Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Attempt to resolve warnings in effect_N_discrete #97

Merged
merged 4 commits into from
Dec 2, 2016
Merged

Attempt to resolve warnings in effect_N_discrete #97

Changes from 3 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
35e6c52
Fix warning message in effect_N_discrete (tested) and effect_N_contin…
rueuntal Dec 2, 2016
669664b
Missed effect_N_continuous (not tested) in previous commit.
rueuntal Dec 2, 2016
bb0a7b9
Similarly remove warning in deltaS_N by avoiding extrapolation of pchip.
rueuntal Dec 2, 2016
d48af2c
Expand rows to be more readable.
rueuntal Dec 2, 2016
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 8 additions & 7 deletions R/mobr.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -240,9 +240,8 @@ deltaS_N = function(comm, ref_dens, inds){
# rescale and interpolate this plot based S to individual based
# using the ref_density (i.e., not the observed density)
rescaled_effort = round(1:nplots * ref_dens)
if (max(rescaled_effort) < max(inds))
warning('Extrapolating the rarefaction curve because the number of rescaled individuals is smaller than the inds argument')
interp_S_samp = pchip(c(1, rescaled_effort), c(1, S_samp), inds)
# No extrapolation of the rescaled rarefaction curve, only interpolation
interp_S_samp = pchip(c(1, rescaled_effort), c(1, S_samp), inds[inds <= max(rescaled_effort)])[1:length(inds)]
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Nice job fixing this! I can see why this code works but it will difficult to understand for future us and other users. If we don't know that R adds NA's to cells that are longer than the vector is defined across we would be scratching our heads right now. I would prefer one step where you define interp_S_samp and then a second step where you add NA's to that vector so that it has the same length as inds. What do you think?

S_indiv = rarefaction(comm, 'indiv', inds)
deltaS = interp_S_samp - S_indiv
out = data.frame(inds = inds, deltaS = deltaS)
Expand Down Expand Up @@ -572,8 +571,8 @@ effect_N_continuous = function(mob_in, S, group_levels, env_levels, group_data,
level_perm = group_levels[j]
comm_level_perm = comm_perm[which(as.character(group_data) == level_perm), ]
group_effect_N_perm = deltaS_N(comm_level_perm, plot_dens,
ind_sample_size)
effect_N_perm[, j] = group_effect_N_perm$deltaS
ind_sample_size[ind_sample_size <= sum(comm_level_perm)])
effect_N_perm[, j] = group_effect_N_perm$deltaS[1:nrow(effect_N_perm)]
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I have the same basic feeling here as in the previous comment.

}
effect_N_perm = effect_N_perm[complete.cases(effect_N_perm), ]
# If the output is not long enough, fill it with NA's
Expand Down Expand Up @@ -614,10 +613,12 @@ effect_N_discrete = function(mob_in, group_levels, ref_group, groups,
for (i in 1:nperm){
# swap plot abu between group 1 and each other group
comm_perm = permute_comm(comm_levels, 'swapN', plot_levels)
min_N = min(sum(comm_perm[plot_levels == as.character(ref_group), ]),
sum(comm_perm[plot_levels == level, ]))
N_eff_perm = sapply(c(as.character(ref_group), level), function(x)
deltaS_N(comm_perm[plot_levels == x, ], plot_dens_level,
ind_sample_size)$deltaS)
null_N_deltaS_mat[i, ] = N_eff_perm[ , 2] - N_eff_perm[ , 1]
ind_sample_size[ind_sample_size <= min_N])$deltaS)
null_N_deltaS_mat[i, ] = (N_eff_perm[ , 2] - N_eff_perm[ , 1])[1:ncol(null_N_deltaS_mat)]
setTxtProgressBar(pb, k)
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

and here, but great job diving in and tracking these problems down. I'll test your code out on the case-studies to see if anything changes drastically on the results.

k = k + 1
}
Expand Down