwApply.Rd b/man/twdtwApply.Rd
diff --git a/man/twdtwClassify.Rd b/man/twdtwClassify.Rd
diff --git a/man/twdtwMatches-class.Rd b/man/twdtwMatches-class.Rd
diff --git a/man/twdtwRaster-class.Rd b/man/twdtwRaster-class.Rd
diff --git a/man/twdtwReduceTime.Rd b/man/twdtwReduceTime.Rd
diff --git a/man/twdtwTimeSeries-class.Rd b/man/twdtwTimeSeries-class.Rd
diff --git a/vignettes/twdtw01.Rmd b/vignettes/twdtw01.Rmd
@@ -60,7 +60,7 @@ weight_fun <- logisticWeight(alpha = -0.1, beta = 50)
 twdtw_matches <- twdtwApply(x = veg_ts, 
                             y = veg_profiles, 
                             weight.fun = weight_fun, 
-                            keep = TRUE) 
+                            keep = TRUE, legacy=TRUE) 
 
 class(twdtw_matches)
 

diff --git a/vignettes/twdtw03-speed.Rmd b/vignettes/twdtw03-speed.Rmd
@@ -46,7 +46,6 @@ samples_cerrado_mod13q1 |>
 
 
 ```{r}
-
 # TODO: 
 #  - twdtwCLassify call for twdtwTimeSeries class and list of data.frame/data.table
 #  - the same as above with the legacy option
-Original file line number
+Diff line change
@@ Expand Up / @@ -46,7 +46,6 @@ samples_cerrado_mod13q1 |> @@
     ```{r}
     # TODO:
     #  - twdtwCLassify call for twdtwTimeSeries class and list of data.frame/data.table
     #  - the same as above with the legacy option
@@ Expand Down @@