acorg/acmacs.r

Acmacs package for R

acmacs.r's Issues

acmacs.map_resolution_test number of replicates

In acmacs.map_resolution_test , there is no option to set the number of replicates/random trials per dimension and proportion left out.
It is useful to increase this to improve the precision of the error estimates.

caught segfault on loading acmacs.r

I and @CaitlinWalker have been trying to install acmacs.r on her mac running os x 10.13.

Installation is fine, but then loading the library results in a caught segfault error: https://gist.github.com/CaitlinWalker/3626c6a964fa161bc46e1531827a941e

Here is the output of sessionInfo() https://gist.github.com/CaitlinWalker/6c7d59ce9816e062b1b88315f0a982f2

acmacs.r 4.5 - unable to load shared object '[...]/acmacs.r.so': libacmacswhoccdata.so.1: cannot open shared object file: No such file or directory

Hi,

I have R 3.6 and am trying to load acmacs.r version 4.5 on Linux (to work with Racmacs), but am constantly faced with this error message:

library(acmacs.r)
Error: package or namespace load failed for ‘acmacs.r’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/vetschool/R/x86_64-pc-linux-gnu-library/3.6/acmacs.r/libs/acmacs.r.so':
libacmacswhoccdata.so.1: cannot open shared object file: No such file or directory

I have Rcpp 1.0.5, devtools, roxygen2, testthat installed.

Please can you advise? (duplicate posted on Racmacs page)

Thank you.

Carlijn

Dimension testing absolute error variability greater than expected from sd

I had originally submitted this to Racmacs, but I realised that the dimensionTestMap function uses acmacs.map_resolution_test

I'm not sure if this is an error or if I'm interpreting the data incorrectly. There is more variability in the average absolute error than I'd expect from it's sd and n.

I used the sd and n to calculate a 95% CI = mean +/- 1.96 * sd / sqrt(n) . I then repeat dimension testing and compare the results. With 5 dimensions and 10 repeats (50 data points), I'd expect 2.5 to be outside the CIs. Most are outside this range.

Example code below

library(Racmacs)

# generate random test data
set.seed(1)
coord <- matrix(rep(runif(10,0,10), times=2), ncol=2, byrow=T)
dist <- as.matrix(dist(coord))+rnorm(100)
max_mat <- matrix(apply(round(dist),2,max), ncol=10, nrow=10, byrow=T)
tab1 <- 10*2^round(max_mat-dist)

# make map
map1 <- make.acmap(table=tab1,
                   number_of_dimensions=2,
                   number_of_optimizations=10,
                   minimum_column_basis="2560", 
                   remove_trapped_points="none",
                   check_for_hemisphering = F)

# dimension test
dim_test <- dimensionTestMap(map1, 1:5, 0.1)

# dimension test x10
dim_tests <- NULL
for (i in 1:10){
  dim_tests[[i]] <- dimensionTestMap(map1, 1:5, 0.1)
}

# plot results
plot(NA, xlim=c(1,5), ylim=c(1,2.5), ylab="Average error", xlab="Dimensions")
for (i in 1:10){
  points(dim_tests[[i]]$av_abs_error, pch=16, cex=0.8, col=rainbow(10)[i])
  lines(dim_tests[[i]]$av_abs_error, col=rainbow(10)[i])
}


points(dim_test$av_abs_error, pch=16)
lines(dim_test$av_abs_error)
arrows(1:5, dim_test$av_abs_error-1.96*dim_test$av_abs_error_sd/sqrt(dim_test$number_of_samples), 
       1:5, dim_test$av_abs_error+1.96*dim_test$av_abs_error_sd/sqrt(dim_test$number_of_samples), 
       code=3, length=0.1, angle=90)

The attached plot show the first dimension test (black) with 95% CI and the subsequent 10 repeats (coloured)

Setting of projection transformation matrix not allowed

Although documented in the help files, the code below:

chart <- new(acmacs.r::acmacs.Chart, path_to_acd1)
chart$projections[[1]]$transformation <- matrix(c(1, 0, 0, 1), nrow=2, byrow=TRUE)

Returns the error:

Error in (new("activeBindingFunction", .Data = function (x)  : 
  property is read only

Session crashes if empty chart name is accessed

A small acmacs.r bug is that if you create a chart without setting the name, then try and access the name you get a pointer error and the session crashes. It might be good to set a default name of an empty string to avoid this?

Frozen merge naming

The name "frozen" has a different meaning in lispmds and acmacs.R , which confused me. In lispmds, "frozen" means that map1 is fixed and the points in map2 (really the data from table2) are optimised. This is a useful feature for merging in less reliable data so it would be helpful to have this functionality. It would also be good to change the name in acmacs.R to avoid other people with experience with lispmds making the same mistake as I did.

(I know you're on holiday so I'm not expecting a reply anytime soon!)