QUICK START QUICK START TRAINING Updated – September 15, 2011.
Quick Start... · ModestR Software Quick start tutorial 2 Contents 1 Introduction
Transcript of Quick Start... · ModestR Software Quick start tutorial 2 Contents 1 Introduction
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ModestR Software Quick start tutorial
2
Contents
1 Introduction .......................................................................................................................... 5
2 First steps with MapMaker ................................................................................................... 5
2.1 Opening MapMaker ...................................................................................................... 6
2.2 Moving across the world map ....................................................................................... 6
2.3 Making a range distribution map in MapMaker ........................................................... 7
2.4 Making a samples distribution map in MapMaker ....................................................... 9
2.5 Modifying samples in a map ....................................................................................... 12
2.6 Importing data to a MapMaker map ........................................................................... 13
2.7 Data cleaning using validation rules ............................................................................ 13
2.8 Using convex hull tool ................................................................................................. 16
2.8.1 Using convex hull with samples .......................................................................... 16
2.8.2 Using convex hull with areas ............................................................................... 19
2.9 Saving a MapMaker map ............................................................................................. 20
2.10 Retrieving a map ......................................................................................................... 21
2.11 Setting the default ModestR database and other preferences in MapMaker ............ 22
2.12 Other useful features .................................................................................................. 22
2.12.1 Querying a point in OpenstreetMaps or GoogleMaps ........................................ 22
2.12.2 Encircling presence areas .................................................................................... 23
2.12.3 Showing environmental data at mouse cursor ................................................... 23
2.12.4 Adding visual templates ...................................................................................... 24
3 First steps in DataManager ................................................................................................. 27
3.1 DataManager user interface ....................................................................................... 27
3.2 Default settings in DataManager ................................................................................ 27
3.3 Creating a new database ............................................................................................. 28
3.4 Adding and managing maps to a database ................................................................. 29
3.5 Opening a map from DataManager ............................................................................ 30
3.6 Processing maps .......................................................................................................... 30
3.7 Exporting data ............................................................................................................. 33
ModestR Software Quick start tutorial
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3.8 Applying convex hull transformation .......................................................................... 34
3.9 Searching maps with no data ...................................................................................... 37
3.10 Forcing maps updating to current map version .......................................................... 37
4 First steps in MRFinder ........................................................................................................ 39
4.1 Default settings in MRFinder ....................................................................................... 39
4.2 Moving across the world map ..................................................................................... 40
4.3 Searching for species in one or more areas ................................................................ 40
4.4 Importing selections .................................................................................................... 40
4.5 Using predefined selections ........................................................................................ 41
4.6 Search options ............................................................................................................. 43
4.7 Filtering species to be processed ................................................................................ 45
4.8 Generating and exporting data ................................................................................... 48
4.9 Managing predefined selections ................................................................................. 49
4.10 Other tools .................................................................................................................. 53
4.10.1 Simplifying/inflating selections ........................................................................... 54
4.10.2 Merging selections .............................................................................................. 54
5 DataManager import/export files format ........................................................................... 55
5.1 Importing taxonomy from a CSV file ........................................................................... 55
5.2 Importing taxonomy from another ModestR database .............................................. 55
5.3 Importing taxonomy from phyloXML files .................................................................. 55
5.4 Importing Map Files from Mapmaker map files ......................................................... 56
5.5 Importing Map Files from another ModestR database............................................... 56
5.6 Importing samples from GBIF online database ........................................................... 57
5.7 Importing samples from CSV files ............................................................................... 58
5.8 Importing samples from Darwin Core Archives .......................................................... 60
5.9 Importing data from distribution models ................................................................... 61
5.10 Exporting taxonomy to a CSV file ................................................................................ 62
5.11 Exporting maps to map independent files .................................................................. 63
5.12 Exporting presence data to CSV data files .................................................................. 63
5.13 Exporting samples to Darwin Core Archive style ........................................................ 66
5.14 Exporting metrics and environmental variables data ................................................. 66
5.15 Exporting latitudinal gradients .................................................................................... 70
5.16 Managing environmental variables ............................................................................. 73
5.17 Exporting summary data ............................................................................................. 75
ModestR Software Quick start tutorial
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5.18 Exporting JPEG images ................................................................................................ 76
6 MapMaker import/export files format ............................................................................... 77
6.1 Import sample data from a CSV file ............................................................................ 77
6.2 Importing samples from GBIF online database ........................................................... 77
6.3 Importing areas from ESRI ASCII probability distribution models .............................. 78
6.4 Importing from ShapeFile files .................................................................................... 79
6.5 Importing from KML files ............................................................................................ 80
6.6 Export map view to an image file ................................................................................ 81
6.7 Export user‐selected zones and samples .................................................................... 81
6.8 Export exact zones and samples ................................................................................. 82
6.9 Export only samples to CSV ......................................................................................... 83
7 MRFinder import/export files format ................................................................................. 84
7.1 Exporting metrics data ................................................................................................ 84
7.2 Exporting latitudinal gradients .................................................................................... 85
7.3 Exporting taxonomy to a CSV file or to clipboard ....................................................... 85
7.4 Exporting maps ............................................................................................................ 85
7.5 Exporting statistical data ............................................................................................. 85
7.6 Exporting region coordinates ...................................................................................... 87
8 Checking for updates ........................................................................................................... 87
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ModestR Software Quick start tutorial
13
to show it). You will find options to validate/unvalidate all selected samples, or only
those that are valid/invalid. To validate/unvalidate all samples of the map, use the
options in the Samples menu of the main menu. Remember that if you manually
validate or invalidate samples, this has two side effects: (a) samples become not
habitat auto‐checked. So they will not be checked anymore, but keep the valid/invalid
status you manually set. And (b) manually validated samples will be took into account
when calculating data (presence or richness for example), while invalidated one will be
stored with the map, but not took into account for any calculation.
Set samples as habitat auto‐checked: if you added or modified samples setting them as
manually validated/unvalidated, you may want to reset them as habitat auto‐checked,
this way MapMaker will automatically check their validity regarding the valid habitats
they have associated. To do that you can select an area that contains the samples you
want to modify using the Freehand or the Rectangle tools from the left tool panel, and
then use the context menu option Selected samples/Set as dynamic samples (pressing
the right mouse button to show it). To make all samples of the map to be dynamic, use
the option in the Samples menu of the main menu.
2.6 ImportingdatatoaMapMakermapBesides importing samples from GBIF or CSV files, as explained below, MapMaker can also
import existing maps or data from other sources, like distribution models generated with
Maxent2, ESRI shapefiles, or KML files. Those importation features are explained in section 0.
2.7 DatacleaningusingvalidationrulesMapMaker incorporates the possibility of using validation rules to determine the validity of
samples as well as areas of presence according to environmental variables. This allows for
example to invalidate samples located in areas that don’t comply with some environmental
conditions such as temperature or altitude values within a certain range. Or to delete from an
area of presence the parts where some environmental conditions are not observed.
Environmental data needed to use this features are not included in ModestR, so they have to
be provided by the user as data files in ESRI ASCII or CSV format. There exist free datasets
available in the Net, such as Bi‐Oracle3 for example that are fully compatible with ModestR.
Therefore, the first step will be to integrate those data in ModestR, to allow it to use them
when needed. To do that, you can use the menu Options/Manage environmental variables,
either in MapMaker or in DataManager. Details about how to integrate environmental data in
ModestR are explained in section 5.16.
2 Futher information about Maxent software can be found in: Steven J. Phillips, Miroslav Dudík (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography 31(2):161‐175. DOI: 10.1111/j.0906‐7590.2008.5203.x
3 Tyberghein L., Verbruggen H., Pauly K., Troupin C., Minur F., de Clerck O. 2012. Bio‐ORACLE: a global
environmental dataset for marine species distribution modelling— Global Ecology and Biogeography, 21: 272–281.
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21
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36
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37
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ModestR Software Quick start tutorial
38
distributed through the ModestR website. When DataManager detects that a new version of
the reference world map has been installed, it will indicates that distribution maps have to be
reprocessed to take into account changes in the new reference world map.
But sometimes you can be sure that some of the maps of your ModestR database don’t need
to be reprocessed. For example, if the modifications in the reference world map only involved
freshwater, the maps of marine species are supposed not to be concerned. As map processing
can be a very time‐consuming task, particularly for expert‐drawn maps, in those cases you can
avoid having to reprocess maps by selecting the branch you want to avoid having to reprocess,
and using the menu option Tools/Force set maps from current branch as updated.
This option only has to be used very carefully, and only if you clearly understand its effects.
Existing processed maps will be just marked as updated, even if they were not processed using
the current world reference map. This way DataManager will then consider them as already
processed with the current reference world map.
Anyway, if you incorrectly used this option, you can always reprocess all maps to come back to
a correct and updated state, as explained in section 3.6 above.
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42
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ModestR Software Quick start tutorial
48
Percentage of species with the lowest AOO: a species will be considered rare if its total
presence area all over the world (AOO) is in the range of the X% species with the
lowest AOO, where X is the value you enter in the corresponding field. In this case, you
can also select the taxonomic level (for example a specific class or order) that will be
took into account to calculate this %, just by selecting it on the tree at the right side.
By default all species in the database are took into account.
Maximum Extent of Occurrence (EOO): a species will be considered rare if its EOO
(calculated using convex hull of its presence data, including only valid habitats for the
species) all over the world is lesser that the value you can enter in Km2.
Percentage of species with the lowest AOO: a species will be considered rare if its EOO
(calculated using convex hull of its presence data, including only valid habitats for the
species) all over the world is in the range of the X% species with the lowest EOO,
where X is the value you enter in the corresponding field. In this case, you can also
select the taxonomic level (for example a specific class or order) that will be took into
account to calculate this %, just by selecting it on the tree at the right side. By default
all species in the database are took into account.
4.8 GeneratingandexportingdataOnce filtered the species you want to include, you can use exportation tools to generate and
export several different data about selected species and in different formats. To select a data
exportation process, you just have to click on the desired button. Some buttons will show you
a little context menu with different options regarding the exportation format, like for example
the Export stats option, that will show a menu to select a flat or a structured CSV format.
The available exportation options are:
Export Metrics: generates and exports metrics about species like richness, rarity, patch
index, etc.
Export gradients: generates and exports latitudinal gradients for several metrics.
Export Stats: generates and exports statistical data about species like occupied area,
maximum and minimum latitude and longitude, real area/reference area ratio, etc.
Export Maps: exports selected species maps in several formats.
Export taxonomy: exports taxonomy of the selected species in several formats.
Export region cords: exports the coordinates of the region selected in the map.
More details about those options and the exported formats can be found in section 0.
Mode
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49
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ModestR Software Quick start tutorial
55
5 DataManagerimport/exportfilesformatIn this section we briefly explain the main file formats used by ModestR DataManager to
import/export data from/to a ModestR database. Remember that some exportation defaults
concerning CSV format can be set in the DataManager default settings (see 3.2).
5.1 ImportingtaxonomyfromaCSVfileYou can import taxonomic data in CSV to a ModestR database using the Import/Import
Taxonomy/From CSV file menu option.
Data to be imported have to be in CSV format, either separated by comma or semicolon. They
can contain headers. You should indicate those options in the dialog box that will appear
before importation. Each row must correspond to a species to be imported. Each row must
contain the class, order, family, genus and species, in this order. Importation process is not
case‐sensitive.
For example, those data will be valid to be imported:
Elasmobranchii;Torpediniformes;Narkidae;Typhlonarke;Typhlonarke aysoni
Elasmobranchii;Torpediniformes;Narkidae;Typhlonarke;Typhlonarke tarakea
Actinopterygii;Zeiformes;Oreosomatidae;Allocyttus;Allocyttus folletti
Actinopterygii;Zeiformes;Oreosomatidae;Allocyttus;Allocyttus guineensis
Actinopterygii;Zeiformes;Zenionidae;Capromimus;Capromimus abbreviatus
Actinopterygii;Zeiformes;Parazenidae;Cyttopsis;Cyttopsis rosea
Taxonomy data will be imported to the currently opened database. All required taxonomic
levels will be added to the database for each species contained in the CSV file. If some taxa
(either a class, order, family, genus or species) already exists in the database, it will be simply
skipped.
5.2 ImportingtaxonomyfromanotherModestRdatabaseYou can import taxonomic data from a ModestR database to the currently opened ModestR
database using the Import/Import Taxonomy/From another ModestR database menu option.
In this case, the expected format of the origin database is the original format of the Modest R
database. No modifications have to be done. Just take into account that this option only
imports taxonomic data, but not existing maps from the origin database.
5.3 ImportingtaxonomyfromphyloXMLfilesYou can import taxonomic data from a phyloXML file to the currently opened ModestR
database using the Import/Import Taxonomy/From phyloXML file menu option. DataManager
will search for <taxonomy> elements to import, using the <rank> element to determine the
taxonomic level of the data. You have to be aware that phyloXML files not always contain
comprehensive taxonomic information, so in some cases DataManager will not be able to
import it. For example, a species name from a phyloXML file will only be imported if all
ModestR Software Quick start tutorial
56
superior levels (until class level) are also mentioned in the phyloXML file, or if the genus level
already exists in the target ModestR database.
5.4 ImportingMapFilesfromMapmakermapfilesYou can import map files to the currently opened ModestR database using the Import/Import
presence data/From map independent files menu option. A similar option, but limiting the
species to be imported to a specific branch of the taxonomic tree can be found in the
contextual menu (clicking with left mouse button on the desired element of the tree), selecting
the option Import presence data for this branch/ From map independent files. ModestR
DataManager can import map files generated with MapMaker and saved as standalone
independent map files (files with .IPMMAC extension). This option will ask the user for
selecting a folder, and it will import all map files from this folder to the currently opened
database. Maps to be imported must contain taxonomic information (at least the species
name), and the species assigned to the map has to already exist in the target ModestR
database.
5.5 ImportingMapFilesfromanotherModestRdatabaseYou can import map files to the currently opened ModestR database using the Import/Import
presence data/ From another ModestR database menu option. In this case, the expected
format of the origin database is the original format of the Modest R database. No
modifications have to be done. Once selected the origin database to import maps from, a
dialog box as seen in the figure will allow setting the importation options. First two options
affect taxonomical data:
Import only maps for species already existing in the current database: if selected, no
new taxa will be added. Therefore only maps corresponding to
class/order/family/genus/species that already exist in the currently opened database
could be imported. If a map for the species X exists in the origin database but the
species X doesn’t exist in the currently opened database, the map will not be
imported.
Import maps from all species of the origin database: if selected, all maps of the origin
database could be imported. Consequently, new taxonomies will be added to currently
opened database if needed. So, if a map for the species X exists in the origin database
but the species X doesn’t exist in the currently opened database, species X will be
added to taxonomical data in the target database (including lower levels if necessary,
like genus, families, etc.) , and the map will be imported.
Take into account that all the superior levels are compared to determine if an imported
species corresponds to an existing species. Even if they have the same name, if they differ in
one superior level (for example they have a different family) two species will be considered as
different during importation.
Next two options affect overwriting maps during importation:
Import only new maps from origin database: if selected, only maps for species that
don’t have maps in the currently opened database will be imported. Existing maps will
not be overwritten. Of course, maps for species that don't exist in the currently
Mode
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ModestR Software Quick start tutorial
60
considered valid or invalid with a precision of ±0.1 minutes5. You can set different
colors for valid an invalid samples to easily distinguish them in the
Options/Preferences menu. Moreover, only valid samples will be used when
processing and extracting data from a map (like presence or richness data). If on the
contrary you don’t set a sample as dynamic, it will be considered as manually
validated/invalidated. By default it will be valid, and you have to manually set it as
invalid if needed. So we strongly recommend you to test the dynamic validation.
Select valid habitats for the samples: you have to select which habitats are valid for the
samples you are importing (this option appears on the left tool panel when manually
adding samples). You can select one or more samples, but it is mandatory to select at
least one habitat. If you selected to make the samples as habitat auto‐checked, those
habitats will be used to validate/invalidate a sample. If you don’t selected to make the
samples as dynamic, this information will NOT be used, as samples have to be
manually validated/invalidated. But it will be stored and used in case you later modify
a sample to make it as habitat auto‐checked.
After importation, you will see the list of species imported, and an Importation Log that
includes information about the imported data and eventual errors, like format problems, or
species not imported because they are not found in the database.
5.8 ImportingsamplesfromDarwinCoreArchivesYou can import samples to a DataManager database from a Darwin Core Archive (DwC), which
is a format notably used to share occurrence data through GBIF (www.gbif.org). To do that,
you can use the Import/ Import presence data/From Darwin Core Archive of occurrences
option, or the analog menu option of the tree contextual menu. In this later case, only samples
for the selected branch will be imported.
The first step will be to selected the Zip file that contains the Darwin Core Archive data.
DataManager only supports Darwin Core Archives that contain a meta.xml file which describes
the structure of the ocurrences file, which can be in CSV or text‐delimited format. Moreover,
the occurrence fields that DataManager will require to import data are class, order, family,
genus, specificEpithet (or alternatively scientificName), taxonRank, decimalLatitude, and
decimalLongitude. If some of these fields are empty, samples cannot be imported.
The next step is to configure the importation setting that will be shown in a dialog bog quite
similar to the shown when importing from CSV sample files or GBIG (see sections above). The
main difference is that you can select to only import samples from species already existing in
the database, or to also import samples for new species. In this last case, new taxons (class,
order, family, genus, or species) will be added to the database if needed, using the information
included in the Darwin Core Archive you are importing.
5 This requires installing the last software updates. Anyway, as freshwater habitats are still being added to ModestR map, samples checking currently only distinguishes between land and sea habitats.
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5.10You
Expor
CSV f
estR Softwar
Valid hab
data you
and add t
Merging
created u
existing m
database
e accepted t
mport a lot
wing imported
0 Exportincan export
rt/Export tax
file in two dif
To a CSV
in the pr
data row
an examp
Class
Elasmobranch
Elasmobranch
Elasmobranch
Elasmobranch
Elasmobranch
Elasmobranch
Elasmobranch
Elasmobranch
Elasmobranch
Elasmobranch
Elasmobranch
Elasmobranch
re
bitats: you ha
are importi
to the map.
method: yo
using impor
maps, so im
e.
his dialog, t
of maps, or
d maps and
ngtaxonotaxonomic
xonomy of se
fferent form
(flat) file: da
references (O
w will contain
ple:
Order
ii Carcharhini
ii Carcharhini
ii Carcharhini
ii Carcharhini
ii Carcharhini
ii Carcharhini
ii Carcharhini
ii Carcharhini
ii Carcharhini
ii Carcharhini
ii Carcharhini
ii Carcharhini
ave to select
ing. Only are
u can select
ted data, to
porting only
he importat
they are co
possible erro
omytoaCdata of an
elected branc
ats:
ata will be ex
Options/Pref
n the class, o
Fam
iformes Carch
iformes Carch
iformes Carch
iformes Carch
iformes Carch
iformes Carch
iformes Carch
iformes Carch
iformes Carch
iformes Carch
iformes Carch
iformes Carch
62
t which habit
eas correspo
t to overwri
o add new d
y data for s
ion process
mplex. Whe
ors will be sh
CSVfileny branch
ch option. Yo
xported to a
ferences me
order, family
mily G
harhinidae Ca
harhinidae Ca
harhinidae Ca
harhinidae Ca
harhinidae Ga
harhinidae G
harhinidae G
harhinidae G
harhinidae G
harhinidae G
harhinidae Iso
harhinidae La
tats (at least
onding to th
te existing m
data to exis
pecies that
will start. T
n the proces
how in the ri
of a DataM
ou will see tw
CSV file usin
enu). First ro
y, genus and
Genus
archarhinus
archarhinus
archarhinus
archarhinus
aleocerdo
lyphis
lyphis
lyphis
lyphis
lyphis
ogomphodon
amiopsis
Q
t one) are va
ose habitats
maps (if any
sting maps,
still don’t ha
This can be t
ss will be co
ght panel.
Manager dat
wo options t
ng the field d
ow will conta
species, in t
Species
Carcharhinus
Carcharhinus s
Carcharhinus s
Carcharhinus t
Galeocerdo cu
Glyphis fowler
Glyphis gange
Glyphis garrick
Glyphis glyphi
Glyphis siame
Isogomphodo
Lamiopsis tem
Quick start tu
alid for the sp
s will be acc
y) with new
or to not m
ave a map
time‐consum
mpleted, a r
tabase usin
to export dat
delimited sel
ain headers.
this order. H
macloti
signatus
sorrah
tilstoni
uvier
rae
eticus
ki
is
ensis
on oxyrhynchus
mminckii
utorial
pecies
cepted
maps
modify
in the
ming if
report
g the
ta to a
lected
. Each
Here is
ModestR Software Quick start tutorial
63
To a structured CSV file: data will be exported to a CSV file using the field delimited
selected in the preferences (Options/Preferences menu). First row will contain
headers. First data row will contain a class. Next row will contain an order of this class,
and so on until species level. Once listed all species of a genus, next genus will be listed
and so on. Last column will contain the number of species in the current taxonomical
level (class, order, family…). Here is an example:
Class Order Family Genus Species Total Species
Elasmobranchii 1122
Carcharhiniformes 273
Carcharhinidae 53
Carcharhinus 31
Carcharhinus acronotus
Carcharhinus albimarginatus
Carcharhinus altimus
Carcharhinus sorrah
Carcharhinus tilstoni
Galeocerdo 1
Galeocerdo cuvier
Glyphis 5
Glyphis fowlerae
Glyphis gangeticus
Glyphis garricki
Glyphis glyphis
Glyphis siamensis
Isogomphodon 1
Isogomphodon oxyrhynchus
Lamiopsis 1
Lamiopsis temminckii
5.11 ExportingmapstomapindependentfilesYou can export maps of any branch of a DataManager database to standalone independent
map files (files with .IPMMAC extension) using the Export/Export maps of selected branch/To
Map independent files option. The exported files can be opened with MapMaker. This option
will ask the user for selecting a folder, and it will export all maps from the currently selected
branch of the database to this folder. Maps exported will contain full taxonomic information.
5.12 ExportingpresencedatatoCSVdatafilesYou can export maps of any branch of a DataManager database to CSV using the
Export/Export maps of selected branch/To presence data and variables option. This feature
also allows including environmental variables in the exported data. This option will show a
dialog box with several selections. A brief explanation of each option of this dialog box will be
shown in an emerging tooltip if you place the mouse on it. On the left groupbox you can select
if the exported data will be exported to one separated file for each species of the selected
branch, or to a single file where all species data will be consecutively stored. In the first case,
you will be asked to select on file name to output, whereas in the second one you will have to
select a folder where exported files will be saved. Remember that characters used as field
delimiter and decimal separator can be selected in the preferences (Options/Preferences
menu).
Mode
The a
"C
"A
"A
"A
"A
"A
estR Softwar
available exp
Valid sam
will only
presence
automati
pseudosa
You can a
sample, u
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for each s
of the sam
The outp
dependin
is the Bat
Class";"Order";"F
Actinopterygii";"A
Actinopterygii";"A
Actinopterygii";"A
Actinopterygii";"A
Actinopterygii";"A
Presence
pseudooc
requiring
generate
zones. If
occurren
export t
pseudosa
re
portation for
mples: this o
be useful if
e) will be ski
cally or m
amples expo
also select if
using the co
right tree, if
selected var
mples.
put will be
ng of selecte
thymetry env
Family";"Genus";"
Ateleopodiforme
Ateleopodiforme
Ateleopodiforme
Ateleopodiforme
Ateleopodiforme
e pseudosa
ccurences fr
g that the m
sample data
the maps yo
ce records (
hose sampl
amples.
mat options
option will ex
the maps co
pped. This o
manually, w
rtation descr
the species
rresponding
f available (s
iable, with th
a CSV file
d settings. A
vironmental
"Species";"Longit
es";"Ateleopodida
es";"Ateleopodida
es";"Ateleopodida
es";"Ateleopodida
es";"Ateleopodida
amples dat
rom rasterize
maps are al
a from range
ou have stor
(i.e. downloa
es (see nex
64
are:
xport only va
ontain samp
option expo
without any
ribed above)
taxonomy w
g checkbox. A
see section 5
he value (if it
with this fo
As well as the
variable:
tude";"Latitude";
ae";"Ateleopus";
ae";"Ateleopus";
ae";"Ateleopus";
ae";"Ateleopus";
ae";"Ateleopus";
ta: this o
ed species m
ready raste
e maps wher
red in the d
aded from G
xt option, “
alid sample d
ple data, as r
rts only sam
y extrapola
).
will be added
And you can
5.16). In this
t exists) of th
ormat. Taxo
e last colum
;"Bathy"
"Ateleopus indic
"Ateleopus indic
"Ateleopus indic
"Ateleopus indic
"Ateleopus japon
option gen
map, so basi
rized (see 3
re species pr
atabase alre
GBIF), it’s pr
“Valid samp
Q
data from m
range data (
mples checke
tion (on t
d at the firsts
n add enviro
case, a colu
his variable a
onomy colum
n of this exa
us";‐35,89022;8,0
us";‐36,11473;7,0
us";‐35,04803;8,0
us";‐35,04403;7,0
nicus";146,558;34
nerates pse
ing on a 1’x
3.6). This op
resence is st
eady are bas
robably pref
ples”) in tu
Quick start tu
maps. Theref
(polygonal a
ed as valid,
the contrar
s columns of
nmental var
umn will be a
at the coord
mns are op
ample, which
031313;‐4558
020963;‐2570
087483;‐4863
077033;‐3023
4,84859;‐5788
eudosample
x1’ cells prec
ption is use
tored as poly
sed on samp
ferable to di
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ore, it
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ygonal
ples or
irectly
rating
ModestR Software Quick start tutorial
65
When selecting this option, Pseudosamples exportation options groupbox on the
bottom will activate to allow configuring pseudosamples generation.
You can also set the precision or density of the samples adjusting the width in minutes
of the cells that will be used. If for example you select 5’ cell width, at most one
sample for each 5’x5’ minutes cell on the world map will be generated, if the species is
present in any point of this cell. You can also set if the sample will be generated with
the coordinates of one corner or center of the cell. The smaller cell you select, the
more numerous samples you have, and with the higher accuracy. But for large zones,
this can result if a too large number of samples. You can also set if a sample has to be
generated if the species is just present in the output cell, or in turn set a threshold of
1’x1’ minutes cells occupation that has to be exceeded to generate a sample for this
cell. For example, if you set a cell output of 5’x5’, you could want that only if a species
occupies at least 20% of this cell (that is 20% of 5x5= 5, so 5 cells of 1’x1’ minutes) a
pseudo sample has to be generated for this 5’x5’ cell.
You can also select if the species taxonomy will be added at the firsts columns of each
sample. And you can add environmental variables from the right tree. In this case, a
column will be added for each selected variable, with the value (if it exists) of this
variable at the coordinates of the pseudosample.
The exported format will be the same than for the previously described option of valid
samples exportation.
Presence areas coordinates: this option will generate a CSV with the description of
each polygonal area selected in the map as occupied by the species (warning! This
polygon will not be clipped to the selected habitat, it will contain all the coordinates
selected by the user, regardless of the habitat).
A Outer/Hole column indicates it the coordinates correspond to the outer limits of the
polygon, or to an inner hole. The type indicates the habitat selected for this zone. A
blank line separates each polygon.
Valid samples contained in the map will also be exported, each one in a line, with the
“FillSample” type. Environmental data cannot be added when using this exportation
option.
Lon Lat Outer(1) /Hole(0) Polygon Type Class Order Family Genus Species
‐56,13 54,79 1 0 Sea ActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐56,13 55,13 1 0 Sea ActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐59,5 47,06 1 0 Sea ActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐59,83 47,4 1 0 Sea ActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐59,83 47,73 1 0 Sea ActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐60,17 47,73 1 0 Sea ActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐60,5 48,07 1 0 Sea ActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐60,84 48,4 1 0 Sea ActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐56,13 54,79 1 0 Sea ActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐77,98 33,94 1 1 FillSampleActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
ModestR Software Quick start tutorial
66
‐76,71 35,97 1 2 FillSampleActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐67 40 1 3 FillSampleActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
‐74,73 40,17 1 4 FillSampleActinopterygiiAcipenseriformesAcipenseridaeAcipenserAcipenser brevirostrum
5.13 ExportingsamplestoDarwinCoreArchivestyleYou can export maps of any branch of a DataManager database to CSV data in a format that
can be easily adapted to generate a Darwin Core Archive (DwC), which is a format used to
share occurrence data through GBIF (www.gbif.org). To do that, you can use the Export/Export
maps of selected branch/To Darwin Core Archive data option, or the analog menu option of
the tree contextual menu. DataManager will add unique ID’s for each occurrence, as required
by DwC format. Exported format will contains headers for each column, and a row for each
sample from each map exported. The format is based on the template provided by GBIF in
http://tools.gbif.org/spreadsheet‐processor/, with 45 data fields for ocurrences, but only some
fields will be filed by DataManager, which are:
• occurrenceID: already explained above.
• class, order, family, genus: taxon names for those levels of the species
• specificEpithet: specific species name. For example, for “Isurus paucus” it will be
“paucus”.
• infraspecificEpithet: if you used subspecies at species level in the database, this field
will be the subspecies name. For example for “Acipenser oxyrinchus desotoi” it will be
“desotoi”. If you used species names, it will be empty. For example, for “Isurus
paucus” it will be empty.
• scientificName: full species name. For example, for “Isurus paucus” it will be “Isurus
paucus”; for “Acipenser oxyrinchus desotoi” it will be “Acipenser oxyrinchus desotoi”.
• taxonRank: rank of the taxon associated to the samples. It will be “species” by default,
but if DataManager detect a species name with three words, it will use “subspecies”
rank. For example, for “Isurus paucus” it will be “species”; for “Acipenser oxyrinchus
desotoi” it will be “Acipenser oxyrinchus desotoi”.
• decimalLatitude, decimalLongitude: coordinates of the samples.
The exported CSV file will be easily opened with a worksheet application like Excel and copied
to the Excel template provided by GBIF in http://tools.gbif.org/spreadsheet‐processor/, to
subsequently generate a Darwin Core Archive.
5.14 ExportingmetricsandenvironmentalvariablesdataDataManager can calculate and export several metrics from maps, like richness data, rarity
index, etc. If you have files containing environmental variables data, you can incorporate them
Mode
to Da
mana
When
menu
settin
estR Softwar
ataManager
age environm
n selecting E
u, or equiva
ngs is shown
You can s
cells that
5’x5’ min
You can s
o R
d
o
o R
o
e
o P
c
e
p
a
o A
o
w
re
to make tha
mental variab
Export/Expor
lent option
:
set the precis
will be used
utes cell on
select which
Richness: the
dimensions. T
one species f
Rarity index f
of the cell, an
each species
Patch index f
cell, and Pi is
each species
previously ca
and explanat
AOO index fo
of the cell, a
world) of eac
t they can b
bles is explai
rt maps of t
in the tree
sion or dens
d. If for exam
the world m
metrics will
e number of
This will be e
or the outpu
for each cell,
nd Areai is th
i present in t
or each cell,
s the Patch d
s i present
alculated wh
ion of patch
r each cell, a
and AOOi is
h species i p
67
be exported a
ined in sectio
the selected
contextual m
ity of the ou
mple you sele
map will be ge
be in the ou
different sp
equivalent to
ut.
, as
∑
he occupied
this cell.
as ∑
distribution i
in this cell.
hen processin
index for ea
as ∑
s the Area O
present in thi
at the same
on 5.16.
branch/To m
menu, a dia
utput adjustin
ect 5’ cell wid
enerated.
utput in the l
pecies presen
o a 0/1 pres
∑ 11
area (taking
∑ 1 w
ndex (taking
Patch inde
ng maps. In
ach species is
1
Of Occupancy
is cell.
Q
time that m
metrics and
log box to s
ng the width
dth, one met
eft selection
nt in each ce
ence matrix
where
g into accoun
here n is th
g into accoun
ex of each s
subsection
s calculated.
where
y (taking int
Quick start tu
etrics. The w
variables in
select expor
h in minutes
tric value for
n tree:
ell of the sel
x if you selec
e n is the ric
nt all the wo
he richness o
nt all the wo
species has
5.17 you ca
e n is the ric
to account a
utorial
way to
main
tation
of the
r each
lected
ct only
chness
rld) of
of the
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been
n find
chness
all the
ModestR Software Quick start tutorial
68
o EOO index for each cell, as ∑ 1 where n is the richness
of the cell, and EOOi is the Extent Of Occurrence (taking into account all the
world and using convex hull method) of each species i present in this cell.
o Latitudinal range index: for each cell, as
∑ 11
where n is the
richness of the cell, and LRi is the latitudinal range (that is, the higher latitude
minus the lower latitude, taking into account all the world) of each species i
present in this cell.
o Habitats area: the area in Km2 for each kind of habitat in this cell. Take into
account that this value is calculated using a raster world map of 1’x1’
precision, making results only roughly approximate, particularly for rivers and
small freshwater areas. Except for the CSV list in columns format, this option
necessarily produce a multiple sheet or multiple file output, as the area
occupied by each type of habitat in each cell will be outputted in a separate
sheet or file.
You can also set richness count method: count a species if it is just present in the
output cell, or in turn set a threshold of 1’x1’ minutes cells occupation that has to be
exceeded to count a species in this cell. For example, if you set a cell output of 5’x5’,
you could want that only if a species occupies at least 20% of this cell (that is 20% of
5x5= 5, so 5 cells of 1’x1’ minutes) the species has to be counted (so the value for this
cell incremented).
You can also select which habitats have to be included in metrics calculus. By default
all habitats are took into account. If you exclude one habitat, all samples or zones with
this associated habitat will be excluded from the metrics calculus.
You can define the zone boundaries to be examined in degrees, with a minimum of a
1ºx1º zone. Take into account that rarity index, patch index and area index are always
calculated in a world basis, independent from the zone boundaries selected for the
output.
You can select how cell coordinates will be shown in output: using the coordinates of
the center or one corner of the cell.
You can also select any environmental variables you want to output, for the precision
and boundaries, and with the same format that you selected. It must be pointed out
that it is also possible to only select environmental variables to output, without
including any metrics. To manage environmental variables see section 5.16.
Finally you can select the output format for presence/richness data, among the following ones:
CSV matrix (longitude X latitude): this format outputs a matrix with coordinates of
each cell at row (longitude)/column(latitude) headers, and metrics data as values for
each cell of the matrix. Here we see an example of richness output for a zone with
longitude from 109 to 120 and latitude from 0 to 11 and with a cell precision of 60’.
Values of longitude and latitude correspond here to the right‐down corner of each cell.
ModestR Software Quick start tutorial
69
On the left the original CSV format is shown. On the right, the same data are presented
in a more friendly way, as displayed in Microsoft Excel for example. The zero value in
the first position of the first row has no signification; it is used to avoid importation
problems with some applications like R.
0;110;111;112;113;114;115;116;117;118;119;1
20
10;1;1;0;0;0;3;0;0;4;3;0
9;0;0;0;0;0;0;0;0;0;11;5
8;0;0;1;0;0;0;0;2;0;4;7
7;0;0;1;0;0;0;0;1;0;2;3
6;0;0;0;0;0;0;2;0;1;12;0
5;0;0;0;0;0;0;1;0;0;0;9
4;0;0;0;0;4;0;0;0;0;6;12
3;1;0;0;0;0;0;0;0;0;3;3
2;0;0;0;0;0;0;0;0;0;0;0
1;0;0;0;0;0;0;0;0;0;1;3
0;0;0;0;0;0;0;0;0;1;0;1
0 110 111 112 113 114 115 116 117 118 119 120
10 1 1 0 0 0 3 0 0 4 3 0
9 0 0 0 0 0 0 0 0 0 11 5
8 0 0 1 0 0 0 0 2 0 4 7
7 0 0 1 0 0 0 0 1 0 2 3
6 0 0 0 0 0 0 2 0 1 12 0
5 0 0 0 0 0 0 1 0 0 0 9
4 0 0 0 0 4 0 0 0 0 6 12
3 1 0 0 0 0 0 0 0 0 3 3
2 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 1 3
0 0 0 0 0 0 0 0 0 1 0 1
As the CSV format does not support several pages, if you select this output format and
several metrics to be outputted, you will be warned that one single CSV file for each
selected metric will be generated. Remember that characters used as field delimiter
and decimal separator can be selected in the preferences (Options/Preferences menu).
CSV list in columns: this format outputs a list with several columns: latitude and
longitude for each cell, and a column for each selected metric. Here we see an
example where a zone with longitude from 110 to 120 and latitude from 0 to 2 with a
precision of 30’. The data are exported in CSV, but in the following example the data
are presented in a friendly way, as displayed in Microsoft Excel for example:
Latitude Longitude Species.Richness Sea.Area Land.Area Small.Rivers.Area
Large.Rivers. Area
Lentic.Waters.Area
2 110,5 1 3090,04356
1,5 110,5 1806,41211 968,580384 315,99288
1 110,5 2 2291,28846 800,403343
0,5 110,5 3 2418,75789 673,404884
0 110,5 4 2339,91575 752,482526
Remember that characters used as field delimiter and decimal separator can be
selected in the preferences (Options/Preferences menu). As this format requires
loading all data to be outputted at the same time, if you select several variables it can
result in a very slow processing or even in an out of memory error (particularly in 32bit
systems).
Excel worksheet (2007 or higher): this format will produce an XML file directly
recognized and readable by Microsoft Excel 2007 or higher. This format has the
advantage of being multipage, so one worksheet is generated for each metric to be
outputted.
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ModestR Software Quick start tutorial
71
You can also select which habitats have to be included in metrics calculus. By default
all habitats are took into account. If you exclude one habitat, all samples or zones with
this associated habitat will be excluded from the calculus.
You can define the zone boundaries to be examined in degrees, with a minimum of a
1ºx1º zone.
Output will be generated as a CSV file with the following columns:
Latitude: top limit of the latitudinal band.
Total.Species.Richness: total richness of the latitudinal band This metric is calculated
globally for all the latitudinal band, without taking into account longitudinal cells.
Mean.Species.Richness: mean of the richness of the cells of the latitudinal band,
taking cells of the longitude width in degrees indicated in the dialog box described
above. That is, the richness of each cell of the longitude width and latitude height in
degrees indicated is calculated for a latitudinal band, and then the mean of all those
values is calculated. All cells are took into account to calculate the mean, even if they
have a richness of zero.
SD.Species.Richness: standard deviation of the richness of the cells of the latitudinal
band, calculated in the same way than Mean.Species.Richness.
Mean.AOO.Index: mean of the AOO (Area Of Occupancy) index metrics calculated for
each one of the cells of the latitudinal band, taking cells of the longitude width in
degrees indicated in the dialog box described above. That is, the AOO index of each
cell of the longitude width and latitude height in degrees indicated is calculated for a
latitudinal band, and then the mean of all those values is calculated. Be aware that
only cells with a richness value bigger than zero (that is, where there at least one
species present) are took into account to calculate the mean. Details about AOO index
metric can be found in section 5.14 above.
SD.AOO.Index: standard deviation of the AOO index of the cells of the latitudinal
band, calculated in the same way than Mean.AOO.Index.
Mean.EOO.Index: mean of the EOO (Extent Of Occurence) index metrics calculated for
each one of the cells of the latitudinal band, taking cells of the longitude width in
degrees indicated in the dialog box described above. That is, the EOO index of each cell
of the longitude width and latitude height in degrees indicated is calculated for a
latitudinal band, and then the mean of all those values is calculated. Be aware that
only cells with a richness value bigger than zero (that is, where there at least one
species present) are took into account to calculate the mean. Details about EOO index
metric can be found in section 5.14 above.
SD.EOO.Index: standard deviation of the EOO index of the cells of the latitudinal band,
calculated in the same way than Mean.EOO.Index.
Mean.Rarity.Index: mean of the rarity index metrics calculated for each one of the
cells of the latitudinal band, taking cells of the longitude width in degrees indicated in
the dialog box described above. That is, the rarity index of each cell of the longitude
width and latitude height in degrees indicated is calculated for a latitudinal band, and
then the mean of all those values is calculated. Be aware that only cells with a richness
value bigger than zero (that is, where there at least one species present) are took into
ModestR Software Quick start tutorial
72
account to calculate the mean. Details about rarity index metric can be found in
section 5.14 above.
SD.Rarity.Index: standard deviation of the area index of the cells of the latitudinal
band, calculated in the same way than Mean.Rarity.Index.
Mean.Patch.Index: mean of the patch index metrics calculated for each one of the
cells of the latitudinal band, taking cells of the longitude width in degrees indicated in
the dialog box described above. That is, the patch index of each cell of the longitude
width and latitude height in degrees indicated is calculated for a latitudinal band, and
then the mean of all those values is calculated. Be aware that only cells with a richness
value bigger than zero (that is, where there at least one species present) are took into
account to calculate the mean. Details about patch index metric can be found in
section 5.14 above.
SD.Patch.Index : standard deviation of the area index of the cells of the latitudinal
band, calculated in the same way than Mean.Patch.Index.
Mean.Latitudinal.Range.Index: mean of the latitudinal range index metrics calculated
for each one of the cells of the latitudinal band, taking cells of the longitude width in
degrees indicated in the dialog box described above. That is, the latitudinal range
index of each cell of the longitude width and latitude height in degrees indicated is
calculated for a latitudinal band, and then the mean of all those values is calculated. Be
aware that only cells with a richness value bigger than zero (that is, where there at
least one species present) are took into account to calculate the mean. Details about
latitudinal range index metric can be found in section 5.14 above.
SD.Latitudinal.Range.Index: standard deviation of the area index of the cells of the
latitudinal band, calculated in the same way than Mean.Latitudinal.Range.Index.
Mean. AOO: mean of the AOO of all species present in the latitudinal band (taking into
account the AOO that each species occupies in all the world, independently from the
range selected for the analysis). This metric is calculated globally for all the latitudinal
band, without taking into account longitudinal cells.
SD.AOO: standard deviation of the AOO of all species present in the latitudinal band
(taking into account the AOO that each species occupies in all the world,
independently from the range selected for the analysis). This metric is calculated
globally for all the latitudinal band, without taking into account longitudinal cells.
Mean. EOO: mean of the EOO of all species present in the latitudinal band (taking into
account the EOO that each species occupies in all the world, independently from the
range selected for the analysis). This metric is calculated globally for all the latitudinal
band, without taking into account longitudinal cells.
SD.EOO: standard deviation of the EOO of all species present in the latitudinal band
(taking into account the EOO that each species occupies in all the world,
independently from the range selected for the analysis). This metric is calculated
globally for all the latitudinal band, without taking into account longitudinal cells.
Mean.Latitudinal.Range: mean of the latitudinal range occupied by all species present
in the latitudinal band (taking into account the area that each species occupies in all
the world, independently from the range selected for the analysis). This metric is
calculated globally for all the latitudinal band, without taking into account longitudinal
cells.
ModestR Software Quick start tutorial
73
SD.Latitudinal.Range: standard deviation of the latitudinal range occupied by all
species present in the latitudinal band (taking into account the area that each species
occupies in all the world, independently from the range selected for the analysis). This
metric is calculated globally for all the latitudinal band, without taking into account
longitudinal cells.
Mean.Patch.Distrib: mean of the patch value of all species present in the latitudinal
band (taking into account the area that each species occupies in all the world,
independently from the range selected for the analysis). In subsection 5.17 you can
find and explanation of patch index for each species is calculated. This metric is
calculated globally for all the latitudinal band, without taking into account longitudinal
cells.
SD.Patch.Distrib: standard deviation of the patch value of all species present in the
latitudinal band (taking into account the area that each species occupies in all the
world, independently from the range selected for the analysis). This metric is
calculated globally for all the latitudinal band, without taking into account longitudinal
cells.
5.16 ManagingenvironmentalvariablesDataManager allows to add environmental variables stored in CSV or ESRI ASC files (i.e. Bi‐
Oracle7) to metrics exportation options (see section 5.14). This option is intended to facilitate
to obtain integrated outputs where metrics and environmental variables for a specific zone are
included.
To Add/modify/delete environmental variables you can use the Options/Manage
environmental variables menu. Then a dialog box will be shown in a tree with the currently
configured variables, ordered using their defined type. If you select a variable in the tree, its
settings will be shown in the right panel, in readonly mode. You can delete a variable by
selecting it in the tree and using Delete Var button or the equivalent option of the contextual
menu (pressing the left‐mouse button). You can edit a variable by selecting it in the tree and
using Edit Var button or the equivalent option of the contextual menu (pressing the left‐mouse
button). The settings of the variable will be shown in the right panel, and the read‐write mode
will be activated to allow modifications. You can select to save or to discard changes using the
corresponding buttons on the bottom.
To add a variable you can use the Add Var button, or select an existing variable in the tree and
select Add Var using this as template option in the contextual menu (pressing the left‐mouse
button).
7 Tyberghein L., Verbruggen H., Pauly K., Troupin C., Minur F., de Clerck O. 2012. Bio‐ORACLE: a global
environmental dataset for marine species distribution modelling— Global Ecology and Biogeography, 21: 272–281.
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ModestR Software Quick start tutorial
83
To KML: in this case a KML file will be generated, with polygons corresponding to the
exact zones occupied by a species, and placemarks for samples. KML files are widely
recognized by GIS software and applications like GoogleMaps or GoogleEarth. Anyway,
we have detected that some applications have problems to correctly read and
interpret KML files generated with this option, because they usually contain very
complex polygons. In this case, shapefiles seem to work better.
To Shapefile: in this case a shapefile will be generated, with polygons corresponding to
exact zones occupied by a species, and points for samples. Shapefiles are widely
recognized by GIS software. MapMaker cannot directly generate shapefiles, but it
generates a temporary KML file and uses GDAL ogr2ogr utility to convert it to shapefile
format. Therefore, you need to have GDAL utilities installed in your computer to use
this option (it is included with ModestR since version 1.3; otherwise you have to
correctly set the ogr2ogr path in MapMaker preferences (see 2.11)). As shapefiles are
usually intended to contain a single type of data, when exporting to shapefile you will
have to select whether exporting zones or samples. Exporting both type of data to the
same file is not supported.
6.9 ExportonlysamplestoCSVYou can export samples contained in a map to a CSV file using the File/Export/Only samples to
CSV menu option. You can select to export only valid samples, or all samples. The output file
format will be like this:
"species";"Longitude";"Latitude"
"Heterodontus francisci";‐118,5;33,5
"Heterodontus francisci";‐118,5;32,5
"Heterodontus francisci";‐118,5;28,5
"Heterodontus francisci";‐117,5;32,5
"Heterodontus francisci";‐110,5;24,5
"Heterodontus galeatus";149,5;6,5
"Heterodontus galeatus";149,5;37,5
"Heterodontus galeatus";150,5;‐4,5
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84
filesformain file forma
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ModestR Software Quick start tutorial
85
In any case, you can modify area boundaries disabling the Clip data to selected region
in the metrics dialog box, and setting different rectangular boundaries.
7.2 ExportinglatitudinalgradientsMRFinder can calculate and export latitudinal gradients for several metrics from maps from
selected species. When selecting Export gradients in the exportation tools of the search result
window (see section 4.7), a dialog box to select exportation settings is shown, with the same
options and operation as the corresponding option in DataManager. You can find more details
about latitudinal gradients exportation in section 5.15.
7.3 ExportingtaxonomytoaCSVfileortoclipboardYou can export taxonomic data of the selected species using the Export taxonomy in the
exportation tools of the search result window (see section 4.7). You will see three options to
export data:
To clipboard: this option will copy the list of names of the selected species to the
clipboard.
To a CSV flat file: this option has the same operation that the corresponding option
of DataManager. You can find more details in section 5.10.
To a CSV structured file: this option has the same operation that the corresponding
option of DataManager. You can find more details in section 5.10.
7.4 ExportingmapsYou can export maps data of the selected species using the Export Maps in the exportation
tools of the search result window (see section 4.7). You will see three options to export data:
To map independent files: this option has the same operation that the
corresponding option of DataManager. You can find more details in section 5.11.
To a CSV file(s): this option has the same operation that the corresponding option
of DataManager. You can find more details in section 5.12.
To summary data: this option has the same operation that the corresponding
option of DataManager. You can find more details in section 5.17.
7.5 ExportingstatisticaldataYou can export statistical data of the selected species using the Export stats in the exportation
tools of the search result window (see section 4.7). You will see two options to export data:
To a CSV structured file: this option will generate a CSV file with the following columns:
o Subclass, Order, Family, Genus and Species: those columns will be shown
in a structured way similar to the used when exporting taxonomy to a CSV
structured file in DataManager (see section 5.10.).
o Total.Species: this column will count the number of species for each
higher taxonomic level, in a structured way similar to the used when
exporting taxonomy to a CSV structured file in DataManager (see section
5.10.).
o Total.Rare.Species: this column is similar to the previous one, but it will
only count the number of rare species for each higher taxonomic level.
ModestR Software Quick start tutorial
86
o Rare.Species: this column contains a “1” value for the rare species,
otherwise it will be empty.
o AOO.km2: this column summarizes the total AOO in Km2 occupied by each
taxonomic level (from species to subclass), but only within the bounds of
the selected area. That is, if you selected an area of 4 Km2, the maximum
value of this column will be 4. This column is calculated with a precision of
±1’x1’.
o Mean.AOO: this column summarizes the mean AOO occupied by the
species of each higher taxonomic level (from genus to subclass), within the
bounds of the selected area.
o SD.AOO: this column summarizes the standard deviation of the area
occupied by the species of each higher taxonomic level (from genus to
subclass), within the bounds of the selected area. If there is only one
species in a higher level (for example in a genus), this value will be
obviously empty.
o Maximum.Latitude: this column summarizes the maximum latitude where
a species is present, for each taxonomic level (from species to subclass),
within the bounds of the selected area.
o Mean.Max.Latitude: this column summarizes the mean of the previous
column for each higher taxonomic level (from genus to subclass), within
the bounds of the selected area.
o SD.Max.Latitude: this column summarizes the standard deviation of the
maximum latitude where species are present for each higher taxonomic
level (from genus to subclass), within the bounds of the selected area. If
there is only one species in a higher level (for example in a genus), this
value will be obviously empty.
o Minimum.Latitude, Mean.Min.Latitude, SD.Min.Latitude: those columns
contain similar result than the three previous ones, but for the minimum
latitude where species are present.
o Maximum.Longitude, Mean.Max.Longitude, SD.Max.Longitude : those
columns contain similar result than the three previous ones, but for the
maximum longitude where species are present.
o Minimum.Longitude, Mean.Min.Longitude. SD.Min.Longitude: those
columns contain similar result than the three previous ones, but for the
minimum longitude where species are present.
o Real.Area.Reference.Area: this column is the ratio between the real area
occupied by a species within the bounds of the selected area, and the
reference or potential area that this species could take up in this selected
area, taking into account the valid habitats for this species. For example, is
a species is only present in marine habitats, only sea areas will be took into
account to calculate reference area for the species. The maximum value of
this column will be obviously 1 (if a species takes up all the areas with valid
habitats for it, into the bounds of the selected area), but take into account
that this column is calculated with a precision of ±1’x1’.
ModestR Software Quick start tutorial
87
o Mean.Real.Area.Reference.Area: this column summarizes the mean of
the real area/reference area ratio explained before, for all species of each
higher taxonomic level (from genus to subclass).
o SD.Real.Area.Reference.Area: this column summarizes the standard
deviation of the real area/reference area ratio explained before, for all
species of each higher taxonomic level (from genus to subclass). If there is
only one species in a higher level (for example in a genus), this value will
be obviously empty.
To a CSV flat file: this option will generate a CSV file where there are no summarize rows
for higher taxonomic levels than species, so only some of the columns described above for
the CSV structured file option will be exported. They are: Subclass, Order, Family, Genus,
Species, Rare.Species, AOO.km2, Maximum.Latitude, Minimum.Latitude,
Maximum.Longitude, Minimum.Longitude, Real.Area.Reference.Area.
7.6 ExportingregioncoordinatesYou can export the coordinates of the region you selected in the map to do a search in
MRFinder using the Export region coords in the exportation tools of the search result window
(see section 4.7). You will see two options to export data:
To clipboard: this option will copy the coordinates (longitude, latitude) of the
vertexes of the selected region to the clipboard.
To a CSV file: : this option will export the coordinates (longitude, latitude) of the
vertexes of the selected region to a CSV file, using the default delimiter and
decimal point settings. The resulting file will look like this:
"Longitude";"Latitude" ‐64,40827;37,33813 ‐66,89748;38,27158 ‐72,4982;39,5162 ‐77,16547;40,1385 ‐81,21043;40,1385
8 CheckingforupdatesModestR is still in development to add new features to applications, as well as to add more
elements to the world reference map. Therefore regular updates are released. You can check
for updates directly from any ModestR application using Help/Check for updates menu option.
This makes that the application connects online to ModestR website to download data and
check for available updates for your installation (no data are sent from your computer to the
Web). If there are new updates, a dialog box with a list of updates will be displayed.
You can also make that ModestR applications check automatically for updates, setting this
options in the Options/Preferences menu option of any of those applications.
Updates have to be downloaded from ModestR website, and installed on your computer
taking into account the path where you have installed ModestR software. Updates will try to
ModestR Software Quick start tutorial
88
install themselves by default in the default ModestR installation path (C:\ModestR). If you have
modified this path when installing ModestR for the first time, you may have to set the correct
path to install updates.