Vieja in Nativida
This is a document that describes the step by step set of analysis I used to explore the fish data from Baja Californa´s Cobi/reef check
Load data
First, this is how you load the data into R
Secondly, we check the dimensions of the dataframe. This is a quick way to check if this is the data that we want to analyze.
## [1] 51902 22Then, if you want to see how the table looks like, the following code shows you the first 10 rows and the selected columns
## [1] "Observer" "Date" "Year"
## [4] "TimeInitial" "TimeFinal" "TransectNumber"
## [7] "Location" "Site" "Zone"
## [10] "Country" "DepthInitial_m" "DepthFinal_m"
## [13] "DepthMax_m" "MidTransDepth_m" "Latitude"
## [16] "Longitude" "Temperature_C" "Visibility_m"
## [19] "Genusspecies" "SizeClass" "SexClass"
## [22] "SpeciesPresOutTrans"## Year Location Site Zone Genusspecies SizeClass
## 1 2013 PuntaPrieta IslaNatividad Reserve Anisotremusdavidsoni NA
## 2 2013 PuntaPrieta IslaNatividad Reserve Caulolatilusprinceps NA
## 3 2013 PuntaPrieta IslaNatividad Reserve Chromispunctipinnis NA
## 4 2013 PuntaPrieta IslaNatividad Reserve Embioticajacksoni NA
## 5 2013 PuntaPrieta IslaNatividad Reserve Girellanigricans NA
## 6 2013 PuntaPrieta IslaNatividad Reserve Halichoeressemicintus 18
## 7 2013 PuntaPrieta IslaNatividad Reserve Halichoeressemicintus 18Take a look at the data
Lets look at how many fish the dataset has for each year at each site
##
## IslaMagdalena IslaNatividad
## 2006 0 2862
## 2007 0 5269
## 2008 0 5559
## 2009 0 8680
## 2010 0 7075
## 2011 0 5915
## 2012 2714 7484
## 2013 0 6344Now lets take a look at the ocurrence of each species of fish present in the dataset per year for the two different sites. This allows you to see which species are present at which years.
## , , .3 = IslaMagdalena
##
## .2
## .1 2006 2007 2008 2009 2010 2011 2012 2013
## Anisotremusdavidsoni 0 0 0 0 0 0 2 0
## Anisotremusdavidsonii 0 0 0 0 0 0 86 0
## Calamusbrachysomus 0 0 0 0 0 0 456 0
## Caulolatilusprinceps 0 0 0 0 0 0 0 0
## Chaetodonhumeralis 0 0 0 0 0 0 113 0
## Chromisatrilobata 0 0 0 0 0 0 151 0
## Chromispunctipinnis 0 0 0 0 0 0 0 0
## Embioticajacksoni 0 0 0 0 0 0 0 0
## Epinephelusanalogus 0 0 0 0 0 0 86 0
## Epinephelusitajara 0 0 0 0 0 0 86 0
## Girellanigricans 0 0 0 0 0 0 0 0
## Halichoeressemicintus 0 0 0 0 0 0 0 0
## Heterodontusfrancisci 0 0 0 0 0 0 0 0
## Holacanthuspasser 0 0 0 0 0 0 35 0
## Holocanthuspasser 0 0 0 0 0 0 86 0
## Hypsypopsrubicundus 0 0 0 0 0 0 274 0
## Johnrandallianigrirostris 0 0 0 0 0 0 100 0
## Mulloidichthysdentatus 0 0 0 0 0 0 95 0
## Mycteropercajordani 0 0 0 0 0 0 86 0
## Mycteropercaprionura 0 0 0 0 0 0 87 0
## Mycteropercarosacea 0 0 0 0 0 0 97 0
## Mycteropercaspp 0 0 0 0 0 0 0 0
## Mycteropercaxenarcha 0 0 0 0 0 0 86 0
## Nicholsinadenticulata 0 0 0 0 0 0 94 0
## Ophiodonelongatus 0 0 0 0 0 0 0 0
## Oxyjuliscalifornica 0 0 0 0 0 0 0 0
## Paralabraxclathratus 0 0 0 0 0 0 87 0
## Paralabraxmaculatofasciatus 0 0 0 0 0 0 98 0
## Paralabraxnebulifer 0 0 0 0 0 0 86 0
## Pomacanthuszonipectus 0 0 0 0 0 0 108 0
## Rhacochilusvacca 0 0 0 0 0 0 0 0
## Rhinobatosproductus 0 0 0 0 0 0 0 0
## Scorpaenichthysmarmoratus 0 0 0 0 0 0 0 0
## Sebastesauriculatus 0 0 0 0 0 0 0 0
## Sebastescarnatus 0 0 0 0 0 0 0 0
## Sebasteschrysomelas 0 0 0 0 0 0 0 0
## Sebastesflavidus 0 0 0 0 0 0 0 0
## Sebastesrastrelliger 0 0 0 0 0 0 0 0
## Sebastessp 0 0 0 0 0 0 0 0
## Sebastessrranoides 0 0 0 0 0 0 0 0
## Semicossyphuspulcher 0 0 0 0 0 0 143 0
## Squatinacalifornica 0 0 0 0 0 0 0 0
## Stereolepisgigas 0 0 0 0 0 0 86 0
## Zancluscornutus 0 0 0 0 0 0 86 0
##
## , , .3 = IslaNatividad
##
## .2
## .1 2006 2007 2008 2009 2010 2011 2012 2013
## Anisotremusdavidsoni 103 141 250 162 260 125 278 279
## Anisotremusdavidsonii 0 0 0 0 0 0 0 0
## Calamusbrachysomus 0 0 0 0 0 0 0 0
## Caulolatilusprinceps 73 102 116 197 144 152 145 103
## Chaetodonhumeralis 0 0 0 0 0 0 0 0
## Chromisatrilobata 0 0 0 0 0 0 0 0
## Chromispunctipinnis 406 1073 1007 2311 1164 952 1562 748
## Embioticajacksoni 66 104 209 190 160 162 151 119
## Epinephelusanalogus 0 0 0 0 0 0 0 0
## Epinephelusitajara 0 0 0 0 0 0 0 0
## Girellanigricans 244 230 187 333 175 199 141 193
## Halichoeressemicintus 493 1034 611 1539 1377 517 829 1031
## Heterodontusfrancisci 67 102 116 140 125 134 125 110
## Holacanthuspasser 0 0 0 0 0 0 0 0
## Holocanthuspasser 0 0 0 0 0 0 0 0
## Hypsypopsrubicundus 185 202 320 404 335 300 305 231
## Johnrandallianigrirostris 0 0 0 0 0 0 0 0
## Mulloidichthysdentatus 0 0 0 0 0 0 0 0
## Mycteropercajordani 66 101 110 137 117 123 116 0
## Mycteropercaprionura 0 0 0 0 0 0 0 0
## Mycteropercarosacea 0 0 0 0 0 0 0 0
## Mycteropercaspp 0 0 0 0 0 0 0 100
## Mycteropercaxenarcha 66 101 110 137 117 123 116 0
## Nicholsinadenticulata 0 0 0 0 0 0 0 0
## Ophiodonelongatus 66 101 110 137 117 123 116 100
## Oxyjuliscalifornica 213 152 318 286 362 537 350 386
## Paralabraxclathratus 163 701 793 997 1105 1001 1381 1028
## Paralabraxmaculatofasciatus 0 0 0 0 0 0 0 0
## Paralabraxnebulifer 66 101 110 158 122 124 116 113
## Pomacanthuszonipectus 0 0 0 0 0 0 0 0
## Rhacochilusvacca 66 101 110 137 117 123 116 112
## Rhinobatosproductus 0 0 0 0 0 7 5 0
## Scorpaenichthysmarmoratus 66 101 112 139 117 123 116 100
## Sebastesauriculatus 0 0 0 0 0 0 0 100
## Sebastescarnatus 0 0 0 0 0 0 0 100
## Sebasteschrysomelas 0 0 0 0 0 0 0 100
## Sebastesflavidus 0 0 0 0 0 0 0 100
## Sebastesrastrelliger 0 0 0 0 0 0 0 100
## Sebastessp 66 101 112 137 117 123 116 0
## Sebastessrranoides 0 0 0 0 0 0 0 100
## Semicossyphuspulcher 255 515 638 865 810 721 1117 786
## Squatinacalifornica 66 101 110 137 117 123 116 100
## Stereolepisgigas 66 105 110 137 117 123 167 105
## Zancluscornutus 0 0 0 0 0 0 0 0Split inside and outside MPAs
Now lets divide the Viejas inside and outside reserves for both Islands
Note: There is no Vieja in Isla Magdalena. Thus we are only going to look at the size frequency for Viejas in Isla Natividad. To do that, we need to compute the following: Rodariog es loco!
## null device
## 1Size diferences
Now lets look if the sizes of these fish are different inside the reserves 
Los datos tienes puras NAs para las viejas en Magdalena
## Year Zone avgSize
## 1 2006 Fished 18.40580
## 2 2007 Fished 20.80071
## 3 2008 Fished 20.23810
## 4 2009 Fished 23.83858
## 5 2010 Fished 21.54229
## 6 2011 Fished 24.06398
## 7 2012 Fished 23.90750
## 8 2013 Fished 29.90172
## 9 2006 Reserve 16.89349
## 10 2007 Reserve 22.96875
## 11 2008 Reserve 20.04785
## 12 2009 Reserve 24.57020
## 13 2010 Reserve 23.75000
## 14 2011 Reserve 22.86713
## 15 2012 Reserve 24.85597
## 16 2013 Reserve 30.05490Plot time series
