[Dplr-commits] r1096 - in pkg/dplR: R man

[noreply at r-forge.r-project.org]

Author: darwinalexander
Date: 2018-05-09 05:02:56 +0200 (Wed, 09 May 2018)
New Revision: 1096

Modified:
   pkg/dplR/R/plotRings.R
   pkg/dplR/man/plotRings.Rd
Log:
Changes to plotRings were done.
- The unit of d2pith now is computed according to the unit assigned in 'length.unit'
- If a value in d2pith is assigned, a new row is added before the first year
- Updated the "Length Radius" code for output data to adapt to the changes of d2pith
- In the help file, the argument "d2pith" was more detailed

Modified: pkg/dplR/R/plotRings.R
===================================================================
--- pkg/dplR/R/plotRings.R	2018-05-06 17:51:35 UTC (rev 1095)
+++ pkg/dplR/R/plotRings.R	2018-05-09 03:02:56 UTC (rev 1096)
@@ -31,31 +31,30 @@
   else if(length.unit == "1/1000 mm") 
     TRW[, 1:4] <- TRW[, 1:4]/1000 
   
+  ## Setting the unit of d2pith
+  if(length.unit == "mm") 
+    d2pith <- d2pith
+  else if(length.unit == "1/10 mm") 
+    d2pith <- d2pith/10 
+  else if(length.unit == "1/100 mm") 
+    d2pith <- d2pith/100
+  else if(length.unit == "1/1000 mm") 
+    d2pith <- d2pith/1000
   
+  
   TRW <- TRW[as.logical((rowSums(is.na(TRW))-length(TRW))),] # It is to remove rows with NAs across all rows
   
   # trw means
   TRW$trw.means <- rowMeans(TRW, na.rm = TRUE)
   
   # Distance to pith (d2pith)
-  # Add d2pith values,  
-  # This code find the index position of the first non-NA value in a 
-  # column:  which.min(is.na(TRW$trwE))
-  # This code check the NA values of d2pith. If there are NA values 
-  # this code do nothing, else sum the individual d2pith values to the 
-  # first ring. 
-  if(!is.na(mean(d2pith, na.rm = TRUE))) {  
-    TRW.d2pith <- TRW[,1:4]
-    if(!is.na(d2pith[1])) {
-      TRW.d2pith$trwN[which.min(is.na(TRW.d2pith$trwN))] <- TRW.d2pith$trwN[which.min(is.na(TRW.d2pith$trwN))]+d2pith[1] }
-    if(!is.na(d2pith[2])) {
-      TRW.d2pith$trwS[which.min(is.na(TRW.d2pith$trwS))] <- TRW.d2pith$trwS[which.min(is.na(TRW.d2pith$trwS))]+d2pith[2] }
-    if(!is.na(d2pith[3])) {
-      TRW.d2pith$trwE[which.min(is.na(TRW.d2pith$trwE))] <- TRW.d2pith$trwE[which.min(is.na(TRW.d2pith$trwE))]+d2pith[3] }
-    if(!is.na(d2pith[4])) {
-      TRW.d2pith$trwW[which.min(is.na(TRW.d2pith$trwW))] <- TRW.d2pith$trwW[which.min(is.na(TRW.d2pith$trwW))]+d2pith[4] }
-    # add d2pith to the first ring of the trw.means
-    TRW$trw.means[1] <- rowMeans(TRW.d2pith[1,], na.rm = TRUE)  
+  # Add a new row with the d2pith value at the first position if this argument is assigned
+  if (!is.na(mean(d2pith, na.rm = T))) {
+    TRW.d2pith <- TRW[1, 1:4]
+    TRW.d2pith[1,] <- NA
+    rownames(TRW.d2pith)[1] <- as.numeric(rownames(TRW))[1]-1 
+    TRW.d2pith$trw.means[1] <-  d2pith 
+    TRW <- rbind(TRW.d2pith, TRW)
   }
   
   # Accumulative trw.means
@@ -201,22 +200,22 @@
   if  ((sum(TRW$trwN, na.rm = TRUE) > 0) & is.na(d2pith[1]))
     print(paste("Length Radius N:  ", round(sum(TRW$trwN, na.rm = TRUE), digits = 2), sep = " ", "mm"))
   else if  ((sum(TRW$trwN, na.rm = TRUE) > 0) & (d2pith[1] > 0))
-    print(paste("Length Radius N:  ", round(sum(TRW.d2pith$trwN, na.rm = TRUE), digits = 2), sep = " ", "mm"))
+    print(paste("Length Radius N:  ", round(sum(TRW$trwN, d2pith, na.rm = TRUE), digits = 2), sep = " ", "mm"))
   
   if  ((sum(TRW$trwS, na.rm = TRUE) > 0) & is.na(d2pith[2]))
     print(paste("Length Radius S:  ", round(sum(TRW$trwS, na.rm = TRUE), digits = 2), sep = " ", "mm"))
   else if  ((sum(TRW$trwS, na.rm = TRUE) > 0) & (d2pith[2] > 0))
-    print(paste("Length Radius S:  ", round(sum(TRW.d2pith$trwS, na.rm = TRUE), digits = 2), sep = " ", "mm"))
+    print(paste("Length Radius S:  ", round(sum(TRW$trwS, d2pith, na.rm = TRUE), digits = 2), sep = " ", "mm"))
   
   if  ((sum(TRW$trwE, na.rm = TRUE) > 0) & is.na(d2pith[3]))
     print(paste("Length Radius E:  ", round(sum(TRW$trwE, na.rm = TRUE), digits = 2), sep = " ", "mm"))
   else if  ((sum(TRW$trwE, na.rm = TRUE) > 0) & (d2pith[3] > 0))
-    print(paste("Length Radius E:  ", round(sum(TRW.d2pith$trwE, na.rm = TRUE), digits = 2), sep = " ", "mm"))
+    print(paste("Length Radius E:  ", round(sum(TRW$trwE, d2pith, na.rm = TRUE), digits = 2), sep = " ", "mm"))
   
   if  ((sum(TRW$trwW, na.rm = TRUE) > 0) & is.na(d2pith[4]))
     print(paste("Length Radius W:  ", round(sum(TRW$trwW, na.rm = TRUE), digits = 2), sep = " ", "mm"))
   else if  ((sum(TRW$trwW, na.rm = TRUE) > 0) & (d2pith[4] > 0))
-    print(paste("Length Radius W:  ", round(sum(TRW.d2pith$trwW, na.rm = TRUE), digits = 2), sep = " ", "mm"))
+    print(paste("Length Radius W:  ", round(sum(TRW$trwW, d2pith, na.rm = TRUE), digits = 2), sep = " ", "mm"))
   
   if (sum(TRW$trw.means, na.rm = TRUE) > 0) 
     print(paste("Length Diameter:  ", round(sum(TRW$trw.means, na.rm = TRUE) * 2/10, digits = 6), sep = " ", "cm"))

Modified: pkg/dplR/man/plotRings.Rd
===================================================================
--- pkg/dplR/man/plotRings.Rd	2018-05-06 17:51:35 UTC (rev 1095)
+++ pkg/dplR/man/plotRings.Rd	2018-05-09 03:02:56 UTC (rev 1096)
@@ -50,8 +50,9 @@
   labels will be shown in upper right corner of the plot.  }
   
   \item{d2pith}{ \code{numeric}. The distance from the innermost 
-  ring to the pith of the tree. It has to be written in the same 
-  unit as in the \code{"length.unit"} argument. }
+  ring to the pith of the tree. It is computed in the same 
+  unit as in the \code{"length.unit"} argument. If a value is assigned, 
+  a new row in the output table will be added at the first year}
 
   \item{col.inrings}{ The color to be used for the interior rings.
   See section \sQuote{Color Specification} for suitable values.  }