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corrections et utilisation du checkpoint pour avoir une reproductibilité

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François Pelletier 2016-03-07 21:19:20 -05:00
parent 7513d17988
commit 9747933582
11 changed files with 7332 additions and 9 deletions
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10
README
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@ -1,3 +1,7 @@
Exploration de données ouvertes: Une forêt de données
Projet compilé: http://rpubs.com/franc00018/159312
Ce projet requiert plusieurs librairies disponibles dans les distributions linux populaires.
Il a été présenté le 5 mars 2016 à la JIDO2016, Le CAMP
http://www.meetup.com/fr-FR/Quebec-Numerique/events/228545895/
@ -23,7 +27,7 @@ texlive-english
Ce projet requiert aussi plusieurs packages R
sur CRAN: (avec install.packages)
reard
readr
magrittr
plyr
dplyr
@ -33,10 +37,12 @@ lubridate
cairoDevice
ggplot2
maptools
rgeos
rgdal
RColorBrewer
pander
rgros
ggmap
prettyR
sur github (avec devtools::install_github)
hadley/multidplyr

18
arbres-gbif.Rmd
View file

@ -8,6 +8,11 @@ output: html_document
```{r global_options, include=FALSE}
knitr::opts_chunk$set(fig.width=12, fig.height=8, fig.path='Figs/',
echo=TRUE, warning=FALSE, message=FALSE)
library("checkpoint")
checkpoint("2016-03-07")
# Chargement des libraries
devtools::install_github("hadley/multidplyr")
source("packages.R")
```
# Une forêt de données:
## Enrichir ses données à l'aide des catalogues de données ouvertes et des interfaces de programmation publiques
@ -20,9 +25,6 @@ L'objectif de ce projet est de tirer un maximum d'information du jeu de données
## Chargement du jeu de données
```{r, echo=FALSE}
# Chargement des libraries
source("packages.R")
# Chargement du jeu de données
dA <- read.csv("ARBRE.csv",sep = "|", dec=",", stringsAsFactors = FALSE) %>%
# Correction des dates qui sont dans un format numérique YYYYMMDDHHMMSS
@ -215,8 +217,8 @@ names(arrqc@data) <- paste0(names(arrqc@data),"_ARR")
coordinates(dA3) = ~ LONGITUDE + LATITUDE
proj4string(dA3) = CRS("+proj=longlat +datum=WGS84")
dA4.1 <- dA3 %>% over(qrtqc) %>% cbind(dA3)
dA4 <- dA3 %>% over(arrqc) %>% cbind(dA4.1)
dA4.1 <- dA3 %>% over(qrtqc) %>% cbind(dA3@data)
dA4 <- dA3 %>% over(arrqc) %>% cbind(dA4.1) %>% cbind(dA3@coords)
save(dA4,file="dA4.RData")
readr::write_csv(dA4,"arbres-augmented.csv")
```
@ -230,12 +232,13 @@ pandoc.table(count_arbre_arr %>% select(NOM_QRT, scientificName, freq))
```
```{r, results='asis'}
count_arbre_arr %>% mutate(image=paste0("![",scientificName,"](",identifier,")")) %>% select(NOM_QRT, image) %>% t %>% pandoc.table()
count_arbre_arr %>% mutate(image=paste0("[",scientificName,"](",identifier,")")) %>% select(NOM_QRT, image) %>% t %>% pandoc.table()
```
## Localisation sur une carte
```{r}
select_for_map <- dA4 %>% select(LONGITUDE,LATITUDE,order)
range_long <- range(select_for_map$LONGITUDE)
range_lat <- range(select_for_map$LATITUDE)
@ -272,8 +275,9 @@ map1 +
## Arbres recensés par quartier
Source: [plotting polygon shapefiles](https://github.com/hadley/ggplot2/wiki/plotting-polygon-shapefiles)
```{r}
#https://github.com/hadley/ggplot2/wiki/plotting-polygon-shapefiles
qrtqc@data$id = rownames(qrtqc@data)
qrtqc.df <- as.data.frame(qrtqc)
qrtqc.fort = fortify(qrtqc, region="id")

4
packages.R
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@ -1,3 +1,4 @@
library(devtools)
library(readr) # lecture et écriture de fichiers tabulés
library(magrittr) # opérateur %>%
library(plyr) # transformation de tableaux de données
@ -9,6 +10,8 @@ library(jsonlite) # Lecture et écriture de JSON
library(parallel) # traitements en parallèle
library(gtools) # fonction smartbind
library(lubridate) # gestion des dates
#library(gpclib) # gestion des polygones pour RGDAL
library(rgeos)
library(rgdal) # lien avec la librairie géospatiale GDAL
library(sp) # Spatial Polygons
library(cairoDevice) # sauvegarde de graphiques
@ -18,5 +21,6 @@ library(RColorBrewer) # librairie de palettes de couleurs
library(pander) # Tables en RMarkdown
library(ggmap) # cartes sur GGplot2
#options(unzip="internal")
#devtools::install_github("hadley/multidplyr")