Table 2 Database of study descriptors and data extracted from published studies.
From: A comprehensive database of thermal developmental plasticity in reptiles
Column | Values | Description |
|---|---|---|
data_no | Integer from 1000 onwards | Unique number assigned to each manuscript or unpublished dataset . This data_no column matches the paper_no column in Citations.csv. |
first_author_surname | Variable | The surname of the first author on the manuscript data was extracted from |
pub_year | Variable | Year the manuscript data was extracted from was published |
order | Crocodilia | Order of the reptile of study species |
Rhynchocephalia | ||
Squamata | ||
Testudines | ||
family | Variable | Family of the reptile of the study species |
genus | Variable | The genus name of the study species |
species | Variable | The species name of the study species |
genus_timetree | Variable | The genus name of the study species in the time-tree database (http://www.timetree.org/). When a study species was not found genus name was kept the same as the paper and cross checked with the EMBL Reptile Database.. |
species_timetree | Variable | The species name of the study species in the time-tree database (http://www.timetree.org/). When a study species was not found species name was kept the same as the paper and cross checked with the EMBL Reptile Database. |
latin_name | Variable | The full latin name (genus and species) of the reptile of study |
specific_location_name | String of location descriptions | Specific location of the study as specified within the manuscript. If more than one detail is provided a comma separates them. Also, if the study animal were sourced from a captive colony or hatchery this is specified in this column. If location data is not specified in the manuscript, these columns are filled in with an ‘NA’. |
city | Variable | The city in which the study was conducted as specified within the manuscript. If this is not specified in the manuscript, these columns are filled in with an ‘NA’. |
state_province | Variable | The state or province in which the study was conducted as specified within the manuscript. If this is not specified in the manuscript, these columns are filled in with an ‘NA’. |
country | Variable | The country in which the study was conducted as specified within the manuscript. If this is not specified in the manuscript, these columns are filled in with an ‘NA’. |
population | Variable | “pop1”, “pop2”, etc: if means within a manuscript were from independent populations (e.g., different species within the same location, across different geographic locations) |
data_year | Mostly numeric | If the year data was collected was specified within the manuscript it is detailed here in a numeric format (i.e., 2018). If data was from multiple years, these are listed and separated by a comma in a string (i.e., 2016, 2017, 2018). |
If study methods indicate that data were collected within a particular year, but the numeric date was not specified, then we have used the test “year” with a number after it (i.e., “year1”). If data were collected over multiple years (pooled), but no numeric dates specified, then these are listed in a string using this alphanumeric format (i.e., “year 1, year2”). | ||
If study year is unspecified, this is coded as “NA”. | ||
egg_design | independent | Reflecting how eggs were allocated to each incubation treatment. |
independent_pseudo | “independent”: each incubation treatment consisted of eggs from independent females with no repeated samples from a single female clutch | |
other | “independent_pseudo”: each incubation treatment treated eggs from the same female as replicates, but there were separate clutches within each treatment (i.e. eggs were not split across treatments) | |
split_clutch | “split_clutch”: distributed a single egg from each clutch within each of the incubation treatments | |
split_psuedo | “split_psuedo”: distributed eggs from a single clutch evenly across multiple incubation treatments, but eggs from the same clutch were in the same incubation treatment | |
“other”: not possible to determine the egg allocation strategy | ||
source_page | Numeric | The page within the manuscript that the data was extracted from |
source | Variable FigNo. | The specific location within the manuscript from where the data was extracted; or ‘author’ if data were supplied via contact with an author of the publication |
Variable TableNo. | ||
Text | ||
Author | ||
trait_cat | Incubation | Each trait was assigned to one of seven traits categories. Examples of traits included in each category include: Incubation – time to hatching in days; Behaviour – Activity, latency to a behaviour; Growth – growth rates of various body regions (snout-vent length, mass, head width and length); Morphology – Mass, snout-vent-length, head width and length, carapace width and length, usually presented in mm and grams; Performance – Sprint speed, maximal run distance, time to run, swimming speed, bite force and pull force, usually in m/s, m, Newtons (N); Physiology – generally hormone concentrations (e.g. testosterone, estrogen), metabolic rate (e.g., VC02/ V02 per time), Carcass ash, dry mass, energy and water content; Survival – primarily contains hatching success, but also survival to a particular age. |
Growth | ||
Morphology | ||
Performance | ||
Physiology | ||
Survival | ||
trait | Variable | The detailed name of the phenotypic trait that relates to the specific name used within the original source. |
simp_trait | Variable | A simplified version of the name of the phenotypic traits that was used in the manuscript in order to produce summary figures for publication. This column is likely to be of most use to users given that it provides a simplified indication of the trait quantified within the study. |
units | Variable | The units that were used to quantify a phenotypic trait |
egg_embryo_ | Egg | Specification of the life stage at which the phenotypic trait was measured. |
hatchling | Embryo | “Egg”: measurements of the egg or portions of the egg prior to the embryo hatching |
Hatchling | “Embryo”: measurements of pre-hatched embryos. Often embryos were removed from eggs prior to hatching and measured on a given trait. | |
“Hatchling”: measurements of offspring at- or post-hatching. | ||
age | Numeric | The age (days post-hatching) at which the phenotypic trait was measured. For survival, the age is the second census date. Egg and embryo measurements given NA. |
sex | females | “females”: all females in sample |
males | “males”: all males in sample | |
mixed | “mixed” mixture of sexes in the sample, or if the sample was unknown | |
other_factors | Describes if the phenotypic trait means integrated other confounding factors that were not otherwise specified in the database (e.g., post-hatching treatments, genetic strains or races, elevation, etc.); otherwise “NA” | |
const_fluct | Const | Simplified categorization of incubation temperature design that is based on the T_fluc column. This column can help users distinguish different experimental designs (see definitions below) across studies. “Range” is defined as the full range of temperatures. For example, if 23 +/− 0.5C, then the range is 1 C |
Fluct | “Const”: range of daily temperature data ≤1 deg. C | |
Irreg | “Fluct”: range of daily temperature data was ≥ 1 deg. C | |
Shift | “Irreg”: temperature profiles vary idiosyncratically, or there was a slight delay between oviposition and the establishment of incubation treatments. | |
“Shift”; temperature profiles shifted during incubation between established temperature treatments as part of the experiment design | ||
T | Numeric | Mean temperature, in degrees Celcius, of the incubation treatment |
T_fluc | Numeric | The range of temperature, in degrees Celcius, of the incubation treatment. For example, if the temperature varied between 20 C and 30 C, with a mean temperature of 25 C this column would contain a 10 (+/− 5 C around the mean). This column can be used to treat temperature fluctuations on a continuous scale or classify experimental designs (as is done in const_fluct) in a user specific way. |
water_potential | Numeric | Water potential of treatment, if specified. Negative integers within this column represent water potential measured in kPa. The other representations of water potential reflect a wetter/drier treatment using the terms used in the manuscript. If water potential was not specified within the paper, or if it was specified using a water to vermiculite ratio, then the uncertainty in specific water potential value was represented using “NA”. |
mean | Numeric | The mean of the phenotypic trait from the incubation treatment |
error | Numeric | The error of the phenotypic trait from the incubation treatment |
N | Numeric | The sample size of the phenotypic trait from the incubation treatment |
error_type | SE | The type of error associated with the data |
SD | “SE”: standard error | |
CI | “SD”: standard deviation | |
P | “CI”: 95% confidence intervals | |
NA | “P”: the data was a proportion of individuals within the treatment, and thus did not have error | |
“NA”: If the error type was not unspecified | ||
data_style | adj | Specification if the data were either raw, or adjusted in some way (e.g., residuals, log transformation, etc.). |
raw | ||
comment_code | Numeric | Numbers associated with a comment code to specify particular issues associated about the papers. These were listed in ascending order, separated by a comma followed by a space. The comment codes represent: |
1=other | ||
2=we assumed or calculated N | ||
3=N reported within the paper is conflicting | ||
4=calculated error from paper | ||
5=assumed error type | ||
6=error uncertain or missing | ||
7=unclear temperature treatment | ||
8=back-calculated hatching success from provided sample sizes | ||
9=data pooled between two+ factors because of presentation or non-significant effects | ||
10=N is missing | ||
11=calculated age | ||
12=assumed trait units through logical deduction | ||
13=potential confounding factors in experimental design | ||
14=unknown trait units | ||
15=citation was used to get experimental information (sex ratio, etc.) | ||
16=Substantial delay between oviposition and entering treatment | ||
comm_text | Text | Explanations, if needed, for the comments codes. |
