standOff, and the article is at its publisher via the link below. When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.| relation to other work | claim_relations | how this paper stands to another: agrees, contradicts, extends, qualifies |
| claim type | claim_type | the shape of the claim: existence, mechanism, method, critique, prediction, null |
| concept edge | concept_edges | an asserted relation between two concepts, with the sentence asserting it |
| concept | concepts | an idea the paper works with, quoted where the paper uses it |
| content tag | content_tags | a finding, definition, quantity, statistic or variable named in the paper |
| contribution | contribution | what the paper claims to add |
| control | controls | an experiment run to eliminate a rival explanation |
| limitation | limitations | what the paper says its evidence cannot support |
| mechanism | mechanisms | how the reported effect is said to come about |
| method | method | how the paper produced its evidence |
| object of study | object_of_study | what the paper is about — the thing it investigates |
| phenomenon | phenomenon | the effect or regularity under study |
| research question | research_question | the question the paper sets itself |
| sense | senses | a distinct use of a term, quoted where the paper fixes it |
Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; 3 of 3 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.
| facet | tag | field | conf. | whose words |
|---|---|---|---|---|
| object_of_study | WHAT A STATISTIC MEANS WHEN THE MODEL GETS COMPLICATED - R-squared and the intra-class correlation for generalized linear mixed models, revisited by the authors of the previous definition and extended to families their own method could not reach Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | object_of_study | the paper's words | |
| research_question | how to define the residual variance term that R-squared needs, when for most distributional families it CANNOT BE SEPARATED into the components the earlier definition assumed Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | research_question | the paper's words | |
| contribution | a general definition of the observation-level variance for non-Gaussian GLMMs via the delta method, the lognormal approximation or the trigamma function - plus a correction to two of their own earlier recommendations Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | contribution | the paper's words | |
| claim_type | method Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_type | the paper's words | |
| phenomenon | one of the most-reported numbers in science, with no single definition once the model has random effects Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | phenomenon | the paper's words | |
| method | formal-model Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: formal-model | method | the paper's words | |
| mechanisms | A NAMING RULE - WHEN A MODIFIER IN A NAME IS LICENSED: `In such a case, the ICC should not be called `ADJUSTED`. For an ICC value to be adjusted for a source of variance, that variance must be more than 0 and omitted from the ICC calculation.` A published condition on the use of one word inside a statistic's name - the same shape as buck2011's rule for when two fields may share an acronym, one level down Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[0] | 0.95 | the tagger's words |
| mechanisms | AND ONE NAME FOR TWO QUANTITIES, KEPT APART BY A SUBSCRIPT: `MARGINAL AND CONDITIONAL R2 differ only in whether the random effect variance is included in the numerator` - the marginal is the proportion explained by the fixed effects, the conditional by fixed AND random. Two numbers a reader will see reported as `R2` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[1] | 0.95 | the tagger's words |
| mechanisms | AND A RENAMING WHERE THE NOTATION DELIBERATELY DOES NOT FOLLOW: `We refer to this generalized version ... as `THE OBSERVATION-LEVEL VARIANCE` here rather than the residual variance (but we keep the notation). Note that the observation-level variance should not be confused with the variance associated with OLRE, which ... can be considered to be A PART OF it.` The name changes, the symbol does not, and the sentence that renames it also warns which neighbouring term it is not Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[2] | 0.95 | the tagger's words |
| mechanisms | AND THE EARLIER DEFINITION WORKED ONLY FOR TWO SPECIAL CASES, SAID PLAINLY: `obtaining for specific distributions is not always possible, because in many families of GLMMs, (observation-level variance) cannot be clearly separated into (overdispersion variance) and (distribution-specific variance). It turns out that binomial and Poisson distributions are special cases where can be usefully calculated ... This is not the case for other families.` The general method was a special case and the authors are the ones who found out Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[3] | 0.95 | the tagger's words |
| mechanisms | AND A DISTINCTION THE AUTHORS WITHDRAW FOR ONE FAMILY AND KEEP FOR ANOTHER: `In the past, we distinguished between ICC on the latent scale and on the observation scale. Such a distinction turns out to be strictly appropriate only for binomial distributions but not for Poisson distributions (and probably also not for other non-Gaussian distributions).` A retraction with its scope stated, including the part they are only probably right about Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[4] | 0.95 | the tagger's words |
| mechanisms | AND THEY NAME WHAT THEY USED TO CALL IT: `note that we would have called 1/lambda THE DISTRIBUTION-SPECIFIC VARIANCE` - the same quantity, the old name, and the new one, in a parenthesis. The corpus has papers that rename things and papers that correct things; this one prints the substitution table Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[5] | 0.95 | the tagger's words |
| mechanisms | AND THE NAMING CHOICE MOVES EVERY REPORTED NUMBER, IN A KNOWN DIRECTION: `the MINIMUM VALUE of 1/(p(1-p)) IS 4, which is larger than pi^2/3 = 3.29, meaning that the use of 1/p(1-p) IN R2 and ICC for binary data will always produce larger values than those using pi^2/3.` Which term you call the denominator decides whether every R2 in a literature is larger or smaller - not a range, a DIRECTION, with a floor. And Browne et al. observed exactly that Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[6] | 0.95 | the tagger's words |
| mechanisms | AND TWO OF THEIR OWN EARLIER RECOMMENDATIONS CONTRADICT EACH OTHER: `In our earlier papers, we proposed to use the exponential of the intercept ... WE ALSO SUGGESTED that it is possible to use the mean of observed values. Unfortunately, these two recommendations are often inconsistent with each other.` Two ways to compute one input, from one paper, that disagree Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[7] | 0.95 | the tagger's words |
| mechanisms | AND THE REASON IS THAT ONE OF THEM ESTIMATES A DIFFERENT LOCATION ENTIRELY: `In fact, exp(beta0) gives the median value of y rather than the mean ... Thus, the use of exp(beta0) will often OVERESTIMATE, providing SMALLER ESTIMATES OF R2 AND ICC ... when lambda is small, the difference can be substantial so the choice of the method needs to be reported for reproducibility.` A methods choice promoted to a reporting requirement because the two answers differ Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[8] | 0.95 | the tagger's words |
| mechanisms | AND THREE ROUTES REACH ONE QUANTITY AND AGREE ONLY ABOVE A THRESHOLD: `ln(1 + 1/lambda) (LOGNORMAL APPROXIMATION), 1/lambda (DELTA METHOD APPROXIMATION) and (TRIGAMMA FUNCTION) GIVE SIMILAR RESULTS WHEN LAMBDA IS GREATER THAN 2. Our recommendation is to use the trigamma function.` Three names, one target, and a condition under which the choice stops mattering Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[9] | 0.95 | the tagger's words |
| limitations | THEIR OWN APPROXIMATION IS NOT THE BEST ONE, AND THEY SAY SO: `A comparison among equations (6.7)-(6.9) is also shown in electronic supplementary material, appendix S3 (it turns out equation (6.8) gives the best approximation). Simulation will give the most accurate conversions when no exact solutions are available.` Equation 6.7 is theirs; 6.8 is McCulloch et al.'s Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[0] | 0.95 | the tagger's words |
| limitations | AND A NEIGHBOURING STATISTIC IS ADMITTED INTO THE FAMILY WITH A HEDGE IN PARENTHESES: the trigamma function has been used for `heritability (which can be seen as a type of ICC although in a strict sense, it is not)`. A kindhood claim and its denial in eleven words - the corpus's `is-a` cannot carry that, so it is here in prose Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[1] | 0.95 | the tagger's words |
| limitations | and one field renames the statistic outright: `a type of ICC is often referred to as repeatability R, where the grouping factor is often individuals that have been phenotyped repeatedly` - ecology and evolution's name for what the rest of the literature calls an intra-class correlation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[2] | 0.95 | the tagger's words |
| controls | deriving the same observation-level variance three independent ways - delta method, lognormal approximation, trigamma function - and comparing them Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a variance term that is an artefact of one derivation; they agree when lambda > 2 and the trigamma is recommended where it applies · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | comparing their own bias-correction approximation against McCulloch et al.'s and Zeger et al.'s, and against simulation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: recommending their own formula without testing it - and the test says somebody else's is better · outcome: failed | controls[1] | 0.95 | the tagger's words |
| controls | requiring that the method used to obtain lambda be reported Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: two papers reporting 'R2' from the same data and the same model with different numbers, because they estimated lambda differently · outcome: partial | controls[2] | 0.95 | the tagger's words |
| concepts | marginal R 2 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: marginal R 2 | concepts[0] | 0.95 | the paper's words |
| concepts | conditional R 2 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: conditional R 2 | concepts[1] | 0.95 | the paper's words |
| concepts | observation-level variance Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: observation-level variance | concepts[2] | 0.95 | the paper's words |
| concepts | distribution-specific variance Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: distribution-specific variance | concepts[3] | 0.95 | the paper's words |
| concepts | median Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: median | concepts[4] | 0.95 | the paper's words |
| concepts | mean Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: mean | concepts[5] | 0.95 | the paper's words |
| senses | `marginal R2` - the proportion of total variance explained by the FIXED effects only; `conditional R2` - by fixed AND random. They `differ only in whether the random effect variance is included in the numerator` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[0] | 0.95 | the tagger's words |
| senses | `observation-level variance` (this paper) - the generalized residual term, explicitly renamed `rather than the residual variance` while KEEPING THE NOTATION, and not to be confused with the variance of an observation-level random effect Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[1] | 0.95 | the tagger's words |
| senses | `distribution-specific variance` - what 1/lambda would have been called in the authors' earlier papers; kept as a separate concept for binomial distributions and declared not analogous Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[2] | 0.95 | the tagger's words |
| senses | `repeatability R` (ECOLOGY AND EVOLUTION) - a type of intra-class correlation where the grouping factor is individuals measured repeatedly Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[3] | 0.95 | the tagger's words |
| senses | `adjusted ICC` - and the condition on the word: an ICC may only be called adjusted if the variance it is adjusted for is `MORE THAN 0 AND OMITTED FROM THE CALCULATION` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[4] | 0.95 | the tagger's words |
| claim_relations | extends → the authors' own earlier definitions of R2_GLMM and ICC_GLMM (Nakagawa & Schielzeth 2013; Nakagawa, Johnson & Schielzeth), which covered only binomial and Poisson families - 'It turns out that binomial and Poisson distributions are special cases' Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[0] | 0.95 | the tagger's words |
| claim_relations | contradicts → their own earlier distinction between ICC on the latent scale and on the observation scale, which 'turns out to be strictly appropriate only for binomial distributions but not for Poisson distributions' Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[1] | 0.95 | the tagger's words |
| concept_edges | marginal R 2 —distinct-from→ conditional R 2 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 0.95 · note: 'As MARGINAL AND…' One name for two numbers, kept apart by a subscript a reader may not carry across papers · the relation stated: the two differ ONLY in whether the random-effect variance is in the numerator - and both are reported as 'R2' also in: marginal R 2 · conditional R 2 | concept_edges[0] | 0.95 | the tagger's words |
| concept_edges | observation-level variance —distinct-from→ distribution-specific variance Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 0.95 · note: 'ARE ANALOGOUS…' The authors previously called one of these by the other's name - 'note that we would have called 1/lambda THE DISTRIBUTION-SPECIFIC VARIANCE' - and the edge records the distinction they drew afterwards · the relation stated: the two observation-level variances are analogous to each other and the distribution-specific variance is not - which is why the term was renamed | concept_edges[1] | 0.95 | the tagger's words |
| concept_edges | median —distinct-from→ mean Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 0.95 · note: 'In fact, exp(beta0) gives the median value of y rather than the mean of y, assuming a Poisson distribution. Thus, the use of exp(beta0) will often overestimate, providing smaller estimates of R2 AND ICC ... when lambda is small, the difference can be substantial so the choice of the method needs to be reported for reproducibility.' A textbook distinction with a reporting requirement attached to it · the relation stated: exp(beta0) estimates the MEDIAN where the formula requires the MEAN, so using it systematically shrinks R2 and ICC | concept_edges[2] | 0.95 | the tagger's words |
| content_tags | A PUBLISHED CONDITION ON A WORD INSIDE A STATISTIC'S NAME: `the ICC should not be called `ADJUSTED` ... that variance must be more than 0 and omitted from the ICC calculation` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[0] | 0.95 | the tagger's words |
| content_tags | AND A RENAMING WHERE THE NOTATION DELIBERATELY DOES NOT FOLLOW: `we refer to this generalized version ... as `THE OBSERVATION-LEVEL VARIANCE` here rather than the residual variance (but we keep the notation)` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[1] | 0.95 | the tagger's words |
| content_tags | AND THE AUTHORS NAME WHAT THEY USED TO CALL IT: `note that we would have called 1/lambda THE DISTRIBUTION-SPECIFIC VARIANCE` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[2] | 0.95 | the tagger's words |
| content_tags | AND THE NAMING CHOICE MOVES EVERY NUMBER IN A KNOWN DIRECTION: `the minimum value of 1/(p(1-p)) IS 4, which is larger than pi^2/3 = 3.29, meaning that the use of 1/p(1-p) IN R2 and ICC for binary data will always produce larger values` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[3] | 0.95 | the tagger's words |
| content_tags | the authors' two earlier recommendations for estimating lambda, exp(beta0) and the mean of observed values, are often inconsistent Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[4] | 0.95 | the tagger's words |
| content_tags | AND A DISTINCTION WITHDRAWN FOR ONE FAMILY AND KEPT FOR ANOTHER: `Such a distinction turns out to be strictly appropriate only for binomial distributions but not for Poisson distributions (and probably also not for other non-Gaussian distributions)` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[5] | 0.95 | the tagger's words |
| content_tags | `quantifies the proportion of variance explained by a statistical model` - and `ESTIMATING R2 FOR GENERALIZED LINEAR MIXED MODELS REMAINS CHALLENGING` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: coefficient of determination | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | `For an ICC value to be adjusted for a source of variance, that variance must be more than 0 and omitted from the ICC calculation` - otherwise `the ICC should not be called `ADJUSTED`` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: adjusted ICC | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | so the choice of term makes every R2 and ICC for binary data larger or smaller, in a fixed direction Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[0] | 0.95 | the tagger's words |
| content_tags | below that the delta method, lognormal approximation and trigamma function diverge Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[1] | 0.95 | the tagger's words |
| content_tags | `Simulation will give the most accurate conversions when no exact solutions are available` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[2] | 0.95 | the tagger's words |
| content_tags | the proportion of variance explained by a grouping factor - called `repeatability R` in ecology and evolution, and a statistic whose `adjusted` variant carries a published condition on the word Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: intra-class correlation coefficient | content_tags.statistics[0] | 0.95 | the tagger's words |
| content_tags | the excess variation the residual term was supposed to separate out - and which `cannot be clearly separated` from the distribution-specific part in most families Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: overdispersion | content_tags.variables[0] | 0.95 | the tagger's words |
Tags that could not be placed in the text:
What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.