dracodoc
commented
4 years ago I explored this for a while:
- In RStudio if you click on a ctmm object, the list viewer will be able to list every slot name properly
ls.strcan handle the names too, but in a slightly different format without indentation
> ls.str(model_try_res[[1]][[1]])
AIC : num 3792
AICc : num 3793
axes : chr [1:2] "x" "y"
BIC : num 3808
circle : num 0
COV : num [1:4, 1:4] 7.12e+13 -2.87e+05 -5.58e+03 6.44e+11 -2.87e+05 ...
COV.mu : num [1:2, 1:2] 2413364 186400 186400 822488
error : logi FALSE
features : chr [1:4] "major" "minor" "angle" "tau position"
isotropic : logi FALSE
loglike : num -1890
mean : chr "stationary"
method : chr "pHREML"
MSPE : Named num [1:2] 52912139 Inf
mu : num [1, 1:2] 41189.9 29.7
omega : num 0
range : logi TRUE
sigma : Formal class 'covm' [package "ctmm"] with 3 slots
tau : Named num 438449- One quick hack is just use ls.str to replace str
str.ctmm <- function(x, ...) {
ls.str(x)
}
> str(model_try_res[[1]][[1]])
AIC : num 3792
AICc : num 3793
axes : chr [1:2] "x" "y"
BIC : num 3808
circle : num 0
COV : num [1:4, 1:4] 7.12e+13 -2.87e+05 -5.58e+03 6.44e+11 -2.87e+05 ...
COV.mu : num [1:2, 1:2] 2413364 186400 186400 822488
error : logi FALSE
features : chr [1:4] "major" "minor" "angle" "tau position"
isotropic : logi FALSE
loglike : num -1890
mean : chr "stationary"
method : chr "pHREML"
MSPE : Named num [1:2] 52912139 Inf
mu : num [1, 1:2] 41189.9 29.7
omega : num 0
range : logi TRUE
sigma : Formal class 'covm' [package "ctmm"] with 3 slots
tau : Named num 438449This is not perfect but I think will serve the purpose. Given that RStudio can display it already, this at least will avoid the previous situation.
jfsmenezes
Some users get confused when inspecting
ctmmobjects on the command lines or when usingstrto inspect the object structure, because the$slot names are all missing. (E.g., https://groups.google.com/forum/#!topic/ctmm-user/Wy8EH-8mwIg )I put a crude
str.ctmm()hack instr.R, but apparently console printing does not callRmethods likeprint()orcat()and is hard coded at a lower level ( https://stackoverflow.com/questions/34638307/changing-how-output-is-printed-to-the-console )The cause, I assume, is because a
ctmmobjectFITis just alistobjectFIT@.Datawith some extra slotsFIT@info, yet the list names are stored in thectmmobject and no names are stored inFIT@.Data, and many baseRfunctions likestr()work withFIT@.Data.So far, I've tried the assignment
names(FIT@.Data) <- names(FIT), but this does nothing.