plotshpcreate.R

Full Tutorial

Tutorial Script

For Argument Details

library("UAStools")
?plotshpcreate

Infile:

For details on infile format please see:

library("UAStools")
?SampleInfile

The infile for plotshpcreate.R requires four columns (Additional columns are permitted but wont be utilize):

• [,3] Plot The number of each plot (numeric)
• [,4] Barcode A unique identifier for each plot (character)
• [,9] Range The range [also called row] number of each plot in the experimental grid (numeric)
• [,10] Row The row [also called column] number of each plot in the experimental grid (numeric)

It is recommended to have repeated Barcodes and Plot numbers if there are multi-row plots (mrowplot= >1) as the plotshpcreatre function accounts for this redundancy within the function.

> head(SampleInfile)  
   Loc Test Plot       Barcode                       Stock                Pedigree Entry Rep Range Row
1 CS17 G2FE    1 CS17-G2FE-001    16.2.19716.04067.0000000 NILASQ4G31I11S3/LH123HT     1   1     4 255
2 CS17 G2FE    1 CS17-G2FE-001    16.2.19716.04067.0000000 NILASQ4G31I11S3/LH123HT    NA   1     4 256
3 CS17 G2FE    2 CS17-G2FE-002 16.2.19716.04555.0000000.m1            2369/LH123HT    NA   1     4 257
4 CS17 G2FE    2 CS17-G2FE-002 16.2.19716.04555.0000000.m1            2369/LH123HT    NA   1     4 258
5 CS17 G2FE    3 CS17-G2FE-003    16.2.19716.04052.0000000 NILASQ4G31I06S2/LH123HT    NA   1     4 259
6 CS17 G2FE    3 CS17-G2FE-003    16.2.19716.04052.0000000 NILASQ4G31I06S2/LH123HT    NA   1     4 260 

Important Infile Format

Barcodes must be unique across all observations if nrowplot=1.

• If every observation of the infile has a unique barcode use: nrowplot==1.

Barcodes must be identical across adjacent rows in a plot if the trial consists of multi-row plots (see table below).

> head(SampleInfile)  
   Loc Test Plot       Barcode                       Stock                Pedigree Entry Rep Range Row
1 CS17 G2FE    1 CS17-G2FE-001    16.2.19716.04067.0000000 NILASQ4G31I11S3/LH123HT     1   1     4 255
2 CS17 G2FE    1 CS17-G2FE-001    16.2.19716.04067.0000000 NILASQ4G31I11S3/LH123HT    NA   1     4 256

AB Line:

• Plotshpcreate was developed for UTM coordinates. Please convert to UTM before attempting to use plotshpcreate.
• Plotshpcreate builds plot polygons based on the A point as a reference and utilized the plot locations in the rectangular grid (Range, Row) of the experimental design to calculate the appropriate geo-locations for the polygon corners.
• The location of "A" is specific and must lie at the bottom left corner of the first plot. More specifically, within the middle of the preceding alley and in the middle of the inter-row space to the left of the first plot (Figure 1).
• The B point is less specific but should be placed in the same inter-row space to accurately capture the angle (i.e. deviation from South/North orientation) of the field (Figure 2).

Figure 1. Example of proper coordinates of the A point.

Figure 2. Example of AB line.

Polygon Dimensions:

rowspc	        Row (i.e. column) spacing of a single row. Default 2.5 feet in reference to 30-inch row spacing.  

rowbuf	        Distance removed from both sides of rowspc to create a buffer zone between plots boundaries.
                    Default is 0.1 feet.  

rangespc        Range (i.e. row) spacing of a single row. This dimension refers to the total plot length 
                including half alley distance on either side of the plot. Default 25 feet. 

rangebuf        Distance removed from both sides of rangespc to create a buffer zone between plots boundaries. 
                Default is 2 feet in reference to four-foot allies. 
                Note: If alleys are 4 feet rangebuf should be set to 2 feet to remove 2 ft from both ends of 
                      the polygon.  

Executing plotshpcreate

ALL EXAMPLES ASSUME DEFAULT FOR ARGUMENTS NOT SHOWN IN CODE EXAMPLE

Ex.1) Single Row Plots

If the trial consists of single-row plots a polygon will be created for each observation if each barcode is unique per observation.

If nrowplots=1 results in an error below, the infile$Barcode is not unique across observations.

Error in validObject(res) :   
  invalid class “SpatialPolygons” object: non-unique Polygons ID slot values

Executable:

#For this example, the plot number in the barcode was replaced with Range_Row
SampleInfile$Barcode<-paste(SampleInfile$Loc,"-",SampleInfile$Test,"-",SampleInfile$Range,"_",SampleInfile$Row,sep="")

### Set the working directory to where you want the files to be saved
setwd("C://Temp")

plotshpcreate(A=c(746374.266,3382152.489), #Point A c(Easting_0.0,Northing_0.0)
              B=c(746476.259,3382265.951), #Point B c(Easting_1.0,Northing_1.0)
              infile=SampleInfile,
              outfile="Ind_plots",
              nrowplot=1,
              field="CS17-G2FE")

Ex.2) Retaining Adjacent Rows in a Plot as Single Polygons

If you have multi-row plots plotshpcreate can create individual .shp files for each row in a plot but subsetting barcodes. Barcode subsetting is numbered left to right by grid location of adjacent rows within a plot.

nrowplot= # of adjacent rows in each plot (must be >1)
multirowind=T

Executable:

### Set the working directory to where you want the files to be saved
setwd("C://Temp")

plotshpcreate(A=c(746239.817,3382052.264), #Point A c(Easting_0.0,Northing_0.0)
              B=c(746334.224,3382152.870), #Point B c(Easting_1.0,Northing_1.0)
              infile=SampleInfile,
              outfile="Ind_Multirow_plots",
              nrowplot=2,
              multirowind=T,
              field="CS17-G2FE")

Ex.3) Combining Multi-row Plots into a Single Polygon

If you have multi-row plots they can be combined by indicating:

nrowplot= # of adjacent rows in each plot (must be >1)
multirowind=F

Adjacent rows identified as the same Infile$Barcode within the infile will be combined to create a single polygon for each plot.

Executable:

### Set the `working directory to where you want the files to be saved
setwd("C://Temp")

plotshpcreate(A=c(746239.817,3382052.264), #Point A c(Easting_0.0,Northing_0.0)
              B=c(746334.224,3382152.870), #Point B c(Easting_1.0,Northing_1.0)
              infile=SampleInfile,
              outfile="Ind_Multirow_plots",
              nrowplot=2,
              multirowind=F,
              field="CS17-G2FE")

Output Files

plotshpcreate outputs are saved to the current working directory

# Find the current working directory
getwd()
# Set working directory example
setwd("C:\\Temp")

1. The plot shapefile ("field"_"output".shp)

2. The buffer shapefile ("field"_"output"_buff.shp)

3. A PDF visualization of the non-oriented shapefile schmatic ("field"_"output"_Square_plots.pdf)

4. A PDF visualization of the oriented shapefile schmatic ("field"_"output"_Rotated_plots.pdf)