R session_REM
Paulina Pawlikowska
2024-11-15
In this session you will learn how to calculate the density of animals using Random Encounter Model (Rowcliffe et al., 2008). In this exercise we will calculate the density of hedgehogs in urban and rural habitat using data from Schaus et al. (2020). The code was also adapted from this publication.
1. Create environment: set working directory and download the necessary packages
There are a few packages available for calculating density with REM. Today we will be using remBoot (Caravaggi, xxxx)
install.packages(“devtools”)
devtools::install_github(“arcaravaggi/remBoot”)
-----how can I hide outputs of that
library(remBoot)
library(readxl)
library(dplyr)## Warning: pakiet 'dplyr' został zbudowany w wersji R 4.3.3##
## Dołączanie pakietu: 'dplyr'## Następujące obiekty zostały zakryte z 'package:stats':
##
## filter, lag## Następujące obiekty zostały zakryte z 'package:base':
##
## intersect, setdiff, setequal, unionLet’s see what format of the data is required for the REM analysis
?remBoot
As we see in the Viewer, to be able to run the model using remBoot, the data has to be structured in a certain way:
-each row will represent one camera trap
-there will be 4 columns: survey location, trapping rate (number of individuals captured), radial* distance to the detected animal (in meters), and angle to the detected animal (in radians**)
*radial-> meaning that it's a radius of the circular space around the camera trap
**radian-> way of expressing time
Additional variables required by the model are:
tm- The total number of hours all cameras were left in-situ at a focal site
v- The distance travelled by the focal species in 24 hours, in kilometres
Let’s upload the data and change it to a dataframe
camDat <- read_excel("camDat.xlsx")
camDat<-as.data.frame(camDat)When you take a look at the camDat dataset, you will notice that there are 2 site locations- urban (Southwell) and rural (Brackenhurst). We will be calculating density for each location separately, so we need to split them into two seperate groups. We first assign them numerical values
camDat$Site[camDat$Site=="Southwell"] <- 1
camDat$Site[camDat$Site=="Brackenhurst2017"] <- 2Make sure that your data has a correct format. Here we will change Site and count to integer
camDat$Site<-as.integer(camDat$Site)
camDat$count<-as.integer(camDat$count)and split by survey
grpDat <- split_dat(camDat)Day range
One of the variables we need to calculate is day range (v), so distance traveled by an animal in a day (24h) in kilometers. Day range is a product of animal speed and time spent active.
Speed
Speed is extracted from camera trap footage. It can be calculated by measuring the distance that the animal traveled in a sequence of pictures that camera trap had captured and dividing it by the time that the animal was present in the camera trap’s detection zone. More automated approaches are being developed, where it will possible to extract the speed from images captured by cameras that were previously calibrated- see Miles et al., 2024.
In our example the mean speed was previously calculated:
0.77km/h for Southwell
0.50km/h for Brackenhurst
Activity
To calculate the time spent active, we will use package activity
library(activity)We will calculate the activity from camera trap footage. We will use the time space between the earliest possible recording of a hedgehog and the latest one as bounds and fit activity model to it.
For this we will need a dataset including hours of hedgehog captures. Let’s start with Southwell data
activity <- read_excel("activity.xlsx")
We will need to change the format of the time to radians (to allow for fitting kernel models?)
Radians are
rad_time <- gettime(activity$Time, tryFormats = "%Y-%m-%d %H:%M:%S", scale = "radian")The gettime function converts the hours in POSITx or character format to radians, which will be recognized by R.
To plot activity model we will have to choose the bounds of activity of hedgehogs
#why do we choose bounds? Because they are nocturnal? when bounds are given, normal kernel distribution is used, truncated at the values of bounds, otherwise it would use circular kernel distribution
#the following step is not easily reproducible, it requires that from the dataset we manually look at which recording is the earliest for hedgehogs and which is the latest. It would be best to find a better approach here.
From the dataset we identify the earliest and the latest hour of capturing a hedgehog. Remember that hedgehogs are nocturnal species, so the beginning of their activity will be the start of the night.
earliest-> 21:22
latest->4:20
We need to identify the radian form of these hours, to provide data to the model in the same format
library("astroFns")
first_video<-hms2rad(h = '21h 22 m')
last_video<-hms2rad(h = '4h 20m')Now we can fit activity model, using fitact function and choosing bounds as the argument
activity<-fitact(rad_time,bounds=c(first_video,last_video), sample = "data")#is bootstrapping here appropriate to get standard error?
activity## An object of class "actmod"
## Slot "data":
## [1] 6.230825430 5.637413484 6.217735460 0.000000000 0.056723201 5.777039824
## [7] 0.309795942 5.777039824 0.693768378 5.921029487 5.929756134 0.973021058
## [13] 6.265732015 0.274889357 0.484328867 0.842121364 0.654498469 0.685041731
## [19] 0.021816616 5.995205981 1.077740813 0.104719755 0.959931089 5.816309732
## [25] 0.209439510 0.335975881 0.178896248 1.125737368 5.929756134 5.969026042
## [31] 6.008295950 6.082472443 6.108652382 6.152285613 0.061086524 0.148352986
## [37] 6.134832321 0.632681854 0.802851456 5.973389365 0.047996554 0.100356432
## [43] 0.405789051 0.061086524 6.073745797 0.026179939 0.318522588 0.475602221
## [49] 0.898844565 0.004363323 0.519235452 0.126536371 5.877396256 5.912302841
## [55] 0.047996554 1.073377490 5.846852994 0.427605667 0.575958653 1.108284075
## [61] 1.012290966 1.082104136 1.034107582 0.292342650 0.309795942 1.060287521
## [67] 0.689405055 1.021017612 6.278821984 0.920661180 0.497418837 0.510508806
## [73] 0.872664626 0.602138592 6.147922290 0.575958653 0.903207888 0.925024504
## [79] 0.981747704 0.863937980 5.598143576 5.598143576 5.995205981 0.183259571
## [85] 0.479965544 0.130899694 0.925024504 0.475602221 0.898844565 0.615228561
## [91] 0.959931089 0.196349541 0.894481242 5.750859885 0.331612558 0.213802833
## [97] 0.711221670 0.004363323 0.222529480 0.746128255 0.423242344 0.885754595
## [103] 0.986111027 6.073745797 0.335975881 6.121742351 0.087266463 0.087266463
## [109] 5.934119457 0.584685299
##
## Slot "wt":
## [1] 1
##
## Slot "bw":
## [1] 0.1753924
##
## Slot "adj":
## [1] 1
##
## Slot "pdf":
## x y se lcl ucl
## [1,] 0.003022733 0.6510740 0.08033044 0.5012526 0.8109646
## [2,] 0.006591948 0.6524628 0.08050497 0.5040201 0.8145248
## [3,] 0.010161163 0.6538160 0.08067679 0.5047228 0.8184560
## [4,] 0.013730379 0.6551061 0.08082946 0.5041248 0.8211026
## [5,] 0.017299594 0.6563774 0.08099048 0.5064281 0.8228014
## [6,] 0.020868810 0.6575637 0.08112002 0.5065680 0.8259444
## [7,] 0.024438025 0.6587293 0.08125729 0.5062228 0.8285580
## [8,] 0.028007240 0.6598270 0.08137439 0.5058603 0.8296106
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## [10,] 0.035145671 0.6618881 0.08159069 0.5069797 0.8316472
## [11,] 0.038714887 0.6628286 0.08167734 0.5079412 0.8325026
## [12,] 0.042284102 0.6637402 0.08176742 0.5087843 0.8332138
## [13,] 0.045853317 0.6645621 0.08182765 0.5101855 0.8336689
## [14,] 0.049422533 0.6653614 0.08189509 0.5129316 0.8341881
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## [16,] 0.056560964 0.6667542 0.08197735 0.5157254 0.8331863
## [17,] 0.060130179 0.6673693 0.08200448 0.5163875 0.8325184
## [18,] 0.063699394 0.6679215 0.08201794 0.5167548 0.8343745
## [19,] 0.067268610 0.6684347 0.08203047 0.5176249 0.8352356
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## [21,] 0.074407041 0.6692624 0.08201089 0.5188838 0.8348904
## [22,] 0.077976256 0.6695690 0.08197511 0.5195440 0.8346500
## [23,] 0.081545471 0.6698434 0.08194262 0.5202036 0.8365627
## [24,] 0.085114687 0.6700462 0.08189314 0.5206279 0.8368829
## [25,] 0.088683902 0.6701930 0.08183492 0.5202047 0.8377192
## [26,] 0.092253118 0.6702921 0.08177237 0.5202178 0.8365317
## [27,] 0.095822333 0.6703118 0.08168924 0.5214585 0.8364215
## [28,] 0.099391548 0.6703077 0.08161429 0.5217466 0.8379095
## [29,] 0.102960764 0.6702016 0.08150736 0.5210555 0.8355233
## [30,] 0.106529979 0.6700721 0.08140895 0.5214658 0.8329095
## [31,] 0.110099195 0.6698653 0.08129131 0.5219128 0.8319239
## [32,] 0.113668410 0.6696126 0.08117068 0.5214680 0.8324336
## [33,] 0.117237625 0.6693066 0.08104342 0.5198162 0.8332690
## [34,] 0.120806841 0.6689334 0.08090192 0.5181588 0.8314228
## [35,] 0.124376056 0.6685303 0.08076619 0.5172576 0.8311806
## [36,] 0.127945272 0.6680398 0.08060530 0.5165012 0.8317673
## [37,] 0.131514487 0.6675278 0.08045459 0.5157281 0.8299307
## [38,] 0.135083702 0.6669381 0.08028362 0.5150810 0.8278709
## [39,] 0.138652918 0.6663141 0.08011572 0.5148416 0.8257446
## [40,] 0.142222133 0.6656355 0.07993982 0.5152785 0.8236876
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## [43,] 0.152929779 0.6633057 0.07937959 0.5146465 0.8205789
## [44,] 0.156498995 0.6624531 0.07919428 0.5137742 0.8208497
## [45,] 0.160068210 0.6615282 0.07898849 0.5131757 0.8180351
## [46,] 0.163637426 0.6605804 0.07879169 0.5135087 0.8166993
## [47,] 0.167206641 0.6595812 0.07858615 0.5134085 0.8163232
## [48,] 0.170775856 0.6585442 0.07837953 0.5132334 0.8158209
## [49,] 0.174345072 0.6574749 0.07817563 0.5115814 0.8128074
## [50,] 0.177914287 0.6563549 0.07796084 0.5102198 0.8133971
## [51,] 0.181483503 0.6552197 0.07775988 0.5082505 0.8121749
## [52,] 0.185052718 0.6540232 0.07753854 0.5068320 0.8130525
## [53,] 0.188621933 0.6528137 0.07733163 0.5090367 0.8122455
## [54,] 0.192191149 0.6515605 0.07711546 0.5079142 0.8111517
## [55,] 0.195760364 0.6502833 0.07690408 0.5050422 0.8098823
## [56,] 0.199329580 0.6489781 0.07669428 0.5047108 0.8071727
## [57,] 0.202898795 0.6476402 0.07647983 0.5043900 0.8063031
## [58,] 0.206468010 0.6462877 0.07627755 0.5034921 0.8036601
## [59,] 0.210037226 0.6448960 0.07606134 0.5031444 0.8013748
## [60,] 0.213606441 0.6434952 0.07586108 0.5029871 0.8003638
## [61,] 0.217175657 0.6420624 0.07565084 0.5022081 0.7982386
## [62,] 0.220744872 0.6406170 0.07545048 0.5000634 0.7948269
## [63,] 0.224314087 0.6391512 0.07525041 0.4982353 0.7913255
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## [65,] 0.231452518 0.6361739 0.07486193 0.4965686 0.7852243
## [66,] 0.235021734 0.6346598 0.07466438 0.4941048 0.7828921
## [67,] 0.238590949 0.6331405 0.07448392 0.4929236 0.7813914
## [68,] 0.242160164 0.6316035 0.07429222 0.4913438 0.7801534
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## [77,] 0.274283103 0.6175427 0.07281321 0.4767033 0.7636374
## [78,] 0.277852318 0.6159751 0.07267166 0.4751962 0.7595845
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## [82,] 0.292129180 0.6097470 0.07214867 0.4696622 0.7536109
## [83,] 0.295698395 0.6082035 0.07203669 0.4674760 0.7508883
## [84,] 0.299267611 0.6066719 0.07191844 0.4653073 0.7492572
## [85,] 0.302836826 0.6051467 0.07181244 0.4647525 0.7477964
## [86,] 0.306406041 0.6036319 0.07170938 0.4642525 0.7452996
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## [88,] 0.313544472 0.6006331 0.07152164 0.4603861 0.7432154
## [89,] 0.317113688 0.5991554 0.07142778 0.4606095 0.7425751
## [90,] 0.320682903 0.5976827 0.07135225 0.4591504 0.7410366
## [91,] 0.324252118 0.5962315 0.07126749 0.4579524 0.7394556
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## [93,] 0.331390549 0.5933615 0.07112848 0.4565177 0.7391946
## [94,] 0.334959765 0.5919492 0.07106506 0.4562377 0.7378387
## [95,] 0.338528980 0.5905491 0.07101065 0.4556577 0.7378256
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## [98,] 0.349236626 0.5864531 0.07086206 0.4534355 0.7337171
## [99,] 0.352805842 0.5851155 0.07082847 0.4531023 0.7317166
## [100,] 0.356375057 0.5838003 0.07079148 0.4528963 0.7295160
## [101,] 0.359944272 0.5824989 0.07076342 0.4525287 0.7274789
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## [104,] 0.370651919 0.5786932 0.07071021 0.4477484 0.7215206
## [105,] 0.374221134 0.5774656 0.07069245 0.4463712 0.7194906
## [106,] 0.377790349 0.5762448 0.07069242 0.4446185 0.7182281
## [107,] 0.381359565 0.5750497 0.07068538 0.4434202 0.7154258
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## [109,] 0.388497996 0.5727008 0.07069636 0.4393649 0.7117748
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## [111,] 0.395636426 0.5704181 0.07072456 0.4383501 0.7098157
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## [114,] 0.406344073 0.5671251 0.07078434 0.4367128 0.7093510
## [115,] 0.409913288 0.5660559 0.07081649 0.4372968 0.7065600
## [116,] 0.413482503 0.5650061 0.07084661 0.4368176 0.7061738
## [117,] 0.417051719 0.5639710 0.07088097 0.4361328 0.7066015
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## [120,] 0.427759365 0.5609504 0.07101027 0.4309833 0.7045679
## [121,] 0.431328580 0.5599801 0.07104694 0.4284637 0.7038691
## [122,] 0.434897796 0.5590156 0.07109954 0.4257694 0.7031468
## [123,] 0.438467011 0.5580703 0.07114558 0.4232412 0.7003181
## [124,] 0.442036227 0.5571361 0.07119780 0.4208564 0.6973802
## [125,] 0.445605442 0.5562150 0.07125260 0.4184254 0.6944264
## [126,] 0.449174657 0.5553100 0.07130357 0.4160712 0.6919079
## [127,] 0.452743873 0.5544123 0.07136633 0.4154237 0.6912848
## [128,] 0.456313088 0.5535354 0.07141513 0.4153175 0.6905601
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## [130,] 0.463451519 0.5518106 0.07153071 0.4132129 0.6889656
## [131,] 0.467020734 0.5509657 0.07159074 0.4119102 0.6876522
## [132,] 0.470589950 0.5501340 0.07164850 0.4107265 0.6873044
## [133,] 0.474159165 0.5493151 0.07170399 0.4095727 0.6871275
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## [153,] 0.545543473 0.5353751 0.07244557 0.3950319 0.6747050
## [154,] 0.549112689 0.5348102 0.07244851 0.3955416 0.6740874
## [155,] 0.552681904 0.5342615 0.07244424 0.3968119 0.6742208
## [156,] 0.556251119 0.5337297 0.07243308 0.3972124 0.6746714
## [157,] 0.559820335 0.5332087 0.07242516 0.3966487 0.6743610
## [158,] 0.563389550 0.5327124 0.07239952 0.3957732 0.6729621
## [159,] 0.566958766 0.5322230 0.07238434 0.3949797 0.6722909
## [160,] 0.570527981 0.5317627 0.07234732 0.3954456 0.6724945
## [161,] 0.574097196 0.5313123 0.07231738 0.3950697 0.6724830
## [162,] 0.577666412 0.5308852 0.07227624 0.3935399 0.6723164
## [163,] 0.581235627 0.5304768 0.07223152 0.3938163 0.6732977
## [164,] 0.584804843 0.5300850 0.07218629 0.3934637 0.6745173
## [165,] 0.588374058 0.5297218 0.07212693 0.3925255 0.6755302
## [166,] 0.591943273 0.5293675 0.07207779 0.3916183 0.6762336
## [167,] 0.595512489 0.5290528 0.07200410 0.3914466 0.6768258
## [168,] 0.599081704 0.5287478 0.07194105 0.3900483 0.6769942
## [169,] 0.602650920 0.5284755 0.07186384 0.3891725 0.6765721
## [170,] 0.606220135 0.5282236 0.07178722 0.3903897 0.6764438
## [171,] 0.609789350 0.5279960 0.07170729 0.3922820 0.6767839
## [172,] 0.613358566 0.5278008 0.07161786 0.3905209 0.6774791
## [173,] 0.616927781 0.5276203 0.07153593 0.3905208 0.6781438
## [174,] 0.620496996 0.5274854 0.07143467 0.3920676 0.6767737
## [175,] 0.624066212 0.5273624 0.07134504 0.3931592 0.6778319
## [176,] 0.627635427 0.5272838 0.07123969 0.3934694 0.6773369
## [177,] 0.631204643 0.5272259 0.07113992 0.3951044 0.6784097
## [178,] 0.634773858 0.5272019 0.07103531 0.3948567 0.6787792
## [179,] 0.638343073 0.5272127 0.07092686 0.3943944 0.6786255
## [180,] 0.641912289 0.5272458 0.07082429 0.3949650 0.6784684
## [181,] 0.645481504 0.5273288 0.07070883 0.3959197 0.6783053
## [182,] 0.649050720 0.5274257 0.07060677 0.3952364 0.6786845
## [183,] 0.652619935 0.5275799 0.07048914 0.3969084 0.6811356
## [184,] 0.656189150 0.5277533 0.07038271 0.3975628 0.6823338
## [185,] 0.659758366 0.5279713 0.07027140 0.3982383 0.6824361
## [186,] 0.663327581 0.5282243 0.07016271 0.3972885 0.6824723
## [187,] 0.666896797 0.5285080 0.07005956 0.3984855 0.6824773
## [188,] 0.670466012 0.5288434 0.06995088 0.3971984 0.6823862
## [189,] 0.674035227 0.5291947 0.06985783 0.3983310 0.6822775
## [190,] 0.677604443 0.5296149 0.06975156 0.3982946 0.6813397
## [191,] 0.681173658 0.5300513 0.06966215 0.4002910 0.6809643
## [192,] 0.684742874 0.5305425 0.06956930 0.4026697 0.6797432
## [193,] 0.688312089 0.5310664 0.06948584 0.4031718 0.6799008
## [194,] 0.691881304 0.5316294 0.06940883 0.4039614 0.6802063
## [195,] 0.695450520 0.5322423 0.06933393 0.4042456 0.6804620
## [196,] 0.699019735 0.5328780 0.06927494 0.4049176 0.6788311
## [197,] 0.702588951 0.5335810 0.06921127 0.4056600 0.6779028
## [198,] 0.706158166 0.5343010 0.06916748 0.4068415 0.6761640
## [199,] 0.709727381 0.5350839 0.06912270 0.4091449 0.6753841
## [200,] 0.713296597 0.5358947 0.06909379 0.4105288 0.6752004
## [201,] 0.716865812 0.5367514 0.06907299 0.4107998 0.6750208
## [202,] 0.720435028 0.5376529 0.06906152 0.4111626 0.6752724
## [203,] 0.724004243 0.5385832 0.06906676 0.4128584 0.6763740
## [204,] 0.727573458 0.5395748 0.06907518 0.4134180 0.6772323
## [205,] 0.731142674 0.5405832 0.06910628 0.4140183 0.6794022
## [206,] 0.734711889 0.5416588 0.06913901 0.4156787 0.6808036
## [207,] 0.738281105 0.5427556 0.06919312 0.4172356 0.6806407
## [208,] 0.741850320 0.5439021 0.06925695 0.4163538 0.6815470
## [209,] 0.745419535 0.5450855 0.06933605 0.4170935 0.6840761
## [210,] 0.748988751 0.5463014 0.06943250 0.4180483 0.6865420
## [211,] 0.752557966 0.5475688 0.06953836 0.4188589 0.6874253
## [212,] 0.756127182 0.5488523 0.06966872 0.4188568 0.6891509
## [213,] 0.759696397 0.5502006 0.06980284 0.4199699 0.6910864
## [214,] 0.763265612 0.5515635 0.06996210 0.4209006 0.6899638
## [215,] 0.766834828 0.5529753 0.07013176 0.4217818 0.6909737
## [216,] 0.770404043 0.5544142 0.07032080 0.4230098 0.6926053
## [217,] 0.773973259 0.5558860 0.07052686 0.4239349 0.6940447
## [218,] 0.777542474 0.5573968 0.07074644 0.4235085 0.6956323
## [219,] 0.781111689 0.5589255 0.07098930 0.4233044 0.6972875
## [220,] 0.784680905 0.5605032 0.07123991 0.4228182 0.6989170
## [221,] 0.788250120 0.5620927 0.07151599 0.4235677 0.7014829
## [222,] 0.791819336 0.5637249 0.07180153 0.4232389 0.7031784
## [223,] 0.795388551 0.5653743 0.07210868 0.4226421 0.7043294
## [224,] 0.798957766 0.5670525 0.07243112 0.4230768 0.7080678
## [225,] 0.802526982 0.5687560 0.07276913 0.4237706 0.7100660
## [226,] 0.806096197 0.5704759 0.07312801 0.4245550 0.7120547
## [227,] 0.809665413 0.5722273 0.07349643 0.4254476 0.7139263
## [228,] 0.813234628 0.5739870 0.07388942 0.4263122 0.7166832
## [229,] 0.816803843 0.5757775 0.07428929 0.4279994 0.7187455
## [230,] 0.820373059 0.5775764 0.07471157 0.4311042 0.7212726
## [231,] 0.823942274 0.5793952 0.07514606 0.4331369 0.7233116
## [232,] 0.827511490 0.5812265 0.07559671 0.4352138 0.7250100
## [233,] 0.831080705 0.5830688 0.07606481 0.4354413 0.7271737
## [234,] 0.834649920 0.5849253 0.07654279 0.4370877 0.7294766
## [235,] 0.838219136 0.5867863 0.07704337 0.4368132 0.7316480
## [236,] 0.841788351 0.5886609 0.07754755 0.4377786 0.7337751
## [237,] 0.845357567 0.5905375 0.07807390 0.4391843 0.7358909
## [238,] 0.848926782 0.5924210 0.07860858 0.4386493 0.7379486
## [239,] 0.852495997 0.5943061 0.07915928 0.4388945 0.7406669
## [240,] 0.856065213 0.5961933 0.07972340 0.4401794 0.7424398
## [241,] 0.859634428 0.5980797 0.08029717 0.4415060 0.7463708
## [242,] 0.863203644 0.5999657 0.08088946 0.4428521 0.7506260
## [243,] 0.866772859 0.6018461 0.08148501 0.4442945 0.7525891
## [244,] 0.870342074 0.6037245 0.08210055 0.4457883 0.7551545
## [245,] 0.873911290 0.6055935 0.08272021 0.4473296 0.7571543
## [246,] 0.877480505 0.6074567 0.08335557 0.4487365 0.7596108
## [247,] 0.881049721 0.6093101 0.08400018 0.4479854 0.7636607
## [248,] 0.884618936 0.6111513 0.08465407 0.4472234 0.7666638
## [249,] 0.888188151 0.6129846 0.08532231 0.4464541 0.7697206
## [250,] 0.891757367 0.6147974 0.08599343 0.4461815 0.7720002
## [251,] 0.895326582 0.6166043 0.08668232 0.4476690 0.7743921
## [252,] 0.898895798 0.6183844 0.08737105 0.4492943 0.7783401
## [253,] 0.902465013 0.6201547 0.08807516 0.4508406 0.7816394
## [254,] 0.906034228 0.6219022 0.08878426 0.4524466 0.7841070
## [255,] 0.909603444 0.6236303 0.08950225 0.4540492 0.7890125
## [256,] 0.913172659 0.6253414 0.09023033 0.4548395 0.7934204
## [257,] 0.916741875 0.6270222 0.09096079 0.4540530 0.7977128
## [258,] 0.920311090 0.6286933 0.09170645 0.4529756 0.8011024
## [259,] 0.923880305 0.6303219 0.09244791 0.4534352 0.8036656
## [260,] 0.927449521 0.6319399 0.09320404 0.4550086 0.8078276
## [261,] 0.931018736 0.6335220 0.09396055 0.4546105 0.8120012
## [262,] 0.934587952 0.6350823 0.09472529 0.4535343 0.8160849
## [263,] 0.938157167 0.6366158 0.09549547 0.4524427 0.8199045
## [264,] 0.941726382 0.6381147 0.09626708 0.4514209 0.8241607
## [265,] 0.945295598 0.6395973 0.09704923 0.4510870 0.8280771
## [266,] 0.948864813 0.6410317 0.09782582 0.4494343 0.8317388
## [267,] 0.952434029 0.6424536 0.09861430 0.4502248 0.8355902
## [268,] 0.956003244 0.6438288 0.09939762 0.4511543 0.8360860
## [269,] 0.959572459 0.6451830 0.10018803 0.4502421 0.8392110
## [270,] 0.963141675 0.6465022 0.10097833 0.4502719 0.8423131
## [271,] 0.966710890 0.6477869 0.10176835 0.4495841 0.8453413
## [272,] 0.970280105 0.6490490 0.10256347 0.4488921 0.8486895
## [273,] 0.973849321 0.6502628 0.10335061 0.4478886 0.8519666
## [274,] 0.977418536 0.6514632 0.10414633 0.4469574 0.8552502
## [275,] 0.980987752 0.6526091 0.10492981 0.4469923 0.8585224
## [276,] 0.984556967 0.6537377 0.10571876 0.4463912 0.8617315
## [277,] 0.988126182 0.6548250 0.10650067 0.4459965 0.8647740
## [278,] 0.991695398 0.6558816 0.10727988 0.4450298 0.8678279
## [279,] 0.995264613 0.6569105 0.10805757 0.4443198 0.8707721
## [280,] 0.998833829 0.6578952 0.10882393 0.4428650 0.8727700
## [281,] 1.002403044 0.6588659 0.10959465 0.4418269 0.8761603
## [282,] 1.005972259 0.6597796 0.11034488 0.4408834 0.8791461
## [283,] 1.009541475 0.6606801 0.11109844 0.4405607 0.8818101
## [284,] 1.013110690 0.6615362 0.11183645 0.4401989 0.8841135
## [285,] 1.016679906 0.6623670 0.11256904 0.4396630 0.8862357
## [286,] 1.020249121 0.6631671 0.11329222 0.4393933 0.8893364
## [287,] 1.023818336 0.6639298 0.11400028 0.4387464 0.8917783
## [288,] 1.027387552 0.6646749 0.11470559 0.4381134 0.8940692
## [289,] 1.030956767 0.6653711 0.11538551 0.4377585 0.8962374
## [290,] 1.034525983 0.6660551 0.11606450 0.4378189 0.8983744
## [291,] 1.038095198 0.6666941 0.11671807 0.4378562 0.9003960
## [292,] 1.041664413 0.6673142 0.11736384 0.4378848 0.9025307
## [293,] 1.045233629 0.6679022 0.11799129 0.4370354 0.9043762
## [294,] 1.048802844 0.6684605 0.11860025 0.4344456 0.9060596
## [295,] 1.052372060 0.6689991 0.11919861 0.4336466 0.9078133
## [296,] 1.055941275 0.6694977 0.11976721 0.4329829 0.9094543
## [297,] 1.059510490 0.6699853 0.12033081 0.4323489 0.9110645
## [298,] 1.063079706 0.6704295 0.12085844 0.4318096 0.9125499
## [299,] 1.066648921 0.6708604 0.12137698 0.4312810 0.9139960
## [300,] 1.070218137 0.6712596 0.12186789 0.4307780 0.9153674
## [301,] 1.073787352 0.6716360 0.12233819 0.4302956 0.9166873
## [302,] 1.077356567 0.6719918 0.12278985 0.4298317 0.9175029
## [303,] 1.080925783 0.6723156 0.12320893 0.4294160 0.9184854
## [304,] 1.084494998 0.6726293 0.12361900 0.4290309 0.9194268
## [305,] 1.088064214 0.6729027 0.12398413 0.4286854 0.9202410
## [306,] 1.091633429 0.6731669 0.12433987 0.4283497 0.9209075
## [307,] 1.095202644 0.6734002 0.12465921 0.4280470 0.9217588
## [308,] 1.098771860 0.6736162 0.12495773 0.4277640 0.9224401
## [309,] 1.102341075 0.6738110 0.12523012 0.4275053 0.9230567
## [310,] 1.105910291 0.6739802 0.12546943 0.4272775 0.9235945
## [311,] 1.109479506 0.6741374 0.12569339 0.4270643 0.9242571
## [312,] 1.113048721 0.6742611 0.12587185 0.4268936 0.9248146
## [313,] 1.116617937 0.6743764 0.12603897 0.4267338 0.9253355
## [314,] 1.120187152 0.6744606 0.12616253 0.4266150 0.9257195
## [315,] 1.123756368 0.6745314 0.12626718 0.4265141 0.9260441
## [316,] 1.127325583 0.6745798 0.12633967 0.4264436 0.9262683
## [317,] 1.130894798 0.6746068 0.12638116 0.4264025 0.9263960
## [318,] 1.134464014 0.6746196 0.12640218 0.4263807 0.9264600
## [319,] 5.593780253 0.2994982 0.08427421 0.1448719 0.4798735
## [320,] 5.597349468 0.2995356 0.08426013 0.1449450 0.4798824
## [321,] 5.600918683 0.2996071 0.08423233 0.1450874 0.4798980
## [322,] 5.604487899 0.2997303 0.08418378 0.1453348 0.4799237
## [323,] 5.608057114 0.2999075 0.08411377 0.1456914 0.4799601
## [324,] 5.611626330 0.3001166 0.08403121 0.1461127 0.4800029
## [325,] 5.615195545 0.3003992 0.08391977 0.1466826 0.4800608
## [326,] 5.618764760 0.3007015 0.08380099 0.1472922 0.4801226
## [327,] 5.622333976 0.3010816 0.08365232 0.1480584 0.4802009
## [328,] 5.625903191 0.3014888 0.08349390 0.1488790 0.4802852
## [329,] 5.629472407 0.3019538 0.08331416 0.1498155 0.4803821
## [330,] 5.633041622 0.3024655 0.08311793 0.1508591 0.4804898
## [331,] 5.636610837 0.3030150 0.08290881 0.1519805 0.4806077
## [332,] 5.640180053 0.3036302 0.08267697 0.1532350 0.4808936
## [333,] 5.643749268 0.3042648 0.08244007 0.1548338 0.4811737
## [334,] 5.647318484 0.3049816 0.08217560 0.1566383 0.4810060
## [335,] 5.650887699 0.3057185 0.08190680 0.1582917 0.4811756
## [336,] 5.654456914 0.3065179 0.08161901 0.1593498 0.4813628
## [337,] 5.658026130 0.3073560 0.08132140 0.1605860 0.4815615
## [338,] 5.661595345 0.3082370 0.08101302 0.1624047 0.4824620
## [339,] 5.665164561 0.3091749 0.08069000 0.1642455 0.4833497
## [340,] 5.668733776 0.3101366 0.08036396 0.1661525 0.4833095
## [341,] 5.672302991 0.3111727 0.08001916 0.1682000 0.4824798
## [342,] 5.675872207 0.3122269 0.07967455 0.1702815 0.4828690
## [343,] 5.679441422 0.3133465 0.07931591 0.1724850 0.4841715
## [344,] 5.683010638 0.3144966 0.07895499 0.1743760 0.4850101
## [345,] 5.686579853 0.3156932 0.07858762 0.1762772 0.4850730
## [346,] 5.690149068 0.3169371 0.07821448 0.1782535 0.4847460
## [347,] 5.693718284 0.3182091 0.07784191 0.1802746 0.4850209
## [348,] 5.697287499 0.3195445 0.07746075 0.1821291 0.4865513
## [349,] 5.700856715 0.3208969 0.07708485 0.1838001 0.4874552
## [350,] 5.704425930 0.3223149 0.07670162 0.1856146 0.4890022
## [351,] 5.707995145 0.3237554 0.07632364 0.1877419 0.4901935
## [352,] 5.711564361 0.3252438 0.07594495 0.1901950 0.4920815
## [353,] 5.715133576 0.3267696 0.07556906 0.1922090 0.4937419
## [354,] 5.718702792 0.3283262 0.07519848 0.1955090 0.4932308
## [355,] 5.722272007 0.3299344 0.07482873 0.1976098 0.4930005
## [356,] 5.725841222 0.3315578 0.07446959 0.1998921 0.4932442
## [357,] 5.729410438 0.3332444 0.07411001 0.2017380 0.4918004
## [358,] 5.732979653 0.3349458 0.07376245 0.2048637 0.4914130
## [359,] 5.736548869 0.3366937 0.07341989 0.2082297 0.4918989
## [360,] 5.740118084 0.3384695 0.07308739 0.2093231 0.4924428
## [361,] 5.743687299 0.3402763 0.07276485 0.2104397 0.4934431
## [362,] 5.747256515 0.3421227 0.07245057 0.2120347 0.4951430
## [363,] 5.750825730 0.3439857 0.07215078 0.2152558 0.4956963
## [364,] 5.754394946 0.3458987 0.07185749 0.2175561 0.4963366
## [365,] 5.757964161 0.3478235 0.07158069 0.2191176 0.4985754
## [366,] 5.761533376 0.3497905 0.07131288 0.2210950 0.4995841
## [367,] 5.765102592 0.3517764 0.07106031 0.2235240 0.5021261
## [368,] 5.768671807 0.3537910 0.07082069 0.2260230 0.5035413
## [369,] 5.772241023 0.3558334 0.07059398 0.2283017 0.5045609
## [370,] 5.775810238 0.3578925 0.07038396 0.2307519 0.5064568
## [371,] 5.779379453 0.3599869 0.07018422 0.2323576 0.5079625
## [372,] 5.782948669 0.3620905 0.07000358 0.2350053 0.5093358
## [373,] 5.786517884 0.3642289 0.06983262 0.2368810 0.5107972
## [374,] 5.790087100 0.3663783 0.06967977 0.2384131 0.5122425
## [375,] 5.793656315 0.3685514 0.06953986 0.2400461 0.5140754
## [376,] 5.797225530 0.3707417 0.06941461 0.2423239 0.5161437
## [377,] 5.800794746 0.3729462 0.06930566 0.2446795 0.5182519
## [378,] 5.804363961 0.3751724 0.06920735 0.2476193 0.5213699
## [379,] 5.807933177 0.3774051 0.06912870 0.2501448 0.5241805
## [380,] 5.811502392 0.3796621 0.06905637 0.2517665 0.5269339
## [381,] 5.815071607 0.3819242 0.06900308 0.2550358 0.5289857
## [382,] 5.818640823 0.3842024 0.06895926 0.2581135 0.5307647
## [383,] 5.822210038 0.3864889 0.06892962 0.2609249 0.5326251
## [384,] 5.825779254 0.3887848 0.06891293 0.2626809 0.5342879
## [385,] 5.829348469 0.3910909 0.06890485 0.2651851 0.5368220
## [386,] 5.832917684 0.3934012 0.06891366 0.2676351 0.5378937
## [387,] 5.836486900 0.3957218 0.06892480 0.2705447 0.5397049
## [388,] 5.840056115 0.3980445 0.06895342 0.2712767 0.5415060
## [389,] 5.843625330 0.4003737 0.06898503 0.2731271 0.5451109
## [390,] 5.847194546 0.4027048 0.06902932 0.2754730 0.5499878
## [391,] 5.850763761 0.4050387 0.06908079 0.2767465 0.5545608
## [392,] 5.854332977 0.4073737 0.06913796 0.2784401 0.5564242
## [393,] 5.857902192 0.4097092 0.06920712 0.2803305 0.5589121
## [394,] 5.861471407 0.4120436 0.06927432 0.2822817 0.5609682
## [395,] 5.865040623 0.4143775 0.06935646 0.2858901 0.5629977
## [396,] 5.868609838 0.4167076 0.06943332 0.2889355 0.5649186
## [397,] 5.872179054 0.4190356 0.06952160 0.2905372 0.5675606
## [398,] 5.875748269 0.4213590 0.06960992 0.2924391 0.5701051
## [399,] 5.879317484 0.4236773 0.06970154 0.2943536 0.5721820
## [400,] 5.882886700 0.4259914 0.06979921 0.2968502 0.5738702
## [401,] 5.886455915 0.4282966 0.06989151 0.2998590 0.5761043
## [402,] 5.890025131 0.4305991 0.06999618 0.3017296 0.5779652
## [403,] 5.893594346 0.4328881 0.07008692 0.3041095 0.5804165
## [404,] 5.897163561 0.4351733 0.07018887 0.3059858 0.5846653
## [405,] 5.900732777 0.4374468 0.07028354 0.3063081 0.5886443
## [406,] 5.904301992 0.4397123 0.07038050 0.3098816 0.5898715
## [407,] 5.907871208 0.4419686 0.07047744 0.3108815 0.5903828
## [408,] 5.911440423 0.4442119 0.07056737 0.3128066 0.5913579
## [409,] 5.915009638 0.4464496 0.07066508 0.3151849 0.5941484
## [410,] 5.918578854 0.4486689 0.07074619 0.3162806 0.5952986
## [411,] 5.922148069 0.4508834 0.07083708 0.3185178 0.5983296
## [412,] 5.925717285 0.4530806 0.07091408 0.3215969 0.5999629
## [413,] 5.929286500 0.4552693 0.07099410 0.3228282 0.6026544
## [414,] 5.932855715 0.4574449 0.07106862 0.3248250 0.6052248
## [415,] 5.936424931 0.4596069 0.07113658 0.3285255 0.6076245
## [416,] 5.939994146 0.4617606 0.07120783 0.3323846 0.6099263
## [417,] 5.943563362 0.4638953 0.07126279 0.3352555 0.6111959
## [418,] 5.947132577 0.4660249 0.07132671 0.3367062 0.6125064
## [419,] 5.950701792 0.4681343 0.07137147 0.3382011 0.6140533
## [420,] 5.954271008 0.4702367 0.07142157 0.3397114 0.6143378
## [421,] 5.957840223 0.4723241 0.07146180 0.3418219 0.6156049
## [422,] 5.961409439 0.4743998 0.07149777 0.3437360 0.6187278
## [423,] 5.964978654 0.4764658 0.07153341 0.3455183 0.6201733
## [424,] 5.968547869 0.4785157 0.07155519 0.3473376 0.6226306
## [425,] 5.972117085 0.4805608 0.07158601 0.3492100 0.6242913
## [426,] 5.975686300 0.4825862 0.07159408 0.3514973 0.6243675
## [427,] 5.979255516 0.4846072 0.07161105 0.3535179 0.6269293
## [428,] 5.982824731 0.4866139 0.07161514 0.3556939 0.6300127
## [429,] 5.986393946 0.4886125 0.07161874 0.3579952 0.6307642
## [430,] 5.989963162 0.4906018 0.07161941 0.3601438 0.6311504
## [431,] 5.993532377 0.4925800 0.07161033 0.3624481 0.6328086
## [432,] 5.997101593 0.4945534 0.07160831 0.3648447 0.6344264
## [433,] 6.000670808 0.4965134 0.07158743 0.3672993 0.6362100
## [434,] 6.004240023 0.4984704 0.07157693 0.3704771 0.6380685
## [435,] 6.007809239 0.5004169 0.07155195 0.3726290 0.6397172
## [436,] 6.011378454 0.5023591 0.07153120 0.3746981 0.6412971
## [437,] 6.014947670 0.5042948 0.07150607 0.3760463 0.6436268
## [438,] 6.018516885 0.5062250 0.07147636 0.3767426 0.6456354
## [439,] 6.022086100 0.5081518 0.07145225 0.3773993 0.6491399
## [440,] 6.025655316 0.5100728 0.07141498 0.3781090 0.6521951
## [441,] 6.029224531 0.5119924 0.07138983 0.3788801 0.6554536
## [442,] 6.032793747 0.5139076 0.07134984 0.3798839 0.6584036
## [443,] 6.036362962 0.5158218 0.07131929 0.3827730 0.6604251
## [444,] 6.039932177 0.5177341 0.07128389 0.3844180 0.6612265
## [445,] 6.043501393 0.5196460 0.07124958 0.3866783 0.6619709
## [446,] 6.047070608 0.5215575 0.07122018 0.3889807 0.6644938
## [447,] 6.050639824 0.5234699 0.07118381 0.3914104 0.6671464
## [448,] 6.054209039 0.5253825 0.07116165 0.3938651 0.6697595
## [449,] 6.057778254 0.5272982 0.07112518 0.3962650 0.6722403
## [450,] 6.061347470 0.5292150 0.07110337 0.3974884 0.6734934
## [451,] 6.064916685 0.5311355 0.07107689 0.4004550 0.6735948
## [452,] 6.068485901 0.5330591 0.07105716 0.4038837 0.6737302
## [453,] 6.072055116 0.5349860 0.07104213 0.4043509 0.6738636
## [454,] 6.075624331 0.5369186 0.07102617 0.4046918 0.6767149
## [455,] 6.079193547 0.5388536 0.07102403 0.4060787 0.6799072
## [456,] 6.082762762 0.5407973 0.07101347 0.4060041 0.6815729
## [457,] 6.086331978 0.5427434 0.07101990 0.4073450 0.6821594
## [458,] 6.089901193 0.5446983 0.07102196 0.4088703 0.6837568
## [459,] 6.093470408 0.5466577 0.07103592 0.4104905 0.6857450
## [460,] 6.097039624 0.5486241 0.07105437 0.4121821 0.6865852
## [461,] 6.100608839 0.5505981 0.07107724 0.4138644 0.6879539
## [462,] 6.104178055 0.5525766 0.07111321 0.4163631 0.6894165
## [463,] 6.107747270 0.5545660 0.07114620 0.4188905 0.6928977
## [464,] 6.111316485 0.5565583 0.07119784 0.4214344 0.6955396
## [465,] 6.114885701 0.5585624 0.07124483 0.4230067 0.6958511
## [466,] 6.118454916 0.5605705 0.07130800 0.4237319 0.6987359
## [467,] 6.122024132 0.5625873 0.07137481 0.4253379 0.7027741
## [468,] 6.125593347 0.5646109 0.07145026 0.4277421 0.7049498
## [469,] 6.129162562 0.5666402 0.07153747 0.4305069 0.7078303
## [470,] 6.132731778 0.5686785 0.07162572 0.4322559 0.7120254
## [471,] 6.136300993 0.5707195 0.07173350 0.4336261 0.7133437
## [472,] 6.139870209 0.5727711 0.07183502 0.4335112 0.7166732
## [473,] 6.143439424 0.5748250 0.07195593 0.4364795 0.7211239
## [474,] 6.147008639 0.5768860 0.07207837 0.4374260 0.7235742
## [475,] 6.150577855 0.5789507 0.07221231 0.4379119 0.7266440
## [476,] 6.154147070 0.5810196 0.07235551 0.4386083 0.7302488
## [477,] 6.157716286 0.5830926 0.07250214 0.4399958 0.7326245
## [478,] 6.161285501 0.5851673 0.07266571 0.4406973 0.7346228
## [479,] 6.164854716 0.5872454 0.07282442 0.4420911 0.7368541
## [480,] 6.168423932 0.5893240 0.07300224 0.4437163 0.7418041
## [481,] 6.171993147 0.5914034 0.07317770 0.4449972 0.7442519
## [482,] 6.175562363 0.5934823 0.07336630 0.4462270 0.7461866
## [483,] 6.179131578 0.5955600 0.07356009 0.4486665 0.7480432
## [484,] 6.182700793 0.5976348 0.07375825 0.4501131 0.7490273
## [485,] 6.186270009 0.5997078 0.07396927 0.4524286 0.7496818
## [486,] 6.189839224 0.6017738 0.07417553 0.4543627 0.7501986
## [487,] 6.193408439 0.6038377 0.07439948 0.4562233 0.7518192
## [488,] 6.196977655 0.6058907 0.07461522 0.4581976 0.7532872
## [489,] 6.200546870 0.6079389 0.07484490 0.4601842 0.7570106
## [490,] 6.204116086 0.6099763 0.07507405 0.4622136 0.7601731
## [491,] 6.207685301 0.6120030 0.07530755 0.4641501 0.7633260
## [492,] 6.211254516 0.6140208 0.07554849 0.4663650 0.7662776
## [493,] 6.214823732 0.6160202 0.07578375 0.4684987 0.7677479
## [494,] 6.218392947 0.6180140 0.07603458 0.4706455 0.7690895
## [495,] 6.221962163 0.6199797 0.07626958 0.4724335 0.7703932
## [496,] 6.225531378 0.6219378 0.07651911 0.4736170 0.7747418
## [497,] 6.229100593 0.6238708 0.07676098 0.4748504 0.7773974
## [498,] 6.232669809 0.6257865 0.07700692 0.4764407 0.7784422
## [499,] 6.236239024 0.6276823 0.07725378 0.4770812 0.7795292
## [500,] 6.239808240 0.6295488 0.07749381 0.4779940 0.7804167
## [501,] 6.243377455 0.6314026 0.07774377 0.4805610 0.7835178
## [502,] 6.246946670 0.6332132 0.07797555 0.4816603 0.7869284
## [503,] 6.250515886 0.6350123 0.07821961 0.4838922 0.7917633
## [504,] 6.254085101 0.6367682 0.07844796 0.4861890 0.7942519
## [505,] 6.257654317 0.6385023 0.07868059 0.4885009 0.7973126
## [506,] 6.261223532 0.6402022 0.07890694 0.4903298 0.7986310
## [507,] 6.264792747 0.6418646 0.07912592 0.4922581 0.7989712
## [508,] 6.268361963 0.6435039 0.07934852 0.4935352 0.8014011
## [509,] 6.271931178 0.6450879 0.07955174 0.4937882 0.8042073
## [510,] 6.275500394 0.6466565 0.07976500 0.4957013 0.8057489
## [511,] 6.279069609 0.6481612 0.07995438 0.4975592 0.8070865
## [512,] 6.282638824 0.6496430 0.08014917 0.4994802 0.8083562
##
## Slot "act":
## act se lcl.2.5% ucl.97.5%
## 0.81273204 0.06863662 0.59057257 0.86182433Results of the model:
act=0.81273204
se= 0.06794684
#how to interpret this result?
##remember to add analysis for Brack!
We then can plot it:
plot(activity,centre="night")
Now we finally can calculate the day range. To do this we multiply average speed by activity level:
#check day_range function