add example_SimASAP.R and Rbuildignore examples

Author: cmlegault

.Rbuildignore

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+^simASAP\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^\./examples$

DESCRIPTION

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 Package: simASAP
 Title: Simulate ASAP Data Sets and Optionally Run Them
-Version: 0.0.0.9004
+Version: 0.0.0.9005
 Authors@R: 
     person(given = "Chris",
            family = "Legault",

examples/example_SimASAP.R

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+# example_SimASAP.R
+# walks the user through a set of examples
+
+library("simASAP")
+library("ggplot2") # shouldn't need to do this but doesn't seem to work otherwise
+
+# first define where your original ASAP run is located
+base.dir <- "C:\\Users\\chris.legault\\Desktop\\testSimASAP"
+my.asap.name <- "simplelogistic"
+
+# run simASAP with defaults to create 10 data sets
+SimASAP(wd=base.dir, asap.name=my.asap.name, nsim=10)
+# the C:\\Users\\chris.legault\\Desktop\\testSimASAP\\sim directory should have been created
+# in this new directory open up two or more of the simplelogistic_simX.dat files
+# and compare the Fleet-1 Catch Data (lines 164-184) and Index-1 and Index-2 Data (lines 281-322)
+# with each other and the original run to see that they have changed
+# can do this by hand or using the ReadASAP3DatFile function
+datorig <- ReadASAP3DatFile(file.path(base.dir, paste0(my.asap.name, ".dat")))
+od <- file.path(base.dir, "sim")
+datsim1 <- ReadASAP3DatFile(file.path(od, paste0(my.asap.name, "_sim1.dat")))
+datsim2 <- ReadASAP3DatFile(file.path(od, paste0(my.asap.name, "_sim2.dat")))
+rbind(datorig$dat$CAA_mats[[1]][1, ],
+      datsim1$dat$CAA_mats[[1]][1, ],
+      datsim2$dat$CAA_mats[[1]][1, ])
+# note the original file has the catch at age in proportions (the first 10 columns),
+# while the simulated files have the catch at age in numbers (which will be converted to proportions by ASAP automatically when the program is run)
+
+# now actually run ASAP for a new set of random errors
+SimASAP(wd=base.dir, asap.name=my.asap.name, nsim=10, runflag=FALSE)