README.md
In frousseu/BDTREScheck: A package for doing checks on the Tree Swallow DB
BDTREScheck
A package for doing checks on the Tree Swallow databases. Will print a list with the results (problematic lines) of the different checks executed.
Installation
To install, do:
# install and load devtools to be able to install packages from GitHub with install_github
install.packages("devtools")
library(devtools)
# install package
install_github("frousseu/BDTREScheck")
library(BDTREScheck)
?checkBD
Column Names Required
adults: ferme, nichoir, id, annee, nnich, idcouvee, heure, jjulien, prefixe, suffixe, idadult, condition, sexe_morpho, age_morpho, sexe_gen, locus_sexe_gen, couleur, age_exact, laile1, laile2, masse, tarse1, tarse2, trougauche, troudroite, pararectrice, plaqueincu, Cause_recapt, commentaire, observateur
chicks: ferme, nichoir, id, annee, nnich, idcouvee, heure, jjulien, prefixe, suffixe, idois, sexe_gen, locus_sexe_gen, condition, numero_oisillon, jour_suivi, envol, masse, 9primaires1, 9primaires2, tarse1, tarse2, commentaires, manipulateur
broods: idcouvee, id, ferme, nichoir, annee, codesp, nnich, noeufs, noisnes, noisenvol, noismort, dispa_ois, dispa_oeufs, abandon, pred_pot, dponte, dincub, declomin, declomax, denvomin, denvomax, dabanmin, dabanmax, idF1, idM1, idF2, idF3, idM2, idM3, Commentaires
How To Use
Run checks:
library(BDTREScheck)
x<-checkBD(
dsn="//argus.dinf.fsci.usherbrooke.ca/DBio_Rech_Data/Projet_Hirondelle/1_Donnees/11_Principales",
year=2015,
adultsNew=NULL,
broodsNew=NULL,
chicksNew=NULL,
adultsOld="Adultes_2004-2015.xlsx",
broodsOld="Couvee_2004-2015.xlsx",
chicksOld="Oisillons_2004-2015.xlsx",
sheet=1
)
Display results:
x
x[4]
Show the list of checks:
checkShow(html=FALSE)
TODO
- add part at the end of Nghia script (already done?)
- find what to do with read_excel warnings on expectation about column format
- change default values of databases names
- think of a way to remove warnings associated with the check on the number of characters based on column names that are not in all databases
- think about the input db type given and arguments options (a data.frame already in the environment, a path to an excel, csv file, a remote database etc.)
- make a few other checks already described, but not code
- looking for more than one label for sex gives a lot of results (with M or F and I), so it may not be the thing to do
Current List Of Checks (updated 2018-02-05)
ID
Checks
1
"GENERAL: Remove rows with NA id's in broodsNew"
2
"GENERAL: Remove rows with NA id's in adultsNew"
3
"GENERAL: Remove rows with NA id's in chicksNew"
4
"GENERAL: Are column names in adult consistent?"
5
"GENERAL: Are column names in chicksNew consistent?"
6
"GENERAL: Are column names in broodsNew consistent?"
7
"GENERAL: Are column names consistant across old and new databases"
8
"ADULTS: Wrong ferme id observed"
9
"NESTLINGS: Wrong ferme id observed"
10
"BROODS: Wrong ferme id observed"
11
"ADULTS: Wrong nichoir id observed"
12
"NESTLINGS: Wrong nichoir id observed"
13
"BROODS: Wrong nichoir id observed"
14
"ADULTS: id column doesn't correspond to ferme + nichoir id"
15
"NESTLINGS: id column doesn't correspond to ferme + nichoir id"
16
"BROODS: id column doesn't correspond to ferme + nichoir id"
17
"ADULTS: idcouv doesn't correspond to ferme + nichoir + annee + nnich column"
18
"NESTLINGS: idcouv doesn't correspond to ferme + nichoir + annee + nnich column"
19
"BROODS: idcouv doesn't correspond to ferme + nichoir + annee + nnich column"
20
"ADULTS: Wrong prefixe name observed (is it a new prefixe?)"
21
"ADULTS: Wrong suffixe name observed (too short/long)"
22
"ADULTS: idadult doesn't correspond to prefixe + suffixe"
23
"ADULTS: idadult doesn't correspond to id + year + LETTER"
24
"NESTLINGS: Wrong prefixe name observed (is it a new prefixe?)"
25
"NESTLINGS: Wrong suffixe name observed (too short/long)"
26
"NESTLINGS: idois doesn't correspond to prefixe + suffixe"
27
"NESTLINGS: idois doesn't correspond to idcouvee + numero_oisillon"
28
"ADULTS: Show all unique values in columns for which the number of possible values is restricted"
29
"BROODS: Show all unique values in columns for which the number of possible values is restricted"
30
"NESTLINGS: Show all unique values in columns for which the number of possible values is restricted"
31
"ADULTS/BROODS: Females assigned to an idcouv in adults db but no female is assigned to this idcouv in broods db (check capture dates)"
32
"ADULTS/BROODS: Females assigned to an idcouv in adults db but not referenced in broods db (idF2 or idF3)"
33
"ADULTS/BROODS: Females captured at a nestbox but not assigned to an idcouv in adults db (check nnich)"
34
"ADULTS/BROODS: Females captured at a nestbox but assigned to a wrong idcouv in adults db (check nnich)"
35
"ADULTS/BROODS: Males assigned to an idcouv in adults db but no male is assigned to this idcouv in broods db (check capture dates or morpho/gen sex identity)"
36
"ADULTS/BROODS: Males assigned to an idcouv in adults db but not referenced in broods db (idM2 or idM3)"
37
"ADULTS/BROODS: Males captured at a nestbox but not assigned to an idcouv in adults db (check nnich)"
38
"ADULTS/BROODS: Males captured at a nestbox but assigned to a wrong idcouv in adults db (check nnich)"
39
"BROODS: Female referenced as second female when only one female captured (change to idF1 - some exceptions possible)"
40
"BROODS: Male referenced as second males when only one male captured (change to idM1)"
41
"BROODS: Two males captured in the same nestbox but not properly reported (idM2 and idM3, not idM1)"
42
"BROODS: Males (idM1) assigned to brood with no nestlings (not coherent)"
43
"ADULTS: Sex/age incoherencies (few exceptions when condition !=0)"
44
"ADULTS: Some colors not in the list of possible values?"
45
"ADULTS: Brown females (>50%) not assigned to SY?"
46
"ADULTS: Individual with a couleur assigned, but without morpho_age (no check for condition != 0)"
47
"ADULTS: Dead individual with a couleur assigned, but without morpho_age (probably nothing to do)"
48
"ADULTS: Capture time outside 06:00 and 20:40 (max)"
49
"NESTLINGS: Capture time outside 06:00 and 20:40 (max)"
50
"ADULTS: Wrong sexe_gen/locus_sexe_gen association (both NA or with values)"
51
"ADULTS: Check for adults with changing sexe_morph (within the current breeding season ONLY)"
52
"ADULTS: Check for adults with changing sexe_morph (across seasons - MUST be concordant (see Donnees_Codes.docx))"
53
"ADULTS: Check for adults with changing sexe_gen (within the current breeding season ONLY)"
54
"ADULTS: Check for adults with changing sexe_gen (across seasons)"
55
"ADULTS: Check for adults with changing locus_sexe_gen (within the current breeding season ONLY)"
56
"ADULTS: Check for adults with changing locus_sexe_gen (across seasons)"
57
"ADULTS: Missing one wing measurement"
58
"ADULTS: Missing one tarsus measurement"
59
"ADULTS: Wing measurement outside the range of likely values (105-128 mm)"
60
"ADULTS: Wing measurement 1 and 2 too far apart (>1 mm)"
61
"ADULTS: Weight measurements outside the range of likely values (15-30g)"
62
"ADULTS: Tarsus measurements outside the range of likely values (10-14 mm)"
63
"ADULTS: tarsus measurement 1 and 2 too far apart (>0.1 mm)"
64
"ADULTS: Wrong condition status"
65
"ADULTS: Wrong plaqueincu status"
66
"ADULTS: Male with brood patch (plaqueincu)"
67
"ADULTS: Wrong Cause_capture status"
68
"ADULTS: Visits are not all 2 days apart for the following farms (maybe caused by presence of NAs)"
69
"NESTLINGS: Visits are not all 2 days apart for the following farms (maybe caused by presence of NAs)"
70
"ADULTS: Check for duplicates using all columns"
71
"BROODS: Check for duplicates using all columns"
72
"CHICKS: Check for duplicates using all columns"
73
"ADULTS: Check for adults with more than one entry for a single date (probably duplicated lines - remove one)"
74
"NESTLINGS: Check for chicks with more than one entry for a single date (probably duplicated lines - remove one)"
75
"NESTLINGS: Check for chicks with more than one entry for a single age"
76
"ADULTS: Check for adults found at more than one farm (maybe not an error)"
77
"NESTLINGS: Check for nestlings found at more than one nestbox"
78
"NESTLINGS/BROODS: Capture date of young is later than the minimal abandonment date if nest was abandoned"
79
"NESTLINGS/BROODS: Capture date of young is before the laying date"
80
"NESTLINGS/BROODS: jjulien of young that doesn't correspond to declomax + jour_suivi"
81
"NESTLINGS: Wrong sexe_gen/locus_sexe_gen association (both NA or with values)"
82
"NESTLINGS: Check for individuals with changing sexe_gen"
83
"NESTLINGS: Check for individuals with changing locus_sexe_gen"
84
"NESTLINGS: Wrong chick conditions (4 possible values; vivant, disparu, mort or disparuj16)"
85
"NESTLINGS: Dead or disappeared nestlings without a 0 for flight code (few exceptions possibles, see comments)"
86
"NESTLINGS: Nestling with disparuj16 condition but without a 1 for flight code"
87
"NESTLINGS: Make sure that living nestlings with a 0 flight code are eventually dead or disappeared"
88
"NESTLINGS: Make sure that no nestling comes back to life"
89
"NESTLINGS: Check that numero_oisillon are from 1 to nb of nestlings"
90
"NESTLINGS: Nestlings which were followed for 12 days or more should have a band number as id and otherwise they should have a farm/brood id (maybe an exception, comments [Oisillon non bagué car trop petit à J12])"
91
"NESTLINGS: Chicks for which there is a band number but it does not correspond to the id of the chick"
92
"NESTLINGS: Missing one wing measurement"
93
"NESTLINGS: Missing one tarsus measurement"
94
"NESTLINGS: 9primaires larger than expected (65 mm, no age consideration)"
95
"NESTLINGS: 9primaires outside the range of likely values at 6-day-old (0 - 10 mm)"
96
"NESTLINGS: 9primaires outside the range of likely values at 12-day-old (5 - 45 mm)"
97
"NESTLINGS: 9primaires outside the range of likely values at 16-day-old (15 - 65 mm)"
98
"NESTLINGS: 9primaires 1 and 2 too far apart (>0.1 mm)"
99
"NESTLINGS: Weight measurements larger than expected (27 g, no age consideration)"
100
"NESTLINGS: Weight measurements outside the range of likely value at 2-days-old (1-8 g)"
101
"NESTLINGS: Weight measurements outside the range of likely value at 6-days-old (2-20 g)"
102
"NESTLINGS: Weight measurements outside the range of likely value at 12-days-old (10-27 g)"
103
"NESTLINGS: Weight measurements outside the range of likely value at 16-days-old (12-27 g)"
104
"NESTLINGS: Tarsus measurements outside the range of likely values (10-14 mm)"
105
"NESTLINGS: Tarsus measurement 1 and 2 too far apart (>0.1 mm)"
106
"NESTLINGS/BROODS: Broods that are in chicks db but not in broods db"
107
"NESTLINGS/BROODS: TRES broods with at least one nestling that are in broods db but not in chicks db"
108
"ADULTS/NESTLINGS: Check for individuals with changing sexe_gen across db"
109
"ADULTS: Check for either missing or wrong age_exact column for individuals hatched in our study system"
110
"BROODS: Check for duplicates in idcouvee"
111
"BROODS: Check for duplicates in id/nnich (change nnich)"
112
"BROODS: Check for missing id (add lines for them)"
113
"BROODS: Wrong codesp (some other species were exceptionnally ringed)"
114
"BROODS: checks if the nnich number is good assuming only one line per brood"
115
"BROODS: Wrong abandon / pred_pot"
116
"BROODS: Wrong chronology in events within a brood"
117
"BROODS: Broods with more nestlings than eggs"
118
"BROODS: More/less nestlings than nestling status (noines != noisenvol + noismort + dispa_ois)"
119
"BROODS: Too much eggs/nestlings within the same brood (8 and more; few exception possible, see comments)"
120
"BROODS: Event dates outside the range of possible values (JJ 95-220)"
121
"BROODS: No fledging or abandon date for TRES broods (exception possibles, see comments"
122
"BROODS: Missing 1 value in declo (min or max)"
123
"BROODS: Missing 1 value in denvo for TRES (min or max)"
124
"BROODS: Wrong denvomin for other species (should be NA)"
125
"BROODS: Missing 1 value in daban (min or max)"
126
"BROODS: Very long time elapse between laying date and incubation initiation (> 2 weeks; 2 different broods?)"
127
"BROODS: Very short time elapse between laying date and incubation initiation (< 5 days)"
128
"BROODS: Very long time elapse between laying date and hatching date (> 4 weeks; 2 different broods?)"
129
"BROODS: Very short time elapse between laying date and hatching date (< 10 days)"
130
"BROODS: Very long time elapse between incubation initiation and hatching date (> 2 weeks; 2 different broods?)"
131
"BROODS: Very short time elapse between incubation initiation and hatching date (< 1 week)"
132
"BROODS: Too long time elapse between minimum and maximum hatching date (> 1 day)"
133
"BROODS: Too long time elapse between minimum and maximum abandon date (> 1 day) when nestlings >=1"
134
"BROODS: Too long time elapse between minimum and maximum fledging date (> 1 week)"
135
"BROODS: Too short time elapse between minimum and maximum fledging date (< 1 day; exception possible, see comments)"
136
"NESTLINGS/BROODS: Inconsistency in the number of nestlings between databases (NESTLINGS: Nois, Nenvol, Ndead, Ndispa - MAYBE some nestlings with num_ois = NA)"
frousseu/BDTREScheck documentation built on Sept. 22, 2023, 3:53 a.m.
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BDTREScheck
A package for doing checks on the Tree Swallow databases. Will print a list with the results (problematic lines) of the different checks executed.
Installation
To install, do:
# install and load devtools to be able to install packages from GitHub with install_github
install.packages("devtools")
library(devtools)
# install package
install_github("frousseu/BDTREScheck")
library(BDTREScheck)
?checkBD
Column Names Required
adults: ferme, nichoir, id, annee, nnich, idcouvee, heure, jjulien, prefixe, suffixe, idadult, condition, sexe_morpho, age_morpho, sexe_gen, locus_sexe_gen, couleur, age_exact, laile1, laile2, masse, tarse1, tarse2, trougauche, troudroite, pararectrice, plaqueincu, Cause_recapt, commentaire, observateur
chicks: ferme, nichoir, id, annee, nnich, idcouvee, heure, jjulien, prefixe, suffixe, idois, sexe_gen, locus_sexe_gen, condition, numero_oisillon, jour_suivi, envol, masse, 9primaires1, 9primaires2, tarse1, tarse2, commentaires, manipulateur
broods: idcouvee, id, ferme, nichoir, annee, codesp, nnich, noeufs, noisnes, noisenvol, noismort, dispa_ois, dispa_oeufs, abandon, pred_pot, dponte, dincub, declomin, declomax, denvomin, denvomax, dabanmin, dabanmax, idF1, idM1, idF2, idF3, idM2, idM3, Commentaires
How To Use
Run checks:
library(BDTREScheck)
x<-checkBD(
dsn="//argus.dinf.fsci.usherbrooke.ca/DBio_Rech_Data/Projet_Hirondelle/1_Donnees/11_Principales",
year=2015,
adultsNew=NULL,
broodsNew=NULL,
chicksNew=NULL,
adultsOld="Adultes_2004-2015.xlsx",
broodsOld="Couvee_2004-2015.xlsx",
chicksOld="Oisillons_2004-2015.xlsx",
sheet=1
)
Display results:
x
x[4]
Show the list of checks:
checkShow(html=FALSE)
TODO
- add part at the end of Nghia script (already done?)
- find what to do with read_excel warnings on expectation about column format
- change default values of databases names
- think of a way to remove warnings associated with the check on the number of characters based on column names that are not in all databases
- think about the input db type given and arguments options (a data.frame already in the environment, a path to an excel, csv file, a remote database etc.)
- make a few other checks already described, but not code
- looking for more than one label for sex gives a lot of results (with M or F and I), so it may not be the thing to do
Current List Of Checks (updated 2018-02-05)
ID Checks 1 "GENERAL: Remove rows with NA id's in broodsNew" 2 "GENERAL: Remove rows with NA id's in adultsNew" 3 "GENERAL: Remove rows with NA id's in chicksNew" 4 "GENERAL: Are column names in adult consistent?" 5 "GENERAL: Are column names in chicksNew consistent?" 6 "GENERAL: Are column names in broodsNew consistent?" 7 "GENERAL: Are column names consistant across old and new databases" 8 "ADULTS: Wrong ferme id observed" 9 "NESTLINGS: Wrong ferme id observed" 10 "BROODS: Wrong ferme id observed" 11 "ADULTS: Wrong nichoir id observed" 12 "NESTLINGS: Wrong nichoir id observed" 13 "BROODS: Wrong nichoir id observed" 14 "ADULTS: id column doesn't correspond to ferme + nichoir id" 15 "NESTLINGS: id column doesn't correspond to ferme + nichoir id" 16 "BROODS: id column doesn't correspond to ferme + nichoir id" 17 "ADULTS: idcouv doesn't correspond to ferme + nichoir + annee + nnich column" 18 "NESTLINGS: idcouv doesn't correspond to ferme + nichoir + annee + nnich column" 19 "BROODS: idcouv doesn't correspond to ferme + nichoir + annee + nnich column" 20 "ADULTS: Wrong prefixe name observed (is it a new prefixe?)" 21 "ADULTS: Wrong suffixe name observed (too short/long)" 22 "ADULTS: idadult doesn't correspond to prefixe + suffixe" 23 "ADULTS: idadult doesn't correspond to id + year + LETTER" 24 "NESTLINGS: Wrong prefixe name observed (is it a new prefixe?)" 25 "NESTLINGS: Wrong suffixe name observed (too short/long)" 26 "NESTLINGS: idois doesn't correspond to prefixe + suffixe" 27 "NESTLINGS: idois doesn't correspond to idcouvee + numero_oisillon" 28 "ADULTS: Show all unique values in columns for which the number of possible values is restricted" 29 "BROODS: Show all unique values in columns for which the number of possible values is restricted" 30 "NESTLINGS: Show all unique values in columns for which the number of possible values is restricted" 31 "ADULTS/BROODS: Females assigned to an idcouv in adults db but no female is assigned to this idcouv in broods db (check capture dates)" 32 "ADULTS/BROODS: Females assigned to an idcouv in adults db but not referenced in broods db (idF2 or idF3)" 33 "ADULTS/BROODS: Females captured at a nestbox but not assigned to an idcouv in adults db (check nnich)" 34 "ADULTS/BROODS: Females captured at a nestbox but assigned to a wrong idcouv in adults db (check nnich)" 35 "ADULTS/BROODS: Males assigned to an idcouv in adults db but no male is assigned to this idcouv in broods db (check capture dates or morpho/gen sex identity)" 36 "ADULTS/BROODS: Males assigned to an idcouv in adults db but not referenced in broods db (idM2 or idM3)" 37 "ADULTS/BROODS: Males captured at a nestbox but not assigned to an idcouv in adults db (check nnich)" 38 "ADULTS/BROODS: Males captured at a nestbox but assigned to a wrong idcouv in adults db (check nnich)" 39 "BROODS: Female referenced as second female when only one female captured (change to idF1 - some exceptions possible)" 40 "BROODS: Male referenced as second males when only one male captured (change to idM1)" 41 "BROODS: Two males captured in the same nestbox but not properly reported (idM2 and idM3, not idM1)" 42 "BROODS: Males (idM1) assigned to brood with no nestlings (not coherent)" 43 "ADULTS: Sex/age incoherencies (few exceptions when condition !=0)" 44 "ADULTS: Some colors not in the list of possible values?" 45 "ADULTS: Brown females (>50%) not assigned to SY?" 46 "ADULTS: Individual with a couleur assigned, but without morpho_age (no check for condition != 0)" 47 "ADULTS: Dead individual with a couleur assigned, but without morpho_age (probably nothing to do)" 48 "ADULTS: Capture time outside 06:00 and 20:40 (max)" 49 "NESTLINGS: Capture time outside 06:00 and 20:40 (max)" 50 "ADULTS: Wrong sexe_gen/locus_sexe_gen association (both NA or with values)" 51 "ADULTS: Check for adults with changing sexe_morph (within the current breeding season ONLY)" 52 "ADULTS: Check for adults with changing sexe_morph (across seasons - MUST be concordant (see Donnees_Codes.docx))" 53 "ADULTS: Check for adults with changing sexe_gen (within the current breeding season ONLY)" 54 "ADULTS: Check for adults with changing sexe_gen (across seasons)" 55 "ADULTS: Check for adults with changing locus_sexe_gen (within the current breeding season ONLY)" 56 "ADULTS: Check for adults with changing locus_sexe_gen (across seasons)" 57 "ADULTS: Missing one wing measurement" 58 "ADULTS: Missing one tarsus measurement" 59 "ADULTS: Wing measurement outside the range of likely values (105-128 mm)" 60 "ADULTS: Wing measurement 1 and 2 too far apart (>1 mm)" 61 "ADULTS: Weight measurements outside the range of likely values (15-30g)" 62 "ADULTS: Tarsus measurements outside the range of likely values (10-14 mm)" 63 "ADULTS: tarsus measurement 1 and 2 too far apart (>0.1 mm)" 64 "ADULTS: Wrong condition status" 65 "ADULTS: Wrong plaqueincu status" 66 "ADULTS: Male with brood patch (plaqueincu)" 67 "ADULTS: Wrong Cause_capture status" 68 "ADULTS: Visits are not all 2 days apart for the following farms (maybe caused by presence of NAs)" 69 "NESTLINGS: Visits are not all 2 days apart for the following farms (maybe caused by presence of NAs)" 70 "ADULTS: Check for duplicates using all columns" 71 "BROODS: Check for duplicates using all columns" 72 "CHICKS: Check for duplicates using all columns" 73 "ADULTS: Check for adults with more than one entry for a single date (probably duplicated lines - remove one)" 74 "NESTLINGS: Check for chicks with more than one entry for a single date (probably duplicated lines - remove one)" 75 "NESTLINGS: Check for chicks with more than one entry for a single age" 76 "ADULTS: Check for adults found at more than one farm (maybe not an error)" 77 "NESTLINGS: Check for nestlings found at more than one nestbox" 78 "NESTLINGS/BROODS: Capture date of young is later than the minimal abandonment date if nest was abandoned" 79 "NESTLINGS/BROODS: Capture date of young is before the laying date" 80 "NESTLINGS/BROODS: jjulien of young that doesn't correspond to declomax + jour_suivi" 81 "NESTLINGS: Wrong sexe_gen/locus_sexe_gen association (both NA or with values)" 82 "NESTLINGS: Check for individuals with changing sexe_gen" 83 "NESTLINGS: Check for individuals with changing locus_sexe_gen" 84 "NESTLINGS: Wrong chick conditions (4 possible values; vivant, disparu, mort or disparuj16)" 85 "NESTLINGS: Dead or disappeared nestlings without a 0 for flight code (few exceptions possibles, see comments)" 86 "NESTLINGS: Nestling with disparuj16 condition but without a 1 for flight code" 87 "NESTLINGS: Make sure that living nestlings with a 0 flight code are eventually dead or disappeared" 88 "NESTLINGS: Make sure that no nestling comes back to life" 89 "NESTLINGS: Check that numero_oisillon are from 1 to nb of nestlings" 90 "NESTLINGS: Nestlings which were followed for 12 days or more should have a band number as id and otherwise they should have a farm/brood id (maybe an exception, comments [Oisillon non bagué car trop petit à J12])" 91 "NESTLINGS: Chicks for which there is a band number but it does not correspond to the id of the chick" 92 "NESTLINGS: Missing one wing measurement" 93 "NESTLINGS: Missing one tarsus measurement" 94 "NESTLINGS: 9primaires larger than expected (65 mm, no age consideration)" 95 "NESTLINGS: 9primaires outside the range of likely values at 6-day-old (0 - 10 mm)" 96 "NESTLINGS: 9primaires outside the range of likely values at 12-day-old (5 - 45 mm)" 97 "NESTLINGS: 9primaires outside the range of likely values at 16-day-old (15 - 65 mm)" 98 "NESTLINGS: 9primaires 1 and 2 too far apart (>0.1 mm)" 99 "NESTLINGS: Weight measurements larger than expected (27 g, no age consideration)" 100 "NESTLINGS: Weight measurements outside the range of likely value at 2-days-old (1-8 g)" 101 "NESTLINGS: Weight measurements outside the range of likely value at 6-days-old (2-20 g)" 102 "NESTLINGS: Weight measurements outside the range of likely value at 12-days-old (10-27 g)" 103 "NESTLINGS: Weight measurements outside the range of likely value at 16-days-old (12-27 g)" 104 "NESTLINGS: Tarsus measurements outside the range of likely values (10-14 mm)" 105 "NESTLINGS: Tarsus measurement 1 and 2 too far apart (>0.1 mm)" 106 "NESTLINGS/BROODS: Broods that are in chicks db but not in broods db" 107 "NESTLINGS/BROODS: TRES broods with at least one nestling that are in broods db but not in chicks db" 108 "ADULTS/NESTLINGS: Check for individuals with changing sexe_gen across db" 109 "ADULTS: Check for either missing or wrong age_exact column for individuals hatched in our study system" 110 "BROODS: Check for duplicates in idcouvee" 111 "BROODS: Check for duplicates in id/nnich (change nnich)" 112 "BROODS: Check for missing id (add lines for them)" 113 "BROODS: Wrong codesp (some other species were exceptionnally ringed)" 114 "BROODS: checks if the nnich number is good assuming only one line per brood" 115 "BROODS: Wrong abandon / pred_pot" 116 "BROODS: Wrong chronology in events within a brood" 117 "BROODS: Broods with more nestlings than eggs" 118 "BROODS: More/less nestlings than nestling status (noines != noisenvol + noismort + dispa_ois)" 119 "BROODS: Too much eggs/nestlings within the same brood (8 and more; few exception possible, see comments)" 120 "BROODS: Event dates outside the range of possible values (JJ 95-220)" 121 "BROODS: No fledging or abandon date for TRES broods (exception possibles, see comments" 122 "BROODS: Missing 1 value in declo (min or max)" 123 "BROODS: Missing 1 value in denvo for TRES (min or max)" 124 "BROODS: Wrong denvomin for other species (should be NA)" 125 "BROODS: Missing 1 value in daban (min or max)" 126 "BROODS: Very long time elapse between laying date and incubation initiation (> 2 weeks; 2 different broods?)" 127 "BROODS: Very short time elapse between laying date and incubation initiation (< 5 days)" 128 "BROODS: Very long time elapse between laying date and hatching date (> 4 weeks; 2 different broods?)" 129 "BROODS: Very short time elapse between laying date and hatching date (< 10 days)" 130 "BROODS: Very long time elapse between incubation initiation and hatching date (> 2 weeks; 2 different broods?)" 131 "BROODS: Very short time elapse between incubation initiation and hatching date (< 1 week)" 132 "BROODS: Too long time elapse between minimum and maximum hatching date (> 1 day)" 133 "BROODS: Too long time elapse between minimum and maximum abandon date (> 1 day) when nestlings >=1" 134 "BROODS: Too long time elapse between minimum and maximum fledging date (> 1 week)" 135 "BROODS: Too short time elapse between minimum and maximum fledging date (< 1 day; exception possible, see comments)" 136 "NESTLINGS/BROODS: Inconsistency in the number of nestlings between databases (NESTLINGS: Nois, Nenvol, Ndead, Ndispa - MAYBE some nestlings with num_ois = NA)"R Package Documentation
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