73 lakes become 78

I have detailed many curious aspects of the remarkable Lake Żabińskie August air-temperature reconstruction by Larocque-Tobler et al (2015). This posts describes yet more – this time in Supplementary Data Figure 1 which shows a redundancy analysis (a type of constrained ordination).

The method

A Redundancy Analysis (RDA) created in CANOCO was also used to determine the fit of downcore samples to the transfer function samples. The RDA constrained to temperature was created with the transfer function samples and the downcore samples added passively to the RDA.

The result

An RDA with downcore samples passively added to the transfer function samples show that no downcore sample was located outside the field determined by the transfer function samples. The eight warmer lakes (17–27.5 °C) in the Canadian transfer function were also found in the same quadrant as the Polish lakes (16.3–18.8 °C) suggesting a similarity between the assemblages in warmer lakes in Canada and those which cover the same temperature gradient in Poland.

The first result is somewhat inevitable given that only the first two axes of the RDA are considered. As a reconstruction diagnostic tool, passive plotting is only really useful if residual distances are small, otherwise the fossil samples might be highly aberrant on axis three and no-one would ever know.

The second result is critically important to the paper which combines calibration sets from Canada and Poland. If the warm Polish and Canadian lakes do not overlap in ordination space, they do not have similar species assemblages and it is likely that an environmental variable other than temperature is driving the difference between them. This would severely damage the motivation for making a combined calibration set.

The figure

sdfig1

A few points are immediately obvious.

  • Unlike perhaps every other RDA I have seen, there is no arrow showing the constraining environmental variable. It should point right from the origin.
  • The axis scales are not identical as the should be (giving undue prominence to the first axis).
  • The second axis of the ordination is mis-labelled as RDA Axis 2. When there is only one constraining variable, there can only be a single constrained axis. The second axis should be PCA axis 1.

None of these points are of any great importance, except that they strongly indicate that the figure was not made in CanoDraw, C2 or the vegan/analogue packages in R which would not make these mistakes.

Much more seriously, while there are 73 Canadian lakes in the archived calibration set (not 72 as the paper reports), there are 78 red squares (perhaps 77 – some overlap) which indicate Canadian lakes in the figure.

The replication

This figure should be easy to replicate from the archived data (full code at https://github.com/richardjtelford/Zabinskie). First, I want to plot just the calibration set lakes, omitting the passive fossil samples.

library(vegan)
library(ggvegan)

mod <- rda(sqrt(spp) ~ env)

scaling <- "sites"
frda <- fortify(mod, display = "sites", scaling = scaling)

#country information
frda$country <- c(rep("Poland", 48), rep("Canada", 73))

g <- ggplot(frda, aes(-Dim1, Dim2, colour = country, shape = country)) + #axis 1 flipped to match published figure
geom_point(size = 2) +
coord_equal() +
labs(x = "RDA1", y = "PCA1", shape = "Country", colour = "Country") +
geom_vline(xintercept = 0) +
geom_hline(yintercept = 0) +
scale_shape_manual(values = c(15, 18)) +
scale_colour_manual(values = c(2, 4))

print(g)

 

unnamed-chunk-1-1

Generally, the replication is similar to the published figure. However, contrary to what LT15 write and show in their figure, there are only two Canadian lakes in the lower-left quadrant with the Polish lakes. The extra Canadian lakes in the Polish quadrant are not due to mis-classification of the lakes, there are no lakes in these positions in the replication. Other changes are the deletion of two lakes at the left side of the upper left quadrant and the addition of one point at the upper-right corner of the upper right quadrant.

I honestly cannot explain how these difference could have occurred.

Adding the fossil sites passively is most easily done with the function timetrack in Gavin Simpson’s analogue package.

tt <- analogue::timetrack(X = spp, passive = fos, env = env, method = "rda", transform = "sqrt", scaling = scaling)

g + geom_point(aes(x = -RDA1, y = PC1), data = as.data.frame(tt$fitted.values), inherit.aes = FALSE, colour = "green", shape = 17) +
scale_shape_manual(name = "", limits = c("Canada", "Poland", "Fossil"), values = c(15, 18, 17)) +
scale_colour_manual(name = "", limits = c("Canada", "Poland", "Fossil"), values = c(2, 4, 3))

timetrack

Well most of the fossil samples are in the same quadrant as LT15 find them, but the pattern is not the same. I have no idea if this is because of different species inclusion rules or what

An earlier version of this post contained a faulty version of the timetrack plot due to my misunderstanding of how analogue::join worked. Gavin kindly updated this function so my code now works.

Posted in Peer reviewed literature, transfer function | Tagged , | 6 Comments

Comment on Lyons et al finally published

After many months, our comment on Lyons et al is finally published [link should give free access].

Lyons et al looked at many community  data sets from the last 300 million years and tested for pairs of species that are more aggregated (co-occur) or segregated than expected by chance. They found that in modern data sets, there are more segregated than aggregated species pairs, and the opposite pattern in fossil data sets, with a breakpoint about 6000 years ago, suggesting a severe impact from early agriculture. This was a surprising finding, especially given the presence-absence data used by the authors.

We argue that Lyons et al result is a product of

  • poor data set selection (some of which were addressed by a corrigendum)
  • artefacts in the breakpoint analysis
  • data-set size related artefacts in the identification of segregated and aggregated species pairs

Together, these problems mean that the results of Lyons et al cannot be substantiated.

Lyons and co-authors, predictable, disagree with our conclusion.

Once I get back to Bergen from Makerere, I plan to write something about the reply, and some of our findings that we didn’t have space for in our comment.

 

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There is no scientific misconduct …

The youngest patient was two years old when she died three months after Professor Paolo Macchiarini’s experimental surgery to replace her trachea. Since then, Macchiarini has been accused of scientific malpractice. An external investigation found that he reported in a paper that ethics approval had been obtained when it had not, misrepresented patients’ outcomes in several papers, and other issues rated as malpractice.

The vice-chancellor at the Karolinska Institute, where Macchiarini worked, decided that Macchiarini acted “without due care”, but that his behaviour “does not qualify as scientific misconduct”.

That might have been the end of the matter but for the work of journalists. Vanity Fair reported Macchiarini’s plans to marry the producer of a TV documentary about his work in a ceremony officiated by Pope Francis at the Pope’s summer residence with guests including Vladimir Putin and Barack Obama. In reality, the Pope plans took him to South America instead of the wedding of the already-married surgeon. Macchiarini’s CV was only slightly less fanciful. Sveriges Television alleged that some Russian patients Macchiarini operated onwere not ill enough to warrant such a risky procedure.

The misconduct investigation into Macchiarini’s work was subsequently reopened: he was fired (and is under investigation for manslaughter by Swedish prosecutors); and the vice-chancellor resigned, as did several eminent scientists, including Nobel-prize judges.

Macchiarini’s work hastened the deaths of several patients, yet until pressurised by the media, the Karolinska Institute was prepared to overlook misconduct. There is no scientific misconduct so severe that distinguished scientists might not seek to ignore it. How can we ensure that university investigations into research misconduct (or indeed other types of misconduct) are thorough and fair, and as importantly, seen to be thorough and fair? Quis custodiet ipsos custodes?

Posted in Misconduct, Uncategorized | Tagged | 1 Comment

Bob Irvine’s zombie paper (hide the tin foil)

A couple of years ago, I criticised a paper by Bob Irvine published by WIT (a publisher on Beal’s List of possibly predatory publishers). Shortly afterwards, the paper was retracted with the editor writing “I have now received the result of a peer evaluation carried out urgently yesterday on the paper you brought into question, and have decided to withdraw it from our eLibrary.”

Recently, a commenter told me that a revised version of the paper was now published.

I don’t know what’s changed in the paper as I didn’t keep a copy of the paper and the journal does not disclose what changed. But I can compare the abstract. It was one paragraph. It is now four paragraphs. The text is otherwise identical (except that “greenhouse” has been mis-corrected to “Green House”). The declaration that Irvine does not understand climate models is still there

Most Coupled Model Intercomparison Project Phase 5 (CMIP5) climate models assume that the efficacy of a solar forcing is close to the efficacy of a similar sized Green House Gas (GHG) forcing.

As are the tin foil experiments.

If the paper was bad enough to merit retraction two years ago, it really isn’t clear why it merits publication now.

 

 

 

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Data archiving at The Holocene: policy and practice

When I read a recent paper in The Holocene,  I wondered, the way one does, if the data were available, and turned to The Holocene’s submission guidelines.

SAGE [the publisher] acknowledges the importance of research data availability as an integral part of the research and verification process for academic journal articles.

The Holocene requests all authors submitting any primary data used in their research articles if the articles are accepted to be published in the online version of the journal, or provide detailed information in their articles on how the data can be obtained. This information should include links to third-party data repositories or detailed contact information for third-party data sources. Data available only on an author-maintained website will need to be loaded onto either the journal’s platform or a third-party platform to ensure continuing accessibility. Examples of data types include but are not limited to statistical data files, replication code, text files, audio files, images, videos, appendices, and additional charts and graphs necessary to understand the original research. The editor can also grant exceptions for data that cannot legally or ethically be released. All data submitted should comply with Institutional or Ethical Review Board requirements and applicable government regulations. For further information, please contact the editorial office.

The policy is not as strong as I would like – it requests rather than requires – and the first sentence of the main paragraph is difficult to parse. What is missing is a requirement for a data availability statement. Nature announced yesterday that this will be required in their journals.

But how well is the data archiving mandate followed? I’m going to look at the latest issue of The Holocene, and see if data has been archived for the papers. Note, I don’t know when this policy came into force so this test of compliance might be unfair if papers were submitted before the policy was announced.

The issue contains twelve research papers: one paper has most of the data in tables within the paper; four have supplementary online material; none link to third-party (e.g., figshare or datadryad), institutional or personal data repositories.

Unfortunately none of the supplementary online material are currently online (8th September). This is a tiny bit hopeless as the papers have been online since April. It would be so cunning to publish the supplementary material at the same time as the paper, ideally with a link from the PDF.

The absence of the supplemental material means that I cannot tell if they archive data or not. Even being optimistic about their contents, there is less than 50% compliance with the data archiving mandate.

It doesn’t have to be this way. The Journal of Ecology had a 93% data archiving compliance rate in 2015.

 

 

 

 

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Czarny Staw Gąsienicowy

Whenever I see a lake, especially one as beautiful as Czarny Staw Gąsienicowy in the High Tatras, I wonder about what hypotheses could be tested with a sediment core.

P1050091

The lake, in a glacial cirque 1624 m a.s.l., is 51 m deep. At that depth, a Kajak corer or a micro-Kullenberg corer would be the obvious corers to use. Both are line-operated, the former would be good for sediment cores up to 50 cm long, the latter has a piston which improved sediment recovery when collecting longer cores (perhaps 2m). Fortunately, that is probably about as much lacustrine sediment as there is in the lake. The lake could be cored from the ice in spring (I’ve never done this – I was supposed to core a Finnish bay, but the ice was too thin), or from a small boat.

There are, not surprisingly, several palaeoecological studies on Czarny Staw Gąsienicowy and neighbouring lakes in the High Tatras (this list does not pretend to be complete – please add any I have missed in the comments).

Sienkiewicz and Gąsiorowsk (2014) take short cores from Czarny Staw Gąsienicowy and two other lakes and investigate the diatom stratigraphies over the last millennium and use EDDI to reconstruct nutrient status. The two other lakes have tourist cabins in their catchment and show eutrophication (the Secchi-disc depth is 12 m – these are not your pea soup eutrophic pond).

Gąsiorowski and Sienkiewicz (2010) investigate diatom and cladoceran stratigraphies from short cores from two lakes south of Czarny Staw Gąsienicowy (not the lakes in Sienkiewicz and Gąsiorowsk (2014)). They infer recent acidification-driven change in the stratigraphies following earlier climate-driven changes.

Kubovčík and Bitušík (2006) examine the chironomid response to pH changes in three lakes with different susceptibility to acidification from the Slovakian side of the Tatra. The best buffered lake shows no change in chironomid assemblages, whereas the least buffered lake has a large change in assemblage composition and a large drop in chironomid abundance.

Šporka et al (2002) investigate several proxies from Nižné Terianske pleso in Slovakia. Spherical carbonaceous particles give a good indication of the timing of atmospheric pollution. The pigment record is ambiguous (as it often is): downcore changes may be driven entirely by diagenesis, but there may also be a signal from changes in trophic state revealed by the other proxies. There was “no clear relationship between chironomid assemblage and temperature change”. Diatom and chrysophyte assemblages appear to have been influenced by acidification and perhaps also by warming.

On a longer time-scale, Marciniak (1986) presents a diatom stratigraphy from a 3 m-long core from Przedni Staw Lake that starts in the Older Dryas. It is a very descriptive paper, the likes of which would be difficult to publish now, and mentions some previous work on the same lake, including Cladoceran analyses.

There are also pollen analytical work including Rybníčková and Rybníček (2006) and Kłapyta et al (2015).

An overview of limnological studies in the Carpathian region, of which the Tatras are a part, is given by Buczkó et al (2009).

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A comment on Lyons et al is published

Alas it is not the comment that I helped write. But hopefully that will be published soon.

To recap, Lyons et al (2016)  report that that the proportion of species pairs that are aggregated (i.e. co-occur) rather than segregated began to decline in the mid-Holocene, coinciding with the spread of agriculture across North America. Concluding that the organization of modern and late Holocene species assemblages

differs fundamentally from that of assemblages over the past 300 million years that pre-date the large-scale impacts of humans.

 

Bertelsmeier and Ollier dispute these findings. Their first objection is that Lyons treat their proportion data as if they comes from a Gaussian distribution. This is an entirely reasonable point to make.

A proportion of 50% of aggregated species could have been calculated either based on one aggregated and one segregated species pair, or based on 100 aggregated and 100 segregated pairs. The reliability of the estimate is clearly not the same. In total, 44% of the proportions are based on 5 or less species pairs from assemblages with several thousand random species pairs.

By using a Gaussian rather than a binomial distribution, Lyons et al give more weight than can be justified to data sets with few significantly aggregated or segregated taxon-pairs where the proportion of significant pairs is inherently uncertain. They also risk that predictions from their model will escape the zero to one range of proportion data (this is guaranteed to happen if the model is extrapolated).

Bertelsmeir and Ollier find that if the breakpoint analysis is re-run using a binomial error distribution, there is no breakpoint at 6000 years BP. Instead, a breakpoint occurs in the very recent data points.

In their reply, Lyons et al naturally object to this. They point out, correctly, that the taxon-pairs are not independent. If there are n taxa, there will be 0.5n(n-1) taxon-pairs and each taxon occurs in n-1 pairs.

Lyons et al find that Akaike information criterion (AIC) provide much stronger support for a breakpoint analysis if the data are assumed to come from a Gaussian distribution (74.6) than using a binomial distribution (637.0). Lower AIC values suggest better models.

Lyons et al conclude that this means their preferred model is better, but it is at best a poor approximation of the error in the data. A better strategy would be to deal with the over-dispersion in the data caused by the non-independence of the taxon-pairs. This could be easily be done by using a quasibinomial error distribution which relaxes the assumption about the relationship between the mean and the variance in the residuals.

Unfortunately, a breakpoint analysis on a GLM fitted with a quasibinomial error distribution does not converge. Even if it had, it would not have an AIC and so could not be compared directly with the Gaussian model, but it would in principle be a much better model. Alternatives for dealing with over-dispersion in proportion data, such as a beta-binomial model, would probably require some effort before the segmented package breakpoint analysis would work with them.

We don’t discuss the problem with the choice of a Gausssian model in our comment. With the word limit, we were restricted to what we saw as the most critical problems (inappropriate dataset selection, including duplicate datasets; pathological behaviour of the breakpoint analysis; and biases in the proportion of aggregated taxon-pairs with dataset size), and wanted to keep the rest of our analysis as close to Lyons et al’s methods as  possible.

In their reply Lyons et al, write that

Bertelsmeier and Ollier argue that datasets with only a few significant pairs should be excluded because those estimates are unreliable.

Except that I don’t think that B&O argues this. They do argue, as shown above, that data sets with few significantly non-random species pairs have less reliable estimates, but not that they should be excluded.

B&O’s second argument is that the temporal extent of each data set in Lyons et al’s analysis is, perhaps not surprisingly, correlated with its age. B&O suggest that this could cause biases in the proportion of aggregated taxon-pairs. I don’t find this argument any more compelling than Lyons et al’s argument that disturbance causes an increase in aggregated taxon-pairs. To me, aggregation and segregation look like different sides of the same coin. If you increase one, you increase the other and the proportion of each stays the same (of course, biases in the numerical methods may create patterns).

Lyons et al

stand by [their] original analyses and conclusions.

Interestingly, one of the original authors did not join the reply. I wonder if publishing a paper that concludes

Because aggregated and segregated species pairs may be shaped by similar processes both can be used to infer processes of community assembly.

which would appear to contradict Lyons et al, had anything to do with this.

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