The vast majority of people looking at your publications are not going
to give a hoot if your paper was published in one of these online
journals or another outlet.  Nearly all journals today are online
journals in spirit because nearly all journals have an online presence
with online access to articles either via pay or open access policies.
 All of the journals you name are legitimate, most have good
reputations or virtually no reputation (SR).  Whether a journal is
open access or not is irrelevant from a quality standpoint.  There are
crap open-access journals and crap print journals, likewise, their are
very good open access journals and print journals.  Recently Nature
elicited an attack on open access journals.  But you must remember
that fake articles submitted to journals can get through peer review.
A recent publication I posted earlier demonstrated that 120 fake
articles made it through peer review on Springer and IEEE in computer
science journals.  That is amazing because the IEEE outlets in
particular are for computer scientists and engineers what Ecology,
American Naturalist, and similar journals are to ecologists.  Things
do get through, but they should not.  I am 90% sure we had a fake
submission this year at HCB, and we rejected it.

PLoS and PLoS One
The PLoS journals have a good reputation period by anyone who
understands what is going on in modern journal publishing.  Of the
PLoS journals, PLoS One is probably the least respected, I will not
address all the reasons, but a primary reason is the falling impact
factor associated with its growing volume.  However, anyone with a
basic understanding of how impact factor is calculated will recognize
that a journal that is growing as rapidly as PLoS One will always
haave a suppressed impact factor because the impact factor is
essentially a mean.  A mean is an appropriate central tendency measure
for a parametric distribution, but not a distribution that is a power
curve, which citation magnitude certainly is.  This feeds into the
growth of PLoS One.  Because citation rate is a power curve, and
because the papers published in the most recent year are always way
more than the number of papers published in the first year of the two
year impact factor, the opportunity for citation is not evenly
distributed between the 2 year old and 1 year old articles.  This is
why the impact factor is suppressed.  The growth of PLoS One is a
sigmoid curve, and if you look at the trajectory for this year, it
will likely have a very slightly larger number of submissions this
year relative to last year, it is now approaching the assymptotic
portion of the sigmoid curve in that publishing numbers is probably
going to level off now.  That will cause the impact factor to rise
likely back into the 4s.  The reptuation of PLoS Biology and the other
PLoS Journals are very high.  One thing to remember about PLoS One is
that the other PLoS journals funnel papers below their standards to
this journal if they believve it is a publishable paper.  Why?  I
suspect it is because papers submitted to the other PLoS Journals are
likely to have cited PLoS articles.  By directing these into PLoS One
this will help rise the impact rating of the other PLoS Journals.
This is very common among publishers today.  ALSO, PLoS journals
publish as accepted, this reduces their impact rating relative to say
Springer journals who pre-release articles 6 mo early.  That 6 mo
window provides an extra 6 mo of citations without eaating up time
time on the 2 year impact factor clock.  I expect this game to be
circumvented by Thomson-Reuters Journal Citation Reports, but maybe
they don't care.

PEERJ
I submitted a paper on occupational health to PEERJ about 6 months
ago, and it got a very very good peer review.  The editor handling my
paper was literally the top expert in the topic I was covering, which
is why I actually sent it there.  PEERJ has no impact factor, and much
of the expectations of PEERJ is that it will be similar to PLoS One.
The big advantage of PEERJ is its publishing costs and based on the
articles that I have seen related to my interests, they ahve been
pretty good.  I expect it to be in some ways better than PLoS One
because so many universities are signing on a group plan.  However,
you also have to question if this is a sustainable model.  Online
presence is pretty cheap, so I expect it will be...or they will raise
the price, change policies!

Ecosphere
I have never used this journal for my own output, but I have read
articles in it and cited many.  The quality seems to be pretty damn
good.

Scientific Reports
I don't think this outlet has the name recognition of the above
journals.  I can't recall ever citing anything from it, and I recently
read a human genetics article in it that I sent to "Highly Respected
Geneticist who is a member of the NAS" asking his view, and I'll just
say it was not very well received!  Notice, all journals publish their
share of bad papers, and I can't recall any of these having to pull a
manuscript for ethical reasons (faked data).  I PERSONALLY see no
advantage to sending a paper to SR over the other outlets you named.

My personal opinion on submitting to journals
Select your journal based on the audience you hope to attract, the
media impact you think might be possible, and the overall quality of
the journal.

Lets say you had a paper in conservation of cumquats.
You look at your results and say, this is extremely important for
Conservation Biologists, but I doubt anyone in the general public will
care.  Then send it to Conservation Biology or Biological
Conservation.  But, if you look at it and think the general public
will also be interested, you might choose to send it to a more general
outlet that gets good media exposure.  However, you might be attacking
the work of the current editor of the journal! Then you might still
opt for the less ideal outlet.  The most critical point will be the
quality of the journal, which you can only define based on your own
and your main research groups' vision of quality.  Its not black and
white.  One well-funded scientist I know publishes almost all his
papers in the same 1-2 journals.  But, most try to spread it around.

Another point when  you publish in regard to audience that is
currently ignored and becoming obsolete. It used to be that if you
paper was a state issue, you sent it to the state academy, if a
regional issue, you sent it to a regional journal, if a national issue
you sent it to a national journal, and if international you sent it to
an international journal.  That entire scope has decayed at least
partly because of Thomson-Reuter's past policies on selecting journals
for inclusion combined with authors who are forced to seek higher
impact ratings, something I believe is unfortunate.  Mostly, you now
try to get your paper into the highest rated journal you can.  This
causes people to shoot the moon too often, clogging up the peer review
process, delaying publication of manuscripts, and ultimately slowing
science.  A few years back I sent a paper to Science and it got
rejected w/o review, big deal.  Then, I sent it to Conservation
Biology and it got rejected without review.  In both cases they said
the article had "too limited of a focus for their general audience."
I ultimately sent it to Journal of Herpetology where it got published.
 You know what?  It is either the most cited paper or the second most
cited paper published since 2007, it has been cited more than
something like 90% of papers from 2007 referenced in the Web of
Science, and its been cited more than 1/3 of papers published in
Science in 2007!  That is as of 2012. I have not checked since.  The
reason I bring this up is not to wave a flag or brag.  Its to point
out that if your paper is a solid article with solid results, people
will notice and it will get its due justice.  There is a point where
published is better than being in review.  Being published means you
complete what you start.  That is the ultimate point.  Whether it be a
tiny note or a mega monograph, if you spent your time starting it, and
you have results, it should be published somewhere.  Finish what you
start.  Sometimes people may ask why you spent that time publishing
the tiny insignificant note.  My response?  Because I finish what I
start.  Being a finisher is a good habit.  Allowing things to site for
years and then get lost to science and society is a very very bad
habit.  The latter also creeps into other things.  Well, my paragraph
note is not important, I'll just leave it sit.  Next thing its 1 page
notes, then 5 page papers, the 20 page papers, then you are sitting in
your office complaining about how you don't have resources to do the
research you want to do because you only want to do research that
results in treatises requiring your own private research facility.  If
you have something to publish, and you think it is worthy of landiing
in "BIG JOURNAL" send it there and work your way down the chain.  But,
if  you look at your study and see it is probably only of interest to
cumquat growers, you might send it to cumquat growers quarterly.
Either way, you are published, and with the large quantity of
scientists who are unable to publish due to ability, health, time, or
resources, no one should complain you are maintaining your
productivity.  However, as you migrate to seasoned scientist it is
expected that you have landed papers in the best outlets in your
field.  WHat those are depends on your field.  Landing in Science or
Nature is partly talent, partly salesmanship, and partly luck.  I know
too many people who never get their, and too many people who its hard
to believe they ever did! :)

I hope this is helpful, I also hope that the alternative views will be
posted because it is important for you to get all sides of this
argument so you can come to your own conclusions about publishing and
decide what you will find most rewarding in the short and long run.

On Thu, Feb 27, 2014 at 8:22 AM, Nathan Lemoine
<[email protected]> wrote:
> Hey ECOLOGers,
>
> I have a question regarding the perception of publishing in open-access 
> journals. First, I really like the idea behind PLoS and PeerJ (particularly 
> PeerJ, due to its more reasonable price). These journals makes science 
> accessible to those who are interested but can't afford the pricey 
> subscription tag of for-profit journals,  and it does work. PLoS is cited by 
> popular magazines (like Men's Health), I hear it referred to on podcasts 
> where the speaker cites an article from PLoS. I see references to PLoS 
> everywhere in the popular literature, etc., much more so than traditional 
> journals. It's pretty amazing how widely read it is.
>
> In theory, it'd be a great principle to adopt a "publish only in open-access 
> journals" philosophy. I'm wondering how this would be received. If someone 
> submits a post-doc, faculty, or grant application with only PLoS, PeerJ, 
> Ecosphere, Scientific Reports, etc. articles, would that place them behind 
> others with the same quantity of publications (and ostensibly same quality of 
> work) in more established journals? I get the sense that it might, which may 
> discourage grad students and other early-career individuals from publishing 
> more in these journals who typically want to have high-impact and 
> well-recognized publications. Am I correct on this, or are times changing?
>
> Nate



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