DOI: 10.5281/zenodo.3955050
title: Core SAFE project small mammal trapping data

description: <b>Description: </b>This is the combined dataset for the SAFE project's core small mammal trapping programme, which was run from 2011-2014 by O.R. Wearn, from 2015-2017 by P. M. Chapman, and from 2018-2019 by S. Heon. In total, trapping grids have been run at 30 sites across the SAFE landscape and control areas, covering blocks D, E, F, OG1, OG2, OG3 and OP2. However, since 2014 trapping has been limited to 12 standard permanent grids which are resampled annually: two in D (the 100ha fragment site), six in E (two each in the 1, 10 and 100ha sites), two in OG2 at the Maliau Basin Conservation area and two in OP2 at the Selangan Batu Oil Palm estate. In 2018, 2 new mammal grids were added : Dmatrix-1 and Ematrix-1 grid. The following grids were dropped E1-1, E10-1, E100-1 and D100-1, while D1-2 and D10-2 were sampled. In 2019, OG2-N, trap lines 1-8 were not accessible due to a massive landslide. In replacement, lines 47-56 were added to the trap grid for OG2-N. trapping grids Dmatrix-2 and Ematrix-2 were also added. All the new grids are reflected on the locations sheet. One standard annual sampling session comprises 96 traps run for seven nights, and the first sheet in the dataset ("Deployment") records this as 672 rows detailing the basic outcome of each trap night in the sampling session. There are several grids which form exceptions to this trapping pattern; details of these are recorded in the metadata. The subsequent two sheets (Corrected_Trapping_Data and Raw_Trapping_Data) form a more detailed record of captured animals. These sheets have the non-capture rows removed, along with most of the basic trap location and state data; however they can easily be linked back to the relevant rows in "Deployment" by the date and the unique trap identifier. At first capture, all possible details of captured animals are recorded, including age, sex, biometric measurements, crude estimates of parasite load, and the ID of any associated samples. All animals captured in good health were fitted with a Passive Integrated Transponder (PIT) Tag so the unique 10-digit alphanumeric number associated with each PIT tag is also recorded. Upon recapture, the animals are merely weighed and the PIT tag number and trap location recorded; this is partly to save time and partly to avoid unneccessary repeat anaesthesia. In 2018, Prevost's squirrel with the species code PVSQ was added into the species list. <br>The entire dataset from 2011-2017 was extensively error-checked by PMC in 2018, then from 2018-2019 by SH with many errors identified, recorded, and where possible, rectified. These errors are most frequently duplications or typos in the PIT tag string. Where these errors are unresolvable, the true unique ID of the individual is no longer certain, and its independence from other individuals cannot be guaranteed. These records will require omitting from most analyses. The detailed dataset with capture data is therefore presented in both its raw and corrected forms. ("Raw_Trapping_Data" and "Corrected_Trapping_Data", respectively). In the corrected datasheet, all the resolvable errors have been corrected, with a brief note made of what was done and why. Notes have also been added to irresolvable errors briefly explaining the problem, and recommending omission from analyses where appropriate. We strongly recommend that all users rely on the corrected version; however we also include the raw data for completeness. In 2018, an additional sheet - general site information details was added<b>Project: </b>This dataset was collected as part of the following SAFE research project: <b>The impacts of tropical forest fragmentation on dispersal behaviour of mammal communities</b><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available here<b>Files: </b>This consists of 1 file: SAFE_Core_Small_Mammal_Data_V3_2019_ROB_SUI.xlsx<b>SAFE_Core_Small_Mammal_Data_V3_2019_ROB_SUI.xlsx</b>This file contains dataset metadata and 4 data tables:<b>Basic trap outcome data</b> (described in worksheet Deployment)Description: This is the basic trapping data covering the outcome of every trap night since the start of the study in 2011. It comprises merely the location and date information for the trap, the person who was responsible for baiting it, the state of the trap and bait on checking, any invertebrates captured, the number of small mammal captures (generally 0 or 1, but occasionally 2) and any notes pertaining to the trap itself.Number of fields: 15Number of data rows: 71123Fields: <b>Grid-Session-Occasion</b>: An identifier for the individual trapping day ("occasion") within a sampling year ("session"). This nomenclature originates from applying Spatially Explicit Capture-Recapture models to this data, however experience suggests this is the most concise, intuitive way of referring to a particular day of trapping (rather than using the actual date). This is applied to all grids which were trapped in the standard pattern of 96 traps run for seven consecutive days. There are five exceptions: OG2-E in 2011, D100-2 in 2011, D100-1 in 2012, F100-1 in 2012, and F100-2 in 2012. These were all trapped in a non-standard pattern (either total trapping effort ≠ 96 traps and 7 days, or there were gaps etween days such that the total trapped duration &gt; 7 days). These exceptions are given NA (Field type: id)<b>Date</b>: The calendar date of trapping (Field type: date)<b>Block</b>: The SAFE sampling block (Field type: categorical)<b>Fragment</b>: The fragment (SAFE landscape; 1, 10, or 100ha) or sub-block (control sites; e.g. OP2, OG1, etc) of the sampling session. (Field type: id)<b>Grid</b>: The grid of the sampling session. There are two grids (1 and 2, numered outwards from the centre of the lock) in each fragment in the SAFE design, and three in each su-block in the control sites (North, East and West). (Field type: id)<b>Point</b>: The camera trap/small mammal sampling point where the trap was located. (Field type: id)<b>Trap</b>: The trap identifier (two traps, A and B, are located within a 5m radius of each sampling point) (Field type: id)<b>Unique_Point_ID</b>: Unique identifier for the sampling point (corresponds to the Locations sheet, and the locations in the Gazeteer) (Field type: location)<b>Unique_Trap_ID</b>: Unique identifier for the individual trap. (Field type: id)<b>State</b>: The state of the trap when checked. (Field type: categorical)<b>Bait</b>: The state of the bait when checked. (Field type: categorical)<b>Invertebrates</b>: Comments on any invertebrates found; in particular the presence of ants is frequently recorded, as these can be a severe danger to small mammals. (Field type: comments)<b>Capture_N</b>: Number of small mammals caught. This is almost invarialy zero or one, however very occasionally two are caught together. Models such as Spatially Explicit Capture Recapture treat small mammal traps as "single-catch" traps, and the model is violated y these occasions - so they are worth flagging up. (Field type: numeric)<b>Who_baited</b>: Person who baited the trap (Field type: comments)<b>Other_Notes</b>: Original supplementary field notes on the trap outcome or the animal captured. On the "Deployment" sheet this column has Been trimmed to only include notes covering the placement and condition of the traps - with notes pertaining to captured animals removed. (Field type: comments)<b>Corrected trapping data</b> (described in worksheet Corrected_Trapping_Data)Description: This is the modified, corrected version of the detailed trapping data covering all the small mammal captures from 2011 (i.e. blank rows are removed). It is directly based on the raw trapping data, however it has been fully verified, with all rectifiable errors corrected. Extra columns are included to: 1.) display any corrections to species ID and PIT tag ID of an individual record, 2.) explain the reason for corrections applied, or any unresolvable errors, and 3.) recommend a record for omission from analyses, where appropriate.Number of fields: 36Number of data rows: 8101Fields: <b>Grid-Session-Occasion</b>: An identifier for the individual trapping day ("occasion") within a sampling year ("session"). This nomenclature originates from applying Spatially Explicit Capture-Recapture models to this data, however experience suggests this is the most concise, intuitive way of referring to a particular day of trapping (rather than using the actual date). This is applied to all grids which were trapped in the standard pattern of 96 traps run for seven consecutive days. There are five exceptions: OG2-E in 2011, D100-2 in 2011, D100-1 in 2012, F100-1 in 2012, and F100-2 in 2012. These were all trapped in a non-standard pattern (either total trapping effort ≠ 96 traps and 7 days, or there were gaps between days such that the total trapped duration &gt; 7 days). These exceptions are given NA (Field type: id)<b>Date</b>: The calendar date of trapping (Field type: date)<b>Unique_Point_ID</b>: Unique identifier for the sampling point (corresponds to the Locations sheet, and the locations in the Gazeteer) (Field type: location)<b>Unique_Trap_ID</b>: Unique identifier for the individual trap. (Field type: id)<b>Species</b>: Raw species ID for the captured animal. All "target" small mammals receive an identifying code for brevity (see the Taxa sheet) while occasional caputures of "non-target" taxa (larger mammals, other vertebrates) are referred to in full. Fully unknown small mammal species are referred to as "Unknown". (Field type: taxa)<b>Species_Validated</b>: Corrected, verified species ID for the captured animal. This should be used in preference to "Species" as any misidentifications have been amended. Codes follow those in the "Raw Taxon" column (Field type: taxa)<b>Species_Uncertainty</b>: Indicates uncertainty around the species identification (after correction). Species IDs are not alwaysCERtain, especially in the case of aberrant individuals, cryptic species or complexes such as Rattus, or heavily scavenged dead indivuduals. (Field type: categorical)<b>New/Recapture</b>: Indicates whether the individual is a new record or a recapture. NB: Biometric data (apart from weight) is not collected for recaptures for reasons of time and ethics (unnecessary anaesthesia). (Field type: categorical)<b>PIT_Tag/ID</b>: Raw individual ID for the captured animal. This is usually a 10-digit numeric or alphanumeric string, the number of the fitted Passive Integrated Transponder (PIT) tag. All zeros in PIT strings are replaced with capital Os due to persistent problems with Excel irreversibly modifying particular string formats (these errors are included in this raw data). Various other "generic" individual IDs have been applied to occasional animals which were untagged but somehow deemed to be otherwise identifiable. The format and use of these varies between fieldworkers and has not been standardised here in this raw verson. (Field type: id)<b>PIT_Tag/ID_Validated</b>: Corrected, validated individual ID for the captured small mammal. This should be used in preference to "PIT_Tag/ID" as resolvable errors have been amended. In some occasional cases this ID does not correspond to the (corrected) PIT tag string. In these cases a standardised generic ID was applied, generally under two possible conditions: 1.) The individual was released alive without tagging but there is effectively no chance of recapture (such as an animal on the last day of trapping in an isolated block which was not trapped subsequently). 2.) The animal was a new, untagged individual found dead in the trap. Case 1: individuals recieve an identifier comprised of the species code and a unique three-digit number e.g. "WH001". Case 2: Individuals recieve a unique two-digit number preceded by "NewDead". (Field type: id)<b>Age</b>: Age of the individual captured. Uncertain ages are given with question marks. Completely unknown or unrecorded age are given as NA. (Field type: categorical trait)<b>Sex</b>: Sex of the individual captured. Uncertain sexes are given with question marks. Completely unknown or unrecorded sexes are given as NA. (Field type: categorical trait)<b>Sexing_Notes</b>: Notes on criteria used for sexing. (Field type: comments)<b>HF</b>: (Left) Hind foot measurement (Field type: numeric trait)<b>E</b>: (Left) Ear length measurement (only rats) (Field type: numeric trait)<b>AGD</b>: Ano-genital distance measurement (only rats) (Field type: numeric trait)<b>HB</b>: Head-body length measurement (only treeshrews, squirrels and some rat species where ID is uncertain) (Field type: numeric trait)<b>T</b>: Tail length measurement (only treeshrews, squirrels and some rat species where ID is uncertain) (Field type: numeric trait)<b>T_%_of_HB</b>: Tail length as a percentage of body head-body length (Field type: numeric trait)<b>MZ</b>: Muzzle length measurement (only treeshrews) (Field type: numeric trait)<b>Bag_W</b>: Mass of the polythene weighing bag (Field type: numeric)<b>Gross_W</b>: Mass of the polythene weighing bag including animal (Field type: numeric)<b>Net_W</b>: Mass of the animal (Field type: numeric)<b>Parasite_Count</b>: Approximate ectoparasite load: rough visual count of the number of fur mites and other ectoparasites shed within the anaesthesia pot during anaesthesia (Field type: numeric trait)<b>Body_Fat</b>: Body fat score: a nine-level categorical score. Only applied from 2017 onwards. (Field type: categorical trait)<b>Injuries</b>: Description of any injuries or visible signs of diease to the captured small mammal. (Field type: comments)<b>Dead</b>: Was the individual found dead, or euthanised in the course of processing? (Field type: categorical trait)<b>Tissue_Sample_ID</b>: Identifier for any tissue samples taken (rats only, from the right ear) (Field type: id)<b>Parasite_Sample_ID</b>: Identifier for any parasite samples taken (Field type: id)<b>Fur_sample_ID</b>: Identifier for any fur samples taken (Field type: id)<b>Faecal_Sample_1_ID</b>: Identifier for any faecal samples taken (for first investigator) (Field type: id)<b>Faecal_Sample_2_ID</b>: Identifier for any faecal samples taken (for second investigator) (Field type: id)<b>Processor</b>: Person who processed the animal (Field type: comments)<b>Omit</b>: Identifies individuals which should be omitted from all analyses ("Y") or some analyses ("SA") due to data errors (Field type: categorical)<b>Correction_Notes</b>: Comments on any corrections made or reasoning for suggesting omissions in "Omit". Omissions are usually due to the individual ID or species ID of a capture being uncertain. Several common omission reasons are recorded with standard prhases in capitals for clarity: these include escapes, animals released untagged for various reasons (including non-target captures), and dead individuals where species identification was impossible or where it was uncertain if the individual was new or a recapture. More complex cases are discussed individually. (Field type: comments)<b>Other_Notes</b>: Original supplementary field notes on the trap outcome or the animal captured. This column includes supporting notes for ID, descriptions of the circumstances of a death, admissions of missing data, etc etc. These have not been error-checked or modified. (Field type: comments)<b>Raw trapping data</b> (described in worksheet Raw_Trapping_Data)Description: This is the unmodified, raw version of the detailed trapping data, covering all the small mammal sampling from 2011 (i.e. blank rows are removed). It is included for information only and we do not recommend that it is used.Number of fields: 32Number of data rows: 8101Fields: <b>Grid-Session-Occasion</b>: An identifier for the individual trapping day ("occasion") within a sampling year ("session"). This nomenclature originates from applying Spatially Explicit Capture-Recapture models to this data, however experience suggests this is the most concise, intuitive way of referring to a particular day of trapping (rather than using the actual date). This is applied to all grids which were trapped in the standard pattern of 96 traps run for seven consecutive days. There are five exceptions: OG2-E in 2011, D100-2 in 2011, D100-1 in 2012, F100-1 in 2012, and F100-2 in 2012. These were all trapped in a non-standard pattern (either total trapping effort ≠ 96 traps and 7 days, or there were gaps between days such that the total trapped duration &gt; 7 days). These exceptions are given NA (Field type: id)<b>Date</b>: The calendar date of trapping (Field type: date)<b>Unique_Point_ID</b>: Unique identifier for the sampling point (corresponds to the Locations sheet, and the locations in the Gazeteer) (Field type: location)<b>Unique Trap ID</b>: Unique identifier for the individual trap. (Field type: id)<b>Species</b>: Raw species ID for the captured animal. All "target" small mammals receive an identifying code for brevity (see the Taxa sheet) while occasional captures of "non-target" taxa (larger mammals, other vertebrates) are referred to in full. Fully unknown small mammal species are referred to as "Unknown". (Field type: taxa)<b>Species Uncertainty</b>: Indicates uncertainty around the species identification. Species IDs are not always certain, especially in the case of aberrant individuals, cryptic species or complexes such as Rattus, or heavily scavenged dead indivuduals. (Field type: categorical)<b>New/Recapture</b>: Indicates whether the individual is a new record or a recapture. NB: Biometric data (apart from weight) is not collected for recaptures for reasons of time and ethics (unnecessary anaesthesia). (Field type: categorical)<b>PIT_Tag/ID</b>: Raw individual ID for the captured animal. This is usually a 10-digit numeric or alphanumeric string, the number of the fitted Passive Integrated Transponder (PIT) tag. All zeros in PIT strings are replaced with capital Os due to persistent problems with Excel irreversibly modifying particular string formats (these errors are included in this raw data). Various other "generic" individual IDs have been applied to occasional animals which were untagged but somehow deemed to be otherwise identifiable. The format and use of these varies between fieldworkers and has not been standardised here in this raw dataset. (Field type: id)<b>Age</b>: Age of the individual captured. Uncertain ages are given with question marks. Completely unknown or unrecorded age are given as NA. (Field type: categorical trait)<b>Sex</b>: Sex of the individual captured. Uncertain sexes are given with question marks. Completely unknown or unrecorded sexes are given as NA. (Field type: categorical trait)<b>Sexing Notes</b>: Notes on criteria used for sexing. (Field type: comments)<b>HF</b>: (Left) Hind foot measurement (Field type: numeric trait)<b>E</b>