Issues I found

Question

Issues I found

Opened this issue 7 years ago · 14 comments

Hola Sarita,

estou modificando o pacote no meu computador e devo enviar um Push request em breve. Alguns erros que eu encontrar ou sugestões vou colocar aqui.

Besos!

Answer 1 · 2017-04-24T18:05:39.000Z

pm_getdara: Error control does not work. When names are not found in paleobioDB error occurs instead of going through:
print ("There is no data that matches your query on the paleobioDB.
Check if the spelling, temporal intervals, etc. are correct")

Also, I changed the way to handle the error (you will see in the push request).

Answer 2 · 2017-04-24T21:22:01.000Z

For consistency, every time the shape file of the time interval is required the function should allow input the name or the shape itself. Currently it is in one way or the other across different functions. Like pm_plo and pm_occraster.

Answer 3 · 2017-04-24T21:30:43.000Z

I suggest remove all the @Usage from the documentation, roxygen fill it automatically and adds the default options, manually writing it only adds errors

Answer 4 · 2017-04-24T21:33:59.000Z

rank_filter needs an error control if length(data$matched_rank) == 0. Otherwise it will give an uninformative error beyond.

Answer 5 · 2017-04-24T21:53:27.000Z

Needs a function to control the wrong interval names. Give more informative errors in general would be nice, this shall not be too much work as the functions have the same inputs in general.

Answer 6 · 2017-04-24T21:54:01.000Z

I am sending my first push, today I got until the pm_occraster

Answer 7 · 2017-04-24T21:59:19.000Z

Access denied... How can I send my changes? can you allow me to edit the repo?

Answer 8 · 2017-04-25T09:27:22.000Z

@BrunoVilela done! you can push now and change whatever you want :-)

Answer 9 · 2017-04-25T15:05:37.000Z

Thanks! pushed the first changes I did.

Answer 10 · 2017-05-17T20:35:10.000Z

pm_occ: "generates a diversity matrix, with the number occurrences of each species, genus, family or order per locality"

what is a diversity matrix (a presence absence?)
which locality?

Answer 11 · 2017-05-17T20:52:51.000Z

Either the pm_richraster or pm_occ_cell is wrong.
Both should result in the same richness map, given the same data and resolution, but doesn't happen:
data <- pm_getdata(base_name = "Canis", interval = "Quaternary")
result <- pm_occ_cell(data, rank = "species", res = 10)

shape<- pm_getmap(interval="Quaternary")
richness<- pm_richraster(shape, data, rank="species")

plot(shape)
plot(rasterize(result[, 1:2], richness, rowSums(result[, -(1:2)])),
col = c(adjustcolor("white", 0), mycols(100)), add = T)

Answer 12 · 2017-05-17T20:53:05.000Z

I will gonna check on this last issue. My guess is that pm_occ_cell is wrong. I found hard to understand the code, it can be done much easier by using the extract function.

Answer 13 · 2017-05-17T21:18:35.000Z

Ok, fixed. I rewrote the function pm_occ_cell. Just pushed last changes.

Answer 14 · 2017-05-18T07:53:27.000Z

One is the number of occurrences, there could be more than one fossil record of e.g. Canis, and the other the number of different species, genus, etc within, e. g. Canidae both maps should be different. One is something between abundance and sampling effort. and the other maps diversity desde Yahoo Mail con Android El Mié 17 17e May 17e 2017 a las 23:18, Bruno Vilela de Moraes e Silva<notifications@github.com> escribió: Ok, fixed. Just pushed last changes. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.