May 28, 2018
Effect of low count sums on quantitative environmental reconstructions: an example using subfossil chironomids. Heiri & Lotter (2001)
Setting minimum head capsule abundance and taxa deletion criteria in chironomid-based inference models. Quinlan & Smol (2001)
How many chironomid head capsules are enough? A statistical approach to determine sample size for palaeoclimatic reconstructions. Larocque (2001)
adjacent samples were pooled to produce a minimum head-capsule count of 50 specimens per sample Heiri and Lotter (2003)
Chironomids were enumerated from subsamples of sediment until >50 headcapsules were counted Lang et al (2017)
A minimum of 50 head capsules were extracted from each sample Langdon et al (2008)
At least 50 head capsules were mounted. Larocque-Tobler et al (2015)
Samples produc[ing] less than 50 head capsules were not included in the subsequent analyses Zhang et al (2017)
Nullius in verba
The reported count sum is testable.
Trivial with archived count data
More challenging with archived percent data
Last Chance Lake (Axford et al 2017)
## # A tibble: 1 x 3 ## `median singletons` mean_singleton prob1 ## <dbl> <dbl> <dbl> ## 1 3 3.227273 0.96
\(\frac{count} {countSum} \times 100 = percent\)
\(\frac{count}{percent} \times 100 = countSum\)
\(\frac{1}{percent} \times 100 = countSum\)
Can estimate uncertainty due to rounding.
At least 50 head capsules were mounted. Larocque et al (2015)
In Lake Żabińskie, the number of head capsules varied from 19 to 68.5 with 29 out of the 89 (33%) samples having abundances lower than 30 Larocque-Tobler et al (2016) [Corrigendum]
## # A tibble: 6 x 5 ## mn est_n est_min est_max n ## <dbl> <dbl> <dbl> <dbl> <dbl> ## 1 20.0 5.000000 4.987531 5.012531 20.0 ## 2 14.3 6.993007 6.968641 7.017544 21.0 ## 3 14.3 6.993007 6.968641 7.017544 21.0 ## 4 12.5 8.000000 7.968127 8.032129 32.0 ## 5 12.2 8.196721 8.163265 8.230453 41.0 ## 6 10.3 9.708738 9.661836 9.756098 43.5
## # A tibble: 61 x 7 ## # Groups: id [9] ## mn est_n n id species percent multiple ## <dbl> <dbl> <dbl> <int> <chr> <dbl> <dbl> ## 1 20.0 5 20 6 Cladopelma lateralis 20.0 1.000 ## 2 20.0 5 20 6 Endochironomus tendens 20.0 1.000 ## 3 20.0 5 20 6 Microtendipes pedellus 20.0 1.000 ## 4 20.0 5 20 6 Paratanytarsus 40.0 2.000 ## 5 12.5 8 32 7 Chironomini 12.5 1.000 ## 6 12.5 8 32 7 Chironomus anthracinus 12.5 1.000 ## 7 12.5 8 32 7 Polypedilum nubeculosum 12.5 1.000 ## 8 12.5 8 32 7 Cricotopus 12.5 1.000 ## 9 12.5 8 32 7 Procladius 12.5 1.000 ## 10 12.5 8 32 7 Endochironomus albipennis 14.1 1.128 ## # ... with 51 more rows
The diatom counts included 400–500 valves per sample and at least 100 valves in 4 diatom-poor samples.
Two hundred grain counts … were made for each level
99.8% of counts are divisible by two
## # A tibble: 54 x 2 ## depth d4 ## <chr> <dbl> ## 1 59052 1.0000000 ## 2 59094 1.0000000 ## 3 59098 0.8666667 ## 4 59097 0.8333333 ## 5 59068 0.8000000 ## 6 59073 0.8000000 ## 7 59066 0.7777778 ## 8 59089 0.7777778 ## 9 59059 0.7500000 ## 10 59054 0.7142857 ## # ... with 44 more rows
Enthusiastic exclusion of rare taxa
Low taxonomic resolution
Misreporting
How large a count sum should be assummed if it is not reported?
Percent should sum to 100 %
1000 simulations 30 taxa rounded to different precisions <> ##Impossible percent integer rule
all percent should be integer multiples of lowest percent value
Discrepancies need to be checked carefully
Taxon | Percent | Estimated |
---|---|---|
Mesocricotopus | 0.826446 | 1.00 |
Corynocera oliveri | 1.652890 | 2.00 |
Eukiefferiella fittkaui | 1.652890 | 2.00 |
Tanytarsus sp | 1.652890 | 2.00 |
Micropsectra radialis | 3.305790 | 4.00 |
Paratanytarsus | 3.305790 | 4.00 |
Protanypus | 3.900000 | 4.72 |
Paracladius | 5.785120 | 7.00 |
Abiskomyia | 6.611570 | 8.00 |
Cricotopus | 8.264460 | 10.00 |
H# maeri | 52.892600 | 64.00 |
## function (x) ## { ## structure(x, class = unique(c("AsIs", oldClass(x)))) ## } ## <bytecode: 0x2868d80> ## <environment: namespace:base>
Near duplicate assemblages should be rare
Counting errors
Counting error with 50 microfossils, true abundance = 20%
Taxon | 1902 | 1940 | 1981 | 1987 |
---|---|---|---|---|
Cladotanytarsus mancus1 | 11.1111 | 11.1111 | 11.1111 | 11.1111 |
Corynoneura | 11.1111 | 11.1111 | 11.1111 | 11.1111 |
Dicrotendipes nervosus | 11.1111 | 11.1111 | 11.1111 | 11.1111 |
Microtendipes pedellus | 11.1111 | 11.1111 | 11.1111 | 11.1111 |
Paratanytarsus | 11.1111 | 11.1111 | 11.1111 | 11.1111 |
Parochlus | 11.1111 | 11.1111 | 11.1111 | 11.1111 |
Procladius | 11.1111 | 11.1111 | 11.1111 | 11.1111 |
Tanytarsus lugens | 11.1111 | 11.1111 | 11.1111 | 11.1111 |
Tanytarsus pallidicornis | 11.1111 | 11.1111 | 11.1111 | 11.1111 |
Find most similar pair of samples
Taxon | 1964 % | 1967 % | 1964 count | 1967 count |
---|---|---|---|---|
Chironomini | 13.2 | 17.1 | 5.0 | 7 |
Cladotanytarsus mancus1 | 14.5 | 14.6 | 5.5 | 6 |
Glyptotendipes pallens | 3.9 | 0.0 | 1.5 | 0 |
Microtendipes pedellus | 14.5 | 14.6 | 5.5 | 6 |
Tanytarsus lactesens | 13.2 | 12.2 | 5.0 | 5 |
Tanytarsus mendax | 14.5 | 14.6 | 5.5 | 6 |
Tanytarsus sp | 26.3 | 26.8 | 10.0 | 11 |
Mistakes, errors and other problems will be discovered
Many mistakes may have little effect
Take care with calculations
Archive code